Article
Biochemical Research Methods
P. T. V. Florentino, F. N. L. Vitorino, D. Mendes, J. P. C. da Cunha, C. F. M. Menck
Summary: By using quantitative proteomic analysis, this study revealed the impact of Trypanosoma cruzi infection on the chromatin of host cells. It was discovered that parasites interfere with DNA metabolism during both early and late infection stages. Proteins related to DNA damage repair, oxidative phosphorylation, and vesicle-mediated transport showed increased abundance in the host chromatin. Additionally, the translocation of Apoptosis-inducing Factor to the host cell nucleus after infection suggests that the parasites can induce a programmed cell death known as Parthanatos. These findings contribute to a better understanding of how parasites manipulate the chromatin of host cells to disseminate infection and provide potential targets for future treatments.
JOURNAL OF PROTEOMICS
(2023)
Article
Multidisciplinary Sciences
Juan Guiza, Francisco Solis, Bernardita Valenzuela, Duxan Arancibia, Pedro Zamorano, Jorge Gonzalez, Jonathan Saavedra, Alan Neely, Magdiel Salgado, Agustin D. Martinez, Juan C. Saez, Jose L. Vega
Summary: Cells of vertebrate and invertebrate organisms communicate through membrane channels specialized in cell-cell communication, which are absent in unicellular organisms. This study discovered a family of large-pore channel proteins called unnexins in kinetoplastids, which share similarities with innexin and pannexin proteins. Specifically, the unnexin1 protein (Unx1) forms membrane channels that allow the influx of Ca2+. Low extracellular Ca2+/Mg2+ levels or extracellular alkalinization increase Unx1 channel activity, while mechanical stretching does not have this effect. Unx1 also plays a role in cell invasion and can be a potential target for developing drugs to treat Trypanosoma cruzi infections.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Parasitology
Paola Garcia-Huertas, Yesid Cuesta-Astroz, Valentina Araque-Ruiz, Nora Cardona-Castro
Summary: During its life cycle, Trypanosoma cruzi undergoes physiological modifications to adapt to insect vector and mammalian host conditions. In this study, transcriptomes of metacyclic trypomastigotes and epimastigotes were analyzed to identify differentially expressed genes involved in metacyclogenesis. The differential gene expression analysis revealed 513 genes, with 221 upregulated and 292 downregulated in metacyclic trypomastigotes. These genes are related to important biological processes in metacyclogenesis and may serve as potential therapeutic targets for Chagas disease.
PARASITOLOGY RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Yuanyuan Liu, Fanhua Shang, Hongying Liu, Lin Kong, Licheng Jiao, Zhouchen Lin
Summary: The study introduces a new momentum acceleration trick into stochastic variance reduced ADMM, proposing an accelerated SVRG-ADMM method for solving machine learning problems. By introducing a linearized proximal update rule, the convergence rate for non-strongly convex problems is improved. In various machine learning problems, ASVRG-ADMM consistently converges faster than state-of-the-art methods.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2021)
Article
Microbiology
Fanny E. Eberhard, Sven Klimpel, Alessandra A. Guarneri, Nicholas J. Tobias
Summary: The study reveals the interactions between the parasites and microbiota in the intestinal tract of triatomine vectors, shedding light on important aspects of the transmission of Chagas disease by triatomine vectors.
