The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships

Buckwheat (Fagopyrum genus, Polygonaceae), is an annual or perennial, herbaceous or semi-shrub dicotyledonous plant. There are mainly three cultivated buckwheat species, common buckwheat (Fagopyrum esculentum) is widely cultivated in Asia, Europe, and America, while Tartary buckwheat (F. tataricum) and F. cymosum (also known as F. dibotrys) are mainly cultivated in China. The genus Fagopyrum is taxonomically confusing due to the complex phenotypes of different Fagopyrum species. In this study, the chloroplast (cp) genomes of three Fagopyrum species, F. longistylum, F. leptopodum, F. urophyllum, were sequenced, and five published cp genomes of Fagopyrum were retrieved for comparative analyses. We determined the sequence differentiation, repeated sequences of the cp genomes, and the phylogeny of Fagopyrum species. The eight cp genomes ranged, gene number, gene order, and GC content were presented. Most of variations of Fagopyrum species cp genomes existed in the LSC and SSC regions. Among eight Fagopyrum chloroplast genomes, six variable regions (ndhF-rpl32, trnS-trnG, trnC, trnE-trnT, psbD, and trnV) were detected as promising DNA barcodes. In addition, a total of 66 different SSR (simple sequence repeats) types were found in the eight Fagopyrum species, ranging from 8 to 16 bp. Interestingly, many SSRs showed significant differences especially in some photosystem genes, which provided valuable information for understanding the differences in light adaptation among different Fagopyrum species. Genus Fagopyrum has shown a typical branch that is distinguished from the Rumex, Rheum, and Reynoutria, which supports the unique taxonomic status in Fagopyrum among the Polygonaceae. In addition, phylogenetic analysis based on the cp genomes strongly supported the division of eight Fagopyrum species into two independent evolutionary directions, suggesting that the separation of cymosum group and urophyllum group may be earlier than the flower type differentiation in Fagopyrum plants. The results of the chloroplast-based phylogenetic tree were further supported by the matK and Internal Transcribed Spacer (ITS) sequences of 17 Fagopyrum species, which may help to further anchor the taxonomic status of other members in the urophyllum group in Fagopyrum. This study provides valuable information and high-quality cp genomes for identifying species and evolutionary analysis for future Fagopyrum research.

A Mathematical Model to Characterize the Role of Light Adaptation in Mammalian Circadian Clock

In response to a light stimulus, the mammalian circadian clock first dramatically increases the expression of Per1 mRNA, and then drops to a baseline even when light persists. This phenomenon is known as light adaptation, which has been experimentally proven to be related to the CRTC1-SIK1 pathway in suprachiasmatic nucleus (SCN). However, the role of this light adaptation in the circadian rhythm remains to be elucidated. To reveal the in-depth function of light adaptation and the underlying dynamics, we proposed a mathematical model for the CRTC1-SIK1 network and coupled it to a mammalian circadian model. The simulation result proved that the light adaptation is achieved by the self-inhibition of the CRTC1/CREB complex. Also, consistently with experimental observations, this adaptation mechanism can limit the phase response to short-term light stimulus, and it also restricts the rate of the phase shift in a jet lag protocol to avoid overly rapid re-entrainment. More importantly, this light adaptation is predicted to prevent the singularity behavior in the cell population, which represents the abolishment of circadian rhythmicity due to desynchronization of oscillating cells. Furthermore, it has been shown to provide refractoriness to successive stimuli with short gap. Therefore, we concluded that the light adaptation generated by the CRTC1-SIK1 pathway in the SCN provides a robust mechanism, allowing the circadian system to maintain homeostasis in the presence of light perturbations. These results not only give new insights into the dynamics of light adaptation from a computational perspective but also lead us to formulate hypotheses about the related physiological significance.

