A kinetic study of mechanically activated atom exchange: the effect of milling frequency and ball mass.

This study investigates the mechanochemical reaction of hydrogen isotope exchange between solid benzoic acid and liquid heavy water. The systematic change of milling conditions revealed that the reaction rate scales with the milling frequency and the mass of the milling balls. The ball size being always the same, faster reactions stem from the use of higher milling frequencies and heavier balls. The kinetic curves are described by a kinetic model that accounts for the statistical, deformational and chemical factors involved in mechanochemical transformations. The results indicate that the reaction is driven by the generation of a new interface area caused by the deformation of the solid reactants.

Mechanochemical ignition of self-propagating reactions in equimolar Al-Ni powder mixtures and multilayers.

This work addresses a long standing question in the field of mechanochemistry, namely the role of mesostructure in the initiation of self-propagating high-temperature reactions in exothermic chemical systems, commonly referred to as ignition. In an attempt to find robust evidence in this regard, we compare the ignition behaviour of equimolar Al-Ni powder mixtures and equimolar Al-Ni multilayers. To achieve the best possible control of experimental conditions and allowing high reproducibility, we used elemental powders sieved in the range between 20 µm and 44 µm, and multilayers with bi-layer thickness between 10 nm and 800 nm. We carried out systematic ball milling experiments involving pristine powder mixtures and multilayers as well as a mix of pristine material and material prone to ignition suitably prepared. Experimental findings suggest that pristine powder mixtures and multilayers with bi-layer thickness of 240 nm have analogous ignition behaviour. Along the same lines, data suggest that pristine powder mixtures undergo ignition when they attain a mesostructure similar to that of multilayers with bi-layer thickness of 10 nm.

Mechanochemically Induced Solid-State Transformations of Levofloxacin.

Levofloxacin hemihydrate (LVXh) is a complex fluoroquinolone drug that exists in both hydrated and anhydrous/dehydrated forms. Due to the complexity of such a compound, the primary aim of this study was to investigate the amorphization capabilities and solid-state transformations of LVXh when exposed to mechanical treatment using ball milling. Spray drying was utilized as a comparative method for investigating the capabilities of complete LVX amorphous (LVXam) formation. The solid states of the samples produced were comprehensively characterized by powder X-ray diffraction, thermal analysis, infrared spectroscopy, Rietveld method, and dynamic vapor sorption. The kinetics of the process and the quantification of phases at different time points were conducted by Rietveld refinement. The impact of the different mills, milling conditions, and parameters on the composition of the resulting powders was examined. A kinetic investigation of samples produced using both mills disclosed that it was in fact possible to partially amorphize LVXh upon mechanical treatment. It was discovered that LVXh first transformed to the anhydrous/dehydrated form γ (LVXγ), as an intermediate phase, before converting to LVXam. The mechanism of LVXam formation by ball milling was successfully revealed, and a new method of forming LVXγ and LVXam by mechanical forces was developed. Spray drying from water depicted that complete amorphization of LVXh was possible. The amorphous form of LVX had a glass transition temperature of 80 °C. The comparison of methods highlighted that the formation of LVXam is thus both mechanism- and process-dependent. Dynamic vapor sorption studies of both LVXam samples showed comparable stability properties and crystallized to the most stable hemihydrate form upon analysis. In summary, this work contributed to the detailed understanding of solid-state transformations of essential fluoroquinolones while employing greener and more sustainable manufacturing methods.

Forecasting the dynamics of a complex microbial community using integrated meta-omics.

Predicting the behaviour of complex microbial communities is challenging. However, this is essential for complex biotechnological processes such as those in biological wastewater treatment plants (BWWTPs), which require sustainable operation. Here we summarize 14 months of longitudinal meta-omics data from a BWWTP anaerobic tank into 17 temporal signals, explaining 91.1% of the temporal variance, and link those signals to ecological events within the community. We forecast the signals over the subsequent five years and use 21 extra samples collected at defined time intervals for testing and validation. Our forecasts are correct for six signals and hint on phenomena such as predation cycles. Using all the 17 forecasts and the environmental variables, we predict gene abundance and expression, with a coefficient of determination ≥0.87 for the subsequent three years. Our study demonstrates the ability to forecast the dynamics of open microbial ecosystems using interactions between community cycles and environmental parameters.

