Tulp1 deficiency causes early-onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish

Mutations in TUB-like protein 1 (TULP1) are associated with severe early-onset retinal degeneration in humans. However, the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish, namely tulp1a and tulp1b. Here, we generated the single knockout (tulp1a(−/−) and tulp1b(−/−)) and double knockout (tulp1-dKO) models in zebrafish. Knockout of tulp1a resulted in the mislocalization of UV cone opsins and the degeneration of UV cones specifically, while knockout of tulp1b resulted in mislocalization of rod opsins and rod-cone degeneration. In the tulp1-dKO zebrafish, mislocalization of opsins was present in all types of photoreceptors, and severe degeneration was observed at a very early age, mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1-dKO retinas. RNA-seq analysis showed that the expression of tektin2 (tekt2), a ciliary and flagellar microtubule structural component, was downregulated in the tulp1-dKO zebrafish. Dual-luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. In addition, ferroptosis might be activated in the tulp1-dKO zebrafish, as suggested by the up-regulation of genes related to the ferroptosis pathway, the shrinkage of mitochondria, reduction or disappearance of mitochondria cristae, and the iron and lipid droplet deposition in the retina of tulp1-dKO zebrafish. In conclusion, our study establishes an appropriate zebrafish model for TULP1-associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2, which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early-onset retinal degeneration

Rod genesis driven by mafba in an nrl knockout zebrafish model with altered photoreceptor composition and progressive retinal degeneration

Neural retina leucine zipper (NRL) is an essential gene for the fate determination and differentiation of the precursor cells into rod photoreceptors in mammals. Mutations in NRL are associated with the autosomal recessive enhanced S-cone syndrome and autosomal dominant retinitis pigmentosa. However, the exact role of Nrl in regulating the development and maintenance of photoreceptors in the zebrafish (Danio rerio), a popular animal model used for retinal degeneration and regeneration studies, has not been fully determined. In this study, we generated an nrl knockout zebrafish model via the CRISPR-Cas9 technology and observed a surprising phenotype characterized by a reduced number, but not the total loss, of rods and over-growth of green cones. We discovered two waves of rod genesis, nrl-dependent and -independent at the embryonic and post-embryonic stages, respectively, in zebrafish by monitoring the rod development. Through bulk and single-cell RNA sequencing, we characterized the gene expression profiles of the whole retina and each retinal cell type from the wild type and nrl knockout zebrafish. The over-growth of green cones and mis-expression of green-cone-specific genes in rods in nrl mutants suggested that there are rod/green-cone bipotent precursors, whose fate choice between rod versus green-cone is controlled by nrl. Besides, we identified the mafba gene as a novel regulator of the nrl-independent rod development, based on the cell-type-specific expression patterns and the retinal phenotype of nrl/mafba double-knockout zebrafish. Gene collinearity analysis revealed the evolutionary origin of mafba and suggested that the function of mafba in rod development is specific to modern fishes. Furthermore, the altered photoreceptor composition and abnormal gene expression in nrl mutants caused progressive retinal degeneration and subsequent regeneration. Accordingly, this study revealed a novel function of the mafba gene in rod development and established a working model for the developmental and regulatory mechanisms regarding the rod and green-cone photoreceptors in zebrafish

The splicing factor DHX38 enables retinal development through safeguarding genome integrity

DEAH-Box Helicase 38 (DHX38) is a pre-mRNA splicing factor and also a disease-causing gene of autosomal recessive retinitis pigmentosa (arRP). The role of DHX38 in the development and maintenance of the retina remains largely unknown. In this study, by using the dhx38 knockout zebrafish model, wedemonstrated that Dhx38 deficiency causes severe differentiation defects and apoptosis of retinal progenitor cells (RPCs) through disrupted mitosis and increased DNA damage. Furthermore, we found a significant accumulation of R-loops in the dhx38-deficient RPCs and human cell lines. Finally, we found that DNA replication stress is the prerequisite for R-loop-induced DNA damage in the DHX38 knockdown cells. Taken together, our study demonstrates a necessary role of DHX38 in the development of retina and reveals a DHX38/R-loop/replication stress/DNA damage regulatory axis that is relatively independent of the known functions of DHX38 in mitosis control

