Effect of collagen denaturation degree on mechanical properties and biological activity of nanofibrous scaffolds.

Further progress in regenerative medicine and bioengineering highly depends on the development of 3D polymeric scaffolds with active biological properties. The most attention is paid to natural extracellular matrix components, primarily collagen. Herein, nonwoven nanofiber materials with various degrees of collagen denaturation and fiber diameters 250-500 nm were produced by electrospinning, stabilized by genipin, and characterized in detail. Collagen denaturation has been confirmed using DSC and FTIR analysis. The comparative study of collagen and gelatin nonwoven materials (NWM) revealed only minor differences in their biocompatibility with skin fibroblasts and keratinocytes in vitro. In long-term subcutaneous implantation study, the inflammation was less evident on collagen than on gelatin NWM. Remarkably, the pronounced calcification was revealed in the collagen NWM only. The results obtained can be useful in terms of improving the electrospinning technology of collagen from aqueous solutions, as well as emphasize the importance of long-term study to ensure proper implementation of the material, taking into account the ability of collagen to provoke calcification.

PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data.

BACKGROUND: Population structure and cryptic relatedness between individuals (samples) are two major factors affecting false positives in genome-wide association studies (GWAS). In addition, population stratification and genetic relatedness in genomic selection in animal and plant breeding can affect prediction accuracy. The methods commonly used for solving these problems are principal component analysis (to adjust for population stratification) and marker-based kinship estimates (to correct for the confounding effects of genetic relatedness). Currently, many tools and software are available that analyze genetic variation among individuals to determine population structure and genetic relationships. However, none of these tools or pipelines perform such analyses in a single workflow and visualize all the various results in a single interactive web application. RESULTS: We developed PSReliP, a standalone, freely available pipeline for the analysis and visualization of population structure and relatedness between individuals in a user-specified genetic variant dataset. The analysis stage of PSReliP is responsible for executing all steps of data filtering and analysis and contains an ordered sequence of commands from PLINK, a whole-genome association analysis toolset, along with in-house shell scripts and Perl programs that support data pipelining. The visualization stage is provided by Shiny apps, an R-based interactive web application. In this study, we describe the characteristics and features of PSReliP and demonstrate how it can be applied to real genome-wide genetic variant data. CONCLUSIONS: The PSReliP pipeline allows users to quickly analyze genetic variants such as single nucleotide polymorphisms and small insertions or deletions at the genome level to estimate population structure and cryptic relatedness using PLINK software and to visualize the analysis results in interactive tables, plots, and charts using Shiny technology. The analysis and assessment of population stratification and genetic relatedness can aid in choosing an appropriate approach for the statistical analysis of GWAS data and predictions in genomic selection. The various outputs from PLINK can be used for further downstream analysis. The code and manual for PSReliP are available at https://github.com/solelena/PSReliP .

Developing core marker sets for effective genomic-assisted selection in wheat and barley breeding programs.

Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are widely cultivated temperate crops. In breeding programs with these crops in Japan, effective genomic-assisted selection was performed by selecting core marker sets from thousands of genome-wide amplicon sequencing markers. The core sets consist of 768 and 960 markers for barley and wheat, respectively. These markers are distributed evenly across the genomes and effectively detect widely distributed polymorphisms in the chromosomes. The core set utility was assessed using 1,032 barley and 1,798 wheat accessions across the country. Minor allele frequency and chromosomal distributions showed that the core sets could effectively capture polymorphisms across the entire genome, indicating that the core sets are applicable to highly-related advanced breeding materials. Using the core sets, we also assessed the trait value predictability. As observed via fivefold cross-validation, the prediction accuracies of six barley traits ranged from 0.56-0.74 and 0.62 on average, and the corresponding values for eight wheat traits ranged from 0.44-0.83 and 0.65 on average. These data indicate that the established core marker sets enable breeding processes to be accelerated in a cost-effective manner and provide a strong foundation for further research on genomic selection in crops.

Sodium alginate-based composites as a collagen substitute for skin bioengineering.

