A5001997933- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Gut microbiota and health
- Enzyme Catalysis and Immobilization
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Probiotics and Fermented Foods
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Process Optimization and Integration
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Shape Memory Alloy Transformations
- Textile materials and evaluations
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Nonlocal and gradient elasticity in micro/nano structures
- Paleopathology and ancient diseases
- Liver Disease Diagnosis and Treatment
- Soybean genetics and cultivation
- GABA and Rice Research
- Evolutionary Game Theory and Cooperation
- Inflammatory Bowel Disease
Colorado State University
2019-2024
Pennsylvania State University
2017-2020
Oak Ridge National Laboratory
2019
Technical University of Denmark
2014-2017
Peking University
2016
Hong Kong Polytechnic University
2001-2014
Food Research Institute
2014
Genome-scale metabolic modeling has become widespread for analyzing microbial metabolism. Extending this established paradigm to more complex communities is emerging as a promising way unravel the interactions and biochemical repertoire of these omnipresent systems. While several techniques have been developed communities, little emphasis placed on need impose time-averaged constant growth rate across all members community ensure co-existence stability. In absence constraint, faster growing...
Abstract Microbial breakdown of organic matter is one the most important processes on Earth, yet controls decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during despite selection effects location, climate season. We generated metagenome-assembled genome library from cadaver-associated soils integrated it with metabolomics data to identify links between...
The gut microbiota modulates obesity and associated metabolic phenotypes in part through intestinal farnesoid X receptor (FXR) signaling. Glycine-β-muricholic acid (Gly-MCA), an FXR antagonist, has been reported to prevent or reverse high-fat diet (HFD)-induced genetic obesity, insulin resistance, fatty liver; however, the mechanism by which these are improved is not fully understood. current study investigated influence of activity on community structure function its impact hepatic lipid...
In a genome-scale metabolic model, the biomass produced is defined to have molecular weight (MW) of 1 g mmol-1. This critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, standard rarely verified in current practice chemical formulae components such as proteins, nucleic acids lipids are often represented by undefined side groups (e.g. X, R).We introduced systematic procedure checking ensuring complete mass...
Abstract Motivation Microbes are essential part of all ecosystems, influencing material flow and shaping their surroundings. Metabolic modeling has been a useful tool provided tremendous insights into microbial community metabolism. However, current methods based on flux balance analysis (FBA) usually fail to predict metabolic regulatory strategies that lead long-term survival stability especially in heterogenous communities. Results Here, we introduce novel reinforcement learning algorithm,...
Rhodosporidium toruloides is a red, basidiomycetes yeast that can accumulate large amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic capabilities, we reconstructed genome-scale model R. IFO0880's network (iRhto1108) accounting for 2204 reactions, 1985 metabolites 1108 genes. In work, integrated supplemented the current knowledge with in-house generated biomass composition experimental measurements pertaining to organism's capabilities. Predictions...
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data quantitative prediction physicochemically biochemically feasible phenotypic states. The COBRA Toolbox is comprehensive software suite interoperable methods. It has found widespread applications in biology, biomedicine, biotechnology because its functions can be flexibly combined to implement tailored protocols any biochemical network. Version 3.0...
Elementary flux mode (EFM) is a fundamental concept as well useful tool in metabolic pathway analysis. One important role of EFMs that every distribution can be decomposed into set and number methods to study distributions originated from it. Yet finding such decompositions requires the complete EFMs, which intractable genome-scale networks due combinatorial explosion.In this article, we proposed an algorithm decompose networks. It iterative scheme mixed integer linear program. Unlike...
Many platform chemicals can be produced from renewable biomass by microorganisms, with organic acids making up a large fraction. Intolerance to the resulting low pH growth conditions, however, remains challenge for industrial production of microorganisms. Issatchenkia orientalis SD108 is promising host because it tolerant acidic conditions as 2.0. With goal systematically assess metabolic capabilities this non-model yeast, we developed genome-scale model I. spanning 850 genes, 1826...
Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria agriculture because they can fix atmospheric nitrogen make it available to legumes through establishment of a symbiotic relationship with their host plants. In this work, we studied fixation process in microsymbiont Sinorhizobium fredii at genome level. A metabolic model was built using annotation literature reconstruct form S. . Genes controlling were identified by simulating gene knockouts....
Microbial metabolic interactions impact ecosystems, human health and biotechnology profoundly. However, their determination remains elusive, invoking an urgent need for predictive models seamlessly integrating metabolism with evolutionary principles that shape community interactions.Inspired by the game theory, we formulated a bi-level optimization framework termed NECom which any feasible solutions are Nash equilibria of microbial with/without outer-level (community) objective function....
Abstract Background Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded flux ranges are often encountered. TICs satisfy the mass balance directionality constraints but violate second law of thermodynamics. Current practices involve implementing additional to ensure not only optimal also loopless distributions. However, mixed integer linear...
Background: The gut microbiota is a heterogeneous group of microbes that spatially distributed along various sections the intestines and across mucosa lumen in each section. Understanding dynamics between differential microbial populations driving forces for observed spatial organization will provide valuable insights into important questions such as nature colonization infant different types inflammatory bowel disease localized regions intestines. However, most studies, sampled only at...
Abstract Microbes are essential part of all ecosystems, influencing material flow and shaping their surroundings. Metabolic modeling has been a useful tool provided tremendous insights into microbial community metabolism. However, current methods based on flux balance analysis (FBA) usually fail to predict metabolic regulatory strategies that lead long-term survival stability especially in heterogenous communities. Here we introduce novel reinforcement learning algorithm, Self-Playing...
Chromosome replication in Escherichia coli is initiated by DnaA. DnaA binds ATP which essential for formation of a DnaA-oriC nucleoprotein complex that promotes strand opening, helicase loading and replisome assembly. Following initiation, DnaAATP converted to DnaAADP primarily the Regulatory Inactivation process (RIDA). In RIDA deficient cells, accumulates leading uncontrolled initiation cell death accumulation DNA breaks. Mutations suppress deficiency either dampen overinitiation or permit...
Abstract Motivation: Elementary flux mode (EFM) is a useful tool in constraint-based modeling of metabolic networks. The property that every distribution can be decomposed as weighted sum EFMs allows certain applications to studying distributions. existence biologically infeasible and the non-uniqueness decomposition, however, undermine applicability such methods. Efforts have been made find feasible by incorporating information from transcriptional regulation thermodynamics. Yet, no attempt...
Gas fermentation provides a promising platform to turn low-cost and readily available single-carbon waste gases into commodity chemicals, such as 2,3-butanediol. Clostridium autoethanogenum is usually used robust flexible chassis for gas fermentation. Here, we leveraged constraint-based stoichiometric modeling kinetic ensemble of the C. metabolic network provide systematic in silico analysis engineering interventions 2,3-butanediol overproduction low carbon substrate loss dissipated CO2. Our...
Abstract Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences subsequently attaching biological information to those elements. DRAM a tool developed annotate bacterial, archaeal, viral genomes derived from pure cultures or metagenomes. goes beyond traditional tools by distilling multiple gene annotations level summaries potential. Despite these benefits, downside requirement large computational resources, which limits its...