Integrative meta-omics in Galaxy and beyond.

BACKGROUND: 'Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as "meta-omics", they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities. RESULTS: In this study, we applied the workflows on a highly efficient cellulose-degrading minimal consortium enriched from a biogas reactor to analyse the key roles of uncultured microorganisms in complex biomass degradation processes. Metagenomic analysis recovered metagenome-assembled genomes (MAGs) for several constituent populations including Hungateiclostridium thermocellum, Thermoclostridium stercorarium and multiple heterogenic strains affiliated to Coprothermobacter proteolyticus. The metagenomics workflow was developed as two modules, one standard, and one optimized for improving the MAG quality in complex samples by implementing a combination of single- and co-assembly, and dereplication after binning. The exploration of the active pathways within the recovered MAGs can be visualized in ViMO, which also provides an overview of the MAG taxonomy and quality (contamination and completeness), and information about carbohydrate-active enzymes (CAZymes), as well as KEGG annotations and pathways, with counts and abundances at both mRNA and protein level. To achieve this, the metatranscriptomic reads and metaproteomic mass-spectrometry spectra are mapped onto predicted genes from the metagenome to analyse the functional potential of MAGs, as well as the actual expressed proteins and functions of the microbiome, all visualized in ViMO. CONCLUSION: Our three workflows for integrative meta-omics in combination with ViMO presents a progression in the analysis of 'omics data, particularly within Galaxy, but also beyond. The optimized metagenomics workflow allows for detailed reconstruction of microbial community consisting of MAGs with high quality, and thus improves analyses of the metabolism of the microbiome, using the metatranscriptomics and metaproteomics workflows.

Mechanochemical Reactions from Individual Impacts to Global Transformation Kinetics.

Typically induced by the mechanical processing of powders in ball mills, mechanochemical transformations are considered to result from the application of mechanical force to solid reactants. However, the undeniable deep connection between the dynamic compaction of powders during impacts and the overall transformation degree has yet to be disclosed. In the present work, we show that the square planar bis(dibenzoylmethanato)NiII coordination compound undergoes trimerization when its powder experiences even a single ball impact. Based on systematic experiments with individual ball impacts and analysis by Raman spectroscopy, we provide here quantitative mapping of the transformation in the powder compact and deduce bulk reaction kinetics from multiple individual impacts.

Mechanochemical effects underlying the mechanically activated catalytic hydrogenation of carbon monoxide.

In this work, we highlight and measure the intensity of mechanochemical effects at work in the hydrogenation of carbon monoxide by comparing the activity of a supported Co-Fe catalyst subjected, respectively, to ball milling and simple powder agitation. Paying due regard to the discontinuous nature of ball milling, we show that mechanochemical hydrogenation proceeds at significantly higher rate and disclose its connection with individual impacts. Experimental evidence suggests that the enhanced catalytic activity we observe can be ascribed to local processes affecting the amount of powder that gets involved in individual impacts.

Extending the Hammett correlation to mechanochemical reactions.

Using Raman in situ monitoring and mechanochemistry-specific kinetic analysis, we find a correlation between the reaction probability and the Hammett constants in a model mechanochemical reaction of imine formation, indicating that the body of knowledge developed in physical-organic chemistry could be transferable to ball milling reactions in the solid state.

Mechanochemical reaction kinetics scales linearly with impact energy.

