Littérature scientifique sur le sujet « Carboxylates platform »

An overview of the recent progress in the designed synthesis, modification and multifunctional applications of mesoporous non-siliceous inorganic–organic hybrid materials including metal phosphonates, carboxylates and sulfonates is presented.

Oil-based biorefineries play a crucial role in the production of key platform chemicals that can be generated via biotechnological processes instead of a petrochemical route. This work focuses on the latex of the fruit of Araujia sericifera, which can be considered a multienzymatic system with applications in key reactions in oil-based biorefineries. The latex of Araujia sericifera (ASL) was used as a novel biocatalyst in the esterification of oleic acid and in the hydrolysis of triglycerides and p-nitrophenyl carboxylates. When ASL was compared to a commercial biocatalyst, it showed an excellent activity in the hydrolysis of soybean oil and p-nitropheyl laurate, and a comparable activity in the esterification reaction.

Herein, we present the synthesis and anion binding studies of a family of homologous molecular receptors 4–7 based on a DITIPIRAM (8-propyldithieno-[3,2-b:2′,3′-e]-pyridine-3,5-di-amine) platform decorated with various urea para-phenyl substituents (NO2, F, CF3, and Me). Solution, X-ray, and DFT studies reveal that the presented host–guest system offers a convergent array of four urea NH hydrogen bond donors to anions allowing the formation of remarkably stable complexes with carboxylates (acetate, benzoate) and chloride anions in solution, even in competitive solvent mixtures such as DMSO-d6/H2O 99.5/0.5 (v/v) and DMSO-d3/MeOH-d3 9:1 (v/v). The most effective derivatives among the series turned out to be receptors 5 and 6 containing electron-withdrawing F- and -CF3para-substituents, respectively.

A series of ditopic ion pair receptors equipped with 4-nitrophenylurea and 1-aza-18-crown-6-ether linked by ortho-(1), meta-(2), and para-(3) substituted benzoic acid were readily synthesized in three steps from commercially available materials. The binding properties of these regioisomeric receptors were determined using UV-vis and 1H NMR spectroscopy in MeCN and in the solid state by single-crystal X-ray diffraction crystallography. The solution studies revealed that, apart from carboxylates, all the anions tested formed stronger complexes in the presence of sodium cations. Receptors 2 and 3 were found to interact with ion pairs with remarkably higher affinity than ortho-substituted 1. 1H NMR titration experiments showed that both urea NH protons interacted with anions with comparable strength in the case of receptors 2 and 3, but only one of the NHs was effective in anion binding in the case of receptor 1. X-ray analysis of the crystal structure of receptor 1 and 1·NaPF6 complex showed that binding was hampered due to the formation of an intramolecular hydrogen bond. Analysis of the crystal structures of 2·NaBr and 3·NaBr complexes revealed that proper mutual orientation of binding domains was responsible for the improved binding of the sodium salts.

A 4-nitro-L-phenylalanine scaffold was used to construct effective ion pair receptors capable of binding anions in an enhanced manner with the assistance of alkali metal cations. A benzocrown ether was linked to a receptor platform via the amide function so as to support the squaramide function in anion binding and to allow all three NHs to act simultaneously. The binding properties of the receptors were determined using UV-vis, 1H NMR, 2D NMR, and DOSY spectroscopy in MeCN and in the solid state by X-ray measurements. Ion pair receptor 2 was found to interact with the most strongly with salts, and the removal of its key structural elements was shown to hinder the receptor action. The amide proton was recognized to switch from having involvement in an intramolecular hydrogen bond to interacting with anions upon complexation. Apart from carboxylates, which promote deprotonation, and other monovalent salts creating 1:1 complexes with the receptor, more complex equilibria were established upon the complexation of 2 with sulfates. Receptor 2 was shown to be capable of the extraction of ion pairs from the aqueous to organic phase and of the cation-enhanced transport chloride and sulfate anions across a bulk chloroform membrane. These features may open the door for its use in regulating ion concertation under interfacial conditions and acting as a potential drug to treat channelopathies.

