Article
Chemistry, Analytical
Carolina Rojas Ramirez, Jessica A. Espino, Lisa M. Jones, Daniel A. Polasky, Alexey I. Nesvizhskii
Summary: Monitoring protein structure before and after environmental alterations can provide insights into protein function. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry allows for monitoring of structural rearrangements by exposing proteins to radicals. However, the challenges of processing FPOP data have limited its proteome-scale uses. In this study, a computational workflow was developed to analyze FPOP data sets more efficiently, enabling the identification of modified peptide spectra at a faster rate than previous methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Neil A. McCracken, Sarah A. Peck Justice, Aruna B. Wijeratne, Amber L. Mosley
Summary: The study introduces a user-friendly analysis of the melt shift calculation workflow and quantitatively assesses the impact of key steps in the analysis workflow on the final output list of stabilized and destabilized proteins. It also presents a more optimized analysis workflow, illustrating the importance of selected calculation steps on the final list of reported proteins of interest in a study. The development of the R based program Inflect offers a valuable resource for the research community to analyze data from TPP and CETSA experiments.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Automation & Control Systems
Le Yao, Zhiqiang Ge
Summary: This article introduces a framework for distributed parallel modeling and monitoring of plant-wide processes with big data, including spatially distributed modeling, hierarchical monitoring, and a mixture probabilistic model for big process data. Performance comparison and visualization experiments demonstrate the reliability and superiority of the proposed algorithm and framework.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2021)
Article
Computer Science, Artificial Intelligence
Tian Wang, Jiahui Chen, Jinhu Lu, Kexin Liu, Aichun Zhu, Hichem Snoussi, Baochang Zhang
Summary: This paper proposes a method called S(2)TAT network for modeling the spatiotemporal relationship of traffic data. The method synchronously models the nonlocal spatiotemporal relationship using an integrated attention mechanism and graph convolution, and handles the heterogeneity of data using timewise graph convolution and multihead mechanism. Experimental results demonstrate the effectiveness of the proposed method.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2023)
Review
Biochemistry & Molecular Biology
Marine Lenon, Rodrigo Arias-Cartin, Frederic Barras
Summary: Iron-sulfur (Fe-S) clusters are important inorganic cofactors involved in various cellular processes. Recent advancements in predicting and identifying Fe-S proteins have allowed for updates in the composition of Escherichia coli Fe-S proteome. Additionally, the damage to Fe-S proteins caused by redox active compounds or contaminant metals is discussed, along with how cells handle this damage through degradation, recycling, or repair.
Article
Engineering, Environmental
Tomoki Yasuda, Shinichi Ookawara, Shiro Yoshikawa, Hideyuki Matsumoto
Summary: This study proposes a machine learning and data-driven framework to identify the optimal descriptor subset for advanced characterization and accurate performance prediction of porous materials in a given application. Two methods were used for descriptor selection and 154 descriptors were evaluated through CFD simulations. The framework identified 11 descriptors and achieved more accurate prediction of permeability compared to existing correlations.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Clinical Neurology
Tingting Jia, Yanni Ma, Fengqin Qin, Feng Han, Chengcheng Zhang
Summary: This study identified 51 genes associated with multiple sclerosis (MS) risk through proteome-wide association study (PWAS) and verified their dysregulated expression at the transcription level. Dysregulation of SHMT1, FAM120B, and ICA1L may contribute to MS risk. These findings provide new insights into the pathogenesis of MS and prioritize potential targets for future therapy research.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2023)
Article
Biochemical Research Methods
Juan R. Lorenzo, Cesar O. Leonetti, Leonardo G. Alonso, Ignacio E. Sanchez
Summary: Researchers have developed a new algorithm for predicting spontaneous protein deamidation, which is faster and similarly accurate compared to current algorithms. The algorithm takes into account sequence propensities and structural protection to predict the half-life of intact form for each protein. The analysis shows that different taxa exhibit different deamidation dynamics.
Article
Cardiac & Cardiovascular Systems
Joanne L. Dunster, Joy R. Wright, Nilesh J. Samani, Alison H. Goodall
Summary: Understanding the factors that contribute to the hemostatic response can help identify individuals at risk of thrombosis. This study compared coagulation proteins in patients with early onset myocardial infarction and healthy controls, and used a mathematical model to investigate the impact of hemostatic factors on the overall response. The results showed significant differences in protein levels between patients and controls, as well as between males and females.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biochemical Research Methods
Katharina Halbach, Timothy Holbrook, Thorsten Reemtsma, Stephan Wagner
Summary: A workflow was developed and implemented for automated combination of spatially resolved LA-ICP-MS data and biological tissue morphology. Using FishImager, biological features are automatically assigned as ROIs and can be analyzed statistically and compared with elemental data. The tool can be used for clinical and ecotoxicological testing, simplifying interpretation of imaging LA-ICP-MS data.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Weishu Zhao, Bozitao Zhong, Lirong Zheng, Pan Tan, Yinzhao Wang, Hao Leng, Nicolas de Souza, Zhuo Liu, Liang Hong, Xiang Xiao
Summary: This study investigates the ancestral metabolism of ancient bacteria and archaea by comparing their protein structures. The research reveals similar physiological and metabolic characteristics between the two groups and identifies conserved metabolic modules. These findings provide a new perspective on reconstructing ancestral metabolism and understanding its origin.
