Production Of Small Molecules Research Articles

Multiscale modelling of bioprocess dynamics and cellular growth

BackgroundFermentation processes are essential for the production of small molecules, heterologous proteins and other commercially important products. Traditional bioprocess optimisation relies on phenomenological models that focus on macroscale variables like biomass growth and protein yield. However, these models often fail to consider the crucial link between macroscale dynamics and the intracellular activities that drive metabolism and proteins synthesis.ResultsWe introduce a multiscale model that not only captures batch bioreactor dynamics but also incorporates a coarse-grained approach to key intracellular processes such as gene expression, ribosome allocation and growth. Our model accurately fits biomass and substrate data across various Escherichia coli strains, effectively predicts acetate dynamics and evaluates the expression of heterologous proteins. By integrating construct-specific parameters like promoter strength and ribosomal binding sites, our model reveals several key interdependencies between gene expression parameters and outputs such as protein yield and acetate secretion.ConclusionsThis study presents a computational model that, with proper parameterisation, allows for the in silico analysis of genetic constructs. The focus is on combinations of ribosomal binding site (RBS) strength and promoters, assessing their impact on production. In this way, the ability to predict bioreactor dynamics from these genetic constructs can pave the way for more efficient design and optimisation of microbial fermentation processes, enhancing the production of valuable bioproducts.

Identification of new SdiA regulon members of Escherichia coli, Enterobacter cloacae, and Salmonella enterica serovars Typhimurium and Typhi.

Many bacterial species detect their own population density through the production, release, and detection of small molecules (quorum sensing). Salmonella and other Enterobacteriaceae have a modified system that detects the N-acyl-homoserine lactones of other bacteria through the solo quorum sensing receptor SdiA, a behavior known as eavesdropping. The roles of sdiA-dependent eavesdropping in the lifecycles of these bacteria are unknown. In this study, we identify sdiA-dependent transcriptional responses in two clinically relevant serovars of Salmonella, Typhimurium and Typhi, and note that their responses are partially conserved. We also demonstrate for the first time that sdiA-dependent regulation of genes is partially conserved in Enterobacter cloacae and Escherichia coli as well, indicating a degree of commonality in eavesdropping among the Enterobacteriaceae.

Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis.

Spirulina is the common name for the edible, nonheterocystous, filamentous cyanobacterium Arthrospira platensis that is grown industrially as a food supplement, animal feedstock, and pigment source. Although there are many applications for engineering this organism, until recently no genetic tools or reproducible transformation methods have been published. While recent work showed the production of a diversity of proteins in A. platensis, including single-domain antibodies for oral delivery, there remains a need for a modular, characterized genetic toolkit. Here, we independently establish a reproducible method for the transformation of A. platensis and engineer this bacterium to produce acetaminophen as proof-of-concept for small molecule production in an edible host. This work opens A. platensis to the wider scientific community for future engineering as a functional food for nutritional enhancement, modification of organoleptic traits, and production of pharmaceuticals for oral delivery.

Removal of enrofloxacin as well as nutrients in mariculture water by Sesuvium portulacastrum system: Insights for biodegradation, ecotoxicity of enrofloxacin

Antibiotic contamination and eutrophication in mariculture have become problems that cannot be ignored, and enrofloxacin (ENR), as an example, is especially widely used in mariculture. This study firstly revealed that Sesuvium portulacastrum, a plant with world-wide distribution in coastal zones, with its rhizosphere microorganisms, could remove ENR as well as nutrients. The S. portulacastrum system could degrade ENR to small-molecule products 1,2,3,4-tetrahydroquinolin-4-ol and (2,4-dihydroxyphenyl)-cyclopropylamine. And there were 81.3–39.2 % removals of ENR with 0.01-100 mg/L. Although ENR significantly influenced functions of rhizosphere microbial community, like decreasing nitrogen fixation, shifting trophic strategies from phototrophy to chemoheterotrophy, nutrients (NH4+-N, NO2−-N, NO3−-N and total dissolved phosphorus) removal of S. portulacastrum system was essentially unaffected at low ENR concentration (< 1 mg/L). The removal mechanism of S. portulacastrum system was explored. Neither of the isolated root exudates and rhizosphere bacteria could degrade ENR, however, without rhizosphere bacteria, ENR removal rate would decrease. Root proteins including oxidase, decarboxylase, dehydrogenase, such as laccase, isocitrate dehydrogenase, delta-1-pyrroline-5-carboxylate dehydrogenase were overexpressed. Additionally, endocytosis is a pathway for antibiotics to enter S. portulacastrum. This study demonstrated that S. portulacastrum system could be used for remediation of antibiotics-nutrients combined pollution, and deepened understanding the antibiotic removal mechanism of macrophytes in mariculture, moreover, provided new macroplant species and a theoretical basis for antibiotics removal in aquatic systems.

