Unité en Sciences Biologiques et Biotechnologies de Nantes

Cancer is a multifactorial disease that is responsible for 10 million deaths per year. The intra- and inter-heterogeneity of malignant tumors make it difficult to develop single targeted approaches. Similarly, their diversity requires various models to investigate the mechanisms involved in cancer initiation, progression, drug resistance and recurrence. Of the in vitro cell-based models, monolayer adherent (also known as 2D culture) cell cultures have been used for the longest time. However, it appears that they are often less appropriate than the three-dimensional (3D) cell culture approach for mimicking the biological behavior of tumor cells, in particular the mechanisms leading to therapeutic escape and drug resistance. Multicellular tumor spheroids are widely used to study cancers in 3D, and can be generated by a multiplicity of techniques, such as liquid-based and scaffold-based 3D cultures, microfluidics and bioprinting. Organoids are more complex 3D models than multicellular tumor spheroids because they are generated from stem cells isolated from patients and are considered as powerful tools to reproduce the disease development in vitro. The present review provides an overview of the various 3D culture models that have been set up to study cancer development and drug response. The advantages of 3D models compared to 2D cell cultures, the limitations, and the fields of application of these models and their techniques of production are also discussed.

Quantum dots (QDs) are highly fluorescent nanoscale crystals with size-dependent emission spectra. Due to their excellent photophysical properties, QDs are a promising alternative to organic fluorescent dyes and fluorescent proteins for cell targeting, imaging, and drug delivery. For biomedical applications, QDs should be chemically modified to be stable in aqueous solutions and tagged with the recognition molecules or drugs. Here, we review surface modification approaches to, and strategies for, conjugation of bioactive molecules with QDs. There are a variety of methods of QD surface modification and QD incorporation into larger delivery systems that yield fluorescent nanocarriers from 10 nm to several micrometers. Conjugates of QDs with peptides, proteins, antibodies, oligonucleotides, and small molecules have been used for fluorescent targeting, tracking, and imaging both in vitro and in vivo. Due to an extremely high stability to photobleaching, QDs were used for long-term visualization. QD applications pave the way for new generations of ultrasensitive detection, diagnostic systems, as well as drug delivery approaches, combining accurate targeting, delivery, and imaging in a single assay.

A novel and straightforward method for the surface acetylation of cellulose nanowhiskers by transesterification of vinyl acetate is proposed. The reaction of vinyl acetate with the hydroxyl groups of cellulose nanowhiskers obtained from cotton linters was examined with potassium carbonate as catalyst. Results indicate that during the first stage of the reaction, only the surface of the nanowhiskers was modified, while their dimensions and crystallinity remained unchanged. With increasing reaction time, diffusion mechanisms controlled the rate, leading to nanowhiskers with higher levels of acetylation, smaller dimensions, and lower crystallinity. In THF, a solvent of low polarity, the suspensions from modified nanowhiskers showed improved stability with increased acetylation.

This study reports the elaboration of water-resistant, antimicrobial, chitosan and paper-based materials as environmentally friendly food packaging materials. Two types of papers were coated with chitosan-palmitic acid emulsions or with a blend of chitosan and O,O'-dipalmitoylchitosan (DPCT). Micromorphology studies showed that inclusion of hydrophobic compounds into the chitosan matrix was enhanced by grafting them onto chitosan and that this led to their penetration of the paper's core. Compared to chitosan-coated papers, the coating of chitosan-palmitic emulsion kept vapor-barrier properties unchanged (239 and 170 g.m(-2).d(-1) versus 241 and 161 g.m(-2).d(-1)), while the coating of chitosan-DPCT emulsion dramatically deteriorated them (441 and 442 g.m(-2).d(-1)). However, contact angle measurements (110-120 degrees after 1 min) and penetration dynamics analysis showed that both strategies improved liquid-water resistance of the materials. Kit-test showed that all hydrophobized chitosan-coated papers kept good grease barrier properties (degree of resistance 6-8/12). Finally, all chitosan-coated materials exhibited over 98% inhibition on Salmonella Typhimurium and Listeria monocytogenes .

