Extreme biomimetics: Preservation of molecular detail in centimeter-scale samples of biological meshes laid down by sponges.
Ontology highlight
ABSTRACT:
SUBMITTER: Petrenko I
PROVIDER: S-EPMC6777968 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The structural biopolymer spongin in the form of a 3D scaffold resembles in shape and size numerous species of industrially useful marine keratosan demosponges. Due to the large-scale aquaculture of these sponges worldwide, it represents a unique renewable source of biological material, which has already been successfully applied in biomedicine and bioinspired materials science. In the present study, spongin from the demosponge Hippospongia communis was used as a microporous template for the development of a new 3D composite containing goethite [α-FeO(OH)]. For this purpose, an extreme biomimetic technique using iron powder, crystalline iodine, and fibrous spongin was applied under laboratory conditions for the first time. The product was characterized using SEM and digital light microscopy, infrared and Raman spectroscopy, XRD, thermogravimetry (TG/DTG), and confocal micro X-ray fluorescence spectroscopy (CMXRF). A potential application of the obtained goethite-spongin composite in the electrochemical sensing of dopamine (DA) in human urine samples was investigated, with satisfactory recoveries (96% to 116%) being obtained.
| S-EPMC10668986 | biostudies-literature
Project description:Mature tooth enamel is acellular and does not regenerate itself. Developing technologies that rebuild tooth enamel and preserve tooth structure is therefore of great interest. Considering the importance of amelogenin protein in dental enamel formation, its ability to control apatite mineralization in vitro, and its potential to be applied in fabrication of future bio-inspired dental material this review focuses on two major subjects: amelogenin and enamel biomimetics. We review the most recent findings on amelogenin secondary and tertiary structural properties with a focus on its interactions with different targets including other enamel proteins, apatite mineral, and phospholipids. Following a brief overview of enamel hierarchical structure and its mechanical properties we will present the state-of-the-art strategies in the biomimetic reconstruction of human enamel.
| S-EPMC4523244 | biostudies-literature
Project description:Biomimetics, a name coined by Otto Schmitt in the 1950s for the transfer of ideas and analogues from biology to technology, has produced some significant and successful devices and concepts in the past 50 years, but is still empirical. We show that TRIZ, the Russian system of problem solving, can be adapted to illuminate and manipulate this process of transfer. Analysis using TRIZ shows that there is only 12% similarity between biology and technology in the principles which solutions to problems illustrate, and while technology solves problems largely by manipulating usage of energy, biology uses information and structure, two factors largely ignored by technology.
| S-EPMC1664643 | biostudies-literature
Project description:Simple and rapid extraction of human genomic DNA remains a bottleneck for genome analysis and disease diagnosis. Current methods using microfilters require cumbersome, multiple handling steps in part because salt conditions must be controlled for attraction and elution of DNA in porous silica. We report a novel extraction method of human genomic DNA from buccal swab and saliva samples. DNA is attracted onto a gold-coated microchip by an electric field and capillary action while the captured DNA is eluted by thermal heating at 70 °C. A prototype device was designed to handle four microchips, and a compatible protocol was developed. The extracted DNA using microchips was characterized by qPCR for different sample volumes, using different lengths of PCR amplicon, and nuclear and mitochondrial genes. In comparison with a commercial kit, an equivalent yield of DNA extraction was achieved with fewer steps. Room-temperature preservation for 1 month was demonstrated for captured DNA, facilitating straightforward collection, delivery, and handling of genomic DNA in an environment-friendly protocol.
| S-EPMC3566295 | biostudies-literature
Project description:Antigen presenting dendritic cells (DCs) and monocytes capture and transport antigens from barrier tissues for presentation to antigen-specific T cells in the draining-lymph nodes (LNs). While DCs enter LNs through afferent lymphatics in a CCR7-dependent manner, how exactly antigen-carrying monocytes reach LNs is less clear since monocytes do not express CCR7 and can also enter LNs via the bloodstream. In steady state, and following injection of several PAMPs, scRNA-seq data on LN mononuclear phagocytes identified LN resident versus migratory type 1 and type 2 conventional (c)DCs despite downregulation of DC subset-defining transcripts, such as Xcr1, Clec9a, H2-Ab1, Sirpa, and Clec10a on migratory cDCs. Migratory cDCs gained expression of transcripts controlling cellular migration such as Ccr7, Ccl17, Ccl22, and Ccl5, while migratory monocytes expressed Ccr5 without Ccr7. Using two tracking methods and a gating strategy that clearly distinguishes migratory CD88hiCD26lo monocytes from CD88-CD26hi cDCs, we found that both captured antigens in the lung and migrated to lung-draining LNs. Using global and mixed-chimeric Ccl5-, Ccr2-, Ccr5-, Ccr7-, and Batf3-deficient mice, we found that CCR5+ monocytes follow CCL5-secreting migratory cDCs to reach the draining LN via lymphatic vessels. In a model of asthma, such recruited monocytes regulated the induction of type 2 immunity. Overall, our data suggest that CCL5-secreting migratory cDCs lay down the chemokine trail for CCR5+ antigen-presenting monocytes to reach draining lymph nodes and regulate adaptive immunity.
