Injectable In Situ Crosslinking Hydrogel for Autologous Fat Grafting.

Autologous fat grafting is hampered by unpredictable outcomes due to high tissue resorption. Hydrogels based on enzymatically pretreated tunicate nanocellulose (ETC) and alginate (ALG) are biocompatible, safe, and present physiochemical properties capable of promoting cell survival. Here, we compared in situ and ex situ crosslinking of ETC/ALG hydrogels combined with lipoaspirate human adipose tissue (LAT) to generate an injectable formulation capable of retaining dimensional stability in vivo. We performed in situ crosslinking using two different approaches; inducing Ca2+ release from CaCO3 microparticles (CMPs) and physiologically available Ca2+ in vivo. Additionally, we generated ex situ-crosslinked, 3D-bioprinted hydrogel-fat grafts. We found that in vitro optimization generated a CMP-crosslinking system with comparable stiffness to ex situ-crosslinked gels. Comparison of outcomes following in vivo injection of each respective crosslinked hydrogel revealed that after 30 days, in situ crosslinking generated fat grafts with less shape retention than 3D-bioprinted constructs that had undergone ex situ crosslinking. However, CMP addition improved fat-cell distribution and cell survival relative to grafts dependent on physiological Ca2+ alone. These findings suggested that in situ crosslinking using CMP might promote the dimensional stability of injectable fat-hydrogel grafts, although 3D bioprinting with ex situ crosslinking more effectively ensured proper shape stability in vivo.

Biomaterial and biocompatibility evaluation of tunicate nanocellulose for tissue engineering.

Extracellular matrix fibril components, such as collagen, are crucial for the structural properties of several tissues and organs. Tunicate-derived cellulose nanofibrils (TNC) combined with living cells could become the next gold standard for cartilage and soft-tissue repair, as TNC fibrils present similar dimensions to collagen, feasible industrial production, and chemically straightforward and cost-efficient extraction procedures. In this study, we characterized the physical properties of TNC derived from aquaculture production in Norwegian fjords and evaluated its biocompatibility regarding induction of an inflammatory response and foreign-body reactions in a Wistar rat model. Additionally, histologic and immunohistochemical analyses were performed for comparison with expanded polytetrafluoroethylene (ePTFE) as a control. The average length of the TNC as determined by atomic force microscopy was tunable from 3 µm to 2.4 µm via selection of a various number of passages through a microfluidizer, and rheologic analysis showed that the TNC hydrogels were highly shear-thinning and with a viscosity dependent on fibril length and concentration. As a bioink, TNC exhibited excellent rheological and printability properties, with constructs capable of being printed with high resolution and fidelity. We found that post-print cross-linking with alginate stabilized the construct shape and texture, which increased its ease of handling during surgery. Moreover, after 30 days in vivo, the constructs showed a highly-preserved shape and fidelity of the grid holes, with these characteristics preserved after 90 days and with no signs of necrosis, infection, acute inflammation, invasion of neutrophil granulocytes, or extensive fibrosis. Furthermore, we observed a moderate foreign-body reaction involving macrophages, lymphocytes, and giant cells in both the TNC constructs and PTFE controls, although TNC was considered a non-irritant biomaterial according to ISO 10993-6 as compared with ePTFE. These findings represent a milestone for future clinical application of TNC scaffolds for tissue repair. One sentence summary: In this study, the mechanical properties of tunicate nanocellulose are superior to nanocellulose extracted from other sources, and the biocompatibility is comparable to that of ePTFE.

Alginate and tunicate nanocellulose composite microbeads - Preparation, characterization and cell encapsulation.