Microfiltration of oil emulsions stabilized by different surfactants

Membrane-based filtration is a promising technique to treat the enormous amounts of oily wastewater, specifically those with micron-sized oil droplets. However, the understanding on the effect of the surfactants, that are inevitably present to stabilize the oil emulsion, on the filtration performance remains poor. This study aimed to investigate the effect of surfactant type (namely, non-ionic Tween 20, positively charged CTAB, and negatively charged SDS) on filtration flux and membrane fouling during the microfiltration of the surfactant-stabilized oil emulsion with mean droplet sizes of approximately 20 μm. The Optical Coherence Tomography (OCT) was employed to quantify the evolution of fouling, and both the DLVO and XDLVO models were used to quantify the oil droplet-membrane and oil droplet-deposited layer interaction energies. Two key understanding on the correlation between the DLVO and XDLVO predictions with flux and fouling were obtained. Firstly, the steep flux enhancement vis-à-vis a DI water feed by the feed containing CTAB-stabilized oil emulsion was tied to the attractive interaction of the surfactant with the membrane, as evident from the DLVO model. This attraction was not related to the extent of membrane fouling, which was relatively lesser for the CTAB-stabilized oil emulsion. Secondly, the extent of membrane fouling was tied to the repulsive energy magnitudes rather than attractive ones, specifically in that the least repulsive energy values of the Tween 20 – stabilized oil emulsion was linked to the most extensive fouling.Economic Development Board (EDB)Ministry of Education (MOE)We acknowledge funding from the Singapore Ministry of Education Academic Research Funds Tier 2 (MOE2014-T2-2-074; ARC16/15) and Tier 1 (2015-T1-001-023; RG7/15), the GSK (GlaxoSmithKline) – EDB (Economic Development Board) Trust Fund, and the Joint Singapore Germany Research Project Fund (SGP-PROG3-019)

Bioaccumulation, trophic transfer and biomagnification of perfluoroalkyl acids (PFAAs) in the marine food web of the South China Sea

Knowledge about bioaccumulation and trophic transfer in food webs is of tremendous importance in contaminant hazards evaluation. Perfluoroalkyl acids (PFAAs) are widely distributed, and its emissions to coastal areas have posed a threat to the health of marine organisms and consumers. In this study, 15 species were sampled from Qinzhou Bay of the South China Sea. The concentrations of PFAAs in organisms were detected by liquid chromatography-mass spectrometry, and the trophic positions of organisms were constructed based on nitrogen isotope analysis. PFAAs were found in all organisms. The contents of PFOS in all organisms were higher than of PFOA, and the proportions of short-chain PFAAs were higher in the low trophic positioned organisms, while long-chain PFAAs were higher in the high trophic positioned organisms. Moreover, the bioaccumulation factors (BAFs) increased with the increasing number of fluorocarbon atoms. The trophic magnification factor (TMF) and the biomagnification factors (BMFs), calculated from the constructed food webs, together suggested potential biomagnification effects of PFOS, while less clear results were found for PFOA. Our results further indicate that previously banned long-chain PFAAs had persistent residuals in this coastal marine ecosystem, and that emerging short-chain PFAAs had high concentrations in some species but showed no biomagnification

Knockout of mafba Causes Inner-Ear Developmental Defects in Zebrafish via the Impairment of Proliferation and Differentiation of Ionocyte Progenitor Cells

Zebrafish is an excellent model for exploring the development of the inner ear. Its inner ear has similar functions to that of humans, specifically in the maintenance of hearing and balance. Mafba is a component of the Maf transcription factor family. It participates in multiple biological processes, but its role in inner-ear development remains poorly understood. In this study, we constructed a mafba knockout (mafba−/−) zebrafish model using CRISPR/Cas9 technology. The mafba−/− mutant inner ear displayed severe impairments, such as enlarged otocysts, smaller or absent otoliths, and insensitivity to sound stimulation. The proliferation of p63+ epidermal stem cells and dlc+ ionocyte progenitors was inhibited in mafba−/− mutants. Moreover, the results showed that mafba deletion induces the apoptosis of differentiated K+-ATPase-rich (NR) cells and H+-ATPase-rich (HR) cells. The activation of p53 apoptosis and G0/G1 cell cycle arrest resulted from DNA damage in the inner-ear region, providing a mechanism to account for the inner ear deficiencies. The loss of homeostasis resulting from disorders of ionocyte progenitors resulted in structural defects in the inner ear and, consequently, loss of hearing. In conclusion, the present study elucidated the function of ionic channel homeostasis and inner-ear development using a zebrafish Mafba model and clarified the possible physiological roles

data_sheet_1.doc

<p>In this study, the dissolution of biomass components—cellulose, hemicellulose, and lignin, and two whole biomasses—switchgrass and poplar in a pyridine based ionic liquid at a low temperature—50°C has been examined, which will provide an opportunity to explore the original structures of biomass components. The following phosphitylation, and ³¹P NMR measurement could provide quantitative results for various hydroxyl groups, including aliphatic, condensed phenolic, guaiacyl phenolic, p-hydroxyl phenyl and carboxylic hydroxyl groups in the biomass components, and whole biomass. By employing various biomass model compounds (glucose, cellotriose, and cellohexose), artificial mixtures of biomass components (cellulose, hemicellulose, and lignin), and computational simulation for the assignments by using density functional theory calculation in Gaussian, reliability and accuracy of this method have been examined as well, which indicated that this method is a reliable and accurate way to quantitatively characterize five different types of hydroxyl groups in biomass and its components.</p