About 1 million people in the world die each year from diseases spread by mosquitoes, and understanding the mechanism of host identification by the mosquitoes through olfaction is at stake. The role of odorant binding proteins (OBPs) in the primary molecular events of olfaction in mosquitoes is becoming an important focus of biological research in this area. Here, we present a comprehensive comparative genomics study of OBPs in the three disease-transmitting mosquito species Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus starting with the identification of 110 new OBPs in these three genomes. We have characterized their genomic distribution and orthologous and phylogenetic relationships. The diversity and expansion observed with respect to the Aedes and Culex genomes suggests that the OBP gene family acquired functional diversity concurrently with functional constraints posed on these two species. Sequences with unique features have been characterized such as the "two-domain OBPs" (previously known as Atypical OBPs) and "MinusC OBPs" in mosquito genomes. The extensive comparative genomics featured in this work hence provides useful primary insights into the role of OBPs in the molecular adaptations of mosquito olfactory system and could provide more clues for the identification of potential targets for insect repellants and attractants.

Neurodegenerative diseases are characterized by the progressive loss of neurons in different regions of the nervous system. Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most prevalent neurodegenerative diseases, and the symptoms associated with these pathologies are closely related to the regions that are most affected by the process of neurodegeneration. Despite their high prevalence, currently, there is no cure or disease-modifying drugs for the treatment of these conditions. In the last decades, due to the need for the development of new treatments for neurodegenerative diseases, several authors have investigated the neuroprotective actions of naturally occurring molecules, such as resveratrol. Resveratrol is a stilbene found in several plants, including grapes, blueberries, raspberries, and peanuts. Studies have shown that resveratrol presents neuroprotective actions in experimental models of AD and PD, however, its clinical application is limited due to its rapid metabolism and low bioavailability. In this context, studies have proposed that structural changes in the resveratrol molecule, including glycosylation, alkylation, halogenation, hydroxylation, methylation, and prenylation could lead to the development of derivatives with enhanced bioavailability and pharmacological activity. Therefore, this review article aims to discuss how resveratrol derivatives could represent viable molecules in the search for new drugs for the treatment of AD and PD.

Macrophages are specialized cells that control tissue homeostasis. They include non-resident and tissue-resident macrophage populations which are characterized by the expression of particular cell surface markers and the secretion of molecules with a wide range of biological functions. The differentiation and polarization of macrophages relies on specific growth factors and their receptors. Macrophage-colony stimulating factor (CSF-1) and interleukine-34 (IL-34), also known as "twin" cytokines, are part of this regluatory landscape. CSF-1 and IL-34 share a common receptor, the macrophage-colony stimulating factor receptor (CSF-1R), which is activated in a similar way by both factors and turns on identical signaling pathways. However, there is some discrete differential activation leading to specific activities. In this review, we disscuss recent progress in understanding of the role of the twin cytokines in macrophage differentiation, from their interaction with CSF-1R and the activation of signaling pathways, to their implication in macrophage polarization of non-resident and tissue-resident macrophages. A special focus on IL-34, its involvement in pathophsyiological contexts, and its potential as a theranostic target for macrophage therapy will be proposed.

Abstract Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have facilitated the prediction of protein properties and the identification of improved mutants. However, epistatic phenomena constitute an obstacle which can impair the predictions in protein engineering. We present an innovative sequence-activity relationship (innov’SAR) methodology based on digital signal processing combining wet-lab experimentation and computational protein design. In our machine learning approach, a predictive model is developed to find the resulting property of the protein when the n single point mutations are permuted (2 n combinations). The originality of our approach is that only sequence information and the fitness of mutants measured in the wet-lab are needed to build models. We illustrate the application of the approach in the case of improving the enantioselectivity of an epoxide hydrolase from Aspergillus niger . n = 9 single point mutants of the enzyme were experimentally assessed for their enantioselectivity and used as a learning dataset to build a model. Based on combinations of the 9 single point mutations (2 9 ), the enantioselectivity of these 512 variants were predicted, and candidates were experimentally checked: better mutants with higher enantioselectivity were indeed found.

Chitosan was chemically modified to produce quaternary ammonium salts in order to improve its antimicrobial activity and physicochemical properties. Quaternization of N-alkyl chitosan derivatives was carried out using alkyl iodide to elaborate water-soluble cationic polyelectrolytes ( N, N, N-trimethylchitosan, TMC). TMC was characterized by (1)H NMR spectroscopy; the quaternization degree was determined from (1)H NMR spectra and by titration of iodide ion. The antibacterial activity of hydroxypropylcellulose (HPC) films or coatings associated with chitosan or TMC as biocide was evaluated against the growth of Listeria monocytogenes and Salmonella typhimurium. The HPC-chitosan and HPC-TMC coatings exhibited a total inhibition on solid medium of both bacterial strains. Experiments conducted in liquid medium showed that the inhibitory activity against the growth of Listeria innocua was improved after chemical modification. Moreover, physicochemical properties of films were evaluated to determine their potential for food applications. The addition of the antibacterial agents showed a significant impact on the moisture barrier and mechanical properties of HPC films.