2569 Background: The HAI of Irinotecan-Oxaliplatin-5-Fluorouracil (IFO) with IV-Cet achieved 29.7% complete uLM-CRC resections (R0+R1) and an overall median survival (OS) of 25.7 months in previously treated pts (Lévi, Ann Oncol 2016). Methods: To identify pharmacogenomic predictors of outcomes, 207 single nucleotide polymorphisms (SNPs) from 34 pharmacology genes were analysed in blood mononuclear cells (ADME PGx, MassArray platform, Sequenom, USA). Relations between SNPs and tumor response, R0+R1, survival, and toxicities were tested using adjusted Mann Whitney, Fisher Exact, Log Rank tests and Hardy-Weinberg Equilibrium. Results: Pts (16F;36M; 33-76 yo; WHO performance status 0-1) received protocol treatment as 2nd (21 pts) or 3-4thline (31 pts). VKORC1 SNPs in promoter (rs9923231) and intron (rs9934438) were consistently associated with early and objective responses, and overall survival. For rs9923231, T/T (N = 8) as compared to C/T (N = 21) had greatest chance of achieving early response (50% vs 5%, p = 0.029) or 4-y survival (46% vs 0%, p = 0.006). VKORC1 SNPs also related to HA thrombosis (rs992331, T/T, 77% vs C/C, 30%, p = 0.04). In contrast, NAT2 SNPs (rs1041983 and rs1801280) were associated with up to 5-fold differences in R0-R1 resection rate. Statistically significant associations (p < 0.05) of SNPs with clinical outcomes were found for oxydo-reduction (CYP2E1 and HA thrombosis; CYP2C9 and diarrhea; CYP2C19 and diarrhea, fatigue, and early response), conjugation (UGT1A1 and diarrhea; NAT2 and fatigue); and transport (ABCB1 or SLC0B3 and neutropenia; SLC22A1 and diarrhea; SLC 15A2 and early response). Conclusions: VKORC1 was highlighted for the first time, as a pharmacogenomic predictor of HAI efficacy for LM-CRC. Conversion-to-resection was associated with NAT2 polymorphism. VKORC1 γ-carboxylates vitamin K-dependent proteins. Its polymorphism guides personalized warfarin dosing. VKORC1 SNPs determination could help identify the uLM-CRC pts who best benefit from intensive HAI therapy. Clinical trial information: NCT00852228.

Waste activated sludge (WAS) is an important residue generated from Wastewater Treatment Plants (WWTPs) with a high amount of organic and inorganic resources. In view of this, WAS management systems have changed towards improving the use of waste biomass as a feedstock for bioenergy generation and nutrient recovery and reuse. This study assessed the potential of using WAS as the main feedstock for the generation of high-value chemicals like volatile fatty acids (VFAs), via the carboxylate platform. In order to achieve that, a series of experiments were conducted with the aim to identify the main process variables controlling VFA production in batch and semi-continuous stirred tank reactors (CSTRs). In the first stage, acidogenic fermentations were run for 21 days using iodoform as an inhibitor of methanogenic bacteria, reaching VFAs yields of 0.238 g TVFAs/g TVSWAS with iodoform (CHI3) in a ratio of 6 mg CHI3/g VSS and an Organic Loading Rate (OLR) of 5 g TVSWAS/L. The second stage comprised the acidogenic fermentation of high pressure thermal hydrolysis (HPTH)-WAS under different pH conditions (4-1) with results of 0.415 g VFAs/g TVS at pH 9.0 and C/N=8.77, which emphasize the strong effect that pH has on VFA production and speciation and, on the inhibition of methane (CH4) generation. In order to improve VFAs production from HPTH-WAS, acidogenic co-fermentations at pH 9.0 were conducted using thermally pre-treated food waste and algal biomass (Chlorella vulgaris). Optimum results reported a yield of 0.496 g VFAs/g TVS at C/N=12.72 for fermentations using a blend of 25% HPTH-WAS/75% HPTH-Food waste and 25% HPTH-WAS/75% HPTH-Chlorella vulgaris with VFA yields of 0.378 g VFAs/g TVS, C/N=5.08. This suggests that HPTH pre-treatment and co-fermentation had a positive effect on the final production of VFAs despite of the C/N ratio used. Finally, experiments using semi-CSTR reactors fed with HPTH-WAS at pH 9.0 reported yields of 0.539, 0.328 and 0.364 g VFAs/g TVS for fermentors with OLRs of 0.3, 0.6 and 1.0 g TVS WAS/L·d, respectively. This suggests that increments in OLR have a null effect on VFAs production. Fermentations working with 0.3 g TVS WAS/L·d presented overall VFAs production which stoichiometrically exceeds in 31% the methane produced in AD experiments ran in this project. The OLR presented a null effect on the speciation of the VFAs as acetic acid was present in concentrations above 80% of the carboxylic acids content in all CSTR experiments. These results confirm the potential opportunities for high-value chemicals production from HPTH-WAS as part of the development of the biorefinery concept in existing WWTPs.

