1
|
Essack M, Salhi A, Stanimirovic J, Tifratene F, Bin Raies A, Hungler A, Uludag M, Van Neste C, Trpkovic A, Bajic VP, Bajic VB, Isenovic ER. Literature-Based Enrichment Insights into Redox Control of Vascular Biology. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1769437. [PMID: 31223421 PMCID: PMC6542245 DOI: 10.1155/2019/1769437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/11/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023]
Abstract
In cellular physiology and signaling, reactive oxygen species (ROS) play one of the most critical roles. ROS overproduction leads to cellular oxidative stress. This may lead to an irrecoverable imbalance of redox (oxidation-reduction reaction) function that deregulates redox homeostasis, which itself could lead to several diseases including neurodegenerative disease, cardiovascular disease, and cancers. In this study, we focus on the redox effects related to vascular systems in mammals. To support research in this domain, we developed an online knowledge base, DES-RedoxVasc, which enables exploration of information contained in the biomedical scientific literature. The DES-RedoxVasc system analyzed 233399 documents consisting of PubMed abstracts and PubMed Central full-text articles related to different aspects of redox biology in vascular systems. It allows researchers to explore enriched concepts from 28 curated thematic dictionaries, as well as literature-derived potential associations of pairs of such enriched concepts, where associations themselves are statistically enriched. For example, the system allows exploration of associations of pathways, diseases, mutations, genes/proteins, miRNAs, long ncRNAs, toxins, drugs, biological processes, molecular functions, etc. that allow for insights about different aspects of redox effects and control of processes related to the vascular system. Moreover, we deliver case studies about some existing or possibly novel knowledge regarding redox of vascular biology demonstrating the usefulness of DES-RedoxVasc. DES-RedoxVasc is the first compiled knowledge base using text mining for the exploration of this topic.
Collapse
Affiliation(s)
- Magbubah Essack
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Adil Salhi
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Julijana Stanimirovic
- Vinca Institute, University of Belgrade, Laboratory for Molecular Endocrinology and Radiobiology, Belgrade, Serbia
| | - Faroug Tifratene
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Arwa Bin Raies
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Arnaud Hungler
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Mahmut Uludag
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Christophe Van Neste
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Andreja Trpkovic
- Vinca Institute, University of Belgrade, Laboratory for Molecular Endocrinology and Radiobiology, Belgrade, Serbia
| | - Vladan P. Bajic
- Vinca Institute, University of Belgrade, Laboratory for Molecular Endocrinology and Radiobiology, Belgrade, Serbia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Esma R. Isenovic
- Vinca Institute, University of Belgrade, Laboratory for Molecular Endocrinology and Radiobiology, Belgrade, Serbia
| |
Collapse
|
2
|
Merkel J, Wollesen T, Lieb B, Wanninger A. Spiral cleavage and early embryology of a loxosomatid entoproct and the usefulness of spiralian apical cross patterns for phylogenetic inferences. BMC DEVELOPMENTAL BIOLOGY 2012; 12:11. [PMID: 22458754 PMCID: PMC3348079 DOI: 10.1186/1471-213x-12-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 03/29/2012] [Indexed: 12/01/2022]
Abstract
Background Among the four major bilaterian clades, Deuterostomia, Acoelomorpha, Ecdysozoa, and Lophotrochozoa, the latter shows an astonishing diversity of bodyplans. While the largest lophotrochozoan assemblage, the Spiralia, which at least comprises Annelida, Mollusca, Entoprocta, Platyhelminthes, and Nemertea, show a spiral cleavage pattern, Ectoprocta, Brachiopoda and Phoronida (the Lophophorata) cleave radially. Despite a vast amount of recent molecular phylogenetic analyses, the interrelationships of lophotrochozoan phyla remain largely unresolved. Thereby, Entoprocta play a key role, because they have frequently been assigned to the Ectoprocta, despite their differently cleaving embryos. However, developmental data on entoprocts employing modern methods are virtually non-existent and the data available rely exclusively on sketch drawings, thus calling for thorough re-investigation. Results By applying fluorescence staining in combination with confocal microscopy and 3D-imaging techniques, we analyzed early embryonic development of a basal loxosomatid entoproct. We found that cleavage is asynchronous, equal, and spiral. An apical rosette, typical for most spiralian embryos, is formed. We also identified two cross-like cellular arrangements that bear similarities to both, a "molluscan-like" as well as an "annelid-like" cross, respectively. Conclusions A broad comparison of cleavage types and apical cross patterns across Lophotrochozoa shows high plasticity of these character sets and we therefore argue that these developmental traits should be treated and interpreted carefully when used for phylogenetic inferences.