The skin is a combination of two different types of tissue-epithelial and connective (mesenchymal). The outer protective layer of the skin, the epidermis, consists of multiple layers of keratinocytes residing on the basement membrane that separates them from the underlying dermis, which consists of a well-vascularized fibrous extracellular matrix seeded mainly by fibroblasts and mesenchymal stromal cells. These skin features suggest that the development of a fibroblast-friendly porous scaffold covered with a flat dense sheath mimicking the basement membrane, and sufficient to support keratinocyte attachment, would be a reasonable approach in the generation of clinically-relevant skin substitutes useful for reconstructive dermatology and burn treatment. Therefore, we developed a procedure to obtain biocompatible composite bilayer scaffolds comprising a spongy dermis-like body (supporting vascularization and appropriate fibroblast and multipotent stromal cell activity) fused with a film-like cover (supporting keratinocyte attachment, growth and differentiation). The sodium alginate (SA), an algae-derived biopolymer, has been used as a base component for these scaffolds while collagen (CL) and fibrinogen (FG) were used as minor additives in variable concentrations. The slow rates of composite SA-based scaffold biodegradation were achieved by using Ba2+ as cross-linking cations. By manipulating the SA/CL/FG ratio we managed to obtain sponge scaffolds with highly interconnected porous structures, with an average pore size ranging from 60 to 300 µm, and sufficient tensile strength (3.12-5.26 MPa). The scaffolds biocompatibility with the major human skin cell types was confirmed by seeding the scaffold sponge compartment with primary skin fibroblasts and subcutaneous adipose-derived stromal cells while the film side biocompatibility was tested using primary human keratinocytes. The obtained results have shown that bilayer alginate-based scaffolds have biological and mechanical properties comparable with CL scaffolds but surpass them in cost efficiency and vascularization ability in the subcutaneous implantation model in laboratory mice.

Agr2-interacting Prod1-like protein Tfp4 from Xenopus laevis is necessary for early forebrain and eye development as well as for the tadpole appendage regeneration.

The Agr family genes, Ag1, Agr2, and Agr3, encode for the thioredoxin domain containing secreted proteins and are specific only for vertebrates. These proteins are attracting increasing attention due to their involvement in many physiological and pathological processes, including exocrine secretion, cancer, regeneration of the body appendages, and the early brain development. At the same time, the mode by which Agrs regulate intracellular processes are poorly understood. Despite that the receptor to Agr2, the membrane anchored protein Prod1, has been firstly discovered in Urodeles, and it has been shown to interact with Agr2 in the regenerating limb, no functional homologs of Prod1 were identified in other vertebrates. This raises the question of the mechanisms by which Agrs can regulate regeneration in other lower vertebrates. Recently, we have identified that Tfp4 (three-fingers Protein 4), the structural and functional homolog of Prod1 in Anurans, interacts with Agr2 in Xenopus laevis embryos. In the present work we show by several methods that the activity of Tfp4 is essential for the tadpole tail regeneration as well as for the early eye and forebrain development during embryogenesis. These data show for the first time the common molecular mechanism of regeneration regulation in amphibians by interaction of Prod1 and Agr2 proteins.

GGDonto ontology as a knowledge-base for genetic diseases and disorders of glycan metabolism and their causative genes.

BACKGROUND: Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides information about these diseases and disorders as well as their causative genes, has been developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. GDGDB currently provides information on about 80 genetic diseases and disorders caused by single-gene mutations in glyco-related genes. Many biomedical resources provide information about genetic disorders and genes involved in their pathogenesis, but resources focused on genetic disorders known to be related to glycan metabolism are lacking. With the aim of providing more comprehensive knowledge on genetic diseases and disorders of glycan biosynthesis and degradation, we enriched the content of the GDGDB database and improved the methods for data representation. RESULTS: We developed the Genetic Glyco-Diseases Ontology (GGDonto) and a RDF/SPARQL-based user interface using Semantic Web technologies. In particular, we represented the GGDonto content using Semantic Web languages, such as RDF, RDFS, SKOS, and OWL, and created an interactive user interface based on SPARQL queries. This user interface provides features to browse the hierarchy of the ontology, view detailed information on diseases and related genes, and find relevant background information. Moreover, it provides the ability to filter and search information by faceted and keyword searches. CONCLUSIONS: Focused on the molecular etiology, pathogenesis, and clinical manifestations of genetic diseases and disorders of glycan metabolism and developed as a knowledge-base for this scientific field, GGDonto provides comprehensive information on various topics, including links to aid the integration with other scientific resources. The availability and accessibility of this knowledge will help users better understand how genetic defects impact the metabolism of glycans as well as how this impaired metabolism affects various biological functions and human health. In this way, GGDonto will be useful in fields related to glycoscience, including cell biology, biotechnology, and biomedical, and pharmaceutical research.

Fibrinogen-modified sodium alginate as a scaffold material for skin tissue engineering.