The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies.

SUMMARYThe human microbiota encompasses the diverse communities of microorganisms that reside in, on, and around various parts of the human body, such as the skin, nasal passages, and gastrointestinal tract. Although research is ongoing, it is well established that the microbiota exert a substantial influence on the body through the production and modification of metabolites and small molecules. Disruptions in the composition of the microbiota-dysbiosis-have also been linked to various negative health outcomes. As humans embark upon longer-duration space missions, it is important to understand how the conditions of space travel impact the microbiota and, consequently, astronaut health. This article will first characterize the main taxa of the human gut microbiota and their associated metabolites, before discussing potential dysbiosis and negative health consequences. It will also detail the microbial changes observed in astronauts during spaceflight, focusing on gut microbiota composition and pathogenic virulence and survival. Analysis will then turn to how astronaut health may be protected from adverse microbial changes via diet, exercise, and antibiotics before concluding with a discussion of the microbiota of spacecraft and microbial culturing methods in space. The implications of this review are critical, particularly with NASA's ongoing implementation of the Moon to Mars Architecture, which will include weeks or months of living in space and new habitats.

Hirocidins, Cytotoxic Metabolites from Streptomyces hiroshimensis, Induce Mitochondrion-Mediated Apoptosis.

Recent advances in whole genome sequencing have revealed an immense microbial potential for the production of therapeutic small molecules, even from well-known producers. To access this potential, we subjected prominent antimicrobial producers to alternative antiproliferative assays using persistent cancer cell lines. Described herein is our discovery of hirocidins, novel secondary metabolites from Streptomyces hiroshimensis with antiproliferative activities against colon and persistent breast cancer cells. Hirocidin A is an unusual nine-membered carbocyclic maleimide and hirocidins B and C are relatives with an unprecedented, bridged azamacrocyclic backbone. Mode of action studies show that hirocidins trigger mitochondrion-dependent apoptosis by inducing expression of the key apoptotic effector caspase-9. The discovery of new cytotoxins contributes to scaffold diversification in anticancer drug discovery and the reported modes of action and concise total synthetic route for variant A set the stage for unraveling specific targets and biochemical interactions of the hirocidins.

Study on the cracking process of epoxy resin under oxygen and water atmosphere based on ReaxFF force field

Amino-cured epoxy resins are widely used in the electrical and electronic industry for their excellent properties. To investigate the mechanism of the effect of O2 and H2O on the pyrolysis behavior of epoxy resin, in this paper, the cross-linked structure of bisphenol A type epoxy resin cured by adducts of diethylenetriamine and butyl glycidyl ether is modeled based on the ReaxFF force field, and the thermal decomposition processes at different temperatures and gas atmospheres were simulated and the pathways of the small molecule products were clarified. The results show that epoxy resin will produce small molecule gas products, such as H2, CO, H2O, OH, CH2O, and free radicals, in the process of pyrolysis; the presence of amino groups also generates nitrogen-containing radicals, such as CN, CH2N, and C2H4N; as the reaction temperature increases, the rate of pyrolysis reaction will be accelerated. The same temperature in oxygen and water atmospheres can accelerate the breakage of epoxy resin main chain by promoting the breakage of carbon and oxygen bonds and, at the same time, promote the generation of small molecule gases, such as H2 and CO.

