Article
Biotechnology & Applied Microbiology
Yuanhao Li, Bo Jiang, Weijun Dai
Summary: Essential genes are crucial for bacterial viability and new drug discovery, but some false positives generated by Tn-seq may result from gene deletions by bacteria themselves. Deleting genes should be considered when evaluating essentiality, as it has been underestimated in previous studies.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Daniel R. Weilandt, Pierre Salvy, Maria Masid, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis
Summary: Large-scale kinetic models are essential for understanding the dynamic and adaptive responses of biological systems, but the lack of computational tools for building and analyzing these models has been a limitation. This study presents a Python package (SKiMpy) that bridges this gap by providing an efficient toolbox for generating and analyzing large-scale kinetic models in various biological domains. The toolbox also allows for efficient parameterization of kinetic models and implementation of multispecies bioreactor simulations.
Article
Biotechnology & Applied Microbiology
Subasree Sridhar, Prerna Bhalla, Justin Kullu, Sriya Veerapaneni, Swagatika Sahoo, Nirav Bhatt, G. K. Suraishkumar
Summary: Reactive species play important roles in many diseases, but are often not adequately modeled in current genome-scale metabolic models. By developing a scalable RS reactions module, researchers were able to integrate RS reactions into human metabolic models and highlight dysregulations in important cancer pathways, suggesting varying susceptibility to ferroptosis-targeting treatments in different cancers.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Blanca M. Perez-Sepulveda, Darren Heavens, Caisey Pulford, Alexander Predeus, Ross Low, Hermione Webster, Gregory F. Dykes, Christian Schudoma, Will Rowe, James Lipscombe, Chris Watkins, Benjamin Kumwenda, Neil Shearer, Karl Costigan, Kate S. Baker, Nicholas A. Feasey, Jay C. D. Hinton, Neil Hall
Summary: An efficient and cost-effective pipeline has been developed for large-scale collection and genome sequencing of bacterial isolates. Through a worldwide collaboration, over 10,000 diverse isolates of Salmonella enterica were collected and sequenced at a reagent cost of less than USD$10 per genome. This method is applicable to other large bacterial collections to support global collaborations.
Article
Oncology
Seungyoon Nam, Yongmin Lee
Summary: Gastric cancer is a deadly cancer with different histological subtypes. This study used transcriptome analysis to identify differential metabolic pathways between the diffuse and intestinal subtypes of gastric cancer, including cholesterol homeostasis, xenobiotic metabolism, fatty acid metabolism, the MTORC1 pathway, and glycolysis.
Article
Biotechnology & Applied Microbiology
Yujuan Zheng, Min Chen, Jiaxin Li, Shuangwen Fei, Shuai Shang, Sixin Liu, Longxiang Liu, Congfa Li
Summary: Novacetimonas cocois WE7, isolated from contaminated coconut milk, has been sequenced to investigate its inefficient synthesis of bacterial cellulose (BC) from glucose. The absence of bcs III operons in WE7 may lead to reduced BC production. WE7 metabolizes carbohydrate carbon sources mainly through the Hexose Monophosphate Pathway (HMP) and tricarboxylic acid (TCA) pathways, with a complete gluconic acid production pathway. This study provides crucial information for understanding BC production and regulation mechanisms in N. cocois and lays a foundation for constructing engineered strains tailored for diverse BC application purposes.
FERMENTATION-BASEL
(2023)
Article
Biotechnology & Applied Microbiology
Jason C. Hyun, Bernhard O. Palsson
Summary: We constructed pangenomes for 183 bacterial species and reconstructed the core genome of the last bacterial common ancestor (LBCA) through integrating pangenomics and phylogenetics. The results showed that the gene content of modern and ancestral core genomes is diverse at the individual gene level but similarly distributed by functional category. The LBCA core genome has fundamental biological systems intact but likely requires additional non-core genes for viability.
Article
Biotechnology & Applied Microbiology
Sina Beier, Nicholas R. Thomson
Summary: Panakeia is an easy-to-use tool that provides a detailed view of the pangenome structure, allowing for the discovery and in-depth analysis of features of interest. It analyzes the synteny and structural patterns of the pangenome, providing insights into the biological diversity and evolution of the studied taxon.
Article
Plant Sciences
Zhenfei Yan, Lijun Sang, Yue Ma, Yong He, Juan Sun, Lichao Ma, Shuo Li, Fuhong Miao, Zixin Zhang, Jianwei Huang, Zengyu Wang, Guofeng Yang
Summary: In this study, a high-quality de novo genome assembly for red clover was obtained, with improved assembly quality compared to previously published genomes. The annotated gene models can serve as important resources for molecular genetic breeding and legume evolution studies. Additionally, the evolutionary relationships between red clover and closely related species were analyzed, providing a foundation for studying the evolution of clover and legumes, genomic analysis of forage grass, and improvement of agronomic traits.