Article
Chemistry, Multidisciplinary
Joan Atcher, Pedro Mateus, Brice Kauffmann, Frederic Rosu, Victor Maurizot, Ivan Huc
Summary: The study demonstrates the orchestration of ever larger conformational changes through the development of increasingly complex foldamers, including the rare motif of aromatic sheets in synthetic foldamer structures. Experimental results confirm the formation of compact dimers through self-assembly of intercalated aromatic strands, and X-ray crystallography and molecular dynamics simulation validate the stability of the two distinct conformational dimeric states and their interconversion possibilities.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Infectious Diseases
Jose A. Perez-Molina, Clara Crespillo-Andujar, Elena Trigo, Sandra Chamorro, Marta F. Arsuaga, Leticia F. Olavarrieta, Beatriz Navia, Oihane L. Martin, Begona L. Monge-Maillo, Francesca Norman, Val L. Lanza, Sergio Serrano-Villar
Summary: Chagas disease (CD) is a neglected disease with significant knowledge gaps regarding its pathogenesis, treatment, and prognostic factors. In this study, we investigated the changes in gut microbiota of CD patients and identified potential disease biomarkers.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Engineering, Electrical & Electronic
Victor Croisfelt, Abolfazl Amiri, Taufik Abrao, Elisabeth de Carvalho, Petar Popovski
Summary: In M-MIMO systems, the issue of sparse linear equations can significantly deteriorate the performance of the RK algorithm. This article introduces three new RK-based low-complexity receiver designs that are more robust against inter-user interference and sparse channel matrices in the XL-MIMO regime. These methods show promise in overcoming previous schemes and approximating the regularized zero-forcing scheme used by SIC receivers.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Emanuella de Castro Andreassa, Marlon Dias Mariano dos Santos, Rafaela Wassmandorf, Helisa Helena Wippel, Paulo Costa Carvalho, Juliana de Saldanha da Gama Fischer, Tatiana de Arruda Campos Brasil de Souza
Summary: Understanding the biochemical changes associated with apoptosis in Trypanosoma cruzi is crucial for drug development and provides insights into the regulation of metabolic and cellular processes in nonmetazoan apoptotic cells. The study revealed that proteins associated with apoptosis in other species are also present in Trypanosoma cruzi, suggesting the preservation and application of apoptotic functions across different organisms, which could serve as potential targets for the treatment of Chagas disease.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2021)
Article
Engineering, Marine
Krzysztof Woloszyk, Yordan Garbatov, Jakub Kowalski
Summary: The work presented here is part of a long-term project that analyzes the structural behavior of aging marine structures. An accelerated corrosion degradation setup was developed to reproduce corroded marine structural specimens of different degrees of degradation, and the corrosion surfaces obtained were highly non-uniform. The developed corrosion degradation controlled experimental setup is efficient in reproducing marine structural specimens of different degrees of degradation for further mechanical testing, as shown by comparing the results with real measurements of ship deck plates.
Article
Computer Science, Hardware & Architecture
Weiwei Cai, Fazhi He, Xiao Lv
Summary: With the advancement of networking technologies and large-scale social computing, multi-user collaboration is becoming popular. Our research focuses on accelerating consistency maintenance algorithms using multi-core processors with a specific focus on commutative replicated data type (CRDT) operations.
JOURNAL OF SUPERCOMPUTING
(2022)
Article
Immunology
Ayorinde Cooley, Kayla J. Rayford, Ashutosh Arun, Fernando Villalta, Maria F. Lima, Siddharth Pratap, Pius N. Nde
Summary: This study reveals that the protozoan parasite Trypanosoma cruzi dysregulates host piRNAs to interfere with the IL-6 signaling pathway during early infection, leading to severe cardiomyopathies. Through computational prediction, specific piRNAs targeting IL-6 and SOCS3 genes were identified. The expression of these piRNAs and target genes was validated in challenged cells. The findings suggest that targeting piRNAs could be a potential therapeutic strategy to mitigate T. cruzi-induced cardiac disorders.
Article
Environmental Sciences
Lola L. B. Visschers, Carlos D. Santos, Aldina M. A. Franco
Summary: Saltwater intrusion can have significant impacts on coastal ecosystems and local livelihoods. This study used satellite imagery to measure changes in mangrove distribution along the northern coast of Brazil over the past 38 years and found that the mangrove area in this region is highly dynamic, with a net gain overall.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Electrical & Electronic
Renke Huang, Yujiao Chen, Tianzhixi Yin, Xinya Li, Ang Li, Jie Tan, Wenhao Yu, Yuan Liu, Qiuhua Huang
Summary: This study proposes a novel derivative-free DRL algorithm called PARS, tailored for load shedding in power system voltage control. It shows better computational efficiency, robustness in learning, scalability, and generalization capability compared to other methods.