Hirocidins, Cytotoxic Metabolites from Streptomyces hiroshimensis, Induce Mitochondrion‐Mediated Apoptosis

AbstractRecent advances in whole genome sequencing have revealed an immense microbial potential for the production of therapeutic small molecules, even from well‐known producers. To access this potential, we subjected prominent antimicrobial producers to alternative antiproliferative assays using persistent cancer cell lines. Described herein is our discovery of hirocidins, novel secondary metabolites from Streptomyces hiroshimensis with antiproliferative activities against colon and persistent breast cancer cells. Hirocidin A is an unusual nine‐membered carbocyclic maleimide and hirocidins B and C are relatives with an unprecedented, bridged azamacrocyclic backbone. Mode of action studies show that hirocidins trigger mitochondrion‐dependent apoptosis by inducing expression of the key apoptotic effector caspase‐9. The discovery of new cytotoxins contributes to scaffold diversification in anticancer drug discovery and the reported modes of action and concise total synthetic route for variant A set the stage for unraveling specific targets and biochemical interactions of the hirocidins.

Electrochemical reduction of CO2 on a CoTPP/MWCNT composite: Investigation of operation parameters influence on CH3OH production by differential electrochemical mass spectrometry (DEMS)

Renewable electricity-driven electrochemical production of small organic molecules, such as CH3OH, from chemical industry waste CO2 feedstock is highly desirable for circular economy. These reactions proceed via multiple intermediate steps which causes high overpotential and poor selectivity imposing a challenge for designing techno-economically viable systems. Proper understanding of the reaction mechanism is essential to overcome those challenges. Herein, we present a simple qualitative analysis to understand the reaction mechanism during electrochemical reduction of CO2 (eCO2R) on a cobalt tetraphenylporphyrin / multiwalled carbon nanotube (CoTPP/MWCNT) composite in the temperature range of 20–50 °C by employing differential electrochemical mass spectrometry (DEMS) in 0.1 M and 0.5 M KHCO3 electrolytes. Interestingly, temperature is observed to strongly affect the onset potentials for product generation in such a way that with the increase of temperature from 20 °C to 50 °C a decrease in the onset potential specifically for methanol formation is observed. Moreover, formaldehyde (HCHO) formation appears to occur at lower overpotentials before the formation of CH3OH which suggests that on the composite electrocatalyst, HCHO is an important intermediate on a route to CH3OH. This work offers valuable information on reaction routes to CH3OH and temperature effects on the eCO2R selectivity on molecular catalysts.

CLOCI: unveiling cryptic fungal gene clusters with generalized detection.

Gene clusters are genomic loci that contain multiple genes that are functionally and genetically linked. Gene clusters collectively encode diverse functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Current detection algorithms focus on canonical 'core' biosynthetic functions many gene clusters encode, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization. We present CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier), an algorithm that identifies gene clusters using multiple proxies of selection for coordinated gene evolution. Our approach generalizes gene cluster detection and gene cluster family circumscription, improves detection of multiple known functional classes, and unveils non-canonical gene clusters. CLOCI is suitable for genome-enabled small molecule mining, and presents an easily tunable approach for delineating gene cluster families and homologous loci.

A comprehensive review of soybean RNL and TIR domain proteins.

Both prokaryotic and eukaryotic organisms use the nucleotide-binding domain/leucine-rich repeat (NBD/LRR)-triggered immunity (NLR-triggered immunity) signaling pathway to defend against pathogens. Plant NLRs are intracellular immune receptors that can bind to effector proteins secreted by pathogens. Dicotyledonous plants express a type of NLR known as TIR domain-containing NLRs (TNLs). TIR domains are enzymes that catalyze the production of small molecules that are essential for immune signaling and lead to plant cell death. The activation of downstream TNL signaling components, such as enhanced disease susceptibility 1 (EDS1), phytoalexin deficient 4 (PAD4), and senescence-associated gene 101 (SAG101), is facilitated by these small molecules. Helper NLRs (hNLRs) and the EDS1-PAD4/SAG101 complex associate after activation, causing the hNLRs to oligomerize, translocate to the plasma membrane (PM), and produce cation-selective channels. According to a recent theory, cations enter cells through pores created by oligomeric hNLRs and trigger cell death. Occasionally, TNLs can self-associate to create higher-order oligomers. Here, we categorized soybean TNLs based on the protein domains that they possess. We believe that TNLs may help soybean plants effectively fight pathogens by acting as a source of genetic resistance. In summary, the purpose of this review is to elucidate the range of TNLs that are expressed in soybean.

