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Epitopes are specific regions on an antigen's surface that the immune system recognizes. Epitopes are usually protein regions on foreign immune-stimulating entities such as viruses and bacteria, and in some cases, endogenous proteins may act as antigens. Identifying epitopes is crucial for accelerating the development of vaccines and immunotherapies. However, mapping epitopes in pathogen proteomes is challenging using conventional methods. Screening artificial neoepitope libraries against antibodies can overcome this issue. Here, we applied conventional sequence analysis and methods inspired in natural language processing to reveal specific sequence patterns in the linear epitopes deposited in the Immune Epitope Database (www.iedb.org) that can serve as building blocks for the design of universal epitope libraries. Our results reveal that amino acid frequency in annotated linear epitopes differs from that in the human proteome. Aromatic residues are overrepresented, while the presence of cysteines is practically null in epitopes. Byte pair encoding tokenization shows high frequencies of tryptophan in tokens of 5, 6, and 7 amino acids, corroborating the findings of the conventional sequence analysis. These results can be applied to reduce the diversity of linear epitope libraries by orders of magnitude.

Protein-based hybrid nanomaterials have recently emerged as promising platforms to fabricate tailored multifunctional biologics for biotechnological and biomedical applications. This work shows a simple, modular, and versatile strategy to design custom protein hybrid nanomaterials. This approach combines for the first time the engineering of a therapeutic protein module with the engineering of a nanomaterial-stabilizing module within the same molecule, resulting in a multifunctional hybrid nanocomposite unachievable through conventional material synthesis methodologies. As the first proof of concept, a multifunctional system was designed ad hoc for the therapeutic intervention and monitoring of myocardial fibrosis. This hybrid nanomaterial combines a designed Hsp90 inhibitory domain and a metal nanocluster stabilizing module resulting in a biologic drug labelled with a metal nanocluster. The engineered nanomaterial actively reduced myocardial fibrosis and heart hypertrophy in an animal model of cardiac remodeling. In addition to the therapeutic effect, the metal nanocluster allowed for in vitro , ex vivo , and in vivo detection and imaging of the fibrotic disease under study. This study evidences the potential of combining protein engineering and protein-directed nanomaterial engineering approaches to design custom nanomaterials as theranostic tools, opening up unexplored routes to date for the next generation of advanced nanomaterials in medicine., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

In this article, we explored the selective antibiofouling capacity acquired by functional wrinkled hydrogel films via a fine tuning of their chemical structure through the gradual insertion of hydrophobic radical groups in their network. The hydrogel consists of three main components: hydroxyethyl methacrylate (HEMA, amphiphilic monomer), trifluoroethyl methacrylate (TFMA, hydrophobic monomer), and poly(ethylene glycol) diacrylate (PEGDA, hydrophilic crosslinking agent). Interestingly, the manipulation of the chemical composition affects both, surface morphology and physicochemical characteristics of the patterns, inducing transitions between different surface microstructures, i.e. from wrinkles to creases, to folds, and to crumples. Contact angle measurements show that the insertion of TFMA produces a slight decrease in surface wettability, remaining however highly hydrophilic. By using confocal Raman spectroscopy, important information about wrinkle formation mechanism could be obtained. The procedure presented in this article involves two consecutive thermal and photopolymerization steps, generating a "pseudo" two-layer system, which contracts at different extents when is exposed to external stimuli, leading to the formation of wrinkled surfaces. Finally, bacterial and cellular adhesion/proliferation studies were carried out, evidencing that the amount of TFMA included clearly reduce the bacterial adhesion while mammalian cells are able to still proliferate., (Copyright © 2018 Elsevier B.V. All rights reserved.)

We report on the fabrication of 3D printed pH-responsive and antimicrobial hydrogels with a micrometer-scale resolution achieved by stereolithography (SLA) 3D printing. The preparation of the hydrogels was optimized by selecting the most appropriate difunctional polyethylene glycol dimethacrylates (testing cross-linking agents with chain lengths ranging from 2 up to 14 units ethylene glycol) and introducing acrylic acid (AA) as a monofunctional monomer. As a result of the incorporation of AA, the hydrogels described are able to reversibly swell and shrink upon environmental changes on the pH, and the swelling extent is directly related to the amount of AA and can be thus finely tuned. More interestingly, upon optimization of the UV penetration depth employing a photoabsorber (Sudan I), a reliable procedure for the fabrication of 3D objects with a high model accuracy is shown. Finally, the antimicrobial properties of all of the hydrogels were demonstrated using Staphylococcus aureus as a bacterial model. We found that even those hydrogels with a low amount of AA monomeric units presented excellent antimicrobial properties against S. aureus .

