Editorial Material
Biochemistry & Molecular Biology
Neil A. Hanchard, Ananyo Choudhury
Summary: This article discusses the release of expanded high-depth sequencing data for the fourth phase of the 1000 Genomes Project. It explores how this dataset can serve as a more comprehensive and accurate resource for global genomics through extensive comparisons and benchmarks.
Article
Chemistry, Physical
Sasan Nouranian, Alireza Asiaee, Farzin Rahmani, Shan Jiang, Alexander M. Lopez, Michael R. Fiske, Jennifer E. Edmunson, Eric T. Fox, William F. Kaukler, Hunain Alkhateb
Summary: This study used classical molecular dynamics simulations to investigate the solvation thermodynamics and structures of potential cationic and anionic species from Martian regolith in two ionic liquids. The research found that the solvation free energies (SFEs) of cationic solutes increase with ion valency and size, while the trends for anionic solutes are more complex due to molecular size and charge. Additionally, temperature had mixed effects on the solvation of cationic solutes, with higher temperatures generally favoring the dissolution of anionic solutes in both ionic liquids.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Marta Byrska-Bishop, Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley J. Abel, Allison A. Regier, Andre Corvelo, Wayne E. Clarke, Rajeeva Musunuri, Kshithija Nagulapalli, Susan Fairley, Alexi Runnels, Lara Winterkorn, Ernesto Lowy, Paul Flicek, Soren Germer, Harrison Brand, Ira M. Hall, Michael E. Talkowski, Giuseppe Narzisi, Michael C. Zody
Summary: The 1000 Genomes Project is the largest open resource of whole-genome sequencing data, and a new high-coverage WGS 1kGP resource has been released, improving the sensitivity and accuracy of variant calls and making it more valuable for association studies.
Article
Multidisciplinary Sciences
Zheng Li, Harsha Rao, Rasha Atwi, Bhuvaneswari M. Sivakumar, Bharat Gwalani, Scott Gray, Kee Sung Han, Thomas A. Everett, Tanvi A. Ajantiwalay, Vijayakumar Murugesan, Nav Nidhi Rajput, Vilas G. Pol
Summary: Ether solvents have poor anodic stabilities in lithium metal batteries. Here, the authors propose a non-aqueous electrolyte solution with a non-polar and non-fluorinated ether solvent. The electrolyte enables stable cycling of high-voltage Li metal batteries in pouch cell configuration.
NATURE COMMUNICATIONS
(2023)
Article
Clinical Neurology
Fulya Akcimen, Jay P. Ross, Calwing Liao, Dan Spiegelman, Patrick A. Dion, Guy A. Rouleau
Summary: The study identified HTT-positive, ATXN2-positive, ATXN3-positive, and possibly ATXN1-positive samples in 0.5% of these populations, indicating the presence of asymptomatic small expanded repeats. There was no correlation between repeat sizes of different genes and the distribution of CAG alleles varied by ethnicity.
MOVEMENT DISORDERS
(2021)
Article
Biochemical Research Methods
Kshitij Srivastava, Anne-Sophie Fratzscher, Bo Lan, Willy Albert Flegel
Summary: This study identified long reference sequences by analyzing homozygous genomic regions in the 1000 Genomes Project database. A total of 902 ACKR1 haplotypes of varying lengths were confirmed, with the longest being 80,584 nucleotides and the shortest being 1,901 nucleotides. The approach of using tracts of homozygosity for definitive reference sequences is scalable and can be applied to any gene.
