Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales.

Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the γ-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution.

Influencing factors for peripheral and posterior lesions in mild non-proliferative diabetic retinopathy-the Kailuan Eye Study.

AIM: To explore the influencing factors of diabetes type 2 patients with mild non-proliferative diabetic retinopathy (NPDR) in the Kailuan area of Tangshan, Hebei Province, China. METHODS: In this non-interventional, retrospective study, 683 patients with type 2 diabetes were included in the Kailuan Diabetic Retinopathy Study involving participants with diabetes in the community-based longitudinal Kailuan Study. Based on the undilated ultra-wide field (200°; UWF) images and partial dilated digital fundus images, the diabetic retinopathy (DR) of the surveyed population was graded. Interobserver agreement was estimated by using Cohen's Kappa statistics. The main outcome indicators included gender, age, weight, height, body mass index, blood pressure, circumferences of neck, waist and hip, current smoking, levels of fasting plasma glucose (FPG), hypersensitive C-reactive protein, creatinine, and cholesterol, etc. According to different lesions' locations of patients with mild NPDR, logistic regression models were used to estimate the odds ratios (ORs) and their 95%CIs of each risk factor. RESULTS: The study group of 683 patients included 570 males and 113 females. The mean age of the patients was 62.18±9.41y. Compared with dilated fundus examinations, there was fair agreement with the level of DR identified on UWF images in 63.91% of eyes (k=0.369, 95%CI, 0.00-0.00). Detected by UWF images, there were 98 patients with mild NPDR having peripheral retinal lesions, 35 patients with mild NPDR having posterior lesions, 44 patients with mild NPDR whose lesions were detected both in and out the standard two fields area, and 336 patients with non obvious DR. Parameters that conferred a statistically significant increased risks for mild NPDR with having peripheral retinal lesions were neck circumstance (OR, 1.124; 95%CI, 1.044-1.211), and with posterior lesions were FPG (OR, 1.052; 95%CI, 1.007-1.099). CONCLUSION: UWF is an effectiveness means of DR screening. Moreover, it is necessary to evaluate peripheral diabetic retinal lesions which can help to estimate the severity of DR. The phenomenon that nonuniform and inhomogeneous distribution of DR lesions has been found. And the influencing factors in mild NPDR are differing by different lesions' locations.

Ocular Axial Length and Diabetic Retinopathy: The Kailuan Eye Study.

Purpose: To examine the role of ocular axial length as an ocular parameter for the prevalence and severity of diabetic retinopathy (DR). Methods: The cross-sectional Kailuan Diabetic Retinopathy Study included patients with diabetes who participated in the community-based longitudinal Kailuan Study and who had undergone ocular fundus photography. The fundus photographs were graded using the Early Treatment of Diabetic Retinopathy Study criteria. Results: The study included 1096 patients with diabetes (mean age: 60.8 ± 9.4 years; axial length: 23.37 ± 0.92 mm). In binary regression analysis, a higher DR prevalence was associated with shorter axial length (P = 0.007; odds ratio [OR]: 0.81; 95% confidence interval [CI]: 0.70, 0.95) after adjusting for longer known duration of diabetes (P = 0.02; OR: 1.13; 95%CI: 1.02, 1.24) and higher fasting blood glucose concentration (P < 0.001; OR: 1.38; 95%CI: 1.26, 1.52). A more severe DR stage was associated (regression coefficient r: 0.46) with shorter ocular axial length (P = 0.047; standardized regression coefficient ß: -0.06) after adjusting for higher fasting blood glucose (P < 0.001; ß: 0.41) and longer known duration of diabetes (P = 0.045; ß: 0.07). Longer axial length was associated with a lower DR prevalence (P = 0.003; ß: -0.10) after adjusting for younger age (P < 0.001), male sex (P < 0.001), higher body mass index (P = 0.016), and lower fasting blood glucose concentration (P = 0.036). Conclusions: After adjusting for systemic risk factors, DR prevalence decreased by 19% (95%CI: 5, 30) for each millimeter increase in axial length. With longer axial length being a surrogate for axial myopia, the marked increase in myopia prevalence worldwide may lead to a relative decrease in the prevalence and incidence of DR in future.

[One-hour post-load plasma glucose: a better indicator of glucose metabolism for obstructive sleep apnea?]

OBJECTIVE: To assess the value of blood glucose at different time points in oral glucose tolerance test (OGTT), particularly one?hour post load plasma glucose (1 hPG), in evaluating glucose metabolism in adult patients with obstructive sleep apnea (OSA). METHODS: Eighty nine adultswith newly diagnosed OSA were analyzed retrospectively for sleep architecture assessed using polysomnography and glucose metabolism assessed by OGTT at different time points (0, 30, 60, 120, and 180 min). Pearson's correlatives and multiple linear regression models were established to investigate the correlations between glucose metabolism and other indices including sleep architecture, apnea hypopnea index (AHI), mean and lowest oxygen saturation (MSO2 and LSO2) and obesity measurements. RESULTS: The majority (67.4%) of the patients had abnormal 1 hPG, and 41.6% had abnormal 2 hPG. 1 hPG was positively correlated with neck circumference (r=0.245), abdomen circumference (r=0.231), systolic blood pressure (r=0.213), diastolic blood pressure (r=0.276) and AHI (r=0.324), and was negatively associated with MSO2 (r=-0.341) and LSO2 (r=-0.387) (all P<0.05). After controlling for age, BMI, neck and abdomen circumferences, 1 hPG was found to inversely correlated with MSO2 (r=-0.253, P=0.032) and LSO2 (r=-0.311, P=0.008). In non-obese OSA subgroup, 1 hPG was significantly associated with OSA-related indices, and regression models showed that LSO2 and N2 were the two most important contributors to 1 hPG (adjusted R2=0.349, P<0.001); plasma glucose at other time points did not show such correlations. CONCLUSIONS: 1 hPG abnormality occurs earlier than 2 hPG in OSA patients. 1 hPG is significantly associated with OSA independent of obesity and may serve as a better index for measuring OSA-related glucose disorder.

iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity.

Lysine succinylation in protein is one type of post-translational modifications (PTMs). Succinylation is associated with some diseases and succinylated sites data just has been found in recent years in experiments. It is highly desired to develop computational methods to identify the candidate proteins and their sites. In view of this, a new predictor called iSuc-PseAAC was proposed by incorporating the peptide position-specific propensity into the general form of pseudo amino acid composition. The accuracy is 79.94%, sensitivity 51.07%, specificity 89.42% and MCC 0.431 in leave-one-out cross validation with support vector machine algorithm. It demonstrated by rigorous leave-one-out on stringent benchmark dataset that the new predictor is quite promising and may become a useful high throughput tool in this area. Meanwhile a user-friendly web-server for iSuc-PseAAC is accessible at http://app.aporc.org/iSuc-PseAAC/. Users can easily obtain their desired results without the need to understand the complicated mathematical equations presented in this paper just for its integrity.