Hot spot prediction in protein-protein interactions by an ensemble system

© 2018 The Author(s). Background: Hot spot residues are functional sites in protein interaction interfaces. The identification of hot spot residues is time-consuming and laborious using experimental methods. In order to address the issue, many computational methods have been developed to predict hot spot residues. Moreover, most prediction methods are based on structural features, sequence characteristics, and/or other protein features. Results: This paper proposed an ensemble learning method to predict hot spot residues that only uses sequence features and the relative accessible surface area of amino acid sequences. In this work, a novel feature selection technique was developed, an auto-correlation function combined with a sliding window technique was applied to obtain the characteristics of amino acid residues in protein sequence, and an ensemble classifier with SVM and KNN base classifiers was built to achieve the best classification performance. Conclusion: The experimental results showed that our model yields the highest F1 score of 0.92 and an MCC value of 0.87 on ASEdb dataset. Compared with other machine learning methods, our model achieves a big improvement in hot spot prediction. Availability:http://deeplearner.ahu.edu.cn/web/HotspotEL.htm

Serum Metabolomic and Lipidomic Profiling Reveals the Signature for Postoperative Obesity among Adult-Onset Craniopharyngioma

Craniopharyngioma patients often suffer from a diminished quality of life after surgery, which is usually associated with metabolic disorders and hypothalamic obesity. However, the precise etiology of these conditions remains elusive. To identify the metabolic changes after surgery, we conducted a cross-sectional study using metabolomic and lipidomic analysis to profile metabolic alterations in adult-onset craniopharyngioma patients with postoperative obesity. A cohort of 120 craniopharyngioma patients who had undergone surgery were examined. Differential analyses, including clinical characteristics, serum metabolome, and lipidome, were conducted across distinct body mass index (BMI) groups. Our findings indicated no statistically significant differences in age, sex, and fasting blood glucose among postoperative craniopharyngioma patients when stratified by BMI. However, a noteworthy difference was observed in uric acid and blood lipid levels. Further investigation revealed that alterations in metabolites and lipids were evidently correlated with increased BMI, indicating that postoperative obesity of craniopharyngioma patients affected their whole-body metabolism. Additionally, the multi-omics analysis identified specific metabolites and lipids, including uric acid and DG(18:2/20:4), as contributors to the metabolic disorders associated with postoperative obesity of craniopharyngioma patients. This work provides valuable insight into the involvement of metabolites and lipids in metabolic disorders subsequent to craniopharyngioma surgery

GL9 from Oryza glumaepatula controls grain size and chalkiness in rice

Grain size is a key factor influencing grain yield and appearance quality in rice. We identified twelve quantitative trait loci (QTL) for grain length (GL), nine for grain width (GW), and nine for 1000-kernel weight (TKW) using GLU-SSSLs, which are single-segment substitution lines with Oryza glumaepatula as donor parent and Huajingxian 74 (HJX74) as recipient parent. Among the QTL, qGL1-2, qGL1-4, qGL9-2, qGW2-2, qGW9-1 and qTKW9-2 contributed to high grain yield. GL9 was identified as a candidate gene for qGL9-2 by map-based cloning and sequencing, and is a novel allele of GS9. The kernel of NIL-gl9 was slenderer and longer than that of HJX74, and the TKW and grain yield per plant of NIL-gl9 were higher than those of HJX74. The proportion of grain chalkiness of NIL-gl9 was much lower than that of HJX74. Thus, gl9 increased grain yield and appearance quality simultaneously. Three pyramid lines, NIL-gs3/gl9, NIL-GW7/gl9 and NIL-gw8/gl9, were developed and the kernel of each was longer than that of the corresponding recipient parent lines. The gl9 allele may be beneficial for breeding rice varieties with high grain yield and good appearance quality

Additional file 1 of Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

Supplementary Material 1: Fig. S1 QTLs for PGC and their positions in the substitution segments in SSSLs. Fig. S2 Development of pyramiding lines with different QTL combinations for PGC. Fig. S3 QTLs for PGC and their substitution segments in 2QLs. Fig. S4 QTLs for PGC and their substitution segments in 3QLs. Fig. S5 QTLs for PGC and their substitution segments in 4QL

Additional file 2 of Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

Supplementary Material 2: Table S1 QTLs for PGC and their position in the substitution segments in SSSLs. Table S2 Substitution segments carrying QTLs for PGC in pyramiding lines. Table S3 The phenotypes of rice chalkiness in 1QLs to 4QLs. Table S4 Additive effects of QTL combinations on PGC in 1QLs to 4QLs. Table S5 Epistatic effects of QTL combinations on PGC in pyramiding lines. Table S6 Average temperatures of 30 days after rice flowering in different cropping season

Table_1_Grain shape is a factor affecting the stigma exsertion rate in rice.xlsx

Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines carrying gs3 and gs3/gw8 showed higher SER. Single-segment substitution lines (SSSLs) carrying gs3, gw5, GW7 or gw8 genes for grain shape and gene pyramiding lines were used to reveal the relationship between grain shape and SER. The results showed that the grain shape regulatory genes had pleiotropic effects on SER. The SERs were affected by grain shapes including grain length, grain width and the ratio of length to width (RLW) not only in low SER background, but also in high SER background. The coefficients of determination (R2) between grain length and SER, grain width and SER, and grain RLW and SER were 0.78, 0.72, and 0.91 respectively. The grain RLW was the most important parameter affecting SER, and a larger grain RLW was beneficial to stigma exsertion. The pyramiding line PL-gs3/GW7/gw8 showed the largest grain RLW and the highest SER, which will be a fine breeding resource. Further research showed that the grain shape regulatory genes had pleiotropic effects on stigma shape, although the R2 values between grain shape and stigma shape, and stigma shape and SER were lower. Our results demonstrate that grain shape is a factor affecting SER in rice, in part by affecting stigma shape. This finding will be helpful for breeding MSLs with high SER in hybrid rice.</p

DataSheet_1_Grain shape is a factor affecting the stigma exsertion rate in rice.docx

Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines carrying gs3 and gs3/gw8 showed higher SER. Single-segment substitution lines (SSSLs) carrying gs3, gw5, GW7 or gw8 genes for grain shape and gene pyramiding lines were used to reveal the relationship between grain shape and SER. The results showed that the grain shape regulatory genes had pleiotropic effects on SER. The SERs were affected by grain shapes including grain length, grain width and the ratio of length to width (RLW) not only in low SER background, but also in high SER background. The coefficients of determination (R2) between grain length and SER, grain width and SER, and grain RLW and SER were 0.78, 0.72, and 0.91 respectively. The grain RLW was the most important parameter affecting SER, and a larger grain RLW was beneficial to stigma exsertion. The pyramiding line PL-gs3/GW7/gw8 showed the largest grain RLW and the highest SER, which will be a fine breeding resource. Further research showed that the grain shape regulatory genes had pleiotropic effects on stigma shape, although the R2 values between grain shape and stigma shape, and stigma shape and SER were lower. Our results demonstrate that grain shape is a factor affecting SER in rice, in part by affecting stigma shape. This finding will be helpful for breeding MSLs with high SER in hybrid rice.</p