Institute of Fundamental Technological Research

Loayza-Aguilar Rómulo E., Carhuapoma-Garay J., Ramos-Falla K., Saldaña-Rojas Guillermo B., Huamancondor-Paz Yolanda P., Campoverde-Vigo L., Merino F., Olivos-Ramirez Gustavo E., Epibionts affect the growth and survival of Argopecten purpuratus (Lamarck, 1819) cultivated in Samanco Bay, Peru, Aquaculture, ISSN: 0044-8486, DOI: 10.1016/j.aquaculture.2023.740042, Vol.578, pp.740042-1-10, 2024

Abstract:
Argopecten purpuratus, a mollusk very cultivated in Peru, is a species whose ecological relations with respect to the epibionts that colonize it are not well known. For that reason, the objective of this research was to determine the effect of epibionts on valvar growth, total weight, gonad weight, adductor muscle weight, and survival of this cultured species in Samanco Bay. Four lanterns of 2 m and 10 floors were placed with 25 organisms, of 7 cm each, per floor, in two treatments: with epibiont removal (T1) and without removal (T2). The data was obtained after harvest, and the epibiont species on the right and left valves were identified and quantified in T1 and T2. In addition, the Absolute Growth Rate (AGR) was calculated for the meristic records, and the t Student test was applied to compare averages. Furthermore, mortality was recorded at harvest. The analyses allowed the identification of 43 epibiont species, 3 of them endolithic. The greatest biomass is of filter feeders: 70.1% in T1 and 90.9% in T2, and concentrated in 4 species, with limited development in T1. The biomass on the right valve at T1 and T2 represented 80.7 and 151.8% of the weight of the organism, respectively, and on the left valve 89.3 and 95.1%. All Absolute Growth Rates at T1 were higher than at T2, although without statistical significance. Mortality at T1 and T2 was negligible. This research has determined that the epibionts S. patagonicus, C. intestinalis, Hidroydes sp., and B. neritina, qualified as engineered species, are the predominant species on A. purpuratus in suspended cultures. Likewise, treatments with epibiont removal showed a lower development of these and 39 other associated species of lesser importance in terms of number and biomass. Our results allow us to infer that the development of epibionts can generate important stress in A. purpuratus, resulting in losses in the profitability of companies dedicated to this activity.

Keywords:
Argopecten purpuratus, Aquaculture, Epibiosis, Biofouling, Bivalve

Rybak D., Rinoldi C., Nakielski P., Du J., Haghighat Bayan Mohammad A., Zargarian Seyed S., Pruchniewski M., Li X., Strojny-Cieślak B., Ding B., Pierini F., Injectable and self-healable nano-architectured hydrogel for NIR-light responsive chemo- and photothermal bacterial eradication, JOURNAL OF MATERIALS CHEMISTRY B , ISSN: 2050-7518, DOI: 10.1039/D3TB02693K, pp.1-21, 2024

Abstract:
Hydrogels with multifunctional properties activated at specific times have gained significant attention in the biomedical field. As bacterial infections can cause severe complications that negatively impact wound repair, herein, we present the development of a stimuli-responsive, injectable, and in situ-forming hydrogel with antibacterial, self-healing, and drug-delivery properties. In this study, we prepared a Pluronic F-127 (PF127) and sodium alginate (SA)-based hydrogel that can be targeted to a specific tissue via injection. The PF127/SA hydrogel was incorporated with polymeric short-filaments (SFs) containing an anti-inflammatory drug – ketoprofen, and stimuli-responsive polydopamine (PDA) particles. The hydrogel, after injection, could be in situ gelated at the body temperature, showing great in vitro stability and self-healing ability after 4 h of incubation. The SFs and PDA improved the hydrogel injectability and compressive strength. The introduction of PDA significantly accelerated the KET release under near-infrared light exposure and extended its release validity period. The excellent composites’ photo-thermal performance led to antibacterial activity against representative Gram-positive and Gram-negative bacteria, resulting in 99.9% E. coli and S. aureus eradication after 10 min of NIR light irradiation. In vitro, fibroblast L929 cell studies confirmed the materials’ biocompatibility and paved the way toward further in vivo and clinical application of the system for chronic wound treatments.

