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[object Object], [object Object]

Molecular Systems Biology • 2025

Successful computational modelling of complex biological phenomena will depend on the seamless sharing of models and hypotheses between researchers of all backgrounds-experimental and theoretical. LimbNET, a new online tool for modelling, simulating and visualising spatiotemporal patterning in limb development, aims to facilitate this process within the limb development community. LimbNET enables remote users to define and simulate arbitrary gene regulatory network (GRN) models of 2D spatiotemporal developmental patterning processes. Researchers can test and compare each others' hypotheses within a common framework. A database of previously created models empowers users to simulate, explore, and extend each others' work. Spatiotemporally varying gene expression intensities, derived from image-based data, are mapped into a standardised computational description of limb growth, integrated within our modelling framework. This enables direct comparison not only between datasets but between data and simulation outputs, closing the feedback loop between experiments and simulation via parameter optimisation. All functionality is accessible through a web browser ( https://limbnet.embl.es ), requiring no special software, and opening the field of image-driven modelling to the full scientific community.

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Natural Resources Conservation and Research • 2023

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[object Object], [object Object], [object Object] et al.

Energies • 2023

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[object Object], [object Object], [object Object] et al.

Scientific Reports • 2025

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FEMS Microbiology Reviews • 2004

Soil sampling for environmental DNA in remote and semi-remote locations is often limited due to logistical constraints surrounding sample preservation, including no or limited access to a freezer. Freezing at - 20 °C is a common DNA preservation strategy, however, other methods such as desiccation, ethanol or commercial preservatives are available as potential alternative DNA preservation methods for room temperature storage. In this study, we assessed five preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel packs, RNAlater, LifeGuard) along with freezing at - 20 °C, against immediate extraction on organic and mineral soils for up to three weeks of preservation. We assessed direct effects on DNA concentration and quality, and used DNA metabarcoding to assess effects on bacterial and fungal communities. Drying with Dry & Dry led to no significant differences from immediate extraction. RNAlater led to lower DNA concentrations, but effects on community structures were comparable to freezing. CD1, LifeGuard and Ethanol either caused immediate significant shifts in community structure, degradation of DNA quality or changes in diversity metrics. Overall, our study supports the use of drying with silica gel packs as a cost-effective, and easily applied method for the short-term storage at room temperature for DNA-based microbial community analyses.

[object Object], [object Object], [object Object] et al.

Materials • 2024

The performance of current biomedical titanium alloys is limited by inflammatory and severe inflammatory conditions after implantation. In this study, a novel Ti-Nb-Zr-Si (TNZS) alloy was developed and compared with commercially pure titanium, and Ti-6Al-4V alloy. Electrochemical parameters of specimens were monitored during 1 h and 12 h immersion in phosphate buffered saline (PBS) as a normal, PBS/hydrogen peroxide (H 2 O 2 ) as an inflammatory, and PBS/H 2 O 2 /albumin/lactate as a severe inflammatory media. The results showed an effect of the H 2 O 2 in inflammatory condition and the synergistic behavior of H 2 O 2 , albumin, and lactate in severe inflammatory condition towards decreasing the corrosion resistance of titanium biomaterials. Electrochemical tests revealed a superior corrosion resistance of the TNZS in all conditions due to the presence of silicide phases. The developed TNZS was tested for subsequent cell culture investigation to understand its biocompatibility nature. It exhibited favorable cell-materials interactions in vitro compared with Ti-6Al-4V. The results suggest that TNZS alloy might be a competitive biomaterial for orthopedic applications.

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[object Object]

Plants • 2022

Agriculture is changing to rely on agroecological practices that take into account biodiversity, and the ecological processes occurring in soils. The use of agricultural biostimulants has emerged as a valid alternative to chemicals to indirectly sustain plant growth and productivity. Certain BS have been shown to select and stimulate plant beneficial soil microorganisms. However, there is a lack of knowledge on the effects and way of action of the biostimulants operating on soil functioning as well as on the extent and dynamic of these effects. In this study we aimed to decipher the way of action of a seaweed and amino-acids based biostimulant intended to be applied on soil crop residues to increase their microbial mineralization and the further release of nutrients. By setting-up a two-phase experiment (soil plant-growing and soil incubation), our objectives were to (1) determine the effects of the soil biostimulant over time on the active soil bacteria and fungi and the consequences on the organic carbon mineralization in bare soils, and (2) assess the biostimulant effects on soil microorganisms relatively to plant legacy effects in planted soils. We demonstrated that the soil biostimulant had a delayed effect on the active soil microorganisms and activated both plant growth promoting bacteria and saprophytes microorganisms at the medium-term of 49 days. However, the changes in the abundances of active microbial decomposers were not associated to a higher mineralization rate of organic carbon derived from soil and/or litter. The present study assessed the biostimulant beneficial effect on active soil microbial communities as similar as or even higher than the legacy effects of either A. thaliana or T. aestivum plants. We specifically showed that the biostimulant increased the active fungal richness to a higher extent than observed in soils that previously grew the two plants tested.