Article
Computer Science, Artificial Intelligence
Saloua Bennani, Sophie Ebersold, Mahmoud El Hamlaoui, Bernard Coulette, Mahmoud Nassar
Summary: This paper presents an approach called CAHM for Collaborative Alignment of Heterogeneous Models, which utilizes collaborative engineering and group decision-making principles to ensure the overall consistency of heterogeneous source models. The approach defines two sub-processes for developing inter-model correspondences and ensuring consistency during model evolution.
INTERNATIONAL JOURNAL OF INFORMATION TECHNOLOGY & DECISION MAKING
(2022)
Article
Transportation Science & Technology
A. U. Z. Patwary, Wei Huang, Hong K. Lo
Summary: This paper introduces a metamodel-based simulation optimization framework for calibrating an agent-based multimodal traffic microsimulator, which combines a simplified multimodal traffic model with the metamodel to enhance the efficiency and adaptability of the calibration process.
TRANSPORTATION RESEARCH PART C-EMERGING TECHNOLOGIES
(2021)
Article
Biotechnology & Applied Microbiology
Sizhe Qiu, Hong Zeng, Zhijie Yang, Wei-Lian Hung, Bei Wang, Aidong Yang
Summary: In this study, a dynamic metagenome-scale metabolic model was built to investigate metabolic interactions between Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in yogurt fermentation. The model, which integrated constrained proteome allocation, was validated by comparing predicted bacterial growth, lactose consumption, and lactic acid production with experimental data. The dynamic simulation revealed the mutual dependence of S. thermophilus and L. d. bulgaricus during yogurt fermentation. This dynamic metabolic model of the yogurt bacterial community provides a foundation for computer-aided process design and control of fermented dairy product production.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Multidisciplinary Sciences
Haoqi Shi, Peiwen Xu, Shengxin Wu, Wen Yu, Yazhi Cheng, Zhihua Chen, Xingyou Yang, Xiangwen Yu, Bingjie Li, Anming Ding, Weifeng Wang, Yuhe Sun
Summary: This study used high-throughput sequencing technology to investigate the composition of rhizosphere bacterial communities in different regions, and found that the composition of rhizosphere bacterial communities varied in different regions and was closely related to soil factors.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Andrew Walakira, Damjana Rozman, Tadeja Rezen, Miha Mraz, Miha Moskon
Summary: Omics data can be integrated into a reference model using different model extraction methods (MEMs) to generate context-specific genome-scale metabolic models (GEMs). The choice of MEM, thresholding rule, and threshold presents a challenge, with differences in model size and variability explained by different MEMs observed. Among the MEMs tested, FASTCORE was found to capture the most true variability in the data, particularly related to gender differences.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Piyush Nanda, Amit Ghosh
Summary: Researchers developed a metabolic model of host human cells infected with SARS-CoV-2, predicting rapid virus growth rates. Flux analysis identified lipid metabolism as severely affected during infection, with key enzymes directly interacting with viral proteins. The study demonstrates the importance of metabolic flux analysis in understanding disease biology and potential therapeutic interventions.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Esther Molina-Menor, Helena Gimeno-Valero, Javier Pascual, Juli Pereto, Manuel Porcar
Summary: The study employed a culturomics approach to investigate the bacterial diversity of the Tabernas Desert, resulting in the isolation of a large collection of 254 bacterial strains. The research revealed the untapped bacterial biodiversity in the Tabernas Desert, and demonstrated the potential of simple strategies to yield a significant number of diverse, previously unreported bacterial strains and species.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biology
Antonio Lazcano, Juli Pereto
Summary: Lynn Margulis' endosymbiotic proposal in the late 1960s was a groundbreaking scientific achievement that revolutionized the discussion on the origin of nucleated cells. Despite some aspects of her proposal being refuted, her advocacy for endosymbiosis has significantly contributed to the study of eukaryotic evolution.
Article
Microbiology
Esther Molina-Menor, Angela Vidal-Verdu, Leila Satari, Alba Calonge-Garcia, Javier Pascual, Juli Pereto, Manuel Porcar
Summary: Two novel strains of Gram-staining-negative, aerobic, cocci-shaped bacteria, isolated from a biocrust sample near the Tabernas Desert in Spain, were identified as new species belonging to the genus Belnapia - Belnapia mucosa sp. nov. and Belnapia arida sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Angela Vidal-Verdu, Adriel Latorre-Perez, Esther Molina-Menor, Joaquin Baixeras, Juli Pereto, Manuel Porcar
Summary: This study highlights the diversity and potential biotechnological applications of bacterial communities residing in marine sediments trapped in artificial containers such as PET bottles and aluminum cans.
Article
Microbiology
Maria Castillo Lopez, Beatriz Galan, Manuel Carmona, Juana Maria Navarro Llorens, Juli Pereto, Manuel Porcar, Luis Getino, Elias R. Olivera, Jose M. Luengo, Laura Castro, Jose Luis Garcia
Summary: The highly xerotolerant bacterium Exiguobacterium sp. Helios isolated from a solar panel in Spain shows close relationship to Exiguobacterium sibiricum 255-15 from Siberian permafrost. Both strains demonstrate higher xerotolerance than the model strain Deinococcus radiodurans, with significant changes observed in cell morphology after desiccation. Apart from remarkable desiccation resistance, strain Helios also produces selenium nanoparticles and has been genetically modified, making it a promising candidate for biotechnological applications.
