A thermodynamic bottleneck in the TCA cycle contributes to acetate overflow in .

During aerobic growth, relies on acetate overflow metabolism, a process where glucose is incompletely oxidized to acetate, for its bioenergetic needs. Acetate is not immediately captured as a carbon source and is excreted as waste by cells. The underlying factors governing acetate overflow in have not been identified.

Pathway Thermodynamic Analysis Postulates Change in Glutamate Metabolism as a Key Factor in Modulating Immune Responses.

Background: Temperature, as seen during fever, plays a pivotal role in modulating immune responses and maintaining cellular homeostasis. Shifts in temperature influence the thermodynamic feasibility of metabolic reactions, with Gibbs free energy (ΔG) serving as a key indicator of the spontaneity of reactions under specific conditions. By altering ΔG in response to temperature changes across various metabolite concentrations and cell types, we can gain insights into the thermodynamic properties of metabolic pathways and identify critical factors involved in metabolism and immune function.

Dissecting metabolic landscape of alveolar macrophage.

The highly plastic nature of Alveolar Macrophage (AM) plays a crucial role in the defense against inhaled particulates and pathogens in the lungs. Depending on the signal, AM acquires either the classically activated M1 phenotype or the alternatively activated M2 phenotype. In this study, we investigate the metabolic shift in the activated phases of AM (M1 and M2 phases) by reconstructing context specific Genome-Scale Metabolic (GSM) models.

Enzyme-constrained Metabolic Model of Identified Glycerol-3-phosphate Dehydrogenase as an Alternate Electron Sink.

, the causative agent of syphilis, poses a significant global health threat. Its strict intracellular lifestyle and challenges in cultivation have impeded detailed metabolic characterization. In this study, we present iTP251, the first genome-scale metabolic model of , reconstructed and extensively curated to capture its unique metabolic features.

A thermodynamic bottleneck in the TCA cycle contributes to acetate overflow in .

During aerobic growth, relies on acetate overflow metabolism, a process where glucose is incompletely oxidized to acetate, for its bioenergetic needs. Acetate is not immediately captured as a carbon source and is excreted as waste by cells. The underlying factors governing acetate overflow in have not been identified.

Deciphering sphingolipid biosynthesis dynamics in cell cultures: Quantitative analysis amid data variability.

Sphingolipids are pivotal for plant development and stress responses. Growing interest has been directed toward fully comprehending the regulatory mechanisms of the sphingolipid pathway. We explore its biosynthesis and homeostasis in cell cultures, shedding light on fundamental metabolic mechanisms.

Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in persistence.

Unlabelled: Upon nutrient starvation, serovar L2 (CTL) shifts from its normal growth to a non-replicating form, termed persistence. It is unclear if persistence reflects an adaptive response or a lack thereof. To understand this, transcriptomics data were collected for CTL grown under nutrient-replete and nutrient-starved conditions.

Optimal Protein Allocation Controls the Inhibition of GltA and AcnB in .

(Ngo) is a major concern for global public health due to its severe implications for reproductive health. Understanding its metabolic phenotype is crucial for comprehending its pathogenicity. Despite Ngo's ability to encode TCA cycle proteins, GltA and AcnB, their activities are notably restricted.

Quantitative Dynamic Analysis of Sphingolipid Biosynthesis in .

Sphingolipids are pivotal for plant development and stress responses. Growing interest has been directed towards fully comprehending the regulatory mechanisms of the sphingolipid pathway. We explore its biosynthesis and homeostasis in cell cultures, shedding light on fundamental metabolic mechanisms.

A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation.

Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolic model, ZMA6517, and contextualized it with heat and cold stress transcriptomics data using expression distributed reaction flux measurement (EXTREAM) algorithm.

Erratum: Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling.

[This corrects the article DOI: 10.1016/j.isci.

Protocol to develop a synthetic biology toolkit for the non-model bacterium R. palustris.

Numerous biology tools are developed to work for model organisms, which, however, do not work effectively in non-model organisms. Here, we present a protocol for developing a synthetic biology toolkit for Rhodopseudomonas palustris CGA009, a non-model bacterium with unique metabolic properties. We describe steps for introducing and characterizing biological devices in non-model bacteria, such as the utilization of fluorescence markers and RT-qPCR.

Synthesis of Mixed-Phase TiO-ZrO Nanocomposite for Photocatalytic Wastewater Treatment.

