Article
Medicine, General & Internal
Shuaishi Gao, Ziwei Dai, Hanyu Xu, Luhua Lai
Summary: In this study, we analyzed the metabolic tasks of different cancer types and established cancer type-specific metabolic models, providing new insights into the development of specific anti-cancer drugs and treatment plans for specific cancer subtypes.
FRONTIERS IN MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Chang Dong, J. Carl Schultz, Wei Liu, Jiazhang Lian, Lei Huang, Zhinan Xu, Huimin Zhao
Summary: This study identified novel targets for enhancing SAM production through genome-scale engineering (GSE) and validated their effects in industrial yeast strains, leading to significant increases in SAM productivity. Transcriptomic and metabolomic analyses were conducted to investigate the molecular mechanisms for enhanced SAM accumulation.
METABOLIC ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Joan Cortada-Garcia, Ronan Daly, S. Alison Arnold, Karl Burgess
Summary: Metabolomics is a powerful tool for identifying genetic targets for bioprocess optimization. In this study, the authors used untargeted and targeted metabolomics data to perform metabolic pathway enrichment analysis and identified genetic targets for bioprocess improvement in a streamlined way. The analysis revealed three significantly modulated pathways during succinate production, including two previously known pathways and a newly identified target. This methodology represents a powerful tool for accelerating bioprocess optimization.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Joan Cortada-Garcia, Ronan Daly, S. Alison Arnold, Karl Burgess
Summary: Metabolomics is a powerful tool for identifying genetic targets for bioprocess optimization. This study introduced the use of metabolic pathway enrichment analysis with targeted and untargeted metabolomics data to streamline the identification of genetic targets for bioprocess improvement. The analysis of an Escherichia coli succinate production bioprocess revealed three significantly modulated pathways, two of which were consistent with previous efforts while the third pathway, ascorbate and aldarate metabolism, was a new target for succinate production.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Michal Marczyk, Vignesh Gunasekharan, David Casadevall, Tao Qing, Julia Foldi, Raghav Sehgal, Naing Lin Shan, Kim R. M. Blenman, Tess A. O'Meara, Sheila Umlauf, Yulia Surovtseva, Viswanathan Muthusamy, Jesse Rinehart, Rachel J. Perry, Richard Kibbey, Christos Hatzis, Lajos Pusztai
Summary: This study examines the expression patterns of isozymes in cancer and identifies potential therapeutic targets. It shows that the loss of isozyme diversity in cancer can be exploited for anticancer therapy.
Article
Biochemistry & Molecular Biology
Koichi Fujisawa, Toshihiko Matsumoto, Naoki Yamamoto, Takahiro Yamasaki, Taro Takami
Summary: Research has found that iron chelation therapy can alter intracellular metabolism and targeting these metabolic changes with combination anticancer therapy can effectively treat liver cancer. By increasing the concentration of DFO, DFO-resistant cell lines were established, and it was discovered that DFO-induced metabolic changes are specific targets for the development of efficient anticancer therapies.
Article
Immunology
Sainan Zhang, Su Liu, Ling Hong, Xiaohui Wang, Lianghui Diao, Songchen Cai, Tailang Yin, Yong Zeng
Summary: Recent studies have suggested that progesterone (P4) may be associated with the metabolic activities and signaling pathways of dendritic cells (DCs), although the underlying mechanisms are yet to be fully understood.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Engineering, Aerospace
Ruijun Hu, Yulin Zhang, Li Fan
Summary: This paper proposes a new method for lunar sun-synchronous roving in robotic polar exploration and investigates the spatiotemporal constraints. By constructing three-dimensional lunar spatiotemporal maps and designing a multi-speed node expansion mechanism and safety optimization algorithms, a new planning algorithm is proposed. Experimental results show that this method has advantages in terms of motion safety and energy reliability.
Article
Biochemistry & Molecular Biology
Seung Hee Lee, Suyeon Cho, Jong Youl Lee, Jung Yeon Hong, Suji Kim, Myong-Ho Jeong, Won-Ho Kim
Summary: Aging is a global problem, with higher prevalence and mortality of arterial and venous thromboembolism (VTE) in the elderly population. This study identifies three specific antithrombotic drug targets through the analysis of platelet proteome in aged mice.
Review
Chemistry, Physical
Xin Pu, Yejun Han
Summary: This review summarizes the methods and processes of biofixation of carbon dioxide, including six natural pathways and the latest variant pathway. It also discusses the factors affecting the efficiency of CO2 fixation and the recent progress in improving it through enzyme and metabolic engineering. The applications and challenges of artificial CO2 fixation pathways are also discussed.