The carboxylate biofuels platform (CBP) involves the conversion of cellulosic biomass into carboxylate salts by a mixed microbial community. Chemical engineering approaches to convert these salts to a variety of fuels (diesel, gasoline, jet fuel) are well established. However, prior to initiation of this project, little was known about the influence of inoculum source on platform performance. The studies in this dissertation test the hypothesis that microbial communities from particular environments in nature (e.g. saline and/or thermal sediments) are pre-adapted to similar industrial process conditions and, therefore, exhibit superior performances. We screened an extensive collection of sediment samples from extreme environments across a wide geographic range to identify and characterize microbial communities with superior performances in the CBP. I sought to identify aspects of soil chemistry associated with superior CBP fermentation performance. We showed that CBP productivity was influenced by both fermentation conditions and inocula, thus is clearly reasonable to expect both can be optimized to target desired outcomes. Also, we learned that fermentation performance is not as simple as finding one soil parameter that leads to increases in all performance parameters. Rather, there are complex multivariate relationships that are likely indicative of trade-offs associated within the microbial communities. An analysis of targeted locus pyrosequence data for communities with superior performances in the fermentations provides clear associations between particular bacterial taxa and particular performance parameters. Further, I compared microbial community compositions across three different process screen technologies employed in research to understand and optimize CBP fermentations. Finally, we assembled and characterized an isolate library generated from a systematic culture approach. Based on partial 16S rRNA gene sequencing, I estimated operational taxonomic units (OTUs), and inferred a phylogeny of the OTUs. This isolate library will serve as a tool for future studies of assembled communities and bacterial adaptations useful within the CBP fermentations. Taken together the tools and results developed in this dissertation provide for refined hypotheses for optimizing inoculum identification, community composition, and process conditions for this important second generation biofuel platform.

