| 1. |
- Hao, Limin, et al.
(author)
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Comprehensive analysis of gene expression patterns of hedgehog-related genes
- 2006
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 7, s. 280-
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Journal article (peer-reviewed)abstract
- Background: The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-terminal domains, and C. elegans encodes dozens of additional proteins containing only these N-terminal domains. These gene families are called warthog, groundhog, ground-like and quahog, collectively called hedgehog (hh)-related genes. Previously, the expression pattern of seventeen genes was examined, which showed that they are primarily expressed in the ectoderm. Results: With the completion of the C. elegans genome sequence in November 2002, we reexamined and identified 61 hh-related ORFs. Further, we identified 49 hh-related ORFs in C. briggsae. ORF analysis revealed that 30% of the genes still had errors in their predictions and we improved these predictions here. We performed a comprehensive expression analysis using GFP fusions of the putative intergenic regulatory sequence with one or two transgenic lines for most genes. The hh-related genes are expressed in one or a few of the following tissues: hypodermis, seam cells, excretory duct and pore cells, vulval epithelial cells, rectal epithelial cells, pharyngeal muscle or marginal cells, arcade cells, support cells of sensory organs, and neuronal cells. Using time-lapse recordings, we discovered that some hh-related genes are expressed in a cyclical fashion in phase with molting during larval development. We also generated several translational GFP fusions, but they did not show any subcellular localization. In addition, we also studied the expression patterns of two genes with similarity to Drosophila frizzled, T23D8.1 and F27E11.3A, and the ortholog of the Drosophila gene dally-like, gpn-1, which is a heparan sulfate proteoglycan. The two frizzled homologs are expressed in a few neurons in the head, and gpn-1 is expressed in the pharynx. Finally, we compare the efficacy of our GFP expression effort with EST, OST and SAGE data. Conclusion: No bona-fide Hh signaling pathway is present in C. elegans. Given that the hh-related gene products have a predicted signal peptide for secretion, it is possible that they constitute components of the extracellular matrix (ECM). They might be associated with the cuticle or be present in soluble form in the body cavity. They might interact with the Patched or the Patched-related proteins in a manner similar to the interaction of Hedgehog with its receptor Patched.
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| 2. |
- Hao, Limin, et al.
(author)
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The hedgehog-related gene qua-1 is required for molting in Caenorhabditis elegans
- 2006
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In: Developmental Dynamics. - : Wiley. - 1058-8388 .- 1097-0177. ; 235:6, s. 1469-1481
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Journal article (peer-reviewed)abstract
- The Caenorhabditis elegans genome encodes ten proteins that share similarity with Hedgehog through the C-terminal Hint/Hog domain. While most genes are members of larger gene families, qua-1 is a single copy gene. Here we show that orthologs of qua-1 exist in many nematodes, including Brugia malayi, which shared a common ancestor with C. elegans about 300 million years ago. The QUA-1 proteins contain an N-terminal domain, the Qua domain, that is highly conserved, but whose molecular function is not known. We have studied the expression pattern of qua-1 in C. elegans using a qua-1::GFP transcriptional fusion. qua-1 is mainly expressed in hyp1 to hyp11 hypodermal cells, but not in seam cells. It is also expressed in intestinal and rectal cells, sensilla support cells, and the P cell lineage in L1. The expression of qua-1::GFP undergoes cyclical changes during development in phase with the molting cycle. It accumulates prior to molting and disappears between molts. Disruption of the qua-1 gene function through an internal deletion that causes a frame shift with premature stop in the middle of the gene results in strong lethality. The animals arrest in the early larval stages due to defects in molting. Electron microscopy reveals double cuticles due to defective ecdysis, but no obvious defects are seen in the hypodermis. Qua domain-only::GFP and full-length QUA-1::GFP fusion constructs are secreted and associated with the overlying cuticle, but only QUA-1::GFP rescues the mutant phenotype. Our results suggest that both the Hint/Hog domain and Qua domain are critically required for the function of QUA-1.
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| 3. |
- Hao, Limin, et al.
(author)
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The hedgehog-related gene wrt-5 is essential for hypodermal development in Caenorhabditis elegans
- 2006
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In: Developmental Biology. - : Elsevier BV. - 0012-1606 .- 1095-564X. ; 290:2, s. 323-336
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Journal article (peer-reviewed)abstract
- The Caenorhabditis elegans genome encodes a series of hedgehog-related genes, which are thought to have evolved and diverged from an ancestral Hh gene. They are classified into several families based on their N-terminal domains. Here, we analyze the expression and function of a member of the warthog gene family, wrt-5, that lacks the Hint/Hog domain. wrt-5 is expressed in seam cells, the pharynx, pharyngeal-intestinal valve cells, neurons, neuronal support cells, the excretory cell, and the reproductive system. WRT-5 protein is secreted into the extracelluar space during embryogenesis. Furthermore, during larval development, WRT-5 protein is secreted into the pharyngeal lumen and the pharyngeal expression changes in a cyclical manner in phase with the molting cycle. Deletion mutations in wrt-5 cause embryonic lethality, which are temperature sensitive and more severe at 15 degrees C than at 25 degrees C. Animals that hatch exhibit variable abnormal morphology, for example, bagging worms, blistering, molting defects, or Roller phenotypes. We examined hypodermal cell junctions using the AJM-1: :GFP marker in the wrt-5 mutant background and observed cell boundary abnormalities in the arrested embryos. AJM-1: :GFP protein is also misplaced in pharyngeal muscle cells in the absence of WRT-5. In conclusion, we show that wrt-5 is an essential gene that - despite its lack of a Hint domain - has multiple functions in C. elegans and is implicated in cell shape integrity.