[object Object], [object Object], [object Object] et al.

Journal of Nanobiotechnology • 2024

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Pharmaceutical Research • 2008

Biological samples are mainly composed of elements with a low atomic number which show a relatively low electron scattering power. For Transmission Electron Microscopy analysis, biological samples are generally embedded in resins, which allow thin sectioning of the specimen. Embedding resins are also composed by light atoms, thus the contrast difference between the biological sample and the surrounding resin is minimal. Due to that reason in the last decades, several staining solutions and approaches, performed with heavy metal salts, have been developed with the purpose of enhancing both the intrinsic sample contrast and the differences between the sample and resin. The best staining was achieved with the uranyl acetate (UA) solution, which has been the election method for the study of morphology in biological samples. More recently several alternatives for UA have been proposed to get rid of its radiogenic issues, but to date none of these solutions has achieved efficiencies comparable to UA. In this work, we propose a different staining solution (X Solution or X SOL), characterized by lanthanide polyoxometalates (LnPOMs) as heavy atoms source, which could be used alternatively to UA in negative staining (NS), in en bloc staining, and post sectioning staining (PSS) of biological samples. Furthermore, we show an extensive chemical characterization of the LnPOM species present in the solution and the detailed work for its final formulation, which brought remarkable results, and even better performances than UA.

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[object Object], [object Object], [object Object] et al.

Ecological Monographs • 2009

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FEMS Microbiology Reviews • 2004

[object Object], [object Object], [object Object] et al.

Scientific Reports • 2018

Ti-24Nb-4Zr-8Sn (Ti2448), a new β-type Ti alloy, consists of nontoxic elements and exhibits a low uniaxial tensile elastic modulus of approximately 45 GPa for biomedical implant applications. Nevertheless, the bio-corrosion resistance and biocompatibility of Ti2448 alloys must be improved for long-term clinical use. In this study, a rapid electrochemical anodization treatment was used on Ti2448 alloys to enhance the bio-corrosion resistance and bone cell responses by altering the surface characteristics. The proposed anodization process produces a unique hybrid oxide layer (thickness 50-120 nm) comprising a mesoporous outer section and a dense inner section. Experiment results show that the dense inner section enhances the bio-corrosion resistance. Moreover, the mesoporous surface topography, which is on a similar scale as various biological species, improves the wettability, protein adsorption, focal adhesion complex formation and bone cell differentiation. Outside-in signals can be triggered through the interaction of integrins with the mesoporous topography to form the focal adhesion complex and to further induce osteogenic differentiation pathway. These results demonstrate that the proposed electrochemical anodization process for Ti2448 alloys with a low uniaxial tensile elastic modulus has the potential for biomedical implant applications.

[object Object], [object Object], [object Object] et al.

ISME Communications • 2025

With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due to diminished phenol oxidase activity, inhibiting resident microbes and promoting carbon stabilization. Pairing microbiome and geochemical measurements along a permafrost thaw-induced saturation gradient in Stordalen Mire, a model Arctic peatland, we confirmed a negative relationship between phenol oxidase expression and saturation but failed to support other trends predicted by the enzyme latch. To inventory alternative polyphenol removal strategies, we built CAMPER, a gene annotation tool leveraging polyphenol enzyme knowledge gleaned across microbial ecosystems. Applying CAMPER to genome-resolved metatranscriptomes, we identified genes for diverse polyphenol-active enzymes expressed by various microbial lineages under a range of redox conditions. This shifts the paradigm that polyphenols stabilize carbon in saturated soils and highlights the need to consider both oxic and anoxic polyphenol metabolisms to understand carbon cycling in changing ecosystems.

[object Object], [object Object], [object Object] et al.

Nature • 2022

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases 1-3 . SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing 4,5 . Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

[object Object], [object Object], [object Object]

Bioengineering • 2024

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Owing to its 100% theoretical salt rejection capability, membrane distillation (MD) has emerged as a promising seawater desalination approach to address freshwater scarcity. Ideal MD requires high vapor permeate flux established by cross-membrane temperature gradient (∆T) and excellent membrane durability. However, it's difficult to maintain constant ∆T owing to inherent heat loss at feedwater side resulting from continuous water-to-vapor transition and prevent wetting transition-induced membrane fouling and scaling. Here, we develop a Ti 3 C 2 T x MXene-engineered membrane that imparts efficient localized photothermal effect and strong water-repellency, achieving significant boost in freshwater production rate and stability. In addition to photothermal effect that circumvents heat loss, high electrically conductive Ti 3 C 2 T x MXene also allows for self-assembly of uniform hierarchical polymeric nanospheres on its surface via electrostatic spraying, transforming intrinsic hydrophilicity into superhydrophobicity. This interfacial engineering renders energy-efficient and hypersaline-stable photothermal membrane distillation with a high water production rate under one sun irradiation.