Collapse
Affiliation(s)
- Julia Merkel
- Johannes Gutenberg University, Institute of Zoology, Mainz, Germany
| | | | | | | |
Collapse
|
3
|
|
4
|
Henry JQ, Perry KJ, Martindale MQ. Cell specification and the role of the polar lobe in the gastropod mollusc Crepidula fornicata. Dev Biol 2006; 297:295-307. [PMID: 16919619 DOI: 10.1016/j.ydbio.2006.04.441] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 03/27/2006] [Accepted: 04/04/2006] [Indexed: 10/24/2022]
Abstract
A small polar lobe forms at the first and second cleavage divisions in the gastropod mollusc Crepidula fornicata. These lobes normally fuse with the blastomeres that give rise to the D quadrant at the two- and four-cell stages (cells ultimately generating the 4d mesentoblast and D quadrant organizer). Significantly, removal of the small polar lobe had no noticeable effect on subsequent development of the veliger larva. The behavior of the polar lobe and characteristic early cell shape changes involving protrusion of the 3D macromere at the 24-cell suggest that the D quadrant is specified prior to the sixth cleavage division. On the other hand, blastomere deletion experiments indicate that the D quadrant is not determined until the time of formation of the 4d blastomere (mesentoblast). In fact, embryos can undergo regulation to form normal-appearing larvae if the prospective D blastomere or 3D macromere is removed. Removal of the 4d mesentoblast leads to highly disorganized, radial development. Removal of the first quartet micromeres at the 8-cell stage also leads to the development of radialized larvae. These findings indicate that the embryos of C. fornicata follow the mode of development exhibited by equal-cleaving spiralians, which involves conditional specification of the D quadrant organizer via inductive interactions, presumably from the first quartet micromeres.
Collapse
Affiliation(s)
- Jonathan Q Henry
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA.
| | | | | |
Collapse
|
5
|
Karcavich R, Doe CQ. Drosophila neuroblast 7-3 cell lineage: a model system for studying programmed cell death, Notch/Numb signaling, and sequential specification of ganglion mother cell identity. J Comp Neurol 2005; 481:240-51. [PMID: 15593370 DOI: 10.1002/cne.20371] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cell lineage studies provide an important foundation for experimental analysis in many systems. Drosophila neural precursors (neuroblasts) sequentially generate ganglion mother cells (GMCs), which generate neurons and/or glia, but the birth order, or cell lineage, of each neuroblast is poorly understood. The best-characterized neuroblast is NB7-3, in which GMC-1 makes the EW1 serotonergic interneuron and GW motoneuron; GMC-2 makes the EW2 serotonergic interneuron and a programmed cell death; and GMC-3 gives rise to the EW3 interneuron. However, the end of this lineage has not been determined. Here, we use positively marked genetic clones, bromodeoxyuridine (BrdU) labeling, mutations that affect Notch signaling, and antibody markers to further define the end of the cell lineage of NB7-3. We provide evidence that GMC-3 directly differentiates into EW3 and that the sibling neuroblast undergoes programmed cell death. Our results confirm and extend previous work on the early portion of the NB7-3 lineage (Novotny et al. [2002] Development 129:1027-1036; Lundell et al. [ 2003] Development 130:4109-4121).
Collapse
Affiliation(s)
- Rachel Karcavich
- Institute of Neuroscience/Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, Oregon 97403, USA
| | | |
Collapse
|
6
|
Fabioux C, Huvet A, Lelong C, Robert R, Pouvreau S, Daniel JY, Minguant C, Le Pennec M. Oyster vasa-like gene as a marker of the germline cell development in Crassostrea gigas. Biochem Biophys Res Commun 2004; 320:592-8. [PMID: 15219870 DOI: 10.1016/j.bbrc.2004.06.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Indexed: 11/16/2022]
Abstract
The oyster vasa-like gene was previously demonstrated to be specifically expressed in germline cells of adult oysters Crassostrea gigas. In the present study, this gene was used as a molecular marker to establish the developmental pattern of germline cells during oyster ontogenesis, using whole-mount in situ hybridization and real-time PCR. The Oyvlg transcripts appeared to be localized to the vegetal pole of unfertilized oocytes and maternally transmitted to embryos. At early development, these maternal transcripts were observed to segregate into a single blastomere, from the CD macromere of 2-cell stage to the 4d mesentoblast of blastula. From late blastula stage, the mesentoblast divided into two cell clumps that migrated to both sides of the larvae body and that would correspond to primordial germ cells (PGCs). Based on these results, we postulate that the germline of C. gigas is specified at early development by maternal cytoplasmic determinants including Oyvlg mRNAs, in putative PGCs that would differentiate into germinal stem cells in juvenile oysters.