Alginate has been used for decades for cell encapsulation. Cellulose nanofibrils (CNF) from tunicates are desirable in biomedicine due to high molecular weight, purity, crystallinity, and sustainable production. We prepared microbeads of 400-600 µm of alginate and tunicate CNF. Greater size, dispersity and aspect ratio were observed in microbeads with higher fractions of CNF. CNF content in Ca-crosslinked alginate microbeads decreased stability upon saline exposure, whereas crosslinking with calcium (50 mM) and barium (1 mM) yielded stable microbeads. The Young's moduli of gel cylinders decreased when exchanging alginate with CNF, and slightly increased permeability to dextran was observed in microbeads containing CNF. Encapsulation of MC3T3 cells revealed high cell viability after encapsulation (83.6 ± 0.4%) in beads of alginate and CNF. NHDFs showed lower viability but optimizing mixing and production techniques of microbeads increased cell viability (from 66.2 ± 5.3% to 72.7 ± 7.5%).

Mechanically Reinforced, Flexible, Hydrophobic and UV Impermeable Starch-Cellulose Nanofibers (CNF)-Lignin Composites with Good Barrier and Thermal Properties.

Bio-based composite films have been widely studied as potential substitutes for conventional plastics in food packaging. The aim of this study was to develop multifunctional composite films by introducing cellulose nanofibers (CNF) and lignin into starch-based films. Instead of costly and complicated chemical modification or covalent coupling, this study optimized the performance of the composite films by simply tuning the formulation. We found that starch films were mechanically reinforced by CNF, with lignin dispersing as nanoparticles embedded in the matrix. The newly built-up hydrogen bonding between these three components improves the integration of the films, while the introduction of CNF and lignin improved the thermal stability of the starch-based films. Lignin, as a functional additive, improved hydrophobicity and blocked UV transmission. The inherent barrier property of CNF and the dense starch matrix provided the composite films with good gas barrier properties. The prepared flexible films were optically transparent, and exhibited UV blocking ability, good oxygen-barrier properties, high hydrophobicity, appreciable mechanical strength and good thermal stability. These characteristics indicate potential utilization as a green alternative to synthetic plastics especially for food packaging applications.

Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments.

Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have applied a prototype version of a phylogenetic microarray to assess the eukaryote community structures of marine sediments from an area with ongoing oil and gas drilling activity. The results were compared with data from both sequencing (metabarcoding) and morphology-based monitoring to evaluate whether microarrays were capable of detecting ecosystem disturbances. A significant correlation between microarray data and chemical pollution indicators, as well as sequencing-based results, was demonstrated, and several potential indicator organisms for pollution-associated parameters were identified, among them a large fraction of microorganisms not covered by traditional morphology-based monitoring. This suggests that microarrays have a potential in future environmental monitoring.

Development and testing of an 18S rRNA phylogenetic microarray for marine sediments.

There is increasing interest in finding new, more efficient methods for routine monitoring of anthropogenic effects on benthic biodiversity and ecosystems. A range of molecular methods have been developed for assessing biodiversity the last decades. Particularly interesting are microarrays targeting phylogenetic marker genes, such as the small subunit of ribosomal RNA in eukaryotes (18S rRNA). This method can detect a large number of taxonomic groups in several samples simultaneously within a relatively short time and has the potential for incorporation in automated remote sensing pipelines. In this study we developed and tested a microarray for eukaryotes in marine sediments. The probes were designed to target 18S rRNA OTUs obtained through metabarcoding of marine sediments. The resulting microarray was tested using both a spiked sample consisting of 50 plasmid-clones and further, samples of genomic DNA extracted from marine sediments. We developed a filtration pipeline to eliminate noise and reduce the number of false positives, making it possible to detect and quantify most of the OTUs with ≥ 0.1% abundance in the spiked sample. Our data indicated that the microarray was specific at higher taxonomic levels. However, the specificity decreased with increasing sequence similarity suggesting cross-hybridization between closely related OTUs. When using genomic DNA isolated from marine sediment there was a positive correlation between hybridization intensity signals and abundance of sequencing reads, suggesting a quantitative behavior of the microarray. Overall, the data suggest a potential for microarrays as a tool for high throughput sediment monitoring.

Increased fitness of a key appendicularian zooplankton species under warmer, acidified seawater conditions.