IEEE TRANSACTIONS ON POWER SYSTEMS
(2022)
Article
Infectious Diseases
Juan Cantizani, Pablo Gamallo, Ignacio Cotillo, Raquel Alvarez-Velilla, Julio Martin
Summary: Chagas disease is caused by Trypanosoma cruzi, with current treatment options limited to two drugs that have suboptimal efficacy and serious adverse effects. Research suggests that compounds with faster action and higher cidal activity may have better prospects for effective treatment of CD.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Barry J. Grant, Lars Skjaerven, Xin-Qiu Yao
Summary: Bio3D is a set of R packages for analyzing biomolecular sequences, structures, and dynamics, with recent developments including segregation into separate packages and introduction of a new method called ensemble difference distance matrix analysis (eDDM). The eDDM approach helps identify residue-wise determinants underlying specific functional processes by calculating and comparing atomic distance matrices across large sets of homologous structures.
Article
Chemistry, Physical
Zirui Zhang, Clarisse G. Ricci, Chao Fan, Li-Tien Cheng, Bo Li, J. Andrew McCammon
Summary: The hybrid approach combines the Monte Carlo method, a variational implicit-solvent model (VISM), and a binary level-set method for simulating biomolecular binding in an aqueous solvent. It estimates the solvation free energy for the biomolecular complex by minimizing the VISM free-energy functional, accurately predicting the electrostatic part of the solvation free energy by shifting the dielectric boundary. The new and fast binary level-set method allows for this functional minimization in each MC move.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Medicinal
Terra Sztain, Rommie Amaro, J. Andrew McCammon
Summary: By using Gaussian accelerated molecular dynamics, this study identified cryptic pockets within the SARS-CoV-2 main protease, revealing druggable conformational states far from the active site. The simulations demonstrated comparable dynamics and pocket volumes to conventional brute force simulations conducted on significantly longer timescales.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Hamidreza Rahmani, Wen Ma, Zhongjun Hu, Nadia Daneshparvar, Dianne W. Taylor, J. Andrew McCammon, Thomas C. Irving, Robert J. Edwards, Kenneth A. Taylor
Summary: The atomic structure of myosin tail in thick filaments isolated from Lethocerus indicus flight muscle is asymmetric, with differences in skip regions and nonhelical C termini. The study provides insights into the uncoiling of coiled-coils at the head-tail junction and sheds light on the complex roles of thick filaments in muscle contraction across species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Terra Sztain, Thomas G. Bartholow, D. John Lee, Lorenzo Casalino, Andrew Mitchell, Megan A. Young, Jianing Wang, J. Andrew McCammon, Michael D. Burkart
Summary: Enzymes in metabolic pathways utilize a variety of regulatory mechanisms to maintain homeostasis, with carrier proteins playing an essential role in substrate shuttling. A unique communication mechanism between ACP and partner enzymes has been demonstrated, showing allosteric regulation dependent on fatty acid chain length. These findings provide insights into cargo communication by ACP and can potentially be used for engineering carrier protein-dependent pathways for specific products.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Surl-Hee Ahn, Sanbo Qin, Jason Z. Zhang, J. Andrew McCammon, Jin Zhang, Huan-Xiang Zhou
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Varnavas D. Mouchlis, Daiki Hayashi, Alexis M. Vasquez, Jian Cao, J. Andrew McCammon, Edward A. Dennis
Summary: Lipoprotein-associated phospholipase A(2) (Lp-PLA(2)) associates with lipoproteins in human plasma and hydrolyzes oxidized phospholipids. The mechanism of enzyme-membrane association and substrate specificity were studied using lipidomics and mass spectrometry techniques.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Thomas G. Laughlin, Amar Deep, Amy M. Prichard, Christian Seitz, Yajie Gu, Eray Enustun, Sergey Suslov, Kanika Khanna, Erica A. Birkholz, Emily Armbruster, J. Andrew McCammon, Rommie E. Amaro, Joe Pogliano, Kevin D. Corbett, Elizabeth Villa
Summary: This study identifies a protein called ChmA as the main component of the bacteriophage nuclear shell. The structure and dynamics of the ChmA shell provide insights into its formation and functions.
