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Extreme biomimetics: Preservation of molecular detail in centimeter-scale samples of biological meshes laid down by sponges.

ABSTRACT: Fabrication of biomimetic materials and scaffolds is usually a micro- or even nanoscale process; however, most testing and all manufacturing require larger-scale synthesis of nanoscale features. Here, we propose the utilization of naturally prefabricated three-dimensional (3D) spongin scaffolds that preserve molecular detail across centimeter-scale samples. The fine-scale structure of this collagenous resource is stable at temperatures of up to 1200°C and can produce up to 4 × 10-cm-large 3D microfibrous and nanoporous turbostratic graphite. Our findings highlight the fact that this turbostratic graphite is exceptional at preserving the nanostructural features typical for triple-helix collagen. The resulting carbon sponge resembles the shape and unique microarchitecture of the original spongin scaffold. Copper electroplating of the obtained composite leads to a hybrid material with excellent catalytic performance with respect to the reduction of p-nitrophenol in both freshwater and marine environments.

SUBMITTER: Petrenko I

PROVIDER: S-EPMC6777968 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Extreme biomimetics: Preservation of molecular detail in centimeter-scale samples of biological meshes laid down by sponges.

Petrenko Iaroslav I Summers Adam P AP Simon Paul P Żółtowska-Aksamitowska Sonia S Motylenko Mykhailo M Schimpf Christian C Rafaja David D Roth Friedrich F Kummer Kurt K Brendler Erica E Pokrovsky Oleg S OS Galli Roberta R Wysokowski Marcin M Meissner Heike H Niederschlag Elke E Joseph Yvonne Y Molodtsov Serguei S Ereskovsky Alexander A Sivkov Viktor V Nekipelov Sergey S Petrova Olga O Volkova Olena O Bertau Martin M Kraft Michael M Rogalev Andrei A Kopani Martin M Jesioniowski Teofil T Ehrlich Hermann H

Science advances 20191004 10

Fabrication of biomimetic materials and scaffolds is usually a micro- or even nanoscale process; however, most testing and all manufacturing require larger-scale synthesis of nanoscale features. Here, we propose the utilization of naturally prefabricated three-dimensional (3D) spongin scaffolds that preserve molecular detail across centimeter-scale samples. The fine-scale structure of this collagenous resource is stable at temperatures of up to 1200°C and can produce up to 4 × 10-cm-large 3D mic ...[more]

PMID: 31620556

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Project description:The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples appears to be the most important factor in regards to the collection and preservation of samples from glacial environments.

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.

Dataset Information

Extreme biomimetics: Preservation of molecular detail in centimeter-scale samples of biological meshes laid down by sponges.

Publications

Extreme biomimetics: Preservation of molecular detail in centimeter-scale samples of biological meshes laid down by sponges.

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