Ocean warming and acidification (OA) may alter the fitness of species in marine pelagic ecosystems through community effects or direct physiological impacts. We used the zooplanktonic appendicularian, Oikopleura dioica, to assess temperature and pH effects at mesocosm and microcosm scales. In mesocosms, both OA and warming positively impacted O. dioica abundance over successive generations. In microcosms, the positive impact of OA, was observed to result from increased fecundity. In contrast, increased pH, observed for example during phytoplankton blooms, reduced fecundity. Oocyte fertility and juvenile development were equivalent under all pH conditions, indicating that the positive effect of lower pH on O. dioica abundance was principally due to increased egg number. This effect was influenced by food quantity and quality, supporting possible improved digestion and assimilation at lowered pH. Higher temperature resulted in more rapid growth, faster maturation and earlier reproduction. Thus, increased temperature and reduced pH had significant positive impacts on O. dioica fitness through increased fecundity and shortened generation time, suggesting that predicted future ocean conditions may favour this zooplankton species.

Correction: DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments.

[This corrects the article DOI: 10.1371/journal.pone.0179443.].

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments.

Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a "sufficient" replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 µm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon-specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod-prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances.

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities.

As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental responses to stressors. The natural heterogeneity and complexity of communities means that accurate monitoring requires high resolution, both temporally and spatially, as well as more complete assessments of taxa. Increased resolution and taxonomic coverage is economically challenging using current microscopy-based monitoring practices. Alternatively, DNA sequencing-based methods have been suggested for cost-efficient monitoring, offering additional insights into ecosystem function and disturbance. Here, we applied DNA metabarcoding of eukaryotic communities in marine sediments, in areas of offshore drilling on the Norwegian continental shelf. Forty-five samples, collected from seven drilling sites in the Troll/Oseberg region, were assessed, using the small subunit ribosomal RNA gene as a taxonomic marker. In agreement with results based on classical morphology-based monitoring, we were able to identify changes in sediment communities surrounding oil platforms. In addition to overall changes in community structure, we identified several potential indicator taxa, responding to pollutants associated with drilling fluids. These included the metazoan orders Macrodasyida, Macrostomida and Ceriantharia, as well as several ciliates and other protist taxa, typically not targeted by environmental monitoring programmes. Analysis of a co-occurrence network to study the distribution of taxa across samples provided a framework for better understanding the impact of anthropogenic activities on the benthic food web, generating novel, testable hypotheses of trophic interactions structuring benthic communities.

Characterization of the 18S rRNA gene for designing universal eukaryote specific primers.

High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. Full primer universality is difficult or impossible to achieve and studies using different primer sets make biodiversity comparisons problematic. The aim of this study was to design and optimize universal eukaryotic primers that could be used as a standard in future biodiversity studies. Using the alignment of all eukaryotic sequences from the publicly available SILVA database, we generated a full characterization of variable versus conserved regions in the 18S rRNA gene. All variable regions within this gene were analyzed and our results suggested that the V2, V4 and V9 regions were best suited for biodiversity assessments. Previously published universal eukaryotic primers as well as a number of self-designed primers were mapped to the alignment. Primer selection will depend on sequencing technology used, and this study focused on the 454 pyrosequencing GS FLX Titanium platform. The results generated a primer pair yielding theoretical matches to 80% of the eukaryotic and 0% of the prokaryotic sequences in the SILVA database. An empirical test of marine sediments using the AmpliconNoise pipeline for analysis of the high throughput sequencing data yielded amplification of sequences for 71% of all eukaryotic phyla with no isolation of prokaryotic sequences. To our knowledge this is the first characterization of the complete 18S rRNA gene using all eukaryotes present in the SILVA database, providing a robust test for universal eukaryotic primers. Since both in silico and empirical tests using high throughput sequencing retained high inclusion of eukaryotic phyla and exclusion of prokaryotes, we conclude that these primers are well suited for assessing eukaryote diversity, and can be used as a standard in biodiversity studies.

A molecular gut content study of Themisto abyssorum (Amphipoda) from Arctic hydrothermal vent and cold seep systems.