Collapse
Affiliation(s)
- C Fabioux
- UMR Physiologie et Ecophysiologie des Mollusques Marins, Ifremer, B.P.70, 29280 Plouzané, France
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Nielsen C. Trochophora larvae: cell-lineages, ciliary bands, and body regions. 1. Annelida and Mollusca. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2004; 302:35-68. [PMID: 14760653 DOI: 10.1002/jez.b.20001] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The trochophora concept and the literature on cleavage patterns and differentiation of ectodermal structures in annelids ("polychaetes") and molluscs are reviewed. The early development shows some variation within both phyla, and the cephalopods have a highly modified development. Nevertheless, there are conspicuous similarities between the early development of the two phyla, related to the highly conserved spiral cleavage pattern. Apical and cerebral ganglia have almost identical origin in the two phyla, and the cell-lineage of the prototroch is identical, except for minor variations between species. The cell-lineage of the metatrochs is almost unknown, but the telotroch of annelids and the "telotroch" of the gastropod Patella originate from the 2d-cell, as does the gastrotroch in the few species which have been studied. The segmented annelid body, i.e. the region behind the peristome, develops through addition of new ectoderm from a ring of 2d-cells just in front of the telotroch. This whole region is thus derived from 2d-cells. Conversely, the mollusc body is covered by descendants of cells from both the C and D quadrants and a growth zone is not apparent. This supports the notion that the molluscs are not segmented like the annelids, and that the repeated structures seen in polyplacophorans and monoplacophorans do not represent a segmentation homologous to that of the annelids.
Collapse
Affiliation(s)
- Claus Nielsen
- Zoological Museum (University of Copenhagen), Universitetsparken 15, DK-2100 Copenhagen, Denmark.
| |
Collapse
|
8
|
Page LR. Apical sensory organ in larvae of the patellogastropod Tectura scutum. THE BIOLOGICAL BULLETIN 2002; 202:6-22. [PMID: 11842011 DOI: 10.2307/1543218] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The apical sensory organ in veliger larvae of a patellogastropod, a basal clade of gastropod molluscs, was studied using ultrastructural and immunohistochemical techniques. Immediately before veligers of Tectura scutum undergo ontogenetic torsion, the apical sensory organ consists of three large cells that generate a very long apical ciliary tuft, two cells that generate a bilateral pair of shorter ciliary tufts, and a neural ganglion (apical ganglion). Putative sensory neurons forming the ganglion give rise to dendrites that extend to the apical surface of the larva and to basal neurites that contribute to a neuropil. The ganglion includes only one ampullary neuron, a distinctive neuronal type found in the apical ganglion of other gastropod veligers. Serotonin immunoreactivity is expressed by a medial and two lateral neurons, all having an apical dendrite, and also by neurites within the neuropil and by peripheral neurites that run beneath the ciliated prototrochal cells that power larval swimming. The three cells generating the long apical ciliary tuft are lost soon after ontogenetic torsion, and the medial serotonergic cell stops expressing serotonin antigenicity in late-stage veligers. The lateral ciliary tuft cells of T. scutum may be homologs of lateral ciliary tuft cells in planktotrophic opisthobranch veligers. A tripartite arrangement of sensory dendrites, as described previously for veligers of other gastropod clades, can be recognized in T. scutum after loss of the apical ciliary tuft cells.
Collapse
Affiliation(s)
- Louise R Page
- Department of Biology, University of Victoria, P.O. Box 3020 STN CSC, Victoria, British Columbia, Canada V8W 3N5.
| |
Collapse
|
9
|
SCHAEFER KURT. Early development and morphogenesis of the intracapsular veliger ofHaminaea navicula(Gastropoda: Opisthobranchia: Bullomorpha). INVERTEBR REPROD DEV 1997. [DOI: 10.1080/07924259.1997.9672610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
10
|
Dictus WJ, Damen P. Cell-lineage and clonal-contribution map of the trochophore larva of Patella vulgata (mollusca). Mech Dev 1997; 62:213-26. [PMID: 9152012 DOI: 10.1016/s0925-4773(97)00666-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Molluscan development is characterised by its extremely regular cleavage pattern. In numerous molluscs the fate of various early-cleavage stage blastomeres has been determined and fate maps have been constructed. On the basis of similarities between these fate maps, a generalised molluscan cell-lineage map has been constructed. Recently, the validity of this map has been challenged. In this study, the cell-lineage of the first-, second-, and third-quartet micromeres and third-generation macromeres of the equally-cleaving gastropod mollusc Patella vulgata was studied by fluorescent cell-lineage tracer injection followed by epifluorescence microscopy and confocal laser scanning microscopy. For the first time, a complete cell-lineage map, in the form of a clonal-contribution map of the trochophore, has been constructed with the use of fluorescent cell-lineage tracers. This map both agrees and differs in a number of respects with the generalised cell-lineage map of molluscs. The most important deviation is that the micromere 2d, formerly referred to as the first somatoblast, is not the only cell that forms the foot and shell gland in Patella.
Collapse
Affiliation(s)
- W J Dictus
- Department of Experimental Zoology, University of Utrecht, The Netherlands
| | | |
Collapse
|