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| 4. |
- Kristan, Matej, et al.
(author)
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The first visual object tracking segmentation VOTS2023 challenge results
- 2023
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In: 2023 IEEE/CVF International conference on computer vision workshops (ICCVW). - : Institute of Electrical and Electronics Engineers Inc.. - 9798350307443 - 9798350307450 ; , s. 1788-1810
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking Segmentation VOTS2023 challenge is the eleventh annual tracker benchmarking activity of the VOT initiative. This challenge is the first to merge short-term and long-term as well as single-target and multiple-target tracking with segmentation masks as the only target location specification. A new dataset was created; the ground truth has been withheld to prevent overfitting. New performance measures and evaluation protocols have been created along with a new toolkit and an evaluation server. Results of the presented 47 trackers indicate that modern tracking frameworks are well-suited to deal with convergence of short-term and long-term tracking and that multiple and single target tracking can be considered a single problem. A leaderboard, with participating trackers details, the source code, the datasets, and the evaluation kit are publicly available at the challenge website1
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| 5. |
- Li, Peng, et al.
(author)
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Transcriptional reactivation of OTX2, RX1 and SIX3 during reprogramming contributes to the generation of RPE cells from human iPSCs
- 2016
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In: International Journal of Biological Sciences. - : Ivyspring International Publisher. - 1449-2288. ; 12:5, s. 505-517
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Journal article (peer-reviewed)abstract
- Directed differentiation of human induced pluripotent stem cells (iPSCs) into retinal pigmented epithelium (RPE) holds great promise in cell replacement therapy for patients suffering from degenerative eye diseases, including age-related macular degeneration (AMD). In this study, we generated iPSCs from human dermal fibroblasts (HDFs) by electroporation with episomal plasmid vectors encoding OCT4, SOX2, KLF4, L-MYC together with p53 suppression. Intriguingly, cell reprogramming resulted in a metastable transcriptional activation and selective demethylation of neural and retinal specification-associated genes, such as OTX2, RX1 and SIX3. In contrast, RPE progenitor genes were transcriptionally silent in HDFs and descendant iPSCs. Overexpression of OCT4 and SOX2 directly stimulated the expression of OTX2, RX1 and SIX3 in HDFs and iPSCs. Luciferase and chromatin immunoprecipitation (ChIP) assays further identified an OCT4- and two SOX2-binding sites located in the proximal promoter of OTX2. Histone acetylation and methylation on the local promoter also participated in the reactivation of OTX2. The transcriptional conversion of RX1 and SIX3 genes partially attributed to DNA demethylation. Subsequently, iPSCs were induced into the RPE cells displaying the characteristics of polygonal shapes and pigments, and expressing typical RPE cell markers. Taken together, our results establish readily efficient and safe protocols to produce iPSCs and iPSC-derived RPE cells, and underline that the reactivation of anterior neural transcription factor OTX2, eye field transcription factor RX1 and SIX3 in iPSCs is a feature of pluripotency acquisition and predetermines the potential of RPE differentiation.
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| 6. |
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| 7. |
- Yang, Tao, et al.
(author)
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Regional frequency analysis and spatio-temporal pattern characterization of rainfall extremes in the Pearl River Basin, China
- 2010
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In: Journal of Hydrology. - : Elsevier BV. - 0022-1694 .- 1879-2707. ; 380:3-4, s. 386-405
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Journal article (peer-reviewed)abstract
- This paper presents a method for regional frequency analysis and spatio-temporal pattern characterization of rainfall-extreme regimes (i.e. extremes, durations and timings) in the Pearl River Basin (PRB) using the well-known L-moments approach together with advanced statistical tests including stationarity test and serial correlation check, which are crucial to the valid use of L-moments for frequency analysis. Results indicate that: (1) the entire Pearl River Basin (40 sites) can be categorized into six regions by cluster analysis together with consideration of the topography and spatial patterns of mean precipitation in the basin. The results of goodness-of-fit measures indicate that the GNO, GLO, GEV, and PE3 distributions fit well for most of the basin for different HOM regions, but their performances are slightly different in term of curve fitting; (2) the estimated quantiles and their biases approximated by Monte Carlo simulation demonstrate that the results are reliable enough for the return periods of less than 100 years; (3) excessive precipitation magnitude records are observed at Guilin region of Guangxi Province and Fogang region of Guangdong Province, which have sufficient climate conditions (e.g. precipitation and humidity) responsible for the frequently occurred flood disasters in the regions. In addition, the spatial variations of precipitation in different return periods (Return period = 1, 10, 50 years to 100 years) increase from the upstream to downstream at the regional scale; (4) the seasonal patterns of precipitation extremes for different topographical regions are different. The major precipitation events of AM1R, AM3R, AM5R and AM7R in regions of low-elevation in lower (south-eastern) part of the basin occur mainly in May, June, July and August, while the main precipitation periods for the mountainous region upstream are June, July and August. Further analysis of the NCAR/NCEP reanalysis data indicates that the eastern Asian summer monsoon and typhoons (or hurricanes) are major metrological driving forces on the precipitation regimes. Additionally, topographical features (i.e. elevation, distance to the sea, and mountain’s influences) also exert different impacts on the spatial patterns of such regimes. To the best of our knowledge, this study is the first attempt to conduct a systematic regional frequency analysis on various annual precipitation extremes (based on consecutive 1-, 3-, 5-, 7-day averages) and to establish the possible links to climate pattern and topographical features in the Pearl River Basin and even in China. These findings are expected to contribute to exploring the complex spatio-temporal patterns of extreme rainfall in this basin in order to reveal the underlying linkages between precipitation and floods from a broad geographical perspective. (C) 2009 Published by Elsevier B.V.
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