The use of DNA as a marker for prey inside the gut of predators has been instrumental in further understanding of known and unknown interactions. Molecular approaches are in particular useful in unavailable environments like the deep sea. Trophic interactions in the deep sea are difficult to observe in situ, correct deep-sea experimental laboratory conditions are difficult to obtain, animals rarely survive the sampling, or the study organisms feed during the sampling due to long hauls. Preliminary studies of vent and seep systems in the Nordic Seas have identified the temperate-cold-water pelagic amphipod Themisto abyssorum as a potentially important predator in these chemosynthetic habitats. However, the prey of this deep-sea predator is poorly known, and we applied denaturing high performance liquid chromatography (DHPLC) to investigate the predator-prey interactions of T. abyssorum in deep-water vent and seep systems. Two deep-water hydrothermally active localities (The Jan Mayen and Loki's Castle vent fields) and one cold seep locality (The Håkon Mosby mud volcano) in the Nordic Seas were sampled, genomic DNA of the stomachs of T. abyssorum was extracted, and 18S rDNA gene was amplified and used to map the stomach content. We found a wide range of organisms including micro-eukaryotes, metazoans and detritus. Themisto abyssorum specimens from Loki's Castle had the highest diversity of prey. The wide range of prey items found suggests that T. abyssorum might be involved in more than one trophic level and should be regarded as an omnivore and not a strict carnivore as have previously been suggested.

Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica.

The pan-global marine appendicularian, Oikopleura dioica, shows considerable promise as a candidate model organism for cross-disciplinary research ranging from chordate genetics and evolution to molecular ecology research. This urochordate, has a simplified anatomical organization, remains transparent throughout an exceptionally short life cycle of less than 1 week and exhibits high fecundity. At 70 Mb, the compact, sequenced genome ranks among the smallest known metazoan genomes, with both gene regulatory and intronic regions highly reduced in size. The organism occupies an important trophic role in marine ecosystems and is a significant contributor to global vertical carbon flux. Among the short list of bona fide biological model organisms, all share the property that they are amenable to long-term maintenance in laboratory cultures. Here, we tested diet regimes, spawn densities and dilutions and seawater treatment, leading to optimization of a detailed culture protocol that permits sustainable long-term maintenance of O. dioica, allowing continuous, uninterrupted production of source material for experimentation. The culture protocol can be quickly adapted in both coastal and inland laboratories and should promote rapid development of the many original research perspectives the animal offers.

Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR).

Quantification of feeding rates and selectivity of zooplankton is vital for understanding the mechanisms structuring marine ecosystems. However, methodological limitations have made many of these studies difficult. Recently, molecular based methods have demonstrated that DNA from prey species can be used to identify zooplankton gut contents, and further, quantitative gut content estimates by quantitative PCR (qPCR) assays targeted to the 18S rRNA gene have been used to estimate feeding rates in appendicularians and copepods. However, while standard single primer based qPCR assays were quantitative for the filter feeding appendicularian Oikopleura dioica, feeding rates were consistently underestimated in the copepod Calanus finmarchicus. In this study, we test the hypothesis that prey DNA is rapidly digested after ingestion by copepods and describe a qPCR-based assay, differential length amplification qPCR (dla-qPCR), to account for DNA digestion. The assay utilizes multiple primer sets that amplify different sized fragments of the prey 18S rRNA gene and, based on the differential amplification of these fragments, the degree of digestion is estimated and corrected for. Application of this approach to C. finmarchicus fed Rhodomonas marina significantly improved quantitative feeding estimates compared to standard qPCR. The development of dla-qPCR represents a significant advancement towards a quantitative method for assessing in situ copepod feeding rates without involving cultivation-based manipulation.

Detection and discovery of crustacean parasites in blue crabs (Callinectes sapidus) by using 18S rRNA gene-targeted denaturing high-performance liquid chromatography.