Article
Biochemistry & Molecular Biology
Surl-Hee Ahn, Gary A. Huber, J. Andrew McCammon
Summary: Intrinsically disordered proteins (IDPs) have attracted significant attention due to their involvement in biological processes and diseases. Computational studies using Brownian dynamics (BD) simulations with a coarse-grained force field for proteins (COFFDROP) have been conducted to complement experimental work. The researchers found that IDPs' properties, such as hydrodynamic radii and entanglement indices, are influenced by salt concentration.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Joshua C. Corpuz, Ashay Patel, Tony D. Davis, Larissa M. Podust, J. Andrew McCammon, Michael D. Burkart
Summary: This study reveals the binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains in non-ribosomal peptide synthetases (NRPSs) using chemical biology approaches. The research also demonstrates the possibility of controlling PCP binding specificity through modifying interfacial interactions.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yohei Takahashi, Krystal C. Bosmans, Po -Kai Hsu, Karnelia Paul, Christian Seitz, Chung-Yueh Yeh, Yuh-Shuh Wang, Dmitry Yarmolinsky, Maija Sierla, Triin Vahisalu, J. Andrew McCammon, Jaakko Kangasjaervi, Li Zhang, Hannes Kollist, Thien Trac, Julian I. Schroeder
Summary: The rise in atmospheric CO2 concentration affects stomatal closing in plants, impacting transpirational water loss, photosynthesis, and growth. This study identifies MPK4/12 and HT1 as the primary CO2 sensors in plants, located upstream of the CBC1 kinase. These findings are significant for understanding the plant response to CO2.
Article
Biochemistry & Molecular Biology
Jui-Hung Weng, Wen Ma, Jian Wu, Pallavi Kaila Sharma, Steve Silletti, J. Andrew McCammon, Susan Taylor
Summary: Mutations in LRRK2 increase the risk of Parkinson's disease, and its pathological functions are often associated with abnormal kinase activity. This study combines enhanced sampling simulations with HDX-MS to investigate the dynamic changes and allosteric communications within the C-terminal domains of LRRK2. It is found that different types of kinase inhibitors stabilize distinct kinase conformations and modulate the interdomain interactions between the kinase and GTPase domains.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Terra Sztain, Joshua C. Corpuz, Thomas G. Bartholow, Javier O. Sanlley Hernandez, Ziran Jiang, Desirae A. Mellor, Graham W. Heberlig, James J. La Clair, J. Andrew Mccammon, Michael D. Burkart
Summary: Carrier-protein-dependent metabolic pathways rely on protein-protein interactions to control enzyme reactivity and timing. Computational methods, such as the improved Rosetta score function, can be used to design customized pathways by optimizing protein-protein interactions. This method provides a promising platform for engineering carrier-protein-dependent pathways.
ACS CHEMICAL BIOLOGY
(2023)
Article
Physics, Applied
Marcus T. Hock, Abigail E. Teitgen, Kimberly J. McCabe, Sophia P. Hirakis, Gary A. Huber, Michael Regnier, Rommie E. Amaro, J. Andrew McCammon, Andrew D. McCulloch
Summary: dATP, a natural analog of ATP, has been shown to enhance cardiac function. In this study, computational modeling was used to investigate the mechanism by which dATP accelerates calcium re-uptake into the sarcoplasmic reticulum during cardiac relaxation. The results showed that dATP interacts with SERCA and increases calcium association rate constants, ultimately leading to accelerated calcium transient decay observed experimentally.
JOURNAL OF APPLIED PHYSICS
(2023)
Article
Chemistry, Physical
Christian Seitz, Ilker Deveci, J. Andrew McCammon
Summary: This study investigates how protein glycosylation and lateral crowding effects modulate the stability and dynamics of influenza neuraminidase. The results show that glycans stabilize the protein structure, while a crowded membrane environment encourages large-scale conformational changes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)