Inelastic collisions of the milling media in ball milling provide energy to the reaction mixture required for chemical transformations. However, movement of the milling media also results in physical mixing of reactants, which may enable a chemical reaction too. Separating the two contributions is challenging and gaining a direct insight into the purely mechanochemically driven reactivity is accordingly hindered. Here, we have applied in situ reaction monitoring by Raman spectroscopy to a suitable, purely mechanically activated, chemical reaction and combined kinetic analysis with numerical simulations to access experimentally unattainable milling parameters. The breadth of milling conditions allows us to establish a linear relationship between the reaction rate and the energy dose received by the sample. Consequently, different kinetic profiles in time scale to the same profile when plotted against the energy dose, which increases with the ball mass, the average ball velocity and the frequency of impacts, but decreases with the hardness of the milling media due to more elastic collisions. The fundamental relationship between kinetics and energy input provides the basis for planning and optimisation of mechanochemical reactions and is essential for transferability of mechanochemical reactions across different milling platforms.

Longitudinal analysis of the faecal microbiome in pigs fed Cyberlindnera jadinii yeast as a protein source during the weanling period followed by a rapeseed- and faba bean-based grower-finisher diet.

The porcine gut microbiome is central to animal health and growth as well as it can be structurally or functionally reshaped by dietary interventions. The gut microbiota composition in relation to Cyberlindnera jadinii yeast as a protein source in a weanling diet was studied previously. Also, there is a mounting body of knowledge regarding the porcine gut microbiome composition in response to the use of rapeseed (Brassica napus subsp. napus) meal, and faba beans (Vicia faba) as protein sources during the growing/finishing period. However, there is limited data on how the porcine gut microbiome respond to a combination of C. jadinii yeast in the weanling phase and rapeseed meal and faba beans in the growing/finishing phase. This work investigated how the porcine faecal microbiome was changing in response to a novel yeast diet with a high inclusion of yeast proteins (40% of crude protein) in a weanling diet followed by a diet based on rapeseed meal and faba beans during the growing/finishing period. The faecal microbiomes of the weanling pigs fed yeast were more diverse with higher relative abundance of Firmicutes over Bacteroidetes compared with those of soybean meal-based diet fed weanlings. Reduced numbers of Prevotella in the yeast fed faecal microbiomes remained a microbiome characteristic up until two weeks after the yeast diet was changed to the rapeseed/faba bean growing finishing diet. A number of differentially abundant bacterial phylotypes along with distinct co-occurrence patterns observed during the growing/finishing period indicated the presence of a "carry-over" effect of the yeast weanling diet onto the faecal microbiomes of the grower/finisher pigs.

hMSCs in contact with DMSO for cryopreservation: Experiments and modeling of osmotic injury and cytotoxic effect.

In this study a combined analysis of osmotic injury and cytotoxic effect useful for the optimization of the cryopreservation process of a cell suspension is carried out. The case of human Mesenchymal Stem Cells (hMSCs) from Umbilical Cord Blood (UCB) in contact with dimethyl sulfoxide (DMSO) acting as Cryo-Protectant Agent (CPA) is investigated from the experimental as well as the theoretical perspective. The experimental runs are conducted by suspending the cells in hypertonic solutions of DMSO at varying osmolality, system temperature, and contact times; then, at room temperature, cells are pelleted by centrifugation and suspended back to isotonic conditions. Eventually, cell count and viability are measured by means of a Coulter counter and flow-cytometer, respectively. Overall, a decrease in cell count and viability results when DMSO concentration, temperature, and contact time increase. A novel mathematical model is developed and proposed to interpret measured data by dividing the cell population between viable and nonviable cells. The decrease of cell count is ascribed exclusively to the osmotic injury caused by expansion lysis: excessive swelling causes the burst of both viable as well as nonviable cells. On the other hand, the reduction of cell viability is ascribed only to cytotoxicity which gradually transforms viable cells into nonviable ones. A chemical reaction engineering approach is adopted to describe the dynamics of both phenomena: by following the kinetics of two chemical reactions during cell osmosis inside a closed system it is shown that the simultaneous reduction of cell count and viability may be successfully interpreted. The use of the Surface Area Regulation (SAR) model recently proposed by the authors allows one to avoid the setting in advance of fixed cell Osmotic Tolerance Limits (OTLs), as traditionally done in cryopreservation literature to circumvent the mathematical simulation of osmotic injury. Comparisons between experimental data and theoretical simulations are provided: first, a nonlinear regression analysis is performed to evaluate unknown model parameters through a best-fitting procedure carried out in a sequential fashion; then, the proposed model is validated by full predictions of system behavior measured at operating conditions different from those used during the best-fit procedure.