In search for a new pro-angiogenic scaffold material suitable for skin bioengineering and grafting therapy, we have fabricated a number of composite sodium alginate (AG)-fibrinogen (FG) sponge scaffolds using the freeze-drying approach. Thrombin was added to drive FG/fibrin conversion, while ε-aminocapronic acid (εAc) was used as antifibrinolytic component. The slow rates of scaffold biodegradation were achieved by using Ca2+ and Mg2+ cations as cross-linking agents. The novel thrombin-modified AG-FG scaffolds with highly interconnected porous structure were evaluated using scanning electron microscopy, tensile testing and pycnometric analysis. The scaffolds were characterized by high porosity and tensile strength, possessing average pore size from about 60 to 300 µm depending on AG/FG ratio and fibrin stabilization. The biocompatibility of thrombin-modified scaffolds with a different AG/FG ratio was tested on human cells with potential applicability to skin tissue engineering: immortalized epidermal keratinocytes (N-TERT), primary skin fibroblasts, endothelial cells (HUVEC) and subcutaneous adipose-derived stromal cells. The scaffolds with low (15%) FG content have shown the highest adhesiveness and survival rates for all types of cells, as compared to the scaffolds with higher FG content. In unstabilized scaffolds, the addition of FG did not stimulate the aortic ring sprouting. At the same time, fibrin stabilization by εAc resulted in significant increase of aortic ring sprouting and more efficient formation of microvascular network. Altogether, obtained results suggest that thrombin-modified alginate sponges can be successfully used as a grafting material by itself to promote skin healing and regeneration and also as a scaffold for three-dimensional bioequivalent construction.

GlyTouCan 1.0--The international glycan structure repository.

Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover the surfaces of many cells, serving as the 'face' of cells, whereby other biomolecules and viruses interact. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or nucleotides. Therefore, the storage of glycan information in databases, let alone their curation, has been a difficult problem. This has caused many duplicated efforts when integration is attempted between different databases, making an international repository for glycan structures, where unique accession numbers are assigned to every identified glycan structure, necessary. As such, an international team of developers and glycobiologists have collaborated to develop this repository, called GlyTouCan and is available at http://glytoucan.org/, to provide a centralized resource for depositing glycan structures, compositions and topologies, and to retrieve accession numbers for each of these registered entries. This will thus enable researchers to reference glycan structures simply by accession number, as opposed to by chemical structure, which has been a burden to integrate glycomics databases in the past.

Octacalcium phosphate ceramics combined with gingiva-derived stromal cells for engineered functional bone grafts.

Biocompatible ceramic fillers are capable of sustaining bone formation in the proper environment. The major drawback of these scaffolding materials is the absence of osteoinductivity. To overcome this limitation, bioengineered scaffolds combine osteoconductive components (biomaterials) with osteogenic features such as cells and growth factors. The bone marrow mesenchymal stromal cells (BMMSCs) and the ß-tricalcium phosphate (ß-TCP) are well-known and characterized in this regard. The present study was conducted to compare the properties of novel octacalcium phosphate ceramic (OCP) granules with ß-TCP (Cerasorb(®)), gingiva-derived mesenchymal stromal cells (GMSCs) properties with the BMMSCs and osteogenic and angiogenic properties of a bioengineered composite based on OCP granules and the GMSCs. This study demonstrates that GMSCs and BMMSСs have a similar osteogenic capacity. The usage of OCP ceramic granules in combination with BMMSCs/GMSCs significantly affects the osteo- and angiogenesis in bone grafts of ectopic models.

Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements.

BACKGROUND: Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS. We have developed a program with a new algorithm to detect the transpositions from NGS data. RESULTS: In the process of tool development, we used next-generation sequence (NGS) data of derivative lines (ttm2 and ttm5) of japonica rice cv. Nipponbare, regenerated through cell culture. The new program, called a transposon insertion finder (TIF), was applied to detect the de novo transpositions of Tos17 in the regenerated lines. TIF searched 300 million reads of a line within 20 min, identifying 4 and 12 de novo transposition in ttm2 and ttm5 lines, respectively. All of the transpositions were confirmed by PCR/electrophoresis and sequencing. Using the program, we also detected new transposon insertions of P-element from NGS data of Drosophila melanogaster. CONCLUSION: TIF operates to find the transposition of any elements provided that target site duplications (TSDs) are generated by their transpositions.

Novel functions of Noggin proteins: inhibition of Activin/Nodal and Wnt signaling.

The secreted protein Noggin1 is an embryonic inducer that can sequester TGFß cytokines of the BMP family with extremely high affinity. Owing to this function, ectopic Noggin1 can induce formation of the headless secondary body axis in Xenopus embryos. Here, we show that Noggin1 and its homolog Noggin2 can also bind, albeit less effectively, to ActivinB, Nodal/Xnrs and XWnt8, inactivation of which, together with BMP, is essential for the head induction. In support of this, we show that both Noggin proteins, if ectopically produced in sufficient concentrations in Xenopus embryo, can induce a secondary head, including the forebrain. During normal development, however, Noggin1 mRNA is translated in the presumptive forebrain with low efficiency, which provides the sufficient protein concentration for only its BMP-antagonizing function. By contrast, Noggin2, which is produced in cells of the anterior margin of the neural plate at a higher concentration, also protects the developing forebrain from inhibition by ActivinB and XWnt8 signaling. Thus, besides revealing of novel functions of Noggin proteins, our findings demonstrate that specification of the forebrain requires isolation of its cells from BMP, Activin/Nodal and Wnt signaling not only during gastrulation but also at post-gastrulation stages.

