and Clostridium spp

The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.

In-depth understanding of local soil chemistry reveals that addition of Ca may counteract the mobilisation of 226Ra and other pollutants before wetland creation on the Grote Nete river banks

The "Sigma plan" https://www.sigmaplan.be/en/ aims to create in Belgium inundation zones along the Grote Nete river to prevent Antwerp from flooding in extreme weather conditions. The riverbanks of the Grote Nete are at some hotspots historically contaminated by the phosphate industry resulting in Naturally Occurring Radionuclides (NOR) legacy. ²²⁶Ra is from a radiation protection point of view one of the most important radionuclides present at the hot spot under study, with a local soil activity concentration higher than 3000 Bq/kg ²²⁶Ra. In this paper, we identify the most relevant mechanisms governing the mobility of ²²⁶Ra. We selected for this study the role of CaSO₄.2H₂O, clay minerals and humic acids as the main contributors determining the speciation of Ra, due to their presence at the hot spot, their cation exchange capacity and their functional group density, respectively. Various novel analytical chemistry approaches were developed to study the prevailing reaction mechanisms that impact the solid-liquid distribution of ²²⁶Ra. We show that ²²⁶Ra coprecipitates in a (Ca,Ra)SO₄ solid solution due to the high Ca²⁺ and SO₄^2- concentrations in the local hot spot. If CaSO₄.2H₂O is not saturated in the soil solution, ²²⁶Ra adsorption to clay minerals counteracts the tendency of ²²⁶Ra partitioning to the liquid phase by interactions with humic and fulvic acids. Interactions between different soil compounds may further alter the partitioning of Ra. As, Cd, Pb and Zn in the hot spot are significantly above background values in Flemish sediments. Pb may be coprecipitated as sulphate salts, whereas Cd and Zn are most probably partially present as arsenate salts. The excess of Zn may interact with humic acids. The observed reaction mechanisms suggest that Ca²⁺ might play a key role in the immobilisation of Ra. The role of Ca²⁺ as immobilisation agent of the other contaminants is discussed.

Sorption of beryllium in cementitious systems relevant for nuclear waste disposal: Quantitative description and mechanistic understanding

Beryllium has applications in fission and fusion reactors, and it is present in specific streams of radioactive waste. Accordingly, the environmental mobility of beryllium needs to be assessed in the context of repositories for nuclear waste. Although cement is widely used in these facilities, Be(II) uptake by cementitious materials was not previously investigated and was hence assumed negligible. Sorption experiments were performed under Ar-atmosphere. Ordinary Portland cement, low pH cement, calcium silicate hydrated (C-S-H) phases and the model system TiO₂ were investigated. Sorption kinetics, sorption isotherms and distribution ratios (R_d, in kg⋅L^-1) were determined for these systems. Molecular dynamics were used to characterize the surface processes driving Be(II) uptake. A strong uptake (5 ≤ log R_d ≤ 7) is quantified for all investigated cementitious systems. Linear sorption isotherms are observed over three orders of magnitude in [Be(II)]_aq, confirming that the uptake is controlled by sorption processes and that solubility phenomena is not relevant within the investigated conditions. The analogous behaviour observed for cement and C-S-H support that the latter are the main sink of beryllium. The two step sorption kinetics is explained by a fast surface complexation process, followed by the slow incorporation of Be(II) in C-S-H. Molecular dynamics indicate that Be(OH)₃^- and Be(OH)₄^2- are sorbed to the C-S-H surface through Ca-bridges. This work provides a comprehensive quantitative and mechanistic description of Be(II) uptake by cementitious materials, whose retention properties can be now reliably assessed for a wide range of boundary conditions of relevance in nuclear waste disposal.

Chemical interactions and mixtures in public health risk assessment: An analysis of ATSDR's interaction profile database

The Agency for Toxic Substances and Disease Registry (ATSDR) develops interaction profiles using binary weight of evidence (BINWOE) methodology to determine interaction directions of common environmental mixtures. We collected direction of interactions, BINWOE score determination, and BINWOE score confidence rating from 13 interaction profiles along with toxicodynamic and toxicokinetic influences on interaction direction. By doing so, we quantified the 1) direction of interaction and indeterminate evaluations; 2) characterized confidence in the BINWOE determinations; and 3) quantified toxicokinetic/toxicodynamic, and other influences on projected BINWOE interaction directions. Thirty-nine percent (130/336) of the attempts to make a BINWOE were indeterminate due to no interaction data or inadequate or conflicting evidence. Out of remaining BINWOEs, 25% were additive, 9% were greater-than-additive, and 27% were less-than-additive interactions. Fifty-five percent of BINWOEs were explained by toxicokinetic interactions, 12% and 5% were explained by toxicodynamic and other explanations, respectively. High quality mixture toxicology in vivo studies along with mixture in vitro and in silico studies will lead to greater confidence in interaction directions and influences. Limitations for interpretation of the data were also included.