The influence of small molecule products on natural ester impregnated cellulose insulation paper under electric-thermal coupling field

Transformer oil-paper insulation materials are vulnerable to insulation failure due to the influence of voltage, high temperature, and other complex conditions. Additionally, during the operation of the transformer, the generation of harmful substances such as small molecule acids and water becomes a significant concern. In this study, we employed molecular simulation technology to investigate the effect of small molecule products on natural ester-impregnated cellulose insulation paper under electric-thermal coupling field. The results show that: under the action of electric-thermal coupling, the introduction of the electric field can weaken the molecular thermal motion to a certain extent, and the higher the temperature, the more pronounced the weakening effect of the electric field. When subjected to an electric-thermal coupling field, the mean square displacement of the cellulose molecular chains inside the models doped with water and formic acid increases compared to the oil-paper composite model, with an increase of 60.13 % and 98.25 %, respectively, at 700 K. The fraction of free volume in the model increases and the cohesive energy density decreases, the diffusion ability of molecules inside the model remains strong. The weakening effect of the electric field does not diminish the hydrolysis reaction between the small molecular products and the cellulose molecular chains. This leads to a decrease in model stability and ultimately to the breakdown of the insulation paper.

LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae.

Temperature is an important control factor for biologics biomanufacturing in precision fermentation. Here, we explored a highly responsive low temperature-inducible genetic system (LowTempGAL) in the model yeast Saccharomyces cerevisiae. Two temperature biosensors, a heat-inducible degron and a heat-inducible protein aggregation domain, were used to regulate the GAL activator Gal4p, rendering the leaky LowTempGAL systems. Boolean-type induction was achieved by implementing a second-layer control through low-temperature-mediated repression on GAL repressor gene GAL80, but suffered delayed response to low-temperature triggers and a weak response at 30°C. Application potentials were validated for protein and small molecule production. Proteomics analysis suggested that residual Gal80p and Gal4p insufficiency caused suboptimal induction. 'Turbo' mechanisms were engineered through incorporating a basal Gal4p expression and a galactose-independent Gal80p-supressing Gal3p mutant (Gal3Cp). Varying Gal3Cp configurations, we deployed the LowTempGAL systems capable for a rapid stringent high-level induction upon the shift from a high temperature (37-33°C) to a low temperature (≤30°C). Overall, we present a synthetic biology procedure that leverages 'leaky' biosensors to deploy highly responsive Boolean-type genetic circuits. The key lies in optimisation of the intricate layout of the multi-factor system. The LowTempGAL systems may be applicable in non-conventional yeast platforms for precision biomanufacturing.

Environmental metabolomics characterization of modern stromatolites and annotation of ibhayipeptolides.

Lithified layers of complex microbial mats known as microbialites are ubiquitous in the fossil record, and modern forms are increasingly identified globally. A key challenge to developing an understanding of microbialite formation and environmental role is how to investigate complex and diverse communities in situ. We selected living, layered microbialites (stromatolites) in a peritidal environment near Schoenmakerskop, Eastern Cape, South Africa to conduct a spatial survey mapping the composition and small molecule production of the microbial communities from environmental samples. Substrate core samples were collected from nine sampling stations ranging from the upper point of the freshwater inflow to the lower marine interface where tidal overtopping takes place. Substrate cores provided material for parallel analyses of microbial community diversity by 16S rRNA gene amplicon sequencing and metabolomics using LC-MS2. Species and metabolite diversities were correlated, and prominent specialized metabolites were targeted for preliminary characterization. A new series of cyclic hexadepsipeptides, named ibhayipeptolides, was most abundant in substrate cores of submerged microbialites. These results demonstrate the detection and identification of metabolites from mass-limited environmental samples and contribute knowledge about microbialite chemistry and biology, which facilitates future targeted studies of specialized metabolite function and biosynthesis.