Review
Agricultural Engineering
Swati Joshi, SukhDev Mishra
Summary: The rising global energy demands and climate crisis have created an unprecedented need for the bio-based circular economy. Metabolic engineering is at the forefront of developing microbial chassis for biofuel bio-foundries to meet the industrial needs for clean energy.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Physical
Se-Si Li, Xiao-Lin Zhao, Yu-Si Liu, Jian-Jun Liu, Kai-Xue Wang, Jie-Sheng Chen
Summary: Rational catalyst design is proposed as an efficient strategy to address the issue of accumulating Li2O2 on the cathode in Li-O-2 batteries (LOBs). Porous Ni2P nanorods with exposed (0001) facets exhibit superior electrochemical performance due to the interaction between exposed facets and the nucleation and growth of LiO2 or Li2O2, resulting in the formation of large Li2O2 sheets and flower-like nanoflake assemblies.
ENERGY STORAGE MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Kun Chen, Shengqiu Liu, Wei Zhu, Panchao Yin
Summary: The study finds that surface engineering of polyoxovanadate (POV) clusters can improve their bioavailability and pharmacokinetic properties, mitigating the adverse effects of vanadium compounds. Surface-engineered POVs have shorter elimination half-life and higher elimination rates, which favor the elimination of possible side effects. In addition, surface engineering significantly increases the oral bioavailability of POVs. These findings suggest that surface engineering is an effective approach to optimize the therapeutic efficacy of POVs and reduce their adverse effects.
Article
Biochemistry & Molecular Biology
Ilkay Irem Ozbek, Kutlu O. Ulgen
Summary: Computer models are used to imitate the characteristics of medulloblastoma (MB) and find effective therapeutic targets with minimal toxic effects on healthy cells. The study suggests that interfering with enzymes related to fatty acid and cholesterol synthesis, suppressing cardiolipin production, and inhibiting tumor-supporting sphingolipid metabolites may be effective approaches for treating MB. Additionally, decreasing succinate synthesis and GABA-catalyzing enzyme activity concurrently may be a promising strategy for metastatic MB.
Article
Biochemical Research Methods
Hong Wang, Jingqing Zhang, Zhigang Lu, Weina Dai, Chuanjiang Ma, Yun Xiang, Yonghong Zhang
Summary: This study developed useful drug repurposing tools based on data-driven modeling and network pharmacology. Hub proteins important in the onset and development of COVID-19 were identified as potential targets for repurposing approved drugs. The study also predicted the therapeutic effects of bioactive herbal ingredients and chemicals using network distance metrics in the protein-protein interaction network. The method proves to be advantageous in feasibility analysis of drug repurposing or drug screening during pandemic outbreaks.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Environmental Sciences
Sergio A. Silva, Angeles Val del Rio, Antonio L. Amaral, Eugenio C. Ferreira, M. Madalena Alves, Daniela P. Mesquita
Summary: Quantitative image analysis (QIA) was used to monitor the morphology of activated sludge during granulation process, allowing for the clear definition of the transition from flocculation to granulation processes. Multivariate statistical analysis of the QIA data successfully distinguished granulation status and predicted sludge settling properties.
Article
Biochemical Research Methods
Vipul P. Rane, Rushikesh H. Patil, Kiran R. Patil, Amin R. Pathan, Sukantakumar Naik, Vinod K. Ahirrao, Rajiv A. Jadhav, Ravindra D. Yeole
Summary: This report describes the identification and quantification of impurities and degradation products in the antibacterial drug WCK 771 using liquid chromatography tandem mass spectrometry. The research developed two methods, one for identification and another for quantification, that are accurate and sensitive. The methods can be used for quality control and stability studies of the drug.
Review
Microbiology
Anna E. Lindell, Maria Zimmermann-Kogadeeva, Kiran R. Patil
Summary: The gut microbiota composition is associated with diseases and medication response, and understanding the factors shaping it is important. In addition to diet, small-molecule drugs and environmental pollutants can also impact the microbiota composition.