Recently, we described a novel denaturing high-performance liquid chromatography (DHPLC) approach useful for initial detection and identification of crustacean parasites. Because this approach utilizes general primers targeted to conserved regions of the 18S rRNA gene, a priori genetic sequence information on eukaryotic parasites is not required. This distinction provides a significant advantage over specifically targeted PCR assays that do not allow for the detection of unknown or unsuspected parasites. However, initial field evaluations of the DHPLC assay suggested that because of PCR-biased amplification of dominant host genes it was not possible to detect relatively rare parasite genes in infected crab tissue. Here, we describe the use of a peptide nucleic acid (PNA) PCR hybridization blocking probe in association with DHPLC (PNA-PCR DHPLC) to overcome inherent PCR bias associated with amplification of rare target genes by use of generic primers. This approach was utilized to detect infection of blue crabs (Callinectes sapidus) by the parasitic dinoflagellate Hematodinium sp. Evaluation of 76 crabs caught in Wassaw Sound, GA, indicated a 97% correspondence between detection of the parasite by use of a specific PCR diagnostic assay and that by use of PNA-PCR DHPLC. During these studies, we discovered one crab with an association with a previously undescribed protist symbiont. Phylogenetic analysis of the amplified symbiont 18S rRNA gene indicated that it is most closely related to the free-living kinetoplastid parasite Procryptobia sorokini. To our knowledge, this is the first report of this parasite group in a decapod crab and of this organism exhibiting a presumably parasitic life history.

Development of a denaturing high-performance liquid chromatography method for detection of protist parasites of metazoans.

Increasingly, diseases of marine organisms are recognized as significant biotic factors affecting ecosystem health. However, the responsible disease agents are often unknown and the discovery and description of novel parasites most often rely on morphological descriptions made by highly trained specialists. Here, we describe a new approach for parasite discovery, utilizing denaturing high-performance liquid chromatography (DHPLC) reverse-phase ion-pairing technology. Systematic investigations of major DHPLC variables, including temperature, gradient conditions, and target amplicon characteristics were conducted to develop a mechanistic understanding of DNA fragment separation by DHPLC. As a model system, 18S rRNA genes from the blue crab (Callinectes sapidus) and a parasitic dinoflagellate Hematodinium sp. were used. Binding of 18S rRNA gene PCR amplicons to the DNA separation column in the presence of triethylammonium acetate (TEAA) was inversely correlated with temperature and could be predicted based on the estimated DNA helicity of the PCR amplicon. Amplicons of up to 498 bp were resolved as single chromatographic peaks if they had high (>95%) DNA helicity. Amplicons that differed by as few as 2 bp could be resolved. Separation of 18S rRNA gene PCR amplicons was optimized by simultaneous manipulation of both temperature and solvent gradients. The optimal conditions included targeting regions of high DNA helicity (>95%), temperatures in the range of 57 to 63 degrees C, and a linear acetonitrile gradient from 13.75 to 17.5% acetonitrile in 0.1 M TEAA (55 to 70% buffer B) over a 9-min period. Under these conditions, amplicons from a variety of parasites and their hosts can be separated and detected by DHPLC.

Endostyle cell recruitment as a frame of reference for development and growth in the Urochordate Oikopleura dioica.

In models of growth and life history, and in molecular and cell biology, there is a need for more accurate frames of reference to characterize developmental progression. In Caenorhabditis elegans, complete fate maps of cell lineage provide such a standard of reference. To be more widely applicable, reference frames should be easier to measure while still providing strong predictive capacity. Towards this aim, we have analyzed growth of the endostyle in the appendicularian Oikopleura dioica at the cellular level, and measured its response to temperature and food availability. Specifically, we test the hypothesis that age of a specific developmental stage in O. dioica can be predicted from the number of endostyle cells and temperature. We show that the endostyle grows by recruiting cells from the posterior tip into the lateral arms of the organ in an anterior-posterior orientation and that the rate of increase in lateral arm endostyle cells is temperature-dependent but unresponsive to nutritional intake. Endostyle cells therefore serve as an accurate and easily measured marker to describe developmental progression. Conceptually, such a method of characterizing developmental progression should help bridge life-history events and molecular mechanisms throughout organismal aging, facilitating cross-disciplinary understanding by providing a common experimental framework.