Product distribution and conversion mechanism of fossil-based biodegradable plastics during rapid pyrolysis

Fast pyrolysis has emerged as a promising technology for converting fossil-based biodegradable plastics (FBBPs) into clean energy and high-value products with rapid volume reduction and efficient utilisation. The degradation mechanism during pyrolysis is crucial, and different chemical structures and reaction processes directly affect the treatment efficiency and economic benefits. In this study, three typical FBBPs, including poly(butylene adipate-co-terephthalate) (PBAT), polybutylene succinate (PBS) and poly(epsilon-caprolactone) (PCL), have been analyzed in rapid pyrolysis experiments and corresponding products. Being pyrolyzed at 550℃, three kinds of FBBPs exhibited distinctly different decomposition behaviors and characteristics. These differences can be attributed to the bond-breaking ways and pyrolysis mechanisms, which enhance the value of products. Specifically, PBS exhibited the highest abundance of bio-oils and particulate matter (total 90.58%) compared to PBAT and PCL, mainly converted to ketones and acids with a homogeneous component distribution, which was likely to help facilitate further utilisation. In addition, the oxygen of PBS remained in the bio-oil fraction while showing high levels of CO in the bio-gas. Moreover, PCL had the highest amount of bio-gas (21.76%) among the three FBBPs, indicating that it was more likely to break into small molecule products. Notably, the broken chains or macro-molecules of PCL were primarily converted into esters, with di(but-2-en-1-yl) adipate accounting for 57.5% of bio-oils. This work elucidated the transformation pathways and mechanism of FBBP pyrolysis, providing guidance for the treatment and resource utilisation of FBBPs.

Characterization of the decomposition behaviors of catalytic pyrolysis of alkaline lignin with the addition of different concentrations of potassium

Investigating the influence of potassium concentration on alkali lignin pyrolysis is beneficial for advancing the technology of biomass catalytic pyrolysis. This study examined the catalytic effects of different concentrations of various potassium compounds on alkali lignin pyrolysis. The impregnation method was employed to load potassium compounds (KCl, K2CO3, and CH3COOK) onto alkali lignin at varying concentrations. The results showed a significant influence of potassium concentration on the catalytic pyrolysis of lignin. Increasing the potassium concentration resulted in higher pyrolysis char yield and lower pyrolysis gas yield. Furthermore, the pyrolytic char with a high concentration of potassium exhibited a distinct surface pore structure that was noticeably eroded by potassium. Furthermore, with an increase in potassium concentration, the removal of side chains, including methoxy, acetyl, and hydroxyethyl groups, became increasingly pronounced, resulting in higher yields of CO2 and phenol. The elevated potassium concentration facilitated the depolymerization of lignin through Cβ-O bond cleavage, promoted the decomposition of intermediate products, and enhanced the formation of small molecule products. Ultimately, a hypothetical mechanism explaining the influence of potassium concentration on alkali lignin pyrolysis was proposed. This study establishes a scientific foundation for the high-value utilization and resource development of alkaline lignin.

Caloric restriction, Sirtuins, and cardiovascular diseases.

Caloric restriction (CR) is a well-established dietary intervention known to extend healthy lifespan and exert positive effects on aging-related diseases, including cardiovascular conditions. Sirtuins, a family of nicotinamide adenine dinucleotide (NAD + )-dependent histone deacetylases, have emerged as key regulators of cellular metabolism, stress responses, and the aging process, serving as energy status sensors in response to CR. However, the mechanism through which CR regulates Sirtuin function to ameliorate cardiovascular disease remains unclear. This review not only provided an overview of recent research investigating the interplay between Sirtuins and CR, specifically focusing on their potential implications for cardiovascular health, but also provided a comprehensive summary of the benefits of CR for the cardiovascular system mediated directly via Sirtuins. CR has also been shown to have considerable impact on specific metabolic organs, leading to the production of small molecules that enter systemic circulation and subsequently regulate Sirtuin activity within the cardiovascular system. The direct and indirect effects of CR offer a potential mechanism for Sirtuin modulation and subsequent cardiovascular protection. Understanding the interplay between CR and Sirtuins will provide new insights for the development of interventions to prevent and treat cardiovascular diseases.

