Integrating Bioinformatics and Machine Learning for Genomic Prediction in Chickens.

Genomic prediction plays an increasingly important role in modern animal breeding, with predictive accuracy being a crucial aspect. The classical linear mixed model is gradually unable to accommodate the growing number of target traits and the increasingly intricate genetic regulatory patterns. Hence, novel approaches are necessary for future genomic prediction. In this study, we used an illumina 50K SNP chip to genotype 4190 egg-type female Rhode Island Red chickens. Machine learning (ML) and classical bioinformatics methods were integrated to fit genotypes with 10 economic traits in chickens. We evaluated the effectiveness of ML methods using Pearson correlation coefficients and the RMSE between predicted and actual phenotypic values and compared them with rrBLUP and BayesA. Our results indicated that ML algorithms exhibit significantly superior performance to rrBLUP and BayesA in predicting body weight and eggshell strength traits. Conversely, rrBLUP and BayesA demonstrated 2-58% higher predictive accuracy in predicting egg numbers. Additionally, the incorporation of suggestively significant SNPs obtained through the GWAS into the ML models resulted in an increase in the predictive accuracy of 0.1-27% across nearly all traits. These findings suggest the potential of combining classical bioinformatics methods with ML techniques to improve genomic prediction in the future.

Genetic improvement of duration of fertility in chickens and its commercial application for extending insemination intervals.

The growth rate of chickens has made remarkable progress in recent decades through continuous breeding efforts. However, this advancement has also led to a decline in fertility among commercially bred chickens. Therefore, it is crucial to understand and improve factors that influence fertility to ensure the continued success of the industry. Here, we conduct a 3-generation selection experiment within 2 purebred female lines, with the aim of increasing the duration of fertility (DF). Duration of fertility refers to the length of time hens remain capable of producing fertilized eggs and is a crucial factor that directly impacts chick output. The results showed that significant genetic progress was achieved in embryo survival rates and the fertility duration day during both the peak and late laying periods. Moreover, after 3 generations of selective breeding, the disparities in embryo survival and chick health rates from setting eggs between 8-d and 5-d insemination intervals in the grandparent stock were significantly reduced. The rates decreased from 1.83% and 2.39 to 0.72% and 0.33%, respectively. Surprisingly, the hatching performances of hens with an 8-d interval were comparable to those hens that had not undergone genetic selection for DF and had a 5-d interval. We further discussed the possibility of extending the insemination interval to 8 d in parent stock for commercial practices. The parental populations exhibited remarkable performance in terms of percentages of embryo survival and healthy chicks from the setting eggs, with rates exceeding 94 and 90%, respectively. Thus, it can be inferred that an extended insemination interval is feasible by genetic selection for DF. These findings will provide valuable insights into the efficacy of genetic selection in enhancing DF and its practical application in commercial breeding programs.

Effect of a modern stroke unit combined with recombinant human tissue-type plasminogen activator intravenous thrombolysis on ischemic cerebral infarction and its influence on limb motor function and activity of daily living.

OBJECTIVE: To observe the effect of a modern stroke unit combined with recombinant human tissue-type plasminogen activator (rt-PA) intravenous thrombolysis on ischemic cerebral infarction and its impact on limb motor function and activity of daily living. METHODS: In this prospective study, 82 patients with ischemic cerebral infarction who received treatment in our hospital were divided into two groups (41 cases in each group) according to the principle of randomized control. In the control group, patients received rt-PA intravenous thrombolysis. In the study group, patients received the modern stroke unit care combined with rt-PA intravenous thrombolysis. Before and after treatment, the clinical treatment efficacy, changes of serum inflammatory cytokines (hypersensitive C-reactive protein (hs-CRP), interleukin-6 (IL-6)), nerve factors (NSE, S100ß), nerve function (neurologic impairment score (NIHSS)), limb motor function (Fugl-Meyer scale score (FMA)) and activity of daily living (Barthel Index score) and adverse reactions were compared between the two groups. RESULTS: The total effective rate in the study group (92.68%) was higher than that in the control group (73.17%, P<0.01). Compared with those before treatment, the scores of NIHSS, FMA and Barthel indexes, and the levels of serum hs-CRP, IL-6, NSE and S100ß were improved in both groups after treatment, and the improvement in the study group was better than that in the control group (all P<0.001). There was no statistically significant difference in the incidence of adverse reactions between the two groups (9.76% vs. 12.20%, P>0.05). CONCLUSION: A modern stroke unit combined with rt-PA intravenous thrombolysis can effectively improve the clinical treatment efficacy, ameliorate the neurological function and limb motor function, reduce inflammatory reactions, promote the recovery of neurological function, and enhance the activity of daily living in the treatment of patients with ischemic cerebral infarction. Therefore, it is safe and worthy of further promotion.

Naringenin alleviates cognition deficits in high-fat diet-fed SAMP8 mice.

Naringenin is a natural dihydro flavonoid that is abundant in grapefruit. Previous studies suggested the cognition protective effect of naringenin in various cognitive deficits models, such as type 2 diabetic rat model and chemicals (e.g., lipopolysaccharide, scopolamine) treated rodents. However, the effects of naringenin on aging animals and the potential mechanisms are still unclear. In this study, we investigated the influence of naringenin administration on learning deficits in aging mice. High-fat diet-fed SAMP8 mice were employed as an age-related model of Alzheimer's disease. Dietary administration of 0.2% naringenin for 12 weeks significantly improved the spatial learning and memory performance of the high-fat diet-fed SAMP8 mice in both Barnes Maze test and Morris Water Maze test. Further mechanism research indicated that naringenin reduced Aß production, tau-hyperphosphorylation, oxidative stress, and neuroinflammation in the brain. This research provides further evidence for the treatment effect of naringenin on Alzheimer's disease. PRACTICAL APPLICATIONS: Naringenin, also known as 4',5,7-thrihydroxyflflavanone, is a natural dihydro flavonoid that is abundant in grapefruit and other citrus fruits. The current study first demonstrated the improvement effect of naringenin on cognition deficits in HFD-fed SAMP8 mice, an aging mouse model. Potential mechanisms were also systematically explained by exploring the amyloid-ß (Aß) accumulation, tau hyperphosphorylation, oxidative stress, and neuroinflammation in the brain of mice. This study provides further evidence for the utilization of naringenin as an effective treatment agent for Alzheimer's disease.