Microinjection-Based RNA Interference Method in the Water Flea, Daphnia pulex and Daphnia magna

It is well known that most daphnid species have several attractive life history characteristics such as cyclical parthenogenesis, environmental sex determination, and predator-induced defense formation. Recent advances in high-throughput omics technologies make it easy to obtain a huge number of potential candidate factors involved in environmental stimuli-triggered phenotypic alterations. Furthermore, our group has developed a microinjection system to introduce foreign materials such as nucleotides and chemicals into the early-stage (one-cell stage) egg of Daphnia pulex and Daphnia magna. Consequently, we established a microinjection-based RNAi system that allows arbitrary gene functions to be investigated. However, this microinjection system does not seem to have pervaded in the daphnid research community due to its low throughput and high level of skills required. In this chapter, we review the microinjection method and its RNAi system in water fleas, D. pulex and D. magna, providing some technical tips and making challenging proposals for the development of novel high-throughput RNAi methods. Finally, we provide an overview of recently developed gene functional analysis methods such as overexpression and genome-editing systems

Outer retinal circular structures in patients with Bietti crystalline retinopathy.

[Background] : Bietti crystalline retinopathy (BCR) is a distinct retinal degenerative disease characterised by retinal degeneration with many yellow–white crystals located mainly at the posterior pole area. Using spectral domain-optical coherence tomography (SD-OCT), the structural change in retina was investigated. [Methods] : Patients diagnosed with BCR (n=12), retinitis pigmentosa (RP, n=292) and cone dystrophy (n=16) were included in this study. The authors mainly examined fundus photographs and SD-OCT, infrared and fundus autofluorescence images of these patients. [Results]: Crystalline deposits were detected in portions of the retinal pigment epithelium that lacked patchy degenerated lesions. SD-OCT revealed that most of the observed crystalline deposits were located adjacent to the inner side of retinal pigment epithelium layer. The change most frequently observed was circular hyper-refractive structures in the outer nuclear layer. Although the structures were considered to be previously reported “tubular formation” or “tubular degeneration”, we determined that many of these circular structures were slices of spherical structures and were typically noted in areas suspected of ongoing active degeneration. [Conclusion] : BCR has characteristic structures in the outer nuclear layer. Although the incidence of the structure varies, it may be characteristic of retinal degeneration and can be found in many retinal degenerative diseases

RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation

Annotation of development-dependent dimorphic genes in gonad during Day 0–12. Annotation of development-dependent significantly up- and down- regulated DEGs at FDR < 0.01 in gonadal regions incubated under MPT and FPT conditions during Day 0 to Day 12. Ordered by decreasing fold change. (XLSX 196 kb

Wide-Field Fundus Autofluorescence Abnormalities and Visual Function in Patients With Cone and Cone-Rod Dystrophies

METHODS. Sixteen patients with cone dystrophy (CD) and 41 patients with cone-rod dystrophy (CRD) were recruited at one institution. The right eye of each patient was included for analysis. We obtained wide-field FAF images using a ultra-widefield retinal imaging device and measured the area of abnormal FAF. The association between the area of abnormal FAF and the results of visual acuity measurements, kinetic perimetry, and electroretinography (ERG) were investigated. RESULTS. The mean age of the participants was 51.4 6 17.4 years, and the mean logarithm of the minimum angle of resolution was 1.00 6 0.57. The area of abnormal FAF correlated with the scotoma measured by the Goldman perimetry I/4e isopter (q ¼ 0.79, P &lt; 0.001). The area also correlated with amplitudes of the rod ERG (q ¼ À0.63, P &lt; 0.001), combined ERG awave (q ¼ À0.72, P &lt; 0.001), combined ERG b-wave (q ¼ À0.66, P &lt; 0.001), cone ERG (q ¼ À0.44, P ¼ 0.001), and flicker ERG (q ¼ À0.47, P &lt; 0.001). CONCLUSIONS. The extent of abnormal FAF reflects the severity of functional impairment in patients with cone-dominant retinal dystrophies. Fundus autofluorescence measurements are useful for predicting retinal function in these patients

Molecular cloning of doublesex genes of four cladocera (water flea) species

BACKGROUND: The gene doublesex (dsx) is known as a key factor regulating genetic sex determination in many organisms. We previously identified two dsx genes (DapmaDsx1 and DapmaDsx2) from a freshwater branchiopod crustacean, Daphnia magna, which are expressed in males but not in females. D. magna produces males by parthenogenesis in response to environmental cues (environmental sex determination) and we showed that DapmaDsx1 expression during embryonic stages is responsible for the male trait development. The D. magna dsx genes are thought to have arisen by a cladoceran-specific duplication; therefore, to investigate evolutionary conservation of sex specific expression of dsx genes and to further assess their functions in the environmental sex determination, we searched for dsx homologs in four closely related cladoceran species. RESULTS: We identified homologs of both dsx genes from, D. pulex, D. galeata, and Ceriodaphnia dubia, yet only a single dsx gene was found from Moina macrocopa. The deduced amino acid sequences of all 9 dsx homologs contained the DM and oligomerization domains, which are characteristic for all arthropod DSX family members. Molecular phylogenetic analysis suggested that the dsx gene duplication likely occurred prior to the divergence of these cladoceran species, because that of the giant tiger prawn Penaeus monodon is rooted ancestrally to both DSX1 and DSX2 of cladocerans. Therefore, this result also suggested that M. macrocopa lost dsx2 gene secondarily. Furthermore, all dsx genes identified in this study showed male-biased expression levels, yet only half of the putative 5’ upstream regulatory elements are preserved in D. magna and D. pulex. CONCLUSIONS: The all dsx genes of five cladoceran species examined had similar amino acid structure containing highly conserved DM and oligomerization domains, and exhibited sexually dimorphic expression patterns, suggesting that these genes may have similar functions for environmental sex determination in cladocerans