BMC BIOINFORMATICS
(2021)
Article
Chemistry, Physical
Emi Minamitani, Ippei Obayashi, Koji Shimizu, Satoshi Watanabe
Summary: High-accuracy prediction of physical properties of amorphous materials is challenging in condensed-matter physics. Machine-learning potentials, using descriptors invariant to symmetry operations, have shown promise in achieving this. In this study, a novel descriptor based on persistent homology was proposed, which demonstrated the ability to predict energy per atom of amorphous carbon and had similar characteristics to a latent space in a graph neural network.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Farideh Badichi Akher, Yinan Shu, Zoltan Varga, Suman Bhaumik, Donald G. Truhlar
Summary: This article presents a method of adding a new type of activation function to a neural network to enforce low-dimensional constraints. By using this method, the interaction potential can be forced to approach zero when subsystems are too far separated to interact, even without sufficient training data. Additionally, improved potential energy surfaces for the 14 lowest (3)A' states of O-3 are provided, and a more general method called parametrically managed diabatization by deep neural network (PM-DDNN) is introduced to add other low-dimensional or lower-level knowledge to machine-learned potentials.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Cheng Cheng, Shigehiko Hayashi
Summary: The study combined computational chemistry and molecular dynamics simulations to investigate the redox process of cytochrome c, successfully evaluating the absolute redox potential and identifying the molecular determinants for the redox potential by unveiling large and nonlinear protein reorganization in the process.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
M. A. Orekhov
Summary: A universal model is proposed for predicting ion diffusivity enhancement in organic liquids based on the interplay between ion diffusivity and coordination number. The model shows good agreement with molecular dynamics simulations and experimental data. The increase in ion coordination number with ion size leads to maxima in ion diffusivity.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Genetics & Heredity
Jeffrey K. Ng, Pankaj Vats, Elyn Fritz-Waters, Stephanie Sarkar, Eleanor I. Sams, Evin M. Padhi, Zachary L. Payne, Shawn Leonard, Marc A. West, Chandler Prince, Lee Trani, Marshall Jansen, George Vacek, Mehrzad Samadi, Timothy T. Harkins, Craig Pohl, Tychele N. Turner
Summary: In this study, a graphics processing units-based workflow was developed to accelerate the detection of de novo variants (DNVs). The workflow was applied to whole-genome sequencing data from different sources, revealing unexpected results in the DNV callsets and potential cell line artifacts. Additionally, mutation signature analysis identified associations with B-cell lymphoma and variants in DNA repair genes. These findings have important implications for reference building and disease-related projects.
Article
Chemistry, Physical
Anupam Anand Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie E. Amaro
Summary: Recent advances in computational power and algorithms have extended the time scales of molecular dynamics (MD) simulations. However, MD simulations still face limitations in observing conformational transitions associated with biomolecular processes. To address this challenge, enhanced sampling techniques such as the weighted ensemble (WE) method have been developed to estimate kinetic rate constants by sampling transitions between metastable states using weighted trajectories. In this study, deep-learned kinetic modeling approaches are introduced to extract statistically relevant information from short MD trajectories and provide a well-sampled initial state distribution for WE simulations. This hybrid approach overcomes statistical bias and produces a refined free energy landscape closer to the steady state, enabling efficient sampling of kinetic properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Zhihong Piao, Xinru Wu, Hong-Rui Ren, Gongxun Lu, Runhua Gao, Guangmin Zhou, Hui-Ming Cheng
Summary: Researchers have designed an electrolyte with exceptional stability, which can suppress lithium dendrite growth, phase transition, and metal dissolution under high temperature and high voltage conditions. This electrolyte exhibits stability over a wide temperature range and retains a high capacity even after a large number of cycles.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Nanoscience & Nanotechnology
Anh Phan, Michail Stamatakis, Carolyn A. Koh, Alberto Striolo
Summary: This study quantifies the interaction energy between gas hydrate nanoparticles dispersed in liquid hydrocarbons in the presence of different antiagglomerants (AAs) through molecular dynamics simulations, showing excellent agreement with experimental data. Entropy, free energy of solvation, and molecular orientation at hydrate-oil interfaces are found to be descriptors that can be used to predict AA performance. These insights could accelerate the design of new AAs and inform future experiments.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Engineering, Chemical
Lucas Paul, Geradius Deogratias, Daniel M. Shadrack, Celestin N. Mudogo, Kelvin M. Mtei, Revocatus L. Machunda, Andrew S. Paluch, Fidele Ntie-Kang
Summary: This study investigates the physical properties of linamarin and how different solvents affect these properties. The results show that water exhibits the strongest interaction with linamarin, and DMSO is the best solvent.