Among all new nanomaterials, metal nanoclusters (NCs) have attracted special attention due to their interesting optical properties, among others. Metal NCs have been recently studied and used as sensors for different analytes. However, there is a need to explore the potential of these new sensors in a systematic manner and to develop new systems to broaden the possibilities that sensing offers to the industry. In this work, we show the potential use of repeat protein scaffolds as versatile templates for the synthesis and stabilization of various metal NCs, specifically Au, Ag, and CuNCs. The resulting protein-metal NCs hybrids are evaluated as sensors for different stimuli such as temperature, ions, or reactive oxygen species (ROS). Among the three protein-metal NCs, all performed nicely as temperature sensors, AuNCs responded to metal ions, and AgNCs were able to detect ROS., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Polymers exhibiting both antimicrobial and biodegradable properties are of great interest for next generation materials in healthcare. Among those, cationic polycarbonates are one of the most promising classes of materials because of their biodegradability, low toxicity, and biocompatibility. They are typically prepared by a chemical postmodification after the polymer has been synthesized. The main problem with the latter is the challenges of ensuring and verifying complete quaternization within the polymer structure. Herein, we report the first example of synthesizing and polymerizing charged aliphatic cyclic carbonates with three different alkane pendant groups ( N -methyl, N -butyl, and N -hexyl) by ring-opening polymerization (ROP). These charged eight-membered cyclic carbonates displayed extraordinary reactivity and were even polymerizable in polar solvents (e.g., DMSO) and in catalyst free conditions that are generally unobtainable for other ring opening polymerization processes. A computational study was carried out and the findings were in agreement with the experimental data in regards to the dramatic increase in reactivity of the charged monomer over their neutral analogs. Furthermore, a series of hydrogels were prepared using the different charged eight-membered cyclic carbonates, and we found it to have a significant impact on the hydrogels' ability to swell and degrade in water. Finally, the hydrogels demonstrated antibacterial activity against Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive). These materials could be ideal candidates for biologically relevant applications where cationic structure is required.

Background: Plasma exchange (PE) therapy has dramatically improved the outcome of thrombotic microangiopathies (TMA) in adults. However, resistance to PE, which indicates a poor prognosis, is observed in 1/3 of patients and remains not fully understood. We evaluated in this study the survival and the long-term outcome of severe TMA treated by PE and identified the predictive factors of resistance to PE and of mortality., Material/methods: Records of adults with severe TMA treated by PE were reviewed. Clinical and biological data, therapeutic delay to PE, plasma volume exchange per procedure, and number of PE sessions were collected. Mortality was assessed at one month and at one-year follow-up. All data were analyzed and compared between survived/deceased and between responder/non-responder patients., Results: Nineteen females and six males were included. Mean age (+/-SD) was 46.8+/-16.3 years, Glasgow coma score 11+/-3, and Sequential Organ Failure Assessment (SOFA) score 5.8+/-2.8. Nineteen patients partially or fully responded to PE. Twenty patients were alive at one month and 19 at one year. The response to PE was the single discriminating parameter between survivors and non-survivors. A longer delay of PE and a neoplastic cause of TMA were significantly higher in the non-responders., Conclusions: Severe TMA treated by PE had a fair prognosis, with a survival rate at 76% after one year of follow-up. Unresponsiveness to PE was the only predictive factor of mortality; a neoplastic etiology of TMA and a longer therapeutic delay of PE were predictive of resistance to PE.

Acting pharmacologically on different transmitter systems has been suggested to have some advantages in patients with substance abuse and may possibly address a larger spectrum of symptoms. One major drawback of using antidepressants addressing several neurotransmitters is that the relative activities on the different neurotransmitters cannot individually be adjusted. Combining antidepressants targeting different neurotransmitter systems may allow adapting the effect on each neurotransmitter system corresponding to patients' response and tolerance. Three cases of patients presenting a substance use disorder with comorbid major depression episodes are presented, who were treated with a reboxetine/escitalopram combination and who showed a rapid response of their depressive syndrome.