Haghighat Bayan Mohammad A., Rinoldi C., Rybak D., Zargarian Seyed S., Zakrzewska A., Cegielska O., Põhako-Palu K., Zhang S., Stobnicka-Kupiec A., Górny Rafał L., Nakielski P., Kogermann K., De Sio L., Ding B., Pierini F., Engineering surgical face masks with photothermal and photodynamic plasmonic nanostructures for enhancing filtration and on-demand pathogen eradication, Biomaterials Science, ISSN: 2047-4849, DOI: 10.1039/d3bm01125a, pp.1-15, 2024

Abstract:
The shortage of face masks and the lack of antipathogenic functions has been significant since the recent pandemic's inception. Moreover, the disposal of an enormous number of contaminated face masks not only carries a significant environmental impact but also escalates the risk of cross-contamination. This study proposes a strategy to upgrade available surgical masks into antibacterial masks with enhanced particle and bacterial filtration. Plasmonic nanoparticles can provide photodynamic and photothermal functionalities for surgical masks. For this purpose, gold nanorods act as on-demand agents to eliminate pathogens on the surface of the masks upon near-infrared light irradiation. Additionally, the modified masks are furnished with polymer electrospun nanofibrous layers. These electrospun layers can enhance the particle and bacterial filtration efficiency, not at the cost of the pressure drop of the mask. Consequently, fabricating these prototype masks could be a practical approach to upgrading the available masks to alleviate the environmental toll of disposable face masks.

Liu L., Sznajder P., Ekiel-Jeżewska M.L., Spectral analysis for elastica dynamics in a shear flow, Physical Review Fluids, ISSN: 2469-990X, DOI: 10.1103/PhysRevFluids.9.014101, Vol.9, No.1, pp.014101-1-12, 2024

Abstract:
We present the spectral analysis of three-dimensional dynamics of an elastic filament in a shear flow of a viscous fluid at a low Reynolds number in the absence of Brownian motion. The elastica model is used. The fiber initially is almost straight at an arbitrary orientation, with small perpendicular perturbations in the shear plane and out-of-plane. To analyze the stability of both perturbations, equations for the eigenvalues and eigenfunctions are derived and solved by the Chebyshev spectral collocation method. It is shown that their crucial features are the same as in the case of the two-dimensional elastica dynamics in shear flow [Becker and Shelley, Phys. Rev. Lett. 87, 198301 (2001)] and the three-dimensional elastica dynamics in the compressional flow [Chakrabarti et al., Nat. Phys. 16, 689 (2020)]. We find a similar dependence of the buckled shapes on the ratio of bending to hydrodynamic forces as in the simulations for elastic fibers of a nonzero thickness [Słowicka et al., New J. Phys. 24, 013013 (2022)].

Pawłowska S., Cysewska K., Ziai Y., Karczewski J., Jasiński P., Molin S., Influence of conductive carbon and MnCo2O4 on morphological and electrical properties of hydrogels for electrochemical energy conversion, Beilstein Journal of Nanotechnology, ISSN: 2190-4286, DOI: 10.3762/bjnano.15.6, pp.57-70, 2024

Keywords:
electrical properties, energy, hydrogel, hydrogen, oxygen evolution reaction, polymer composites

Nazish J., Sohail M., Mahmood A., Shah Syed A., Qalawlus Aya Hamid M., Khaliq T., Nanocrystals loaded collagen/alginate-based injectable hydrogels: A promising biomaterial for bioavailability improvement of hydrophobic drugs, Journal of Drug Delivery Science and Technology, ISSN: 1773-2247, DOI: 10.1016/j.jddst.2023.105291, Vol.91, pp.105291-1-16, 2024

Abstract:
The study aims to improve the solubility of poorly soluble drug by developing an optimized formulation of nanocrystals and extend its release profile by incorporating optimized nanocrystals in a biopolymer based injectable hydrogel. Nanocrystals of Silymarin (SM) were developed by anti-solvent precipitation technique followed by homogenization. Various stabilizers were investigated and combination of polyvinyl pyrrolidine K30 (PVP K30) and sodium lauryl sulfate (SLS) in a specific ratio was chosen as a stabilizer for nanocrystals. The optimized nanocrystals possessed mean particle size 172 ± 5.23 nm and PDI of 0.228 ± 0.02. Sodium alginate (Alg) and collagen (Col) based injectable hydrogel in combination with pluronic F127 showed good biocompatibility, mechanical strength and biodegradability. The developed formulation was characterized by scanning electron microscopy (SEM), thermogravimetric analysis (TGA), Fourier transform infra-red spectroscopy (FT-IR) and X-ray diffraction (XRD) analysis. The results of FT-IR and TGA showed structural cross-linking between polymers and promising thermal stability of formulation with increasing temperature, respectively. The nanocrystals loaded Alg-Col-F127 injectable hydrogel was degraded completely in 48 h. The results of in vitro release studies and in vivo pharmacokinetic profiling of silymarin nanocrystals laden Alg-Col-F127 injectable hydrogel exhibited controlled release behavior as compared to coarse silymarin suspension and silymarin nanocrystals. Therefore, nanosuspension integrated biopolymer-based hybrid injectable hydrogel system may be used to assist solubility and bioavailability enhancement as well as serve as platform to provide controlled drug release.