NATURE REVIEWS MICROBIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Primrose Boynton, Kiran R. Patil, Irene Stefanini, Rike Stelkens, Francisco A. Cubillos
Correction
Biochemical Research Methods
Vipul P. Rane, Vinod K. Ahirrao, Kiran R. Patil, Rajiv A. Jadhav, Ravindra D. Yeole
Letter
Ecology
Daniel Machado, Kiran R. R. Patil
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Natalia Gabrielli, Christoniki Maga-Nteve, Eleni Kafkia, Mandy Rettel, Jakob Loeffler, Stephan Kamrad, Athanasios Typas, Kiran Raosaheb Patil
Summary: By using C-13 isotope tracing, we identified cross-fed metabolites in co-cultures of Saccharomyces cerevisiae and Lactococcus lactis. Our results showed that the yeast utilized galactose and lactic acid as carbon sources, and revealed a complex pattern of amino acid exchange between the two species. This study demonstrates the utility of C-13-based proteomics for uncovering microbial interactions.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Gavin D. Garland, Kiran R. Patil, Suzanne D. Turner, Anne E. Willis
Summary: Most small-molecule drugs for cancer treatment in the past 40 years are derived from natural compounds. Bacteria can provide a large number of resources for developing new anti-cancer therapeutics to tackle the diversity of malignant diseases. However, achieving selective targeting of cancer cells is challenging.
Article
Biology
Mueberra Fatma Cesur, Arianna Basile, Kiran Raosaheb Patil, Tunahan Cakir
Summary: The high conservation of disease-associated genes between drosophila and humans enables the use of drosophila as a model organism to study metabolic disorders. In this study, a comprehensive genome-scale metabolic network model of drosophila was developed using an orthology-based approach. The resulting model, iDrosophila1, showed superior or comparable results compared to other available fly models and was able to successfully elucidate metabolic pathways in response to Parkinson's disease. Overall, iDrosophila1 is a promising tool for investigating system-level metabolic alterations in drosophila.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Karin Mitosch, Martin Beyss, Prasad Phapale, Bernhard Drotleff, Katharina Noh, Theodore Alexandrov, Kiran R. Patil, Athanasios Typas
Summary: To investigate how pathogenic bacteria adapt and obtain essential nutrients from mammalian host cells, researchers developed a stable isotopic labeling method to track Salmonella enterica metabolites during intracellular proliferation. By combining liquid chromatography-mass spectrometry (LC-MS) with metabolic modeling, they identified carbon sources, metabolic pathways, and reaction rates used by Salmonella. The study highlighted the significance of the Entner-Doudoroff pathway and phosphoenolpyruvate carboxylase in the intracellular proliferation of Salmonella. Furthermore, the metabolic labeling strategy opens new avenues for understanding pathogen metabolism inside host cells.
Review
Microbiology
Christian Kost, Kiran Raosaheb Patil, Jonathan Friedman, Sarahi L. Garcia, Markus Ralser
Summary: Microbial communities are shaped by ecological and environmental interactions, where antagonistic and synergistic interactions play important roles in driving their structure and dynamics.
NATURE MICROBIOLOGY
(2023)
Review
Engineering, Environmental
Daniela P. Mesquita, Cristina Quintelas, Eugenio C. Ferreira
Summary: Microplastics (MP) are commonly found in our daily life and can enter terrestrial and aquatic ecosystems through wastewater treatment plants (WWTPs), causing adverse effects on water quality, aquatic life, and soil and groundwater contamination. Despite efforts to remove MP in WWTPs, many particles are still released into natural water bodies.
ENVIRONMENTAL SCIENCE-ADVANCES
(2023)
Article
Engineering, Environmental
Antonio Melo, Joana Costa, Cristina Quintelas, Eugenio C. Ferreira, Daniela P. Mesquita
Summary: This study assessed the impact of Desloratadine on the performance of activated sludge and the production of extracellular polymeric substances (EPS) in a wastewater treatment process. The results showed that high concentrations of Desloratadine reduced the removal of chemical oxygen demand and ammonium, and increased the production of EPS. Fluorescence analysis revealed differences in the chemical structure of EPS caused by Desloratadine exposure.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Engineering, Environmental
Cristiano Leal, Daniela P. P. Mesquita, Antonio L. Amard, Eugenio C. C. Ferreira, Angeles Val del Rio
Summary: This study successfully predicted the morphological and structural parameters of sludge in the presence of pharmaceutical active compounds using a sequencing batch reactor with aerobic granular sludge. These results highlight the importance of this method for monitoring dysfunctions in aerobic granular sludge.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Engineering, Environmental
Cyntia Ely, Irina S. Moreira, Joao Paulo Bassin, Daniela P. Mesquita, Joana Costa, Eugenio C. Ferreira, Marcia W. C. Dezotti, Paula M. L. Castro
Summary: An AGS SBR reactor adapted to salinity was used for the treatment of synthetic saline wastewater containing EDCs. The results showed that E2 was completely biodegraded, while the removal efficiency of EE2 and BPA was lower. The activity of phosphate-accumulating organisms was affected by EDCs, but the activity of ammonium- and nitrite-oxidizing bacteria was not significantly affected. The microbial diversity increased after the addition of EDCs.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)