Open cultures of anaerobic reactor systems convert organic wastes or biomass residues into mainly short-chain carboxylates with two to five carbon atoms. The short-chain carboxylates can be converted into the highly reduced end product methane by methanogenic consortia in anaerobic digestion. Microbial chain elongation such as via the reverse ꞵ-oxidation pathway was found as an alternative electron sink with the same anaerobic reactor microbiota. In natural ecosystems such as rumen microbial ecosystem, some anaerobic bacteria are known to produce medium-chain carboxylates (e.g., n-caproate and n-caprylate) through reverse ꞵ-oxidation. The carboxylate platform aims to recover carbon from waste streams or biomass residues by anaerobic fermentation in the form of medium-chain carboxylates. It has created great opportunities to replace chemicals derived from non-sustainable sources such as fossil feedstock. Mixed culture fermentation is commonly employed for the chain elongation processes. The diverse microbial chain elongation communities contain different functional groups involved in the processes of hydrolysis and fermentation of available organic compounds as well as the conversion of intermediates to medium-chain carboxylates. In general, the underlying metabolism and ecological interactions of the chain elongation communities are not well understood. This PhD thesis centres on the metabolism and ecological interactions in closed model ecosystems (i.e., anaerobic bioreactors) involved in microbial chain elongation with lactate. In the first chapter, a model ecosystem with reduced complexity was developed by using lactate and xylan as defined carbon sources to simulate the feedstock conditions of caproate-producing bioreactors operated with corn silage. Feeding defined carbon sources enabled balancing of electron and carbon flows. By preventing continuous inoculation, the simplified community of enrichment cultures allowed to study the metabolic and community dynamics in a clearer manner than open reactor systems. During a long-term reactor experiment, four succession stages including adaptation, stage I (high medium-chain carboxylate-producing period), transition and stage II (high butyrate-producing period) were observed. Co-occurrence networks of species based on 16S rRNA amplicon sequences and associations with process parameters were analysed to infer potential metabolic functions and microbial interactions. The results suggested that the process included diverse functions of xylan hydrolysis, xylose fermentation and chain elongation with lactate as electron donor. The inferred interactions such as cooperation between lactic acid bacteria and chain-elongating bacteria, as well as competition between medium-chain carboxylate-producing bacteria and butyrate-producing bacteria, resulted in the community development over four succession stages. In this closed model ecosystem, the chain-elongating bacteria were outcompeted by butyrate-producing bacteria under constant conditions, leading to the increase of butyrate yield at the cost of n-caproate and n-caprylate yields. The second chapter tested the effects of shortening the hydraulic retention time on the community assembly and functioning in the model ecosystems, aiming to quantitatively predict ecophysiological functions of the microbial communities. For the process performance, higher productivities and yields of n-caproate and n-caprylate were achieved by reducing the hydraulic retention time from 8 days to 2 days in two continuous reactors. A predictive model was generated by applying the random forest approach using 16S rRNA amplicon sequencing data. More than 90% accuracy in the quantitative prediction of n-caproate and n-caprylate productivities was achieved. Four inferred bioindicators belonging to the genera Olsenella, Lactobacillus, Syntrophococcus and Clostridium IV suggested their relevance to the higher carboxylate productivity at shorter hydraulic retention time. Combined with metagenomics, the recovery of metagenome-assembled genomes of these bioindicators confirmed their genetic potential to perform key steps of carboxylate production. Besides, functional redundancy in the conversion of xylan and lactate to n-butyrate, n-caproate and n-caprylate was revealed, with the relevant bioindicators increasing in relative abundance. Thus, the involved metabolic pathways were strongly coupled to the decrease in hydraulic retention time. In general, the developed machine learning framework to identify bioindicators and to quantitatively predict process performance is transferable to other ecosystem processes and microbial systems where community dynamics is linked to key functions. In the third chapter, the effects of pH increase on the chain elongation community assembly and functioning were tested based on the developed model ecosystems. The increase in pH from 5.5 to 6.0 caused fluctuations in the yields of n-butyrate, n-caproate and n-caprylate. After the pH disturbance, the carboxylate yields returned to the previous values while the communities developed to a different state, observed as decrease in diversity and evenness and increase in richness. Some taxa shifted from rare to abundant, reflecting strong selective effects of lower pH values. By applying Aitchison PCA clustering, linear mixed effect models and random forest classification, the different pH preferences of the potential chain elongators Clostridium IV and Clostridium sensu stricto were identified. By constructing networks for different pH levels, the cooperation of the chain elongator Clostridium IV with lactic acid bacteria switches from Olsenella to Lactobacillus along the pH increase, revealing the plasticity of the food web of chain elongation communities. Compared with the previously observed results of decreasing the hydraulic retention time, pH increase induced dramatic shifts in the community assembly but exhibited no strong effects on community functioning in terms of medium-chain carboxylate production. High functional redundancy was indicated despite the reactors being long-term closed systems. In parallel to the reactor experiments, pure cultures of chain-elongating clostridial strains were isolated, representing three novel species. Their genomes were assembled using a hybrid short and long read sequencing approach. The three novel strains produced n-caproate, n-butyrate, iso-butyrate and acetate from lactate in batch cultivation at pH 5.5, with the confirmation of their genetic background of lactate-based chain elongation and using CoA transferase as the terminal enzyme. Their genomes show substantial genetic heterogeneity but contain highly conserved genes involved in lactate oxidation, reverse ꞵ-oxidation, hydrogen formation and either of two types of energy conservation systems (Rnf and Ech). The genetic background of lactate-based chain elongation in these isolates and other experimentally validated chain-elongating strains was analysed by comparative genomics. The chain elongation-specific core-genome was indicated to encode the pathways for reverse ꞵ-oxidation, hydrogen formation and energy conservation while chain-elongating species displayed substantial genome heterogeneity. Further research is needed to elucidate the pathways for iso-butyrate formation in these strains. In summary, model communities of chain elongation processes were enriched and further shaped by alternations of pH and hydraulic retention time in long-term bioreactor experiments. The metabolism and ecological interactions of reactor microbiota involved in microbial chain elongation with lactate were elucidated by using 16S rRNA amplicon sequencing and metagenomics coupled to network analysis, statistical modelling and machine learning, which also sparkled new insights into the relationship between microbial chain elongation community diversity and functioning. The isolation of novel chain-elongating species further expands our knowledge on the metabolism of chain elongation bacteria. Finally, a better understanding of the rules governing community assembly is key to accelerate the development of microbiota-based biotechnologies.:Abbreviations ...................................................................................................1 List of figures ...................................................................................................4 List of tables.....................................................................................................9 Zusammenfassung ........................................................................................12 Summary .......................................................................................................17 1 Introduction .................................................................................................21 1.1 Reactor microbiota................................................................................21 1.2 Carboxylate platform.............................................................................21 1.3 Microbial chain elongation ....................................................................22 1.4 Methods for investigating reactor microbiota ........................................24 1.4.1 PCR-based methods ......................................................................24 1.4.2 Metagenomics ................................................................................25 1.4.3 Culture-dependent methods...........................................................27 1.5 Aims of this study..................................................................................28 2 Research chapters......................................................................................29 2.1 Competition between butyrate fermenters and chain-elongating bacteria limits the efficiency of medium-chain carboxylate production .....................29 2.1.1 Main text.........................................................................................30 2.1.2 Supplementary information.............................................................43 2.2 Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture .47 2.2.1 Main text.........................................................................................48 2.2.2 Supplementary information.............................................................83 2.3 Effects of pH increase on microbial chain elongation and community dynamics in closed bioreactor ecosystems...............................................104 2.3.1 Main text.......................................................................................105 2.3.2 Supplementary information...........................................................134 2.4 Draft genome sequences of three Clostridia isolates involved in lactate-based chain elongation.............................................................................148 2.5 Three novel Clostridia isolates produce n-caproate and iso-butyrate from lactate: comparative genomics of chain-elongating bacteria ....................151 2.5.1 Main text.......................................................................................152 2.5.2 Supplementary information...........................................................192 3 General discussion ...................................................................................196 3.1 Understanding microbial community assembly in model ecosystems 196 3.2 Linking microbial community structure to functioning..........................199 3.3 Moving from intriguing science to real-world practice – Microbiota-based biotechnology ...........................................................................................200 4 References ...............................................................................................202 5 Appendix...................................................................................................208 5.1 Declaration of authorship....................................................................208 5.2 Coauthor contributions........................................................................209 5.3 Curriculum Vitae .................................................................................213 5.4 List of publications and conference contributions ...............................215 5.5 Acknowledgements.............................................................................218