Keywords:
Nanocrystals, Injectable hydrogel, Hydrophobic drug, Solubility, Bioavailability

Cofas Vargas L.F.^♦, Azevedo Rodrigo M., Poblete S., Chwastyk M., Poma Bernaola A.M.^♦, The GōMartini Approach: Revisiting the Concept of Contact Maps and the Modelling of Protein Complexes, ACTA PHYSICA POLONICA A, ISSN: 0587-4246, DOI: 10.12693/APhysPolA.145.S9, Vol.145, No.3, pp.S9-S20, 2024

Abstract:
We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g., distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust Gō-Martini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based Gō--like approach to the study of protein–sugar complexes, and the limitations of this approach are also discussed. The Gō-Martini approach was first introduced by Poma et al. (J. Chem. Theory Comput. 13, 1366 (2017)) in Martini 2 force field, and recently, it has gained the status of gold standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support for this approach in the context of the biophysical community.

Keywords:
Martini 3,Structure-based coarse-graining,SMFS,biomolecules,GoMartini

Ray A., Thu Thi Minh T., Santos Natividade Rita d., Azevedo Rodrigo M., Joshua S., Danahe M., Koehler M., Simon P., Qingrong Z., Fabrice B., Laurent G., Poma Bernaola A.M., Alsteens D., Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2, ACS Nanoscience Au, ISSN: 2694-2496, DOI: 10.1021/acsnanoscienceau.3c00060, pp.1-10, 2024

Abstract:
The SARS-CoV-2 pandemic spurred numerous research endeavors to comprehend the virus and mitigate its global severity. Understanding the binding interface between the virus and human receptors is pivotal to these efforts and paramount to curbing infection and transmission. Here we employ atomic force microscopy and steered molecular dynamics simulation to explore SARS-CoV-2 receptor binding domain (RBD) variants and angiotensin-converting enzyme 2 (ACE2), examining the impact of mutations at key residues upon binding affinity. Our results show that the Omicron and Delta variants possess strengthened binding affinity in comparison to the Mu variant. Further, using sera from individuals either vaccinated or with acquired immunity following Delta strain infection, we assess the impact of immunity upon variant RBD/ACE2 complex formation. Single-molecule force spectroscopy analysis suggests that vaccination before infection may provide stronger protection across variants. These results underscore the need to monitor antigenic changes in order to continue developing innovative and effective SARS-CoV-2 abrogation strategies.

Keywords:
SARS-Cov-2,Molecular Dynamics ,Immunity,SMFS,Nanomechanics,Free Energy,Jarzynski,Receptor,Protein complex,interfaces

Ziai Y., Lanzi M., Rinoldi C., Zargarian Seyed S., Zakrzewska A., Kosik-Kozioł A., Nakielski P., Pierini F., Developing strategies to optimize the anchorage between electrospun nanofibers and hydrogels for multi-layered plasmonic biomaterials, Nanoscale Advances, ISSN: 2516-0230, DOI: 10.1039/d3na01022h, pp.1-13, 2024

Abstract:
Polycaprolactone (PCL), a recognized biopolymer, has emerged as a prominent choice for diverse biomedical endeavors due to its good mechanical properties, exceptional biocompatibility, and tunable properties. These attributes render PCL a suitable alternative biomaterial to use in biofabrication, especially the electrospinning technique, facilitating the production of nanofibers with varied dimensions and functionalities. However, the inherent hydrophobicity of PCL nanofibers can pose limitations. Conversely, acrylamide-based hydrogels, characterized by their interconnected porosity, significant water retention, and responsive behavior, present an ideal matrix for numerous biomedical applications. By merging these two materials, one can harness their collective strengths while potentially mitigating individual limitations. A robust interface and effective anchorage during the composite fabrication are pivotal for the optimal performance of the nanoplatforms. Nanoplatforms are subject to varying degrees of tension and physical alterations depending on their specific applications. This is particularly pertinent in the case of layered nanostructures, which require careful consideration to maintain structural stability and functional integrity in their intended applications. In this study, we delve into the influence of the fiber dimensions, orientation and surface modifications of the nanofibrous layer and the hydrogel layer's crosslinking density on their intralayer interface to determine the optimal approach. Comprehensive mechanical pull-out tests offer insights into the interfacial adhesion and anchorage between the layers. Notably, plasma treatment of the hydrophobic nanofibers and the stiffness of the hydrogel layer significantly enhance the mechanical effort required for fiber extraction from the hydrogels, indicating improved anchorage. Furthermore, biocompatibility assessments confirm the potential biomedical applications of the proposed nanoplatforms.