Review
Biotechnology & Applied Microbiology
Adil Alsiyabi, Niaz Bahar Chowdhury, Dianna Long, Rajib Saha
Summary: This article discusses the importance of reconstruction and analysis of metabolic models, introducing the biological relevance of steady-state modeling methods and kinetic modeling techniques, as well as their roles in prediction and experimental validation.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Biochemistry & Molecular Biology
Hai Duc Nguyen, Min -Sun Kim
Summary: Curcumin has therapeutic benefits for MetS and its components through multiple molecular mechanisms, with PPARG as a key transcription factor. Curcumin targets miRNAs that are associated with various metabolic disorders. Furthermore, curcumin exhibits favorable physicochemical properties and pharmacokinetics.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Alexander Reiter, Jian Asgari, Wolfgang Wiechert, Marco Oldiges
Summary: Metabolic footprinting is a holistic approach for gathering large-scale metabolomic information of a biological system, which is crucial for systems biology and bioprocess development. This study presents a workflow for automatically building an organism-specific comprehensive metabolome analysis method using genome-scale model information. The method was applied to Saccharomyces cerevisiae and validated with high efficiency. Additionally, it can be extended to other microbial systems.
Article
Biology
Abdullahi Dandare, Ghulam Rabia, Muhammad Jawad Khan
Summary: The study aimed to predict therapeutic targets and construct a biomarker panel for early detection of metabolic syndrome (MS) using non-coding RNAs, including circRNAs, lncRNAs, and miRNAs. Analysis revealed a strong association of multiple miRNAs with the pathogenesis of MS, affecting pathways related to glucose and lipid homeostasis, inflammatory responses, and insulin resistance. Interactions of specific miRNAs with key genes suggest the potential for designing a biomarker panel for early detection and molecular management of MS.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Multidisciplinary Sciences
Ferran Muinos, Francisco Martinez-Jimenez, Oriol Pich, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Summary: This study proposes using mutations observed in tumors to build machine learning models that outperform experimental methods in identifying driver mutations, demonstrating the role of mutation probability in shaping the landscape of observed driver mutations.
Article
Multidisciplinary Sciences
Yuebin Wang, Wenqiang Li, Luxi Wang, Jiali Yan, Gang Lu, Ning Yang, Jieting Xu, Yuqing Wang, Songtao Gui, Gengshen Chen, Shuyan Li, Chengxiu Wu, Tingting Guo, Yingjie Xiao, Marilyn L. Warburton, Alisdair R. Fernie, Thomas Dresselhaus, Jianbing Yan
Summary: This study separates the Ga1 locus into two functional components and identifies seven linked genes encoding three types of proteins through genetic analysis.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Younes M. Rashad, Elsayed S. Abdel Razik, Doaa B. Darwish
Summary: This study investigated the antifungal activity of lavender essential oil against Fusarium solani, the causal agent of sorghum damping-off. The results showed that lavender EO exhibited potent antifungal activity, possibly attributed to specific compounds identified by GC-MS analysis. Transmission electron microscopy revealed abnormal ultrastructures in the fungal mycelium treated with lavender EO. Real-time PCR investigations demonstrated that certain genes were overexpressed in response to lavender EO. Under greenhouse conditions, treating sorghum grains with lavender EO significantly reduced disease severity and enhanced plant growth parameters and antioxidant activities. The findings suggest the potential use of lavender EO for control of sorghum damping-off, although further field evaluations are needed.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Chao-Ting Cheng, Jin-Mei Lai, Peter Mu-Hsin Chang, Yi-Ren Hong, Chi-Ying F. Huang, Feng-Sheng Wang
Summary: A fuzzy hierarchical optimization framework was proposed to identify essential targets in the genome-scale metabolic networks of cancer cells. The framework was able to convert a multiobjective optimization problem into a trilevel maximizing decision-making problem using fuzzy set theory. The study identified essential genes mostly associated with cholesterol biosynthesis, nucleotide metabolisms, and the glycerophospholipid biosynthetic pathway, with some genes specific to colorectal cancer subtypes.
Article
Toxicology
Karolina Kopanska, Pablo Rodriguez-Belenguer, Jordi Llopis-Lorente, Beatriz Trenor, Javier Saiz, Manuel Pastor
Summary: In silico methods can be used to assess the arrhythmogenic properties of drug candidates early on. This research focuses on developing uncertainty quantification methods for predictions made by multi-level proarrhythmia models. By using probabilistic simulations and replacing single-point estimates with distributions, this approach provides a more comprehensive understanding of drug effects. The methodology was tested on a series of well-characterized marketed drugs.