[object Object], [object Object], [object Object] et al.

Nature Communications • 2018

Terpenes constitute the largest and structurally most diverse natural product family. Most terpenoids exhibit a stereochemically complex macrocyclic core, which is generated by C-C bond forming of aliphatic oligo-prenyl precursors. This reaction is catalysed by terpene synthases (TPSs), which are capable of chaperoning highly reactive carbocation intermediates through an enzyme-specific reaction. Due to the instability of carbocation intermediates, the proteins' structural dynamics and enzyme:substrate interactions during TPS catalysis remain elusive. Here, we present the structure of the diterpene synthase CotB2, in complex with an in crystallo cyclised abrupt reaction product and a substrate-derived diphosphate. We captured additional snapshots of the reaction to gain an overview of CotB2's catalytic mechanism. To enhance insights into catalysis, structural information is augmented with multiscale molecular dynamic simulations. Our data represent fundamental TPS structure dynamics during catalysis, which ultimately enable rational engineering towards tailored terpene macrocycles that are inaccessible by conventional chemical synthesis.

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[object Object], [object Object], [object Object] et al.

ACS ES&T Water • 2023

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[object Object], [object Object], [object Object] et al.

FEMS Microbiology Reviews • 2023

[object Object], [object Object], [object Object] et al.

Metabolic Engineering • 2020

[object Object], [object Object], [object Object] et al.

Environmental Science Processes & Impacts • 2020

Wastewater treatment plants (WWTPs) are one of the largest biotechnology applications in the world and are of critical importance to modern urban societies. An accurate evaluation of the microbial dark matter (MDM, microorganisms whose genomes remain uncharacterized) proportions in WWTPs is of great value, while there is no such research yet. This study conducted a global meta-analysis of MDM in WWTPs with 317,542 prokaryotic genomes from the Genome Taxonomy Database and proposed a "wanted list" for priority targets in further investigations of activated sludge.

[object Object], [object Object], [object Object] et al.

Nature Communications • 2016

Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.

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[object Object], [object Object], [object Object] et al.

Drug Delivery and Translational Research • 2023

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Bioresources and Bioprocessing • 2017

[object Object], [object Object], [object Object] et al.

Frontiers in Pharmacology • 2022

To investigate how the ulcerative colitis (UC) be treated with Chinese herbal medicines (CHM), using Chinese medicine (CM) pattern (zheng) identification, in the current clinical practice.

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[object Object], [object Object], [object Object] et al.

Journal of Fungi • 2024

Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved.

[object Object], [object Object], [object Object] et al.

Toxics • 2022

The large-scale application of organic pollutants (OPs) has contaminated the air, soil, and water. Persistent OPs enter the food supply chain and create several hazardous effects on living systems. Thus, there is a need to manage the environmental levels of these toxicants. Microbial glycoconjugates pave the way for the enhanced degradation of these toxic pollutants from the environment. Microbial glycoconjugates increase the bioavailability of these OPs by reducing surface tension and creating a solvent interface. To date, very little emphasis has been given to the scope of glycoconjugates in the biodegradation of OPs. Glycoconjugates create a bridge between microbes and OPs, which helps to accelerate degradation through microbial metabolism. This review provides an in-depth overview of glycoconjugates, their role in biofilm formation, and their applications in the bioremediation of OP-contaminated environments.

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[object Object], [object Object], [object Object] et al.

Foods • 2023

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The accelerating energy demands of the increasing global population and industrialization has become a matter of great concern all over the globe. In the present scenario, the world is witnessing a considerably huge energy crisis owing to the limited availability of conventional energy resources and rapid depletion of non-renewable fossil fuels. Therefore, there is a dire need to explore the alternative renewable fuels that can fulfil the energy requirements of the growing population and overcome the intimidating environmental issues like greenhouse gas emissions, global warming, air pollution etc. The use of microorganisms such as bacteria has captured significant interest in the recent era for the conversion of the chemical energy reserved in organic compounds into electrical energy. The versatility of the microorganisms to generate renewable energy fuels from multifarious biological and biomass substrates can abate these ominous concerns to a great extent. For instance, most of the microorganisms can easily transform the carbohydrates into alcohol. Establishing the microbial fuel technology as an alternative source for the generation of renewable energy sources can be a state of art technology owing to its reliability, high efficiency, cleanliness and production of minimally toxic or inclusively non-toxic byproducts. This review paper aims to highlight the key points and techniques used for the employment of bacteria to generate, biofuels and bioenergy, and their foremost benefits.

[object Object], [object Object], [object Object] et al.

Nature Communications • 2021