Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions

Corals are the main primary producers of coral reefs and build the three-dimensional reef structure that provides habitat to more than 25% of all marine eukaryotes. They harbor a complex consortium of microorganisms, including bacteria, archaea, fungi, viruses, and protists, which they rely on for their survival. The symbiosis between corals and bacteria is poorly studied, and their symbiotic relationships with intracellular bacteria are only just beginning to be acknowledged. In this review, we emphasize the importance of characterizing intracellular bacteria associated with corals and explore how successful approaches used to study such microorganisms in other systems could be adapted for research on corals. We propose a framework for the description, identification, and functional characterization of coral-associated intracellular bacterial symbionts. Finally, we highlight the possible value of intracellular bacteria in microbiome manipulation and mitigating coral bleaching.

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Effect of Surface Topography Parameters on Friction and Wear of Random Rough Surface

Materials ◽

10.3390/ma12172762 ◽

2019 ◽

Vol 12 (17) ◽

pp. 2762 ◽

Cited By ~ 4

Author(s):

Ruimin Shi ◽

Bukang Wang ◽

Zhiwei Yan ◽

Zongyan Wang ◽

Lei Dong

Keyword(s):

Surface Topography ◽

Fluid Dynamic ◽

Dynamic Pressure ◽

Functional Characterization ◽

Three Dimensional ◽

Measuring System ◽

Height Distribution ◽

Worn Surface ◽

The Relationship

In order to explore the relationship between the surface topography parameters and friction properties of a rough contact interface under fluid dynamic pressure lubrication conditions, friction experiments were carried out. The three-dimensional surface topography of specimens was measured and characterized with a profile microscopy measuring system and scanning electron microscope. The friction coefficient showed a trend of decreasing first and then increasing with the increase in some surface topography parameters at lower pressure, such as the surface height arithmetic mean Sa, surface height distribution kurtosis Sku, surface volume average volume Vvv, and surface center area average void volume Vvc, which are the ISO 25178 international standard parameters. The effects of surface topographic parameters on friction were analyzed and the wear mechanism of the worn surface was presented. The wear characteristics of the samples were mainly characterized as strain fatigue, grinding, and scraping. The results provide a theoretical basis for the functional characterization of surface topography.

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Self-Contained Three-Dimensional Bioprinter for Applications in Cardiovascular Research

Journal of Medical Devices ◽

10.1115/1.4043960 ◽

2019 ◽

Vol 13 (3) ◽

Cited By ~ 1

Author(s):

Prabhuti Kharel ◽

Likitha Somasekhar ◽

Amy Vecheck ◽

Kunal Mitra

Keyword(s):

Functional Characterization ◽

Three Dimensional ◽

Environmental Parameters ◽

3D Bioprinting ◽

Cardiovascular Research ◽

Form Complex ◽

Tissue Constructs ◽

Long Duration ◽

Selection Of

Bioprinting is a technique of creating 3D cell-laden structures by accurately dispensing biomaterial to form complex synthetic tissue. The printed constructs aim to mimic the native tissue by preserving the cell functionality and viability within the printed structure. The 3D bioprinting system presented in this paper aims to facilitate the process of 3D bioprinting through its ability to control the environmental parameters within an enclosed printing chamber. This design of the bioprinter targets to eliminate the need for a laminar flow hood, by regulating the necessary environmental conditions important for cell survival, especially during long duration prints. A syringe-based extrusion (SBE) deposition method comprising multiple nozzles is integrated into the system. This allows for a wider selection of biomaterials that can be used for the formation of the extracellular matrix (ECM). Tissue constructs composed of alginate-gelatin hydrogels were mixed with fibrinogen and human endothelial cells which were then characterized and compared using two methodologies: casted and bioprinted. Furthermore, vasculature was incorporated in the bioprinted constructs using sacrificial printing. Structural and functional characterization of the constructs were performed by assessing rheological, mechanical properties, and analyzing live-dead assay measurements.

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Functional Characterization of Three-Dimensional Cortical Cultures for In Vitro Modeling of Brain Networks

iScience ◽

10.1016/j.isci.2020.101434 ◽

2020 ◽

Vol 23 (8) ◽

pp. 101434

Author(s):

Yu-Ting L. Dingle ◽

Volha Liaudanskaya ◽

Liam T. Finnegan ◽

Kyler C. Berlind ◽

Craig Mizzoni ◽

...

Keyword(s):

Functional Characterization ◽

Brain Networks ◽

Three Dimensional ◽

In Vitro Modeling ◽

Cortical Cultures

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Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs

Journal of Marine Science and Engineering ◽

10.3390/jmse7020027 ◽

2019 ◽

Vol 7 (2) ◽

pp. 27 ◽

Cited By ~ 12

Author(s):

Atsuko Fukunaga ◽

John Burns ◽

Brianna Craig ◽

Randall Kosaki

Keyword(s):

Fractal Dimension ◽

Coral Reefs ◽

Three Dimensional ◽

Ecological Monitoring ◽

Benthic Habitat ◽

Fish Assemblage Structure ◽

Benthic Habitats ◽

Single Measure ◽

Curvature Measures

Long-term ecological monitoring of reef fish populations often requires the simultaneous collection of data on benthic habitats in order to account for the effects of these variables on fish assemblage structure. Here, we described an approach to benthic surveys that uses photogrammetric techniques to facilitate the extraction of quantitative metrics for characterization of benthic habitats from the resulting three-dimensional (3D) reconstruction of coral reefs. Out of 92 sites surveyed in the Northwestern Hawaiian Islands, photographs from 85 sites achieved complete alignment and successfully produced 3D reconstructions and digital elevation models (DEMs). Habitat metrics extracted from the DEMs were generally correlated with one another, with the exception of curvature measures, indicating that complexity and curvature measures should be treated separately when quantifying the habitat structure. Fractal dimension D64, calculated by changing resolutions of the DEMs from 1 cm to 64 cm, had the best correlations with other habitat metrics. Fractal dimension was also less affected by changes in orientations of the models compared to surface complexity or slope. These results showed that fractal dimension can be used as a single measure of complexity for the characterization of coral reef habitats. Further investigations into metrics for 3D characterization of habitats should consider relevant spatial scales and focus on obtaining variables that can complement fractal dimension in the characterization of reef habitats.