Cellular pathways of recombinant adeno-associated virus production for gene therapy

Recombinant adeno-associated viruses (rAAVs) are among the most important vectors for in vivo gene therapies. With the rapid development of gene therapy, current rAAV manufacturing capacity faces a challenge to meet the emerging demand for these therapies in the future. To examine the bottlenecks in rAAV production during cell culture, we focus here on an analysis of cellular pathways of rAAV production, based on an overview of assembly mechanisms first in the wild-type (wt) AAV replication and then in the common methods of rAAV production. The differences analyzed between the wild-type and recombinant systems provide insights into the mechanistic differences that may correlate with viral productivity. Based on these analyses, we identify potential barriers to high productivity of rAAV and discuss future directions for improvement to meet the emerging needs set by the growth of rAAV-based therapy and the needs of patients.

Adverse outcome pathways: Application to enhance mechanistic understanding of neurotoxicity

Recent developments have prompted the transition of empirically based testing of late stage toxicity in animals for a range of different endpoints including neurotoxicity to more efficient and predictive mechanistically based approaches with greater emphasis on measurable key events early in the progression of disease. The adverse outcome pathway (AOP) has been proposed as a simplified organizational construct to contribute to this transition by linking molecular initiating events and earlier (more predictive) key events at lower levels of biological organization to disease outcomes. As such, AOPs are anticipated to facilitate the compilation of information to increase mechanistic understanding of pathophysiological pathways that are responsible for human disease.

In this review, the sequence of key events resulting in adverse outcome (AO) defined as parkinsonian motor impairment and learning and memory deficit in children, triggered by exposure to environmental chemicals has been briefly described using the AOP framework. These AOPs follow convention adopted in an Organization for Economic Cooperation and Development (OECD) AOP development program, publically available, to permit tailored application of AOPs for a range of different purposes.

Due to the complexity of disease pathways, including neurodegenerative disorders, a specific symptom of the disease (e.g. parkinsonian motor deficit) is considered as the AO in a developed AOP. Though the description is necessarily limited by the extent of current knowledge, additional characterization of involved pathways through description of related AOPs interlinked into networks for the same disease has potential to contribute to more holistic and mechanistic understanding of the pathophysiological pathways involved, possibly leading to the mechanism-based reclassification of diseases, thus facilitating more personalized treatment.

Application of the adverse outcome pathway (AOP) concept to structure the available in vivo and in vitro mechanistic data for allergic sensitization to food proteins

BACKGROUND

The introduction of whole new foods in a population may lead to sensitization and food allergy. This constitutes a potential public health problem and a challenge to risk assessors and managers as the existing understanding of the pathophysiological processes and the currently available biological tools for prediction of the risk for food allergy development and the severity of the reaction are not sufficient. There is a substantial body of in vivo and in vitro data describing molecular and cellular events potentially involved in food sensitization. However, these events have not been organized in a sequence of related events that is plausible to result in sensitization, and useful to challenge current hypotheses. The aim of this manuscript was to collect and structure the current mechanistic understanding of sensitization induction to food proteins by applying the concept of adverse outcome pathway (AOP).

MAIN BODY

The proposed AOP for food sensitization is based on information on molecular and cellular mechanisms and pathways evidenced to be involved in sensitization by food and food proteins and uses the AOPs for chemical skin sensitization and respiratory sensitization induction as templates. Available mechanistic data on protein respiratory sensitization were included to fill out gaps in the understanding of how proteins may affect cells, cell-cell interactions and tissue homeostasis. Analysis revealed several key events (KE) and biomarkers that may have potential use in testing and assessment of proteins for their sensitizing potential.

CONCLUSION

The application of the AOP concept to structure mechanistic in vivo and in vitro knowledge has made it possible to identify a number of methods, each addressing a specific KE, that provide information about the food allergenic potential of new proteins. When applied in the context of an integrated strategy these methods may reduce, if not replace, current animal testing approaches. The proposed AOP will be shared at the www.aopwiki.org platform to expand the mechanistic data, improve the confidence in each of the proposed KE and key event relations (KERs), and allow for the identification of new, or refinement of established KE and KERs.