Light-induced blockage of cell division with a chromatin-targeted phototoxic fluorescent protein.

Proteins of the GFP (green fluorescent protein) family are widely used as passive reporters for live cell imaging. In the present study we used H2B (histone H2B)-tKR (tandem KillerRed) as an active tool to affect cell division with light. We demonstrated that H2B-tKR-expressing cells behave normally in the dark, but transiently cease proliferation following green-light illumination. Complete light-induced blockage of cell division for approx. 24 h was observed in cultured mammalian cells that were either transiently or stably transfected with H2B-tKR. Illuminated cells then returned to normal division rate. XRCC1 (X-ray cross complementing factor 1) showed immediate redistribution in the illuminated nuclei of H2B-tKR-expressing cells, indicating massive light-induced damage of genomic DNA. Notably, nondisjunction of chromosomes was observed for cells that were illuminated during metaphase. In transgenic Xenopus embryos expressing H2B-tKR under the control of tissue-specific promoters, we observed clear retardation of the development of these tissues in green-light-illuminated tadpoles. We believe that H2B-tKR represents a novel optogenetic tool, which can be used to study mitosis and meiosis progression per se, as well as to investigate the roles of specific cell populations in development, regeneration and carcinogenesis in vivo.

Far-red fluorescent tags for protein imaging in living tissues.

A vast colour palette of monomeric fluorescent proteins has been developed to investigate protein localization, motility and interactions. However, low brightness has remained a problem in far-red variants, which hampers multicolour labelling and whole-body imaging techniques. In the present paper, we report mKate2, a monomeric far-red fluorescent protein that is almost 3-fold brighter than the previously reported mKate and is 10-fold brighter than mPlum. The high-brightness, far-red emission spectrum, excellent pH resistance and photostability, coupled with low toxicity demonstrated in transgenic Xenopus laevis embryos, make mKate2 a superior fluorescent tag for imaging in living tissues. We also report tdKatushka2, a tandem far-red tag that performs well in fusions, provides 4-fold brighter near-IR fluorescence compared with mRaspberry or mCherry, and is 20-fold brighter than mPlum. Together, monomeric mKate2 and pseudo-monomeric tdKatushka2 represent the next generation of extra-bright far-red fluorescent probes offering novel possibilities for fluorescent imaging of proteins in living cells and animals.

Bright far-red fluorescent protein for whole-body imaging.

For deep imaging of animal tissues, the optical window favorable for light penetration is in near-infrared wavelengths, which requires proteins with emission spectra in the far-red wavelengths. Here we report a far-red fluorescent protein, named Katushka, which is seven- to tenfold brighter compared to the spectrally close HcRed or mPlum, and is characterized by fast maturation as well as a high pH-stability and photostability. These unique characteristics make Katushka the protein of choice for visualization in living tissues. We demonstrate superiority of Katushka for whole-body imaging by direct comparison with other red and far-red fluorescent proteins. We also describe a monomeric version of Katushka, named mKate, which is characterized by high brightness and photostability, and should be an excellent fluorescent label for protein tagging in the far-red part of the spectrum.

The homeodomain factor Xanf represses expression of genes in the presumptive rostral forebrain that specify more caudal brain regions.

Early development of the rostral forebrain (RF) in vertebrates is accompanied by the inhibition of two homeobox regulators, Otx2 and Pax6 in the rostral sector of the anterior neural plate, further giving rise to the RF. However, the precise molecular mechanism and meaning of this inhibition is still obscure. We now demonstrate that the activity of the Anf homeodomain protein is necessary and sufficient for the anterior inhibition of Otx2 and Pax6. Specifically, we show that knockdown of the Xenopus laevis Anf, Xanf, by antisense morpholino oligonucleotides results in the anterior expansion of Otx2 and Pax6 expression into the presumptive RF territory. Furthermore, by overexpressing hormone-inducible activator- and repressor-fused variants of Xanf in the absence of protein synthesis, we present evidence that Xanf can directly downregulate Otx2 and Pax6 but not the more rostrally expressed Bf1, Bf2, Fgf8 and Nkx2.4. These results explain how the inhibitory activity of Xanf can discriminate RF regulators in favor of posterior forebrain ones. Assuming that the Anf type of homeobox is specific for vertebrates, our data suggest that the emergence of Anf in evolution could be a critical event for RF development in vertebrates through the elimination of homologues of modern posterior forebrain regulators from the rostral sector of the anterior neural plate.