Article
Biochemistry & Molecular Biology
Luz N. Irazazabal, William F. Porto, Isabel C. M. Fensterseifer, Eliane S. F. Alves, Carolina O. Matos, Antonio C. S. Menezes, Mario R. Felicio, Sonia Goncalves, Nuno C. Santos, Suzana M. Ribeiro, Vincent Humblot, Luciano M. Liao, Ali Ladram, Octavio L. Franco
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2019)
Article
Biology
A. Nonino, J. M. Nascimento, C. C. Mascarenhas, J. F. Mazzeu, R. W. Pereira, R. H. Jacomo
BRAZILIAN JOURNAL OF MEDICAL AND BIOLOGICAL RESEARCH
(2019)
Article
Cell Biology
Teresa Raquel Tavares Serejo, Amandda Evelin Silva-Carvalho, Luma Dayane de Carvalho Filiu Braga, Francisco de Assis Rocha Neves, Rinaldo Wellerson Pereira, Juliana Lott de Carvalho, Felipe Saldanha-Araujo
Article
Plant Sciences
Yohanna Evelyn Miotto, Carolina Tessele, Ana Beatriz Costa Czermainski, Diogo Denardi Porto, Vitor da Silveira Falavigna, Tiago Sartor, Amanda Malvessi Cattani, Carla Andrea Delatorre, Sergio Amorim de Alencar, Orzenil Bonfim da Silva-Junior, Roberto Coiti Togawa, Marcos Mota do Carmo Costa, Georgios Joannis Pappas Jr, Priscila Grynberg, Paulo Ricardo Dias de Oliveira, Marcus Vinicius Kvitschal, Frederico Denardi, Vanessa Buffon, Luis Fernando Revers
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Pharmacology & Pharmacy
Jeeser Alves Almeida, Daisy Motta-Santos, Bernardo Assis Petriz, Clarissa Pedrosa Da Costa Gomes, Murilo Esteves Nogueira, Rinaldo Wellerson Pereira, Ronaldo Carvalho Araujo, Jonato Prestes, Octavio Luiz Franco
CLINICAL AND EXPERIMENTAL HYPERTENSION
(2020)
Article
Biochemistry & Molecular Biology
Wendell Jacinto Pereira, Arthur Tavares de Oliveira Melo, Alexandre Siqueira Guedes Coelho, Fabiana Aparecida Rodrigues, Sujan Mamidi, Sergio Amorim de Alencar, Anna Cristina Lanna, Paula Arielle Mendes Ribeiro Valdisser, Claudio Brondani, Ivanildo Ramalho do Nascimento-Junior, Tereza Cristina de Oliveira Borba, Rosana Pereira Vianello
GENETICS AND MOLECULAR BIOLOGY
(2020)
Article
Biochemical Research Methods
L. L. S. Monteiro, O. L. Franco, S. A. Alencar, W. F. Porto
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2019)
Article
Biochemistry & Molecular Biology
Karla Cristina do Vale Ferreira, Leonardo Ferreira Fialho, Octavio Luiz Franco, Sergio Amorim de Alencar, William Farias Porto
CHEMICAL BIOLOGY & DRUG DESIGN
(2020)
Article
Environmental Sciences
Caio Victor Sousa, Rinaldo Wellerson Pereira, Thomas Rosemann, Pantelis T. Nikolaidis, Beat Knechtle
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2020)
Article
Veterinary Sciences
Getulio P. de Oliveira Jr, William F. Porto, Cintia C. Palu, Lydyane M. Pereira, Essandra M. M. Reis, Tatiana G. Marcola, Antonio R. Teixeira-Neto, Octavio L. Franco, Rinaldo W. Pereira
Summary: This study evaluated the effects of 160 km endurance racing on horse plasma extracellular particles and their miRNA population. The results showed an increase in extracellular particle concentration and diameter during endurance racing, as well as changes in miRNA expression levels.