NATURE COMMUNICATIONS
(2022)
Article
Computer Science, Artificial Intelligence
Misuk Kim
Summary: Real-time processing and analysis of data are crucial in financial markets due to their direct impact on profits. This study introduces a novel data mining framework focusing on interpretability, prediction metrics, and reporting methods, which was applied to financial prediction problems with successful results.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Chemistry, Analytical
Guoqi Liu, Thomas Ulrich, Fei Xia, Yang Xiao
Summary: Photomicrography, Bayesian regression, and trace element and isotope ratio maps have been effectively used to overcome the challenges in U-Pb dating of hydrothermal and hydrothermal accessory minerals. The software Brama performs outlier processing, baseline correction, isotope calculation, and Bayesian regression, resulting in high resolution spatial maps and age results. Brama's data can also be used in other calculation methods for mineral ages.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Jinhui Liu, Xing Wei, Chengxin Wu, Lingna Zheng, Meng Wang, Mingli Chen, Jianhua Wang
Summary: Single particle-inductively coupled plasma-mass spectrometry (SP-ICP-MS) is a powerful technique for nanoparticle characterization, but its accuracy is influenced by data acquisition rate and processing methods. This work discusses the effects of dwell times ranging from microseconds to milliseconds on data forms in SP-ICP-MS analysis, and provides detailed analysis and processing methods for different dwell times, including the measurement of transport efficiency, distinction of signal and background, evaluation of diameter limit of detection, and quantification of mass, size, and particle number concentration. This study offers valuable data support and guidance for researchers in SP-ICP-MS analysis.
ANALYTICA CHIMICA ACTA
(2023)
Article
Engineering, Electrical & Electronic
Yongxiang Lei
Summary: This article proposes a new unified optimal prediction control framework (ConFrame) for the industrial mining system. The framework integrates optimal and nonlinear control for the industrial paste-filling system and provides a unified consideration for the full-scale paste-filling process. The proposed algorithm is able to achieve high accuracy and robustness in prediction and control performance.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2023)
Article
Genetics & Heredity
Mengling Qi, Peter D. Stenson, Edward Ball, John A. Tainer, Albino Bacolla, Hildegard Kehrer-Sawatzki, David N. Cooper, Huiying Zhao
Summary: Microdeletions and gross deletions are important causes of human inherited disease, and their genomic locations are influenced by the DNA sequence environment. This study analyzed the DNA sequences near breakpoint junctions and found correlations between the frequencies of non-B DNA-forming repeats, GC-content, specific sequence motifs, and deletion length. The study also proposed using a deletion length cut-off of 25-30 bp to functionally distinguish microdeletions from gross deletions.
Article
Biochemical Research Methods
Aries Aisporna, H. Paul Benton, Andy Chen, Rico J. E. Derks, Jean Marie Galano, Martin Giera, Gary Siuzdak
Summary: Neutral loss (NL) spectral data is a valuable resource for molecular discovery and similarity analysis. Researchers have created a MS2 to NL converter and developed the METLIN-NL database to enhance unknown identification and complement existing fragment ion databases.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Multidisciplinary Sciences
Xiang Feng, Gerrit J. Schut, Dominik K. Haja, Michael W. W. Adams, Huilin Li
Summary: Electron bifurcation allows energetically unfavorable biochemical reactions to occur. This study reports a new bifurcating flavoenzyme structure that couples hydrogen oxidation with NAD reduction through electron transfer. By elucidating its structure and function, we gain a deeper understanding of the electron transfer pathways in hydrogenases.
Article
Cell Biology
Alexandra Berroyer, Albino Bacolla, John A. Tainer, Nayun Kim
Summary: Top1 plays a critical role in maintaining stability at G4-forming genomic loci, and its inhibition by anticancer drugs can lead to increased genomic instability. CPT-resistant Top1 mutants enhance G4-induced recombination and synergize with Nsr1 to exacerbate genomic instability, complicating patient treatment.
