Creation of accurate 3D models of harbor porpoises (Phocoena phocoena) using 3D photogrammetry

Creating accurate 3D models of marine mammals is valuable for assessment of body condition, computational fluids dynamics models of locomotion, and for education. However, the methods for creating 3D models are not well-developed. We used photography and video to create 3D photogrammetry models of harbor porpoises (Phocoena phocoena). We accessed one live adult female (155.5 cm total length), and two dead animals, one juvenile (110 cm total length) and one calf (88 cm total length). We accessed the two dead individuals through a stranding network in Germany, and the live individual through the Fjord and Baelt research center in Denmark. For all porpoises, we used still photographs from hand-held cameras, drone video, and synchronized GoPro videos to create 3D photogrammetric models. We used Blender software, and other 3D reconstruction software, to recreate the 3D body meshes, and confirmed the accuracy of each of the 3D body meshes by comparing digital measures on the 3D models to original measures taken on the specimens. We also provide a colored, animated version of the live harbor porpoise for educational purposes. These open-access 3D models can be used to develop methods to study body morphometrics and condition, and to study bioenergetics and locomotion costs.     

Fantastic databases and where to find them: Web applications for researchers in a rush

Public databases are essential to the development of multi-omics resources. The amount of data created by biological technologies needs a systematic and organized form of storage, that can quickly be accessed, and managed. This is the objective of a biological database. Here, we present an overview of human databases with web applications. The databases and tools allow the search of biological sequences, genes and genomes, gene expression patterns, epigenetic variation, protein-protein interactions, variant frequency, regulatory elements, and comparative analysis between human and model organisms. Our goal is to provide an opportunity for exploring large datasets and analyzing the data for users with little or no programming skills. Public user-friendly web-based databases facilitate data mining and the search for information applicable to healthcare professionals. Besides, biological databases are essential to improve biomedical search sensitivity and efficiency and merge multiple datasets needed to share data and build global initiatives for the diagnosis, prognosis, and discovery of new treatments for genetic diseases. To show the databases at work, we present a a case study using ACE2 as example of a gene to be investigated. The analysis and the complete list of databases is available in the following website <https://kur1sutaru.github.io/fantastic_databases_and_where_to_find_them/>.     

Iron-dependent vs. iron-independent cold-induced injury to cultured rat hepatocytes: a comparative study in physiological media and organ preservation solutions

We previously described the entity of cold-induced apoptosis to rat hepatocytes and characterized its major, iron-dependent pathway. However, after cold incubation in some solutions, e.g. cell culture medium, hepatocytes show an additional, yet uncharacterized component of cold-induced injury. We here assessed the effects of organ preservation solutions on both components of cold-induced injury and tried to further characterize the iron-independent component. None of the preservation solutions (University of Wisconsin, histidine-tryptophan-ketoglutarate, Euro-Collins, histidine-lactobionate, sodium-lactobionate-sucrose and Celsior solutions) provided significant protection against cold-induced cell injury (LDH release after 24-h cold incubation/3h rewarming >65% for all solutions); three solutions even enhanced cold-induced injury. However, when the predominant iron-dependent mechanism was eliminated by the addition of iron chelators, all preservation solutions yielded hepatocyte protection that was clearly superior to the one obtainable in cell culture medium or Krebs-Henseleit buffer with iron chelators (LDH release after 24-h cold incubation/3h rewarming 相似文献   

An atlas of differential gene expression during early Xenopus embryogenesis

We have carried out a large-scale, semi-automated whole-mount in situ hybridization screen of 8369 cDNA clones in Xenopus laevis embryos. We confirm that differential gene expression is prevalent during embryogenesis since 24% of the clones are expressed non-ubiquitously and 8% are organ or cell type specific marker genes. Sequence analysis and clustering yielded 723 unique genes displaying a differential expression pattern. Of these, 18% were already described in Xenopus, 47% have homologs and 35% are lacking significant sequence similarity in databases. Many of them encode known developmental regulators. We classified 363 of the 723 genes for which a Gene Ontology annotation for molecular function could be attributed and found 'DNA binding' and 'enzyme' the most represented terms. The most common protein domains encoded in these embryonic, differentially expressed genes are the homeobox and RNA Recognition Motif (RRM). Fifty-nine putative orthologs of human disease genes, and 254 organ or cell specific marker genes were identified. Markers were found for nasal placode and archenteron roof, organs for which a specific marker was previously unavailable. Markers were also found for novel subdomains of various other organs. The tissues for which most markers were found are muscle and epidermis. Expression of cell cycle regulators fell in two classes, containing proliferation-promoting and anti-proliferative genes, respectively. We identified 66 new members of the BMP4, chromatin, endoplasmic reticulum, and karyopherin synexpression groups, thus providing a first glimpse of their probable cellular roles. Cluster analysis of tissues to measure tissue relatedness yielded some unorthodox affinities besides expectable lineage relationships. In conclusion, this study represents an atlas of gene expression patterns, which reveals embryonic regionalization, provides novel marker genes, and makes predictions about the functional role of unknown genes.     

Development of an enzyme-linked immunoreceptor assay (ELIRA) for quantification of the biological activity of recombinant human bone morphogenetic protein-2

Human bone morphogenetic protein-2 is a representative of the transforming growth factor-beta (TGF-beta) superfamily of cytokines. It was produced in high-cell-density cultivations of recombinant Escherichia coli leading to the formation of inclusion bodies with aggregated inactive protein so that the protein had to be solubilized and renatured. Thus, the biological activity of the recombinant protein had to be determined. To avoid time-consuming cell-based assays or radioactive labelling of proteins enzyme-linked immunoreceptor assays were developed. They were based on the specific interaction between the biologically active protein and its receptors, of which the extracellular ligand binding domains were tagged with the Fc part of human IgG and expressed in insect cells. The amount of bound ligand, corresponding to the biologically active recombinant protein, was determined via enzyme-labelled antibodies. Application to various batches of protein showed that not only the amount of active protein could be quantified but also the quality of the protein preparations could be evaluated in significantly shorter analysis times than with conventional cell-based assays.