Understanding the mechanism of tree anchorage in a forest is a priority because of the increase in wind storms in recent years and their projected recurrence as a consequence of global warming. To characterize anchorage mechanisms during tree uprooting, we developed a generic finite element model where real three‐dimensional (3D) root system architectures were represented in a 3D soil. The model was used to simulate tree overturning during wind loading, and results compared with real data from two poplar species ( Populus trichocarpa and P. deltoides ). These trees were winched sideways until failure, and uprooting force and root architecture measured. The uprooting force was higher for P. deltoides than P. trichocarpa , probably due to its higher root volume and thicker lateral roots. Results from the model showed that soil type influences failure modes. In frictional soils, e.g., sandy soils, plastic failure of the soil occurred mainly on the windward side of the tree. In cohesive soils, e.g., clay soils, a more symmetrical slip surface was formed. Root systems were more resistant to uprooting in cohesive soil than in frictional soil. Applications of this generic model include virtual uprooting experiments, where each component of anchorage can be tested individually.

PURPOSE OF REVIEW: This article gives a brief overview of the most recent developments in osteosarcoma treatment, including targeting of signaling pathways, immune checkpoint inhibitors, drug delivery strategies as single or combined approaches, and the identification of new therapeutic targets to face this highly heterogeneous disease. RECENT FINDINGS: Osteosarcoma is one of the most common primary malignant bone tumors in children and young adults, with a high risk of bone and lung metastases and a 5-year survival rate around 70% in the absence of metastases and 30% if metastases are detected at the time of diagnosis. Despite the novel advances in neoadjuvant chemotherapy, the effective treatment for osteosarcoma has not improved in the last 4 decades. The emergence of immunotherapy has transformed the paradigm of treatment, focusing therapeutic strategies on the potential of immune checkpoint inhibitors. However, the most recent clinical trials show a slight improvement over the conventional polychemotherapy scheme. The tumor microenvironment plays a crucial role in the pathogenesis of osteosarcoma by controlling the tumor growth, the metastatic process and the drug resistance and paved the way of new therapeutic options that must be validated by accurate pre-clinical studies and clinical trials.

Environmentally friendly and potentially bioactive food packaging based on chitosan-coated papers were elaborated. The morphology and the microstructure of these new materials were characterized by infrared spectroscopy and scanning electron microscopy. These observations suggested that the chitosan penetrated deeply into the paper, embedding the cellulose fibers, instead of forming a layer as expected. Through the barrier properties against moisture, the liquid water sensitivity, and NMR-relaxometry measurements, the water interactions were evaluated on the chitosan films and the chitosan-coated papers. They revealed that the coating by a chitosan film forming solution improved the paper moisture barrier properties but the surface hydrophilicity remained high. Relaxometry studies showed that, due to its hydrophilic character, chitosan controlled the interaction with water, despite the very low amount of deposit. On the other hand, the mechanical properties of papers were unmodified by the chitosan coating, which did not fundamentally affect the solid structure of the papers.

This study presents a predictive dynamic model developed to analyse the mechanical response of trees submitted to a turbulent airflow. This finite-element model integrates a three-dimensional description of tree architecture and is driven by fluctuating drag forces applied on all parts. For validation purposes, instantaneous wind velocities and wind-induced stem displacements of two trees were recorded in a mature Maritime pine stand (Pinus pinaster) at several heights. The tree geometrical and physical characteristics were measured to describe their architecture. No model parameter was adjusted. Tree motions appear to be driven by wind pulses reflecting turbulence intermittency. No evidence is found for resonant behaviour. In the mean wind direction, the simulated oscillations agree well with the measured time series. The underestimation of tree movement in the cross-stream direction outlines the importance of torque behaviour on the predictive accuracy of the model. The mechanical transfer functions of the modelled trees show vibration peak frequencies very similar to the measured ones. At higher frequencies, the simulated damping appears overestimated, with the set of parameters used. The model provides a sound basis to further investigate the influence of tree aerial architecture and turbulence structure on tree stability to wind.

Abstract Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.

For decades, radiotherapy and chemotherapy were the two only approaches exploiting DNA repair processes to fight against cancer. Nowadays, cancer therapeutics can be a major challenge when it comes to seeking personalized targeted medicine that is both effective and selective to the malignancy. Over the last decade, the discovery of new targeted therapies against DNA damage signalling and repair has offered the possibility of therapeutic improvements in oncology. In this review, we summarize the current knowledge of DNA damage signalling and repair inhibitors, their molecular and cellular effects, and future therapeutic use.