Comprehensive molecular diagnosis of a large cohort of Japanese retinitis pigmentosa and Usher syndrome patients by next-generation sequencing. Invest Ophthalmol Vis Sci

PURPOSE. Retinitis pigmentosa (RP), a major cause of blindness in developed countries, has multiple causative genes; its prevalence differs by ethnicity. Usher syndrome is the most common form of syndromic RP and is accompanied by hearing impairment. Although molecular diagnosis is challenging, recent technological advances such as targeted highthroughput resequencing are efficient screening tools. METHODS. We performed comprehensive molecular testing in 329 Japanese RP and Usher syndrome patients by using a custom capture panel that covered the coding exons and exon/ intron boundaries of all 193 known inherited eye disease genes combined with Illumina HiSequation 2500. Candidate variants were screened using systematic data analyses, and their potential pathogenicity was assessed according to the frequency of the variants in normal populations, in silico prediction tools, and compatibility with known phenotypes or inheritance patterns. RESULTS. Molecular diagnoses were made in 115/317 RP patients (36.3%) and 6/12 Usher syndrome patients (50%). We identified 104 distinct mutations, including 66 novel mutations. EYS, USH2A, and RHO were common causative genes. In particular, mutations in EYS accounted for 15.0% of the autosomal recessive/simplex RP patients or 10.7% of the entire RP cohort. Among the 189 previously reported mutations detected in the current study, 55 (29.1%) were found commonly in Japanese or other public databases and were excluded from molecular diagnoses. CONCLUSIONS. By screening a large cohort of patients, this study catalogued the genetic variations involved in RP and Usher syndrome in a Japanese population and highlighted the different distribution of causative genes among populations

Characterization of evolutionary trend in squamate estrogen receptor sensitivity

Steroid hormones are a key regulator of reproductive biology in vertebrates, and are largely regulated via nuclear receptor families. Estrogen signaling is regulated by two estrogen receptor (ER) subtypes alpha and beta in the nucleus. In order to understand the role of estrogen in vertebrates, these ER from various species have been isolated and were functionally analyzed using luciferase reporter gene assays. Interestingly, species difference in estrogen sensitivity has been noted in the past, and it was reported that snake ER displayed highest estrogen sensitivity. Here, we isolated additional ER from three lizards: chameleon (Bradypodion pumilum), skink (Plestiodon finitimus), and gecko (Gekko japonicus). We have performed functional characterization of these ERs using reporter gene assay system, and found high estrogen sensitivity in all three species. Furthermore, comparison with results 2 from other tetrapod ER revealed a seemingly uniform gradual pattern of ligand sensitivity evolution. In silico 3D homology modeling of the ligand-binding domain revealed structural variation at three sites, helix 2, and juncture between helices 8 and 9, and caudal region of helix 10/11. Docking simulations indicated that predicted ligand-receptor interaction also correlated with the reporter assay results, and overall squamates displayed highest stabilized interactions. The assay system and homology modeling system provides tool for in-depth comparative analysis of estrogen function, and provides insight toward the evolution of ER among vertebrates.This study was partially funded by the Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan (YO, SM, TI), Japan Society for the Promotion of Science (RY), UK-Japan Research Collaboration Grants from the Ministry of the Environment, Japan, and by the NIBB International Collaborative Research Initiative (SM, TI).http://www.elsevier.com/locate/ygcen2017-11-30hb2016Paraclinical Science

Insights into epigenetic regulation of cyp19a via comparative analysis using the scombrid chub mackerel as model

Sexual development and reproduction are largely linked to epigenetic changes in many fish species. However, understanding of epigenetic regulation in scombrid species, such as tunas and mackerels, is limited. This study investigates DNA methylation’s impact on cyp19a expression, crucial for estrogen synthesis, focusing on chub mackerel. Given the commercial significance of scombrids and susceptibility of marine fish to environmental changes, elucidating epigenetic mechanisms, particularly in the context of global warming, becomes imperative. We aimed to generalize observations from chub mackerel to other scombrids. Additionally, we studied DNA methylation patterns across fish with different sexual systems to understand aromatase regulation’s phenotypic plasticity. Our in silico analysis revealed highly conserved promoter sequences within scombrids, sharing TFBS like Foxl2, FOS::JUN, ESRR, and Sox3, while CpG content varies. This indicates a conserved regulatory network controlling gene expression. We found sexual dimorphism in DNA methylation, with males hypermethylated and aromatase expression downregulated. Despite similar dnmt1 expression, tet1, tet2, and tet3 were higher expressed in females, suggesting that the observed DNA methylation patterns are maintained through active demethylation rather than differential methylation. Gonochoristic Japanese anchovy and protogynous bamboo leaf wrasse displayed similar trends, but species-specific methylation patterns highlight DNA methylation’s complex role in gonadal changes. In vitro assays confirmed methylation’s regulatory role and identified an SF-1 binding site relevant for promoter activation in chub mackerel. Another studied SF-1 site, present in both chub mackerel and bamboo leaf wrasse, showed regulatory effects, indicating potential similar regulatory mechanisms for cyp19a expression. Overall, our findings suggest that while global methylation affects cyp19a transcription, the variation in CpG density and location could be introducing nuances in its epigenetic regulation. This study contributes to our understanding of the cyp19a regulation in fish gonad maturation