Mechanochemistry: New Tools to Navigate the Uncharted Territory of "Impossible" Reactions.

Mechanochemical transformations have made chemists enter unknown territories, forcing a different chemistry perspective. While questioning or revisiting familiar concepts belonging to solution chemistry, mechanochemistry has broken new ground, especially in the panorama of organic synthesis. Not only does it foster new "thinking outside the box", but it also has opened new reaction paths, allowing to overcome the weaknesses of traditional chemistry exactly where the use of well-established solution-based methodologies rules out progress. In this Review, the reader is introduced to an intriguing research subject not yet fully explored and waiting for improved understanding. Indeed, the study is mainly focused on organic transformations that, although impossible in solution, become possible under mechanochemical processing conditions, simultaneously entailing innovation and expanding the chemical space.

Chemical effects induced by the mechanical processing of granite powder.

Starting from 1970s, the use of mechanical forces to induce chemical transformations has radically changed vast areas of metallurgy and materials science. More recently, mechanochemistry has expanded to core sectors of chemistry, showing the promise to deeply innovate chemical industry while enhancing its sustainability and competitiveness. We are still far, however, from unveiling the full potential of mechanical activation. This study marks a step forward in this direction focusing on the chemical effects induced on the surrounding gaseous phase by the mechanical processing of granite. We show that fracturing granite blocks in oxygen can result in the generation of ozone. The refinement of coarse granite particles and the friction between fine ones are also effective in this regard. Combining experimental evidence related to the crushing of large granite samples by uniaxial compression and the ball milling of coarse and fine granite powders, we develop a model that relates mechanochemical ozone generation to the surface area effectively affected by fracture and frictional events taking place during individual impacts. We also extend the investigation to gaseous phases involving methane, oxygen, benzene and water, revealing that chemical transformations occur as well.

Estimation of Nanoporous Au Young's Modulus from Serial Block Face-SEM 3D-Characterisation.

Nanoporous Au has been subjected to serial block face-scanning electron microscopy (SBF-SEM) 3D-characterisation. Corresponding sections have been digitalized and used to evaluate the associated mechanical properties. Our investigation demonstrates that the sample is homogeneous and isotropic. The effective Young's modulus estimated by an analytical multiscale approach agrees remarkably well with the values stated in the literature.

Hardening of Nanoporous Au Induced by Exposure to Different Gaseous Environments.

This work focuses on the mechanical behaviour of nanoporous Au samples alternately exposed to ozone and carbon dioxide. Nanoporous Au was fabricated by freely corroding the Ag70Au30 parent alloys prepared by mechanical alloying in the form of powder and subsequently compacted by cold pressing. Dealloying was performed in acidic solution, and conditions were suitably adjusted to obtain fine nanoporous Au structures with ligaments about 15 nm thick. Nanoporous Au samples with increasingly thicker ligaments, up to about 40 nm, were fabricated by annealing the pristine nanoporous Au structure for different time intervals at 473 K. For all of the samples, the cyclic variation of gaseous atmosphere results in a macroscopic strain variation due to the occurrence of surface oxidation and reduction processes. We show that the reiterated cyclic exposure to the different gases also induces the progressive hardening of nanoporous Au, which can be ascribed to irreversible strain contributions. For nanoporous Au samples with ligaments that are 15 nm thick, after 50 exposure cycles, the yield strength increases approximately from 49 MPa to 57 MPa. A systematic investigation on coarser nanoporous Au structures indicates that, with the same exposure cycles, the degree of hardening decreases with the ligament thickness.