ARCHIVES OF TOXICOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Aldrin Y. Cantila, Nur Shuhadah Mohd Saad, Junrey C. Amas, David Edwards, Jacqueline Batley
Summary: Canola is the most economically significant Brassica oilseed globally, but its production can be limited by blackleg disease caused by Lepstosphaeria maculans. Research has shown that genetic resistance against blackleg comes in two forms: qualitative resistance mediated by R genes and quantitative resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Clinical Neurology
David M. Ritter, Paul S. Horn, Katherine D. Holland
Summary: The study demonstrates that the pathogenicity of KCNQ channel variants in neonatal epilepsy can be accurately predicted by a novel KCNQ Index, with higher accuracy compared to other prediction algorithms. However, further work is needed to accurately predict the patient's epilepsy phenotype.
PEDIATRIC NEUROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Gokhan Zengin, Mohamad Fawzi Mahomoodally, Evren Yildiztugay, Sharmeen Jugreet, Shafi Ullah Khan, Stefano Dall'Acqua, Adriano Mollica, Abdelhakim Bouyahya, Domenico Montesano
Summary: This study examined the chemical composition and biological activities of essential oils obtained from three endemic Prangos species from Turkey. The essential oils showed free radical scavenging potential and tyrosinase inhibitory activity, making them potential natural antioxidants and anti-hyperpigmentation agents.
Article
Multidisciplinary Sciences
Shuo Feng, Joel A. Dubin
Summary: Utilizing eICU database, this study aimed to identify variables within the first 24 hours of ICU stay that may lead to potential errors in predicting in-hospital mortality by APACHE IVa scoring system. Different sets of predictors were associated with Type I and Type II errors, and important recommendations were provided for preventing errors in APACHE predictions.
SCIENTIFIC REPORTS
(2021)
Article
Infectious Diseases
Tomasz Bogiel, Malgorzata Prazynska, Joanna Kwiecinska-Pirog, Agnieszka Mikucka, Eugenia Gospodarek-Komkowska
Summary: The study compared the frequency of selected enzymatic virulence factor genes among non-duplicated carbapenem-resistant P. aeruginosa isolates, finding a higher prevalence of alkaline protease gene and a 37.4% detection rate for neuraminidase-1 gene. Significant differences in the prevalence of lasB and nan1 were observed between MBL-positive and MBL-negative strains.
Article
Multidisciplinary Sciences
Joao Luiz de Lemos Padilha Pitta, Crhisllane Rafaele dos Santos Vasconcelos, Gabriel da Luz Wallau, Tulio de Lima Campos, Antonio Mauro Rezende
Summary: Using Random Forest and Support Vector Machine (SVM) algorithms, predictions of protein-protein interactions between two ZIKV strains and human proteomes were made, revealing biologically meaningful interactions. Enrichment analysis identified pathways related to viral infection and neurological development for both ZIKV strains, with differences observed in the JAK-STAT pathway between strains PE243 and FSS13025.
Article
Multidisciplinary Sciences
Gi Bae Kim, Ye Gao, Bernhard O. Palsson, Sang Yup Lee
Summary: Transcription factors are proteins that regulate gene expression by binding to specific DNA sequences, traditionally predicted through sequence homology analysis. However, the development of the deep learning-based tool DeepTFactor has shown high performance in predicting transcription factors efficiently and accurately, even for those with no homology to reported ones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Ke Chen, Amitesh Anand, Connor Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Bernhard O. Palsson
Summary: The study analyzed Escherichia coli phenotypes using genome-scale models, revealing a stratified distribution influenced by different ATP generation strategies. This mechanistic approach offers a fundamental understanding of fitness landscape, bacterial physiology, and evolution dynamics.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Akanksha Rajput, Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk, Bernhard O. Palsson
Summary: TCSs play a crucial role in bacterial pathogenicity and antibiotic resistance. The ESKAPEE pathogens exhibit closed pangenomes for TCS, indicating their potential as drug targets. Mutation in certain TCSs may lead to cell lethality, highlighting their importance in bacterial fitness.
Article
Medicine, Research & Experimental
Travis Nemkov, Davide Stefanoni, Aarash Bordbar, Aaron Issaian, Bernhard O. Palsson, Larry J. Dumont, Ariel Hay, Anren Song, Yang Xia, Jasmina S. Redzic, Elan Z. Eisenmesser, James C. Zimring, Steve Kleinman, Kirk C. Hansen, Michael P. Busch, Angelo D'Alessandro
Summary: Computational models suggest that mature erythrocytes may be affected by common drugs. High-throughput drug screenings show that many drugs impact erythrocyte metabolism, with machine learning models accurately predicting these effects. Certain drugs like ranitidine can improve erythrocyte metabolism and storage quality, indicating potential for enhancing blood transfusion outcomes.
Article
Biochemical Research Methods
Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson
Summary: The article introduces the MASSpy package, an open-source computational framework for dynamic modeling of metabolism using mass action kinetics and detailed chemical mechanisms. By adding dynamic modeling tools to the COBRApy package, MASSpy provides a unified framework for constraint-based and kinetic modeling of metabolic networks. MASSpy supports high-performance dynamic simulation using libRoadRunner: the Systems Biology Markup Language (SBML) simulation engine.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Correction
Multidisciplinary Sciences
Woori Kim, Soonkyu Hwang, Namil Lee, Yongjae Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Summary: The paper has been corrected and the details can be found at the provided link.