Application of Angio Optical Coherence Tomography and Flash Electroretinogram in the Study of Retinal Morphology and Function in High Myopia

Purpose: Using optical coherence tomography (OCTA) and flash electroretinography (F-ERG), we investigated changes to the retinal micromorphology and the overall function of the retina in eyes with different degrees of high myopia. Design: Case-control study. Participants: A total of 64 cases of 118 eyes with axial high myopia with diopters ranging from -−6.0 D to −15.0D were included in the study. The individuals were 18-40 years old.Methods: Subjects were divided into three groups according to the axial length (AL) of the eye and the spherical equivalent (SE)of the lens: the high myopia group (AL: ≤26 mm and SE: −6.0D to −9.0D) with 32 eyes, the ultra-high myopia group (AL: 26-28 mm and SE: -9.25D to -12.0D) with 43 eyes, and the extremely high myopia group (AL: ≥28 mm and SE: −12.25D to −15.0D) with 43 eyes. We used the OCTA measurements macular foveal retinal thickness (MRT), foveal avascular zone (FAZ), and superficial macular and deep retinal microvascular density, and the F-ERG measurements retinal dark-adaptation a-wave and b-wave, oscillation potential (OP) wave, light adaptation a-wave and b-wave, and 30-Hz flicker light amplitudes, which represent the functional state of the retina.Results: The differences in retinal thickness in the macular area between the three groups were only statistically significant within 1 mm of the fovea (P = 0.006). MRT was positively correlated with AL (r = 0.278, P = 0.002) and negatively correlated with SE (R = −0.200, P = 0.031). The difference in the FAZ area between the three groups was also statistically significant (P = 0.036), and FAZ was negatively correlated with AL (r = −0.377, p < 0.001) and positively correlated with SE (r = 0.192, P < 0.5). Both the superficial and deep blood flow density of the macular fovea were positively correlated with AL (p < 0.001). The superficial parafoveal blood flow density was negatively correlated with AL (r = −0.280, P = 0.002) but positively correlated with SE (R = 0.254, P = 0.006). The overall blood flow density of the deep retina, the parafoveal blood flow density, and the blood flow density around the fovea were negatively correlated with AL (p < 0.001) and positively correlated with myopic SE (p < 0.001). The dark-adaptation b-wave, maximum comprehensive response a-wave and b-wave, OP wave, bright-adaptation a-wave and b-wave, and 30-Hz flicker amplitudes of the retina were negatively correlated with AL and positively correlated with SE. The amplitudes of light adaptation a-wave and b-wave were[1] negatively correlated with the foveal avascular density (p < 0.001), and the average amplitude of the OP wave was positively correlated with the superficial retinal avascular density (p < 0.001).Conclusions: Before obvious pathological changes or central vision damage, the morphology and function of the macular area show subtle changes in patients with high myopia. As the degree of myopia increases and the axis of the eye increases, the activity of the cone cells in high myopia eyes decreases and the microvascular circulation in the inner retina and function of inner layer cells, such as non-proa cells, are affected. The changes of retinal dark adaptation are more sensitive than those of bright adaptation, which indicates that retinal rod cell damage may be earlier than cone cell damage in high myopia. Therefore, we believe that the combined use of OCTA and F-ERG can help in the early diagnosis and monitoring of patients at a high risk of myopia and to guide their clinical treatment.Because the p-value is clearly provided, the term “significantly” is not necessary (removed to reduce wordiness).