Investigation on the Thermodynamic Stability of Nanocrystalline W-Based Alloys: A Combined Theoretical and Experimental Approach.

The stability of nanostructured metal alloys is currently being extensively investigated, and several mathematical models have been developed to describe the thermodynamics of these systems. However, model capability in terms of thermal stability predictions strongly relies on grain boundary-related parameters that are difficult to measure or estimate accurately. To overcome this limitation, a novel theoretical approach is proposed and adopted in this work to identify W-based nanocrystalline alloys which are potentially able to show thermodynamic stability. A comparison between model outcomes and experimental findings is reported for two selected alloys, namely W-Ag and W-Al. Experimental results clearly highlight that W-Ag mixtures retain a segregated structure on relatively coarse length scales even after prolonged mechanical treatments. Moreover, annealing at moderate temperatures readily induces demixing of the constituent elements. In contrast, homogeneous nanostructured W-Al solid solutions are obtained by ball milling of elemental powders. These alloys show enhanced thermal stability with respect to pure W even at high homologous temperatures. Experimental evidences agree with model predictions for both the investigated systems.

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.

The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

Mechanochemical Rearrangements.

Molecular rearrangements are a powerful tool for constructing complex structures in an atom- and step-economic manner, translating multistep transformations into an intrinsically more sustainable process. Mechanochemical molecular rearrangements become an even more appealing eco-friendly synthetic approach, especially for preparing active pharmaceutical ingredients (APIs) and natural products. Still in their infancy, rearrangements promoted by mechanochemistry represent a promising approach for chemists to merge molecular diversity and green chemistry perspectives toward more selective and efficient syntheses with a reduced environmental footprint.

Mantis: flexible and consensus-driven genome annotation.

BACKGROUND: The rapid development of the (meta-)omics fields has produced an unprecedented amount of high-resolution and high-fidelity data. Through the use of these datasets we can infer the role of previously functionally unannotated proteins from single organisms and consortia. In this context, protein function annotation can be described as the identification of regions of interest (i.e., domains) in protein sequences and the assignment of biological functions. Despite the existence of numerous tools, challenges remain in terms of speed, flexibility, and reproducibility. In the big data era, it is also increasingly important to cease limiting our findings to a single reference, coalescing knowledge from different data sources, and thus overcoming some limitations in overly relying on computationally generated data from single sources. RESULTS: We implemented a protein annotation tool, Mantis, which uses database identifiers intersection and text mining to integrate knowledge from multiple reference data sources into a single consensus-driven output. Mantis is flexible, allowing for the customization of reference data and execution parameters, and is reproducible across different research goals and user environments. We implemented a depth-first search algorithm for domain-specific annotation, which significantly improved annotation performance compared to sequence-wide annotation. The parallelized implementation of Mantis results in short runtimes while also outputting high coverage and high-quality protein function annotations. CONCLUSIONS: Mantis is a protein function annotation tool that produces high-quality consensus-driven protein annotations. It is easy to set up, customize, and use, scaling from single genomes to large metagenomes. Mantis is available under the MIT license at https://github.com/PedroMTQ/mantis.

A phenomenological kinetic equation for mechanochemical reactions involving highly deformable molecular solids.

With its ability to enable solvent-free chemical reactions, mechanochemistry promises to open new and greener synthetic routes to chemical products of industrial interest. Its practical exploitation requires understanding the relationships between processing variables, powders' mechanical behaviour, and chemical reactivity. To this aim, rationalizing experimental kinetics is of paramount importance. In this work, we propose a phenomenological kinetic model that could help experimentalists to disentangle the mechanical, chemical, and statistical factors underlying mechanochemical reactions. The model takes into account the statistical nature of ball milling and relates the global kinetic curve that can be obtained experimentally to the deformation and chemical processes that occur on the mesoscopic and microscopic scales during individual impacts. We show that our model equations can satisfactorily best fit experimental datasets, providing information on the underlying mechanochemistry.