The use of TiO nanoparticles for photocatalysis for the degradation of organic dyes under UV light for wastewater treatment has been widely studied. However, the photocatalytic characteristics of TiO nanoparticles are inadequate due to their UV light response and higher band gap. In this work, three nanoparticles were synthesized: (i) TiO nanoparticle was synthesized by a sol-gel process.

Supplementation of Sulfide or Acetate and 2-Mercaptoethane Sulfonate Restores Growth of the Δ Deletion Mutant during Methylotrophic Methanogenesis.

Methanogenic archaea are important organisms in the global carbon cycle that grow by producing methane gas. is a methanogenic archaeum that can grow using methylated compounds, carbon monoxide, or acetate and produces renewable methane as a byproduct. However, there is limited knowledge of how combinations of substrates may affect metabolic fluxes in methanogens.

Opening the door to nitrogen fixation in oxygenic phototrophs.

Conveying biological nitrogen fixation (BNF) to photosynthetic species may be the next agricultural revolution, yet poses major engineering challenges. Liu et al. created a diazotrophic strain of a previously non-nitrogen-fixing species, the cyanobacterium Synechocystis sp.

Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 through a Genome-Scale Metabolic and Expression Model.

Rhodopseudomonas palustris CGA009 is a Gram-negative purple nonsulfur bacterium that grows phototrophically by fixing carbon dioxide and nitrogen or chemotrophically by fixing or catabolizing a wide array of substrates, including lignin breakdown products for its carbon and fixing nitrogen for its nitrogen requirements. It can grow aerobically or anaerobically and can use light, inorganic, and organic compounds for energy production. Due to its ability to convert different carbon sources into useful products during anaerobic growth, this study reconstructed a metabolic and expression (ME) model of R.

Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling.

Pancreatic ductal adenocarcinoma (PDAC) is a major research focus because of its poor therapy response and dismal prognosis. PDAC cells adapt their metabolism to the surrounding environment, often relying on diverse nutrient sources. Because traditional experimental techniques appear exhaustive to find a viable therapeutic strategy, a highly curated and omics-informed PDAC genome-scale metabolic model was reconstructed using patient-specific transcriptomics data.

Rhodopseudomonas palustris: A biotechnology chassis.

Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production.

Early detection of Parkinson disease using stacking ensemble method.

Parkinson's disease (PD) is a common progressive neurodegenerative disorder that occurs due to corrosion of the substantianigra, located in the thalamic region of the human brain, and is responsible for the transmission of neural signals throughout the human body using brain chemical, termed as "dopamine." Diagnosis of PD is difficult, as it is often affected by the characteristics of the medical data of the patients, which include the presence of various indicators, imbalance cases of patients' data records, similar cases of healthy/affected persons, etc. Hence, sometimes the process of diagnosis may also be affected by human error.

Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium .

Harnessing the unique biochemical capabilities of non-model microorganisms would expand the array of biomanufacturing substrates, process conditions, and products. There are non-model microorganisms that fix nitrogen and carbon dioxide, derive energy from light, catabolize methane and lignin-derived aromatics, are tolerant to physiochemical stresses and harsh environmental conditions, store lipids in large quantities, and produce hydrogen. Model microorganisms often only break down simple sugars and require low stress conditions, but they have been engineered for the sustainable manufacture of numerous products, such as fragrances, pharmaceuticals, cosmetics, surfactants, and specialty chemicals, often by using tools from synthetic biology.

Heterologous phasin expression in CGA009 for bioplastic production from lignocellulosic biomass.

CGA009 is a metabolically robust microbe that can utilize lignin breakdown products to produce polyhydroxyalkanoates (PHAs), biopolymers with the potential to replace conventional plastics. Our recent efforts suggest PHA granule formation is a limiting factor for maximum production of the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) by The Phap1 phasin () from the PHB-producing model bacterium H16 was expressed in with the aim of overproducing PHBV from the lignin breakdown product coumarate by fostering smaller and more abundant granules. Expression of yielded PHBV production from aerobically (0.

Staphylococcal ClpXP protease targets the cellular antioxidant system to eliminate fitness-compromised cells in stationary phase.

The transition from growth to stationary phase is a natural response of bacteria to starvation and stress. When stress is alleviated and more favorable growth conditions return, bacteria resume proliferation without a significant loss in fitness. Although specific adaptations that enhance the persistence and survival of bacteria in stationary phase have been identified, mechanisms that help maintain the competitive fitness potential of nondividing bacterial populations have remained obscure.