Article
Microbiology
Francesco Smedile, Dionysis Foustoukos, Sushmita Patwardhan, Kelli Mullane, Ian Schlegel, Michael W. Adams, Gerrit J. Schut, Donato Giovannelli, Costantino Vetriani
Summary: Physiological and gene expression studies of deep-sea bacteria under pressure conditions similar to their natural habitat are important for understanding their growth kinetics and metabolic adaptations. This study focused on Campylobacterium Nautilia sp. strain PV-1, a piezophilic bacterium that displays unique protein expression patterns in response to different hydrostatic pressure regimes. The findings suggest that pressure adaptation extends to enzymes involved in central metabolic pathways.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Carlos Guijas, Andrew To, J. Rafael Montenegro-Burke, Xavier Domingo-Almenara, Zaida Alipio-Gloria, Bernard P. Kok, Enrique Saez, Nicole H. Alvarez, Kristen A. Johnson, Gary Siuzdak
Summary: Obesity rates have doubled since the 1980s and are closely associated with metabolic diseases. Balancing energy homeostasis by increasing brown-like adipocytes in white adipose tissue (WAT) is a potential therapeutic approach. Zafirlukast, a drug used to treat asthma, has been found to induce the differentiation of white adipocytes into functional brown adipocytes. However, it is toxic to human cells at high dosages. The endogenous metabolite myristoylglycine has been discovered as a potential alternative to zafirlukast in inducing brown adipocyte differentiation.
Article
Ecology
Jennifer L. Goff, Yan Chen, Michael P. Thorgersen, Linh T. Hoang, Farris L. Poole II, Elizabeth G. Szink, Gary Siuzdak, Christopher J. Petzold, Michael W. W. Adams
Summary: Multiple heavy metal contamination is a common global problem that can disrupt microbial biogeochemical cycling. However, there is a lack of studies on the effects of combinations of heavy metals on bacteria. In this study, we assessed the impact of eight metal contaminants on cell processes using a multiomics approach. The combination of metals had unexpected effects on cell physiology, including a disruption of iron homeostasis and decreased activity of important enzymes. This research highlights the need for multi-metal studies to understand the impacts of complex contaminants on microbial systems.
Article
Biochemistry & Molecular Biology
Amer Bralic, Muhammad Tehseen, Mohamed A. Sobhy, Chi-Lin Tsai, Lubna Alhudhali, Gang Yi, Jina Yu, Chunli Yan, Ivaylo Ivanov, Susan E. Tsutakawa, John A. Tainer, Samir M. Hamdan
Summary: Nucleotide excision repair (NER) is crucial for removing bulky DNA lesions, and this study reveals that the XPG nuclease plays a dual role in lesion recognition and excision. XPG stimulates TFIIH-dependent dsDNA unwinding and cleavage activity, and this coordination requires a DNA bubble longer than 15 nucleotides.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Naseer A. Kutchy, Amelia Palermo, Rong Ma, Zhong Li, Alexandria Ulanov, Shannon Callen, Gary Siuzdak, Sabita Roy, Shilpa Buch, Guoku Hu
Summary: Morphine administration causes distinct metabolic changes, with acute and chronic use leading to different plasma metabolite concentrations. The alterations in metabolites are linked to the development of tolerance to morphine's analgesic effects. The study also identified metabolites that were differentially affected by acute versus chronic morphine use, suggesting that metabolic changes may be mitigated by prolonged exposure to the drug.
Letter
Biochemical Research Methods
Erin S. Baker, Corey Hoang, Winnie Uritboonthai, Heino M. Heyman, Brian Pratt, Michael MacCoss, Brendan MacLean, Robert Plumb, Aries Aisporna, Gary Siuzdak
Editorial Material
Endocrinology & Metabolism
Gary Siuzdak
Summary: Recent advances in mass spectrometry imaging, specifically the development of nano secondary ion mass spectrometry, have made subcellular quantitative analysis a reality, allowing for absolute quantification at the organelle level.
Article
Environmental Sciences
Michael P. Thorgersen, Jennifer L. Goff, Farris L. Poole, Kathleen F. Walker, Andrew D. Putt, Lauren M. Lui, Terry C. Hazen, Adam P. Arkin, Michael W. W. Adams
Summary: Environmental contamination affects microbial communities by limiting diversity and total metabolic activity. The study investigates metal contamination in sediment and finds that the operational speciation of certain elements changes due to contamination. Furthermore, the availability of essential elements also changes. The decreased operational speciation of phosphorus in contaminated sediment may increase the dependence of microbial communities on other phosphorus sources.
ENVIRONMENTAL POLLUTION
(2023)
Review
Biochemistry & Molecular Biology
Atanu Mondal, Apoorva Bhattacharya, Vipin Singh, Shruti Pandita, Albino Bacolla, Raj K. Pandita, John A. Tainer, Kenneth S. Ramos, Tej K. Pandita, Chandrima Das
Summary: From initiation to progression, cancer cells experience a variety of internal and external stresses, leading to changes in their epigenome and transcriptome. Understanding the stress response pathways of cancer cells is crucial for developing novel anticancer therapies.
MOLECULAR AND CELLULAR BIOLOGY
(2022)