Upon emergence of modern anticancer therapy, medical community is divided into two opposite camps, one of them claiming absolute necessity of using isolated or synthesized chemical compounds for efficient patient treatment and another one advocating alternative cancer therapies, in particular those based on natural sources, including extracts from plants. It seems, in reality, that the two camps are reconcilable: while natural sources, plant extracts or juices play both curative and protective role, drugs represent the ultimate possibility to inhibit or reverse tumor development. In this paper we tried to analyze anti-breast cancer potencies of quite a few extracts from different plant sources and to compare their anti-proliferative efficiency of crude extracts with actions of their purified ingredients.

A large number of retaining glycosidases catalyze both hydrolysis and transglycosylation reactions, but little is known about what determines the balance between these two activities (transglycosylation/hydrolysis ratio). We previously obtained by directed evolution the mutants F401S and N282T of Thermus thermophilus β-glycosidase (Ttβ-gly, glycoside hydrolase family 1 (GH1)), which display a higher transglycosylation/hydrolysis ratio than the wild-type enzyme. In order to find the cause of these activity modifications, and thereby set up a generic method for easily obtaining transglycosidases from glycosidases, we determined their X-ray structure. No major structural changes could be observed which could help to rationalize the mutagenesis of glycosidases into transglycosidases. However, as these mutations are highly conserved in GH1 β-glycosidases and are located around the -1 site, we pursued the isolation of new transglycosidases by targeting highly conserved amino acids located around the active site. Thus, by single-point mutagenesis on Ttβ-gly, we created four new mutants that exhibit improved synthetic activity, producing disaccharides in yields of 68-90% against only 36% when native Ttβ-gly was used. As all of the chosen positions were well conserved among GH1 enzymes, this approach is most probably a general route to convert GH1 glycosidases into transglycosidases.

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.

Abstract Resol type resins were prepared in alkaline conditions (potassium hydroxide or potassium carbonate) using furfural obtained by acid hydrolysis of abundant renewable resources from agricultural and forestry waste residues. The structures of the resins were fully determined by 1 H, 13 C, and 2D NMR spectrometries with the help of four models compounds synthesized specially for this study. MALDI‐Tof mass spectrometry experiments indicated that a majority of linear oligomers and a minority of cyclic ones constituted them. Composites were prepared with furfural–phenol resins and sisal fibers. These fibers were chosen mainly because they came from natural lignocellulosic material and they presented excellent mechanical properties. Thermal analyses (dTG and DSC) and electron microscopy images indicated that the composites displayed excellent adhesion between resin and fibers. Impact strength measurement showed that mild conditions were more suitable to prepare thermosets. Nevertheless, mild conditions induced a high‐diffusion coefficient for water absorption by composites. Composites with good properties could be prepared using high proportion of materials obtained from biomass without formaldehyde. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008

ABSTRACT: Locoregional failure (LRF) in patients with breast cancer post-surgery and post-irradiation is linked to a dismal prognosis. In a refined new model, we identified ectonucleotide pyrophosphatase/phosphodiesterase 1/CD203a (ENPP1) to be closely associated with LRF. ENPP1hi circulating tumor cells (CTC) contribute to relapse by a self-seeding mechanism. This process requires the infiltration of polymorphonuclear myeloid-derived suppressor cells and neutrophil extracellular trap (NET) formation. Genetic and pharmacologic ENPP1 inhibition or NET blockade extends relapse-free survival. Furthermore, in combination with fractionated irradiation, ENPP1 abrogation obliterates LRF. Mechanistically, ENPP1-generated adenosinergic metabolites enhance haptoglobin (HP) expression. This inflammatory mediator elicits myeloid invasiveness and promotes NET formation. Accordingly, a significant increase in ENPP1 and NET formation is detected in relapsed human breast cancer tumors. Moreover, high ENPP1 or HP levels are associated with poor prognosis. These findings unveil the ENPP1/HP axis as an unanticipated mechanism exploited by tumor cells linking inflammation to immune remodeling favoring local relapse. SIGNIFICANCE: CTC exploit the ENPP1/HP axis to promote local recurrence post-surgery and post-irradiation by subduing myeloid suppressor cells in breast tumors. Blocking this axis impairs tumor engraftment, impedes immunosuppression, and obliterates NET formation, unveiling new opportunities for therapeutic intervention to eradicate local relapse and ameliorate patient survival. This article is highlighted in the In This Issue feature, p. 1171.