Genetic Profile and Associated Characteristics of 150 Korean Patients with Retinitis Pigmentosa

Purpose. Retinitis pigmentosa (RP) shows great diversity between genotypes and phenotypes, and it is important to identify the causative genes. This study aimed to analyze the molecular profiles, associated ocular characteristics, and progression of RP in Korean patients. Methods. All the genetic variants in patients with RP, identified using targeted next-generation sequencing (NGS) with a panel of 88 RP-related genes between November 2018 and November 2019, were retrospectively reviewed. All the patients underwent comprehensive ophthalmological evaluations, and their clinical and family histories were recorded. The best-corrected visual acuity (BCVA) deterioration and photoreceptor disruption progression rates were determined based on the major causative mutational genes using nonlinear mixed models, and the differences among them were investigated using the interaction effect. Results. Among the 144 probands, 82 variants in 24 causative genes were identified in 77 families (53.5%). Most of the RP cases were associated with autosomal recessive variants (N = 64 (44.4%)), followed by autosomal dominant (N = 10 (6.9%)) and X-linked variants (N = 3 (2.1%)). The four most frequently affected genes were EYS (N = 15 (10.4%)), USH2A (N = 12 (8.3%)), PDE6B (N = 9 (6.3%)), and RP1 (N = 8 (5.6%)). Epiretinal membranes and cystoid macular edema were frequently noted in the patients with USH2A (75.0%) and PDE6B (50.0%) variants, respectively. During the follow-up period, the BCVA and photoreceptor disruption changes were significantly different among the patients carrying the four common causative genes ( P = 0.014 and 0.034, resp.). Patients with PDE6B variants showed faster BCVA changes (0.2 LogMAR/10 years), and those with USH2A variants showed the fastest ellipsoid zone disruptions (−170.4 µm/year). Conclusion. In conclusion, our genetic analysis using targeted NGS provides information about the prevalence of RP-associated mutations in Korean patients. Delineating clinical characteristics according to genetic variations may help clinicians identify subtype features and predict the clinical course of RP.

Increasing root penetration into a different environment is more important than improving rooting depth

Deep rooting is often thought as a promising phenotype for resource extraction, but on soils with constraints, desired rooting depth was rarely observed. We hypothesised that if the genetic effect on root growth and rooting depth were separated from other effects, the determinants of root growth and rooting depth could be quantified. The conventional core-breaking method was used to measure root growth of wheat at two sites in two successive years under rain fed conditions. The Bayesian hierarchical nonlinear mixed models (HNLMMs) were employed to estimate root distribution, heritability and rooting depth. We found that root penetration from the non-sodic top to the sodic subsoil was most critical in determining rooting depth. Our study indicates that focusing on root-soil interaction at the transition layer where soil constraints start to emerge would lead to a more effective solution to develop resilient roots. Our work not only serves as a guide for selecting genotypes in pot trials, but also provides a theoretical support to breed advance crops with better soil adaptation.

Selection of nonlinear mixed models for growth curves of dairy buffaloes (Bubalus bubalis)

The determination of livestock growth patterns is important for meat or milk production systems, and nonlinear models are used to summarize and interpret the information. The aim of this study was to more accurately estimate growth curve parameters in buffalo cows by evaluating and selecting nonlinear mixed models that employ different types of residuals and include or not contemporary groups (CG) as a covariate. Weight records from 720 animals obtained over a period of 60 months were used. The growth curves were fit using nonlinear mixed-effects models. The Bertalanffy, Gompertz and Logistic models were evaluated. Modelling residuals using four structures (constant, combined, exponential and proportional) and the inclusion or not of CG in the models were also evaluated. The Akaike information criterion (AIC) and Bayesian information criterion (BIC) were used to select the model. In addition to estimating the parameters of the nonlinear growth models and their correlations, the instantaneous growth rate and inflection point were obtained. The Bertalanffy model with a combined residual structure and CG exhibited the lowest AIC and BIC values. Asymptotic weight (A) estimates ranged from 621.8 to 742.1 kg, and the maturity rate (k) ranged from 0.068 to 0.115 kg/month. The correlation between A and k ranged from −0.32 to −0.82 among the models evaluated. The selection criteria indicated that the Bertalanffy model was the most suitable for growth curve analysis in buffaloes.

172 Standardized total tract digestible phosphorus requirement of 11- to 23-kg pigs fed diets containing phytase

The objective of this study was to determine the standardized total tract digestible phosphorus (STTD P) requirement of nursery pigs from 11 to 23 kg fed diets containing 1,000 phytase units (FYT). A total of 2,140 barrows and gilts (PIC 359×Camborough, initial BW 11.1 ± 0.24 kg) were used in a 21-d growth trial with 24 to 27 pigs per pen and 12 pens per treatment in a randomized complete block design. The 7 dietary treatments consisted of 0.30, 0.33, 0.38, 0.43, 0.48, 0.53, and 0.58% STTD P, which represented 90, 100, 115, 130, 145, 160 and 175%, respectively, of the NRC (2012) requirement estimate for STTD P for pigs weighing 11 to 23 kg. All diets contained 1,000 FYT of Ronozyme Hiphos 2500 (DSM Nutritional Products, Inc., Parsippany, NJ) with assumed release values of 0.15% available P and 0.132% STTD P. Treatments were achieved by increasing the amount of calcium carbonate and monocalcium phosphate at the expense of corn, while maintaining a similar 1.17:1 total Ca:total P ratio across treatments. Experimental data were analyzed with pen as the experimental unit, using generalized linear and nonlinear mixed models, which included quadratic polynomial, broken-line linear, and broken-line quadratic models. Increasing STTD P quadratically improved (P < 0.05) ADG and feed efficiency (G:F). Final BW and ADFI increased linearly (P < 0.05) up to the highest STTD P level. Income over feed cost improved quadratically (P < 0.05), with the highest income observed at 0.43% STTD P. The broken-line linear plateau was estimated at 0.40% STTD P for ADG and at 0.37% STTD P for G:F. In conclusion, the estimated STTD P requirement for nursery pigs from 11 to 23 kg fed diets containing 1,000 FYT were greater than NRC (2012) requirement estimates and ranged from 0.37 to 0.43% to optimize performance and economic return.