Blue–Yellow VEP with Projector-Stimulation in Glaucoma

Background and aim In the past, increased latencies of the blue-on-yellow pattern visually evoked potentials (BY-VEP), which predominantly originate in the koniocellular pathway, have proven to be a sensitive biomarker for early glaucoma. However, a complex experimental setup based on an optical bench was necessary to obtain these measurements because computer screens lack sufficient temporal, spatial, spectral, and luminance resolution. Here, we evaluated the diagnostic value of a novel setup based on a commercially available video projector. Methods BY-VEPs were recorded in 126 participants (42 healthy control participants, 12 patients with ocular hypertension, 17 with “preperimetric” glaucoma, and 55 with perimetric glaucoma). Stimuli were created with a video projector (DLP technology) by rear projection of a blue checkerboard pattern (460 nm) for 200 ms (onset) superimposed on a bright yellow background (574 nm), followed by an offset interval where only the background was active. Thus, predominantly S-cones were stimulated while L- and M-cone responses were suppressed by light adaptation. Times of stimulus onset to VEP onset-trough (N-peak time) and offset-peak (P-peak time) were analyzed after age-correction based on linear regression in the normal participants. Results The resulting BY-VEPs were quite similar to those obtained in the past with the optical bench: pattern-onset generated a negative deflection of the VEP, whereas the offset-response was dominated by a positive component. N-peak times were significantly increased in glaucoma patients (preperimetric 136.1 ± 10 ms, p < 0.05; perimetric 153.1 ± 17.8 ms, p < 0.001) compared with normal participants (123.6 ± 7.7 ms). Furthermore, they were significantly correlated with disease severity as determined by visual field losses retinal nerve fiber thinning (Spearman R = –0.7, p < 0.001). Conclusions Video projectors can be used to create optical stimuli with high temporal and spatial resolution, thus potentially enabling sophisticated electrophysiological measurements in clinical practice. BY-VEPs based on such a projector had a high diagnostic value for detection of early glaucoma. Registration of study Registration site: www.clinicaltrials.gov Trial registration number: NCT00494923.

Dopamine D1 and D4 receptors contribute to light adaptation in ON-sustained retinal ganglion cells

The adaptation of ganglion cells to increasing light levels is a crucial property of the retina. The retina must respond to light intensities that vary by 10-12 orders of magnitude, but the dynamic range of ganglion cell responses covers only ~3 orders of magnitude. Dopamine is a crucial neuromodulator for light adaptation and activates receptors in the D1 and D2 families. D1Rs are expressed on horizontal cells and some bipolar, amacrine and ganglion cells. In the D2 family D2Rs are expressed on dopaminergic amacrine cells and D4Rs are primarily expressed on photoreceptors. However, the roles of activating these receptors to modulate the synaptic properties of the inputs to ganglion cells are not yet clear. Here we used single cell retinal patch-clamp recordings from the mouse retina to determine how activating D1Rs and D4Rs changed the light-evoked and spontaneous excitatory inputs to ON-sustained (ON-s) ganglion cells. We found that both D1R and D4R activation decrease the light-evoked excitatory inputs to ON-s ganglion cells, but that only the sum of the peak response decrease due to activating the two receptors was similar to the effect of light adaptation to a rod-saturating background. The largest effects on spontaneous excitatory activity of both D1R and D4R agonists was on the frequency of events, suggesting that both D1Rs and D4Rs are acting upstream of the ganglion cells.

EML1 is essential for retinal photoreceptor localization and light detection

Calcium regulates the response sensitivity, kinetics and adaptation in photoreceptors. In striped bass cones, this calcium feedback includes direct modulation of the transduction cyclic nucleotide-gated (CNG) channels by the calcium-binding protein CNG-modulin. However, the possible role of EML1, the mammalian homolog of CNG-modulin, in modulating phototransduction in mammalian photoreceptors has not been examined. Here, we used mice expressing mutant Eml1 to investigate its role in the development and function of mouse photoreceptors using immunostaining, in-vivo and ex-vivo retinal recordings, and single-cell suction recordings. We found that the mutation of Eml1 causes significant changes in the mouse retinal structure characterized by mislocalization of rods and cones in the inner retina. Consistent with the fraction of mislocalized photoreceptors, rod and cone-driven retina responses were reduced in the mutants. However, the Eml1 mutation had no effect on the dark-adapted responses of rods in the outer nuclear layer. Notably, we observed no changes in the cone sensitivity in the Eml1 mutant animals, either in darkness or during light adaptation, ruling out a role for EML1 in modulating cone CNG channels. Together, our results suggest that EML1 plays an important role in retina development but does not modulate phototransduction in mammalian rods and cones.