Article
Microbiology
Soonkyu Hwang, Namil Lee, Donghui Choe, Yongjae Lee, Woori Kim, Yujin Jeong, Suhyung Cho, Bernhard O. Palsson, Byung-Kwan Cho
Summary: In this study, transcriptional regulatory elements in Streptomyces clavuligerus were identified using genome-wide transcript 3'-end positions and transcription units. The study revealed the importance of transcript 3'-end positions in controlling transcription levels and the potential for designing engineering tools to enhance secondary metabolite production based on these findings.
Article
Biochemistry & Molecular Biology
Jean-Christophe Lachance, Dominick Matteau, Joelle Brodeur, Colton J. Lloyd, Nathan Mih, Zachary A. King, Thomas F. Knight, Adam M. Feist, Jonathan M. Monk, Bernhard O. Palsson, Pierre-Etienne Jacques, Sebastien Rodrigue
Summary: Mesoplasma florum, a fast-growing near-minimal organism, was used as a model to explore rational genome designs and construct the iJL208 metabolic model. Through this work, a rational approach to genome design was established, laying the groundwork for model-driven whole-genome engineering.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ye Gao, Hyun Gyu Lim, Hans Verkler, Richard Szubin, Daniel Quach, Irina Rodionova, Ke Chen, James T. Yurkovich, Byung-Kwan Cho, Bernhard O. Palsson
Summary: This study experimentally evaluated 40 uncharacterized proteins in Escherichia coli, confirming 34 as DNA-binding proteins and inferring potential functions for 10 of them. The research significantly expanded the number of confirmed TFs, provided putative functions for newly discovered TFs, and confirmed the functions of four representative TFs through mutant phenotypes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Amir Akbari, James T. Yurkovich, Daniel C. Zielinski, Bernhard O. Palsson
Summary: The study investigates how abiotic constraints shape metabolism in Escherichia coli. It reveals that these constraints are fundamental in driving the evolution of high-affinity phosphate transporters, regulating transcriptional responses to osmotic and acid stress. Understanding these constraints is crucial for comprehending the outcomes of evolutionary adaptation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Colton J. Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O. Palsson
Summary: Escherichia coli can adapt its amino acid and cofactor usage based on different growth environments, as predicted by metabolic models. These models can also be used to study antibiotic resistance and proteome composition, showcasing the intricate properties of functional proteomes in supporting various E. coli lifestyles.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Anand V. Sastry, Nicholas Dillon, Amitesh Anand, Saugat Poudel, Ying Hefner, Sibei Xu, Richard Szubin, Adam M. Feist, Victor Nizet, Bernhard Palsson
Summary: Machine learning analysis of transcriptomics data in Escherichia coli K-12 MG1655 revealed the relationship between antibiotic susceptibility and medium composition. Independent component analysis showed that complex phenotypic changes induced by environmental conditions or antibiotic treatment are linked to the action of a few key transcriptional regulators. Integration of machine learning with biochemical knowledge identified medium-dependent shifts in respiration and iron availability that influence antibiotic susceptibility.
Article
Biology
Henrique Machado, Yara Seif, George Sakoulas, Connor A. Olson, Ying Hefner, Amitesh Anand, Ying Z. Jones, Richard Szubin, Bernhard O. Palsson, Victor Nizet, Adam M. Feist
Summary: Henrique Machado and colleagues describe mutational mechanisms associated with MRSA vancomycin resistance in Staphylococcus aureus using adaptive laboratory evolution experiments focused on tolerance. Their results reveal environment-dependent mutational strategies to vancomycin tolerization and the impact of mutations in regulatory genes, providing insight into the development of antibiotic resistance under multiple conditions.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biology
Irina A. Rodionova, Ye Gao, Anand Sastry, Ying Hefner, Hyun Gyu Lim, Dmitry A. Rodionov, Milton H. Saier, Bernhard O. Palsson
Summary: The study reveals that the putative transporter gene, ydhC, and its regulator, ydhB, are involved in purine transportation, with YdhB activating the expression of the ydhC gene in E. coli. The authors propose renaming the regulator PunR and the transporter PunC.
COMMUNICATIONS BIOLOGY
(2021)
Article
Genetics & Heredity
Donghui Choe, Richard Szubin, Saugat Poudel, Anand Sastry, Yoseb Song, Yongjae Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Summary: RNA sequencing techniques have enabled systematic elucidation of gene expression, transcription start sites, transcript 3' ends, and post-transcriptional processes. A low-cost and highly efficient method called RiboRid has been developed to remove over 90% of rRNA in cells for various transcriptomic studies. This method promises to be robust for large-scale high-throughput bacterial transcriptomic studies.