Article
Computer Science, Artificial Intelligence
Charilaos Akasiadis, Miguel Ponce-de-Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
Summary: Computational systems and methods play an important role in biological research, particularly in the understanding and treatment of cancer. This study combines a simulator for tumor cell growth and a genetic algorithm to find effective parameter configurations for drug treatments. Experimental results demonstrate the effectiveness and computational efficiency of the approach.
COMPUTATIONAL INTELLIGENCE
(2022)
Article
Microbiology
Leila Satari, Esther Molina-Menor, Angela Vidal-Verdu, Javier Pascual, Juli Pereto, Manuel Porcar
Summary: A novel bacterium strain M10.9XT, a Gram-stain-negative, non-motile, halophilic bacterium, was isolated from the inner sediment of an aluminium can collected from the Mediterranean Sea. It belongs to a new species within the genus Sagittula.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Angela Vidal-Verdu, Daniela Gomez-Martinez, Adriel Latorre-Perez, Juli Pereto, Manuel Porcar
Summary: Bioprospecting of microorganisms for bioremediation of fuel or oil spills is often done in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing, microbial communities below the lids of fuel deposits in diesel and gasoline cars were analyzed, revealing potential candidates for bioremediation based on their differential growth and degradation patterns. GC-MS analysis of selected strains showed Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera as promising candidates for diesel degradation, with the latter potentially representing a new species with hydrocarbon degrading capabilities.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biochemistry & Molecular Biology
Miguel Ponce-de-Leon, Arnau Montagud, Charilaos Akasiadis, Janina Schreiber, Thaleia Ntiniakou, Alfonso Valencia
Summary: The study used multi-scale models to investigate the complex phenomenon of cell resistance in cancer treatment, demonstrating the importance of considering cells' spatial geometry and population variability when optimizing treatment strategies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Matthew Smith, Miguel Ponce-de-Leon, Alfonso Valencia
Summary: This paper analyzes the causal impact of policy makers in Cataluna, Spain on mobility and COVID19 incidence. The study finds that the decision to close all bars and restaurants for a 5 week period led to a significant reduction in mobility and a slowed incidence rate of COVID19.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Angela Vidal-Verdu, Esther Molina-Menor, Leila Satari, Javier Pascual, Juli Pereto, Manuel Porcar
Summary: A novel Gram-negative, aerobic, motile, rod-shaped, grey bacterium named Maritalea mediter-ranea was isolated from plastic debris in the shallow waters of the Mediterranean Sea (Valencia, Spain). This bacterium is catalase-and oxidase-positive and can grow under mesophilic, neutrophilic, and halophilic conditions.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Arnau Montagud, Miguel Ponce-de-Leon, Alfonso Valencia
Summary: Agent-based modelling has been proven useful in biomedical projects, but current models suffer from limitations such as small scale, lack of cell-specific characterisation, and oversimplified environment description. Tools that allow scalable and real-sized simulations are needed to capture cell-to-cell heterogeneity and system-wide emerging properties in biomedical scenarios. Efforts have been made to implement technologies for simulations at the giga-scale, and improvement in key areas is necessary to achieve simulations closer to digital twins.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2021)
Article
Engineering, Environmental
R. Mailler, M. Ponce de Leon, V Rocher, P. Ginisty
Summary: This study evaluated a new mini screw decanter and investigated the impact of acceleration, relative velocity, and feeding conditions on separation performance. The results demonstrated good sensitivity and consistent trends of the method, as well as a good correspondence between lab-scale and full-scale performances. Additionally, the behavior of five sludges based on their physico-chemical characteristics was compared, showing the applicability and consistency of the method.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
History & Philosophy Of Science
Juli Pereto, Manuel Porcar
Summary: The concept of standardization plays a crucial role in industrial production, but the extent to which it can be achieved in the biological realm is a question that this paper seeks to answer.
METODE SCIENCE STUDIES JOURNAL
(2021)
Article
Health Care Sciences & Services
Alberto Ferrari, Enrico Santus, Davide Cirillo, Miguel Ponce-de-Leon, Nicola Marino, Maria Teresa Ferretti, Antonella Santuccione Chadha, Nikolaos Mavridis, Alfonso Valencia
Summary: The study utilizes an expanded SIR model and considers population density differences to simulate the impact of contact-tracing apps in response to the COVID-19 epidemic.
Results show that even with a small fraction of users, app-mediated contact-tracing can successfully mitigate the epidemic, but containment may be more challenging in areas with higher population density.
This work emphasizes the importance of region-specific demographic and mobility factors for achieving maximum efficacy in addressing COVID-19.
NPJ DIGITAL MEDICINE
(2021)