Gas-to-Biochar Byproducts of Pyrolysis and Gasification of Star Anise Biomass

In a transition to a circular economy, second-generation biomass energy has come to the forefront. The present study is aimed at characterizing biochar and byproducts of the pyrolysis of star anise residue (ANI) in the N2 and CO2 atmospheres as well as the kinetics and optimal reaction mechanisms based on the Flynn–Wall–Ozawa and Coats-Redfern methods. The ANI pyrolysis involved three stages, with the first one (161.5–559.1°C) as the main phase. The activation energy was lower in the N2 atmosphere than in the CO2 atmosphere (179.44–190.17 kJ/mol). The primary volatile products generated during the ANI pyrolysis were small molecule products (H2O, CO2, CO, and CH4), organic acids, alcohols, and ketones. The atmosphere type exerted a minimal impact on the types of gases released, with the CO2 atmosphere increasing CO and CH4 emissions. The pyrolytic oil of ANI contained a variety of organic compounds, including alcohols, phenols, ketones, acids, sugars, and other nitrogen- and oxygen-containing cyclic compounds, with its predominant compounds being acids, esters, ketones, and sugars. The elevated temperature range of 300–700°C enhanced the charring degree of the ANI biochar. The biochar showed stronger aromaticity in the CO2 atmosphere but better granularity in the N2 atmosphere. This study introduced an innovative perspective by showcasing the potential of ANI as a promising biomass source for energy generation and underscored its abundance, sustainability, and applicability as a raw material in fragrance production. It also emphasized the significance of CO2-reuse technology as a means to mitigate CO2 emissions. The findings of this work offer a theoretical and practical basis for the comprehensive utilization and efficient disposal of star anise residues.

The heat transfer mechanism coupling pyrolysis and flow of hydrocarbon fuel in heated tube under supercritical pressure

The coupling mechanism between pyrolysis and fluid flow of endothermic hydrocarbon fuels plays a crucial role in the design of regenerative cooling systems for advanced aircraft. In this work, the convective heat transfer for HF-1 with pyrolysis including 18 species and 24 reactions is numerically investigated in a horizontal circle tube under supercritical pressure (5 MPa). The results show that the mechanism of small molecule products on different heat transfer phenomena varies. In the inlet heat transfer deterioration region, small molecule products exacerbate the non-uniform radial distribution of fluid density and dynamic viscosity. At the outlet position, it significantly enhances the physical heat sink of the mixture with its high thermal conductivity and specific heat capacity. Additionally, the aromatic hydrocarbons significantly contribute to non-uniformities in thermal conductivity and specific heat capacity due to the low specific heat capacity and thermal conductivity in inlet HTD region. When the radial non-uniformity coefficient of fuel conversion keeps between −0.1 and 0, the pyrolysis of the fuel enhances heat transfer, remarkably.

Thermal chemistry and decomposition behaviors of energetic materials with trimerizing furoxan skeleton

AbstractTrimerizing furoxans are ideal molecular skeletons for the construction of high energetic substances due to their compact structures and high enthalpy of formations. To explore and compare the thermal behaviors of energetic materials with tandem trimerizing furoxan molecular skeleton, we reported the first systematic research on the thermochemical behaviors and decomposition mechanism of 3,4‐bis(3‐fluorodinitromethylfuroxan‐4‐yl)furoxan (BFTF), 3,4‐bis(3‐cyanofurazan)furazan oxide (BCTFO) and benzotrifuroxan (BTF). According to the research results of the DSC‐TG experiments, both the substituted furoxan based energetic compounds (BCTFO and BFTF) exhibited low melting points and complicated thermal decomposition behaviors around 240 °C, while the melting point of unsubstituted furoxan (BTF) was much higher. Their detailed decomposition mechanisms were proposed based on the experimental results through tandem techniques including in‐situ FTIR spectroscopy method and DSC‐TG‐FTIR‐MS quadruple technology, which indicated that the cleavage of substituent would trigger the decompositions of BFTF and the decomposition of trimerizing furoxan skeletons almost synchronous occurrence with substituents in BCTFO. The self‐oxidation‐reduction of the linear and annular trimerizing furoxans lead to similar decomposition fragmented small molecule products.