FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research.

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.

Transient effect of suction on the retinal neurovasculature in myopic patients after small-incision lenticule extraction.

PURPOSE: To characterize retinal neurovasculature changes after small-incision lenticule extraction (SMILE) in myopic patients. SETTING: Ophthalmic Center, the Second Affiliated Hospital of Guangzhou Medical University, China. DESIGN: Prospective interventional study. METHODS: The corrected distance visual acuity/uncorrected distance visual acuity, corrected intraocular pressure (CIOP), and corneal tomography were evaluated at baseline (PRE), postoperative day (POD) 1, and POD 7. Ganglion cell-inner plexiform layer (GCIPL) and peripapillary retinal nerve fiber layer (pRNFL) thicknesses were measured. The vessel area densities (VADs, %), vessel skeleton densities (VSDs, %), vessel diameter index (VDI), and fractal dimensions (Dbox) of the superficial vascular plexus (SVP) and deep vascular plexus (DVP) were measured in a circular area (ϕ 2.5 mm) centered on the fovea. RESULTS: A total of 38 myopic patients were recruited. The GCIPL thickness was increased after SMILE at POD 1 and POD 7 (P < .01) but no significant changes in the pRNFL thickness. The VAD, VSD, and Dbox of the SVP were decreased at POD 1 (P < .01), but not at POD 7. The VDI in small vessels of the SVP and DVP was decreased at POD 1 (P < .05) and increased at POD 7 (P < .05). Changes in CIOP were positively correlated with changes in the GCIPL thickness. Changes in CIOP were negatively correlated with changes in the VAD of small vessels and the Dbox of total vessels in the DVP. Changes in CIOP were negatively correlated with the VSD and VDI of small vessels in the DVP and changes in the VDI of big vessels in the SVP. CONCLUSIONS: The transient fluctuations in the retinal neurovasculature after SMILE may represent a characteristic homeostasis pattern in patients after refractive surgery.

Enhanced functional properties of human limbal stem cells by inhibition of the miR-31/FIH-1/P21 axis.

OBJECTIVE: On the basis of the functional roles of the embryonic stem cell niche (ESCN) in the human limbal stem cells (LSCs), we proposed to explore the potential roles of microRNAs in regulating the self-renewal and differentiation of LSCs cultured in the ESCN. METHODS: The LSCs were cultured in different media, either in CnT-20 media or in CnT-20 + 20% ES culture supernatant (ESC-CM). The LSCs cultured in ESC-CM were then transfected with microRNA-31 (miR-31) mimic or antago-31. The colony-forming efficiency (CFE) was analysed. Cell cycle, apoptosis, mitochondrial potential and reactive oxygen species were analysed by flow cytometry, and quantitative real-time PCR was used to determine the expression levels of FIH-1, P21, P63, ABCG2, CK3, microRNA-31, microRNA-143, microRNA-145 and microRNA-184. Indirect immunostaining was employed to detect the expression of P63, ABCG2, survivin, connexin-43 and CK3. Western blot was employed to detect the expression of FIH-1, P63, P21, CK3, caspase 3, Tcf4, ß-catenin, survivin, GSK3ß and pGSK3ß. RESULTS: Compared with cells grown in CnT-20, the level of miR-31 in cells grown in ESC-CM was lower. We investigated the roles that miR-31 and FIH-1 play in regulating the functional properties of LSCs. We used antagomirs (antago) to reduce the level of miR-31 in LSCs. Antago-31 increased FIH-1 levels and significantly reduced P21 expressional level in LSCs compared to irrelevant-antago (Ir-antago) treatment. The downregulation of miR-31 in LSCs promotes the maintenance of stemness. CONCLUSION: ES culture supernatant (ESC-CM) regulates the fate of LSCs in part by inhibiting the miR-31/FIH-1/P21 axis. This study may have a high impact on the expansion of LSCs in regenerative medicine, especially for ocular surface reconstruction.