2022-10-17 | GSE215299 | GEO
Project description:BackgroundThis paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea's efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as "source" of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation.MethodsWe focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a "Hennigian forest"). The binary representations of the genomic (DNA) data have been made by script 1001. The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data.Principle findingsThe binary matrix may be easily re-written as a set of rooted trees (maximal relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, in principle can help to identify clades despite the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data.DiscussionOur proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual "data" also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the "direct" alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major differences between our recent proposal and the 3TA, as originally designed and implemented: (1) the 3TA deals with the three-taxon statements or minimal relationships. According to the logic of 3TA, the set of the minimal trees must be established as a binary matrix and used as an input for the parsimony program. In this paper, we operate directly with maximal relationships written just as trees, not as binary matrices, while also using the Average Consensus method instead of the MP analysis. The solely 'reversal'-based groups can always be found by our method without the separate scoring of the putative reversals before analyses.
| S-EPMC5522724 | biostudies-literature
Project description:Significance: The recently reported solvent-based optical clearing method FDISCO can preserve various fluorescent signals very well. However, the strict low-temperature storage condition of FDISCO is not conducive to long-time or repetitive imaging usually conducted at room temperature. Therefore, it is important to solve the contradiction between fluorescence preservation and imaging condition. Aim: We develop a modified FDISCO clearing method, termed FDISCO+, to change the preservation condition from low temperature to room temperature. Approach: Two alternative antioxidants were screened out to effectively inhibit the peroxide generation in the clearing agent at room temperature, enabling robust fluorescence preservation of cleared samples. Results: FDISCO+ achieves comparable fluorescence preservation with the original FDISCO protocol and allows long-time storage at room temperature, making it easier for researchers to image and preserve the samples. Conclusions: FDISCO+ is expected to be widely used due to its loose operation requirements.
| S-EPMC8427119 | biostudies-literature
Project description:Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples
| PRJEB49125 | ENA
Project description:The thermomechanical response of Omp2a, a representative porin used for the fabrication of smart biomimetic nanomembranes, has been characterized using microcantilever technology and compared with standard proteins. For this purpose, thermally induced transitions involving the conversion of stable trimers to bigger aggregates, local reorganizations based on the strengthening or weakening of intermolecular interactions, and protein denaturation have been detected by the microcantilever resonance frequency and deflection as a function of the temperature. Measurements have been carried out on arrays of 8-microcantilevers functionalized with proteins (Omp2a, lysozyme and bovine serum albumin). To interpret the measured nanofeatures, the response of proteins to temperature has been also examined using other characterization techniques, including real time wide angle X-ray diffraction. Results not only demonstrate the complex behavior of porins, which exhibit multiple local thermal transitions before undergoing denaturation at temperatures higher than 105 °C, but also suggest a posttreatment to control the orientation of immobilized Omp2a molecules in functionalized biomimetic nanomembranes and, thus, increase their efficacy in ion transport.
| S-EPMC6644815 | biostudies-literature
Project description:Biomineralization in general is based on electrostatic interactions and molecular recognition of organic and inorganic phases. These principles of biomineralization have also been utilized and transferred to bio-inspired synthesis of functional materials during the past decades. Proteins involved in both, biomineralization and bio-inspired processes, are often piezoelectric due to their dipolar character hinting to the impact of a template's piezoelectricity on mineralization processes. However, the piezoelectric contribution on the mineralization process and especially the interaction of organic and inorganic phases is hardly considered so far. We herein report the successful use of the intrinsic piezoelectric properties of tobacco mosaic virus (TMV) to synthesize piezoelectric ZnO. Such films show a two-fold increase of the piezoelectric coefficient up to 7.2 pm V(-1) compared to films synthesized on non-piezoelectric templates. By utilizing the intrinsic piezoelectricity of a biotemplate, we thus established a novel synthesis pathway towards functional materials, which sheds light on the whole field of biomimetics. The obtained results are of even broader and general interest since they are providing a new, more comprehensive insight into the mechanisms involved into biomineralization in living nature.
| S-EPMC4876381 | biostudies-literature