TY - JOUR A1 - Zhang, Yonghong A1 - Zheng, Lanlan A1 - Zheng, Yan A1 - Zhou, Chao A1 - Huang, Ping A1 - Xiao, Xiao A1 - Zhao, Yongheng A1 - Hao, Xincai A1 - Hu, Zhubing A1 - Chen, Qinhua A1 - Li, Hongliang A1 - Wang, Xuanbin A1 - Fukushima, Kenji A1 - Wang, Guodong A1 - Li, Chen T1 - Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum JF - Frontiers in Plant Science N2 - Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue, and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance. KW - genome assembly KW - resveratrol biosynthesis KW - whole-genome duplication KW - medicinal plant KW - stress tolerance KW - Polygonum cuspidatum Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-189279 SN - 1664-462X VL - 10 ER - TY - JOUR A1 - Tsai, Yu-Chen A1 - Grimm, Stefan A1 - Chao, Ju-Lan A1 - Wang, Shih-Chin A1 - Hofmeyer, Kerstin A1 - Shen, Jie A1 - Eichinger, Fred A1 - Michalopoulou, Theoni A1 - Yao, Chi-Kuang A1 - Chang, Chih-Hsuan A1 - Lin, Shih-Han A1 - Sun, Y. Henry A1 - Pflugfelder, Gert O. T1 - Optomotor-blind negatively regulates Drosophila eye development by blocking Jak/STAT signaling JF - PLoS ONE N2 - Organ formation requires a delicate balance of positive and negative regulators. In Drosophila eye development, wingless (wg) is expressed at the lateral margins of the eye disc and serves to block retinal development. The T-box gene optomotor-blind (omb) is expressed in a similar pattern and is regulated by Wg. Omb mediates part of Wg activity in blocking eye development. Omb exerts its function primarily by blocking cell proliferation. These effects occur predominantly in the ventral margin. Our results suggest that the primary effect of Omb is the blocking of Jak/STAT signaling by repressing transcription of upd which encodes the Jak receptor ligand Unpaired. KW - morphogenetic furrow progression KW - cell fate KW - compartment boundary KW - reporter gene KW - compound eye KW - gene expression KW - retinal differentiation KW - acts downstream KW - imaginal disk KW - glial cells Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143577 VL - 10 IS - 3 ER - TY - JOUR A1 - Chen, Si A1 - Waxman, Susannah A1 - Wang, Chao A1 - Atta, Sarah A1 - Loewen, Ralitsa A1 - Loewen, Nils A. T1 - Dose-dependent effects of netarsudil, a Rho-kinase inhibitor, on the distal outflow tract JF - Graefe's Archive for Clinical and Experimental Ophthalmology N2 - Purpose To characterize the effects of netarsudil on the aqueous humor outflow tract distal to the trabecular meshwork (TM). Wehypothesized that netarsudil increases outflow facility in eyes with and without circumferential ab interno trabeculectomy (AIT)that removes the TM. Methods Sixty-four porcine anterior segment cultures were randomly assigned to groups with (n= 32) and without circumferential AIT (n= 32). Cultures were exposed to 0.1, 1, and 10μM netarsudil (N= 8 eyes per concentration). For each concentration,IOP and vessel diameters were compared with their respective pretreatment baselines. Outflow tract vessel diameters wereassessed by spectral-domain optical coherence tomography (SDOCT) and rendered in 4D (XYZ time series). Results Netarsudil at 1μM reduced IOP both in eyes with TM (−0.60 ± 0.24 mmHg,p= 0.01) and in eyes without TM (−1.79 ±0.42 mmHg,p< 0.01). At this concentration, vessels of the distal outflow tract dilated by 72%. However, at 0.1μMnetarsudilelevated IOP in eyes with TM (1.59 ± 0.36 mmHg,p< 0.001) as well as in eyes without TM (0.23 ± 0.32 mmHg,p<0.001). Vessels of the distal outflow tract constricted by 31%. Similarly, netarsudil at a concentration of 10μM elevated IOP both in eyeswith TM (1.91 ± 0.193,p< 0.001) and in eyes without TM (3.65 ± 0.86 mmHg,p< 0.001). At this concentration, outflow tractvessels constricted by 27%. Conclusion In the porcine anterior segment culture, the dose-dependent IOP changes caused by netarsudil matched the diameterchanges of distal outflow tract vessels. Hyper- and hypotensive properties of netarsudil persisted after TM removal KW - Rho-kinase inhibitor KW - Netarsudil KW - Distal outflow trac KW - Anterior chamber perfusion model KW - Porcine eye Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-231893 SN - 0721-832X VL - 258 ER - TY - JOUR A1 - Waxman, Susannah A1 - Strzalkowska, Alicja A1 - Wang, Chao A1 - Loewen, Ralitsa A1 - Dang, Yalong A1 - Loewen, Nils A. T1 - Tissue-engineered anterior segment eye cultures demonstrate hallmarks of conventional organ culture JF - Graefe’s Archive for Clinical and Experimental Ophthalmology N2 - Background Glaucoma is a blinding disease largely caused by dysregulation of outflow through the trabecular meshwork (TM), resulting in elevated intraocular pressure (IOP). We hypothesized that transplanting TM cells into a decellularized, tissue-engineered anterior segment eye culture could restore the outflow structure and function. Methods Porcine eyes were decellularized with freeze–thaw cycles and perfusion of surfactant. We seeded control scaffolds with CrFK cells transduced with lentiviral vectors to stably express eGFP and compared them to scaffolds seeded with primary TM cells as well as to normal, unaltered eyes. We tracked the repopulation behavior, performed IOP maintenance challenges, and analyzed the histology. Results Transplanted cells localized to the TM and progressively infiltrated the extracellular matrix, reaching a distribution comparable to normal, unaltered eyes. After a perfusion rate challenge to mimic a glaucomatous pressure elevation, transplanted and normal eyes reestablished a normal intraocular pressure (transplanted = 16.5 ± 0.9 mmHg, normal = 16.9 ± 0.9). However, eyes reseeded with eGFP-expressing CrFK cells could not regulate IOP, remaining high and unstable (27.0 ± 6.2 mmHg) instead. Conclusion Tissue-engineered anterior segment scaffolds can serve as readily available, scalable ocular perfusion cultures. This could reduce dependency on scarce donor globes in outflow research and may allow engineering perfusion cultures with specific geno- and phenotypes. KW - ocular anterior segment perfusion culture KW - tissue engineering KW - aqueous humor outflow KW - trabecular meshwork Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-323845 VL - 261 IS - 5 ER -