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Characterization of Leucetta prolifera, a calcarean cyanosponge from south-western Australia, and its symbionts

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415000491 ◽

2015 ◽

Vol 96 (2) ◽

pp. 541-552 ◽

Cited By ~ 5

Author(s):

Jane Fromont ◽

Megan J. Huggett ◽

Sabine K. Lengger ◽

Kliti Grice ◽

Christine H.L. Schönberg

Keyword(s):

Western Australia ◽

Pulse Amplitude ◽

Individual Sample ◽

Bacterial Symbionts ◽

16S Rdna Gene ◽

Symbiotic Relationships ◽

The Individual ◽

The Relationship ◽

V3 Region

The biology and ecology of calcarean sponges are not as well understood as they are for demosponges. Here, in order to gain new insights, particularly about symbiotic relationships, the calcarean sponge Leucetta prolifera was sampled from south-western Australia and examined for its assumed photosymbionts. Pulse amplitude modulated fluorometry and extraction of photopigments established that the sponge was photosynthetic. Molecular analysis of the bacterial symbionts via sequencing of the V1–V3 region of the 16S rDNA gene confirmed that between 5 and 22% of all sequences belonged to the phylum Cyanobacteria, depending on the individual sample, with the most dominant strain aligning with Hormoscilla spongeliae, a widely distributed sponge symbiont. Analysis of fatty acids suggested that the sponge obtains nutrition through photosynthates from its symbionts. The relationship is assumed to be mutualistic, with the sponge receiving dietary support and the cyanobacteria sheltering in the sponge tissues. We list all Calcarea presently known to harbour photosymbionts.

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Functional Characterization of 21 Rare Allelic CYP1A2 Variants Identified in a Population of 4773 Japanese Individuals by Assessing Phenacetin O-Deethylation

Journal of Personalized Medicine ◽

10.3390/jpm11080690 ◽

2021 ◽

Vol 11 (8) ◽

pp. 690

Author(s):

Masaki Kumondai ◽

Evelyn Marie Gutiérrez Rico ◽

Eiji Hishinuma ◽

Yuya Nakanishi ◽

Shuki Yamazaki ◽

...

Keyword(s):

Enzymatic Activity ◽

Protein Function ◽

Rare Variants ◽

Functional Characterization ◽

Three Dimensional ◽

Additional Information ◽

Metabolic Reactions ◽

Underlying Mechanisms ◽

Cytochrome Content

Cytochrome P450 1A2 (CYP1A2), which accounts for approximately 13% of the total hepatic cytochrome content, catalyzes the metabolic reactions of approximately 9% of frequently used drugs, including theophylline and olanzapine. Substantial inter-individual differences in enzymatic activity have been observed among patients, which could be caused by genetic polymorphisms. Therefore, we functionally characterized 21 novel CYP1A2 variants identified in 4773 Japanese individuals by determining the kinetic parameters of phenacetin O-deethylation. Our results showed that most of the evaluated variants exhibited decreased or no enzymatic activity, which may be attributed to potential structural alterations. Notably, the Leu98Gln, Gly233Arg, Ser380del Gly454Asp, and Arg457Trp variants did not exhibit quantifiable enzymatic activity. Additionally, three-dimensional (3D) docking analyses were performed to further understand the underlying mechanisms behind variant pharmacokinetics. Our data further suggest that despite mutations occurring on the protein surface, accumulating interactions could result in the impairment of protein function through the destabilization of binding regions and changes in protein folding. Therefore, our findings provide additional information regarding rare CYP1A2 genetic variants and how their underlying effects could clarify discrepancies noted in previous phenotypical studies. This would allow the improvement of personalized therapeutics and highlight the importance of identifying and characterizing rare variants.

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Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

Nature Communications ◽

10.1038/s41467-021-27800-9 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

Diyan Li ◽

Chunyou Ning ◽

Jiaman Zhang ◽

Yujie Wang ◽

Qianzi Tang ◽

...

Keyword(s):

Granulosa Cells ◽

Functional Characterization ◽

Three Dimensional ◽

Range Interaction ◽

Ample Evidence ◽

Chromatin Architecture ◽

Complex Biological Process ◽

Preovulatory Follicles ◽

Long Range Interaction

AbstractFolliculogenesis is a complex biological process involving a central oocyte and its surrounding somatic cells. Three-dimensional chromatin architecture is an important transcription regulator; however, little is known about its dynamics and role in transcriptional regulation of granulosa cells during chicken folliculogenesis. We investigate the transcriptomic dynamics of chicken granulosa cells over ten follicular stages and assess the chromatin architecture dynamics and how it influences gene expression in granulosa cells at three key stages: the prehierarchical small white follicles, the first largest preovulatory follicles, and the postovulatory follicles. Our results demonstrate the consistency between the global reprogramming of chromatin architecture and the transcriptomic divergence during folliculogenesis, providing ample evidence for compartmentalization rearrangement, variable organization of topologically associating domains, and rewiring of the long-range interaction between promoter and enhancers. These results provide key insights into avian reproductive biology and provide a foundational dataset for the future in-depth functional characterization of granulosa cells.

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