Using mixed-culture fermentation, the carboxylate platform produces carboxylic acids, which are chemically converted into chemicals and fuels. To optimize the mixed-acid fermentation, different bioreactor configurations and operating modes were investigated. Intermittent air exposure did not affect fermentation performance and bacterial profiles, but reduced the high-molecular-weight carboxylic acids. The microbial flora contained strict and facultative microbes, suggesting the presence of a facultative anaerobic community existing in a biofilm. Compared to countercurrent trains, propagated fixed-bed fermentations have similar selectivity and acid distribution, but lower yield, conversion, productivity, and acid concentration. One- to six-stage countercurrent fermentations were operated with similar conditions. Fewer stages increased conversion, whereas more stages increased acid concentration and selectivity. One to four stages achieved similar yield, and four to six stages achieved similar maximum acid concentration. Maximum conversion was achieved with a single stage. Recycling residual biomass retained microorganisms and nutrients and increased yield and productivity. Relative to lower biomass reflux, higher reflux increased conversion, decreased selectivity, and did not affect yield. The recommended carbon-nitrogen ratio is ~24 g carbon/g nitrogen. In four-stage fermentations, recycle to the second fermentor and in parallel to the first three fermentors was optimal. Fermentations with excess or insufficient nitrogen had higher selectivity, but decreased yield and conversion. The glucose-utilization assay is a rapid and repeatable method for determining the amount of microbial activity in a sample. This method determined ~25% efficiency of a new cell separation method. In continuous fermentation, compared to no cell recycle, recycling cellular biomass increased selectivity and yield, but decreased conversion. Compared to lower cell reflux, higher reflux increased productivity, yield, and conversion, but decreased selectivity. Compared to residual biomass recycle, cell recycle had increased selectivity and yield, but decreased conversion. A new method to screen and rank inoculum sources from natural environments was successfully developed and tested.