EQUINE VETERINARY JOURNAL
(2021)
Article
Hematology
Alexandre Nonino, Paulo Vidal Campregher, Fabio Pires de Souza Santos, Juliana Forte Mazzeu, Rinaldo Wellerson Pereira
INTERNATIONAL JOURNAL OF HEMATOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Leane Perim Rodrigues, Vitoria Rodrigues Teixeira, Thuany Alencar-Silva, Bianca Simonassi-Paiva, Rinaldo Wellerson Pereira, Robert Pogue, Juliana Lott Carvalho
Summary: Aging is a natural physiological process that leads to various challenges due to cell senescence, which can have negative consequences for health. Immunosenescence, as a result of aging, alters the functionality of the immune system.
CYTOKINE & GROWTH FACTOR REVIEWS
(2021)
Article
Genetics & Heredity
Amy H. Y. Lee, William F. Porto, Celio de Faria, Simoni C. Dias, Sergio A. Alencar, Derek J. Pickard, Robert E. W. Hancock, Octavio L. Franco
Summary: The study sequenced 70 extensively drug resistant clinical isolates of Klebsiella pneumoniae from Brasilia's hospitals in Brazil, with majority belonging to a single clonal complex. Various resistance mechanisms were identified, with beta-lactamase production being the most notable association with the bacteria.
MICROBIAL GENOMICS
(2021)
Article
Genetics & Heredity
Ariadne R. Lima, Barbara M. Ferreira, Chaofan Zhang, Angad Jolly, Haowei Du, Janson J. White, Moez Dawood, Tulio C. Lins, Marcela A. Chiabai, Ellen Beusekom, Mara S. Cordoba, Erica C. C. Caldas Rosa, Hulya Kayserili, Virginia Kimonis, Erica Wu, Cecilia Mellado, Vineet Aggarwal, Antonio Richieri-Costa, Decio Brunoni, Talyta M. Cano, Alexander A. L. Jorge, Chong A. Kim, Rachel Honjo, Debora R. Bertola, Raissa M. Dandalo-Girardi, Yavuz Bayram, Alper Gezdirici, Elif Yilmaz-Gulec, Evren Gumus, Gulay C. Yilmaz, Nobuhiko Okamoto, Hirofumi Ohashi, Zeynep Coban-Akdemir, Tadahiro Mitani, Shalini N. Jhangiani, Donna M. Muzny, Neysa A. P. Regattieri, Robert Pogue, Rinaldo W. Pereira, Paulo A. Otto, Richard A. Gibbs, Bassam R. Ali, Hans Bokhoven, Han G. Brunner, V. Reid Sutton, James R. Lupski, Angela M. Vianna-Morgante, Claudia M. B. Carvalho, Juliana F. Mazzeu
Summary: Robinow syndrome is a rare genetic disorder characterized by craniofacial dysmorphisms, disproportionate-limb short stature, and genital hypoplasia. It is caused by disturbances in the noncanonical WNT-pathway, with ROR2 gene variants being a common cause. This study identified multiple ROR2 variants in patients with autosomal recessive Robinow syndrome and characterized the phenotypic spectrum of the syndrome.
Article
Biochemistry & Molecular Biology
Daniel O. Freire, Nicolau B. da Cunha, Michel L. Leite, Alessandra G. C. Kostopoulos, Sheila N. B. da Silva, Adolfo C. B. de Souza, Diego O. Nolasco, Octavio L. Franco, Marcia R. Mortari, Simoni C. Dias