Advances in alternative splicing identification: deep learning and pantranscriptome

In plants, alternative splicing is a crucial mechanism for regulating gene expression at the post-transcriptional level, which leads to diverse proteins by generating multiple mature mRNA isoforms and diversify the gene regulation. Due to the complexity and variability of this process, accurate identification of splicing events is a vital step in studying alternative splicing. This article presents the application of alternative splicing algorithms with or without reference genomes in plants, as well as the integration of advanced deep learning techniques for improved detection accuracy. In addition, we also discuss alternative splicing studies in the pan-genomic background and the usefulness of integrated strategies for fully profiling alternative splicing

Tooth loss, denture use, and all-cause and cause-specific mortality in older adults: a community cohort study

ObjectivesThe available evidence on the connections between tooth loss, denture use, and mortality from all causes or specific causes among older adults is inconclusive. Therefore, we aimed to investigate the association between tooth loss, denture use, and all-cause and cause-specific mortality in older adults.MethodsA cohort of 5,403 participants aged 65 and older were recruited in the 2014 Chinese Longitudinal Healthy Longevity Survey wave and followed up in the 2018 wave. Cox proportional hazard models were used to examine the association between the number of natural teeth, denture use, and all-cause and cause-specific mortality.ResultsDuring a mean (SD) follow-up of 3.1  years (1.3), 2,126 deaths (39.3%) occurred. Individuals with 0 and 1–9 teeth had higher mortality due to all-cause, cardiovascular disease (CVD), cancer, and other causes (all p-trend <0.05) than those with 20+ teeth. At the same time, no association was found with respiratory disease mortality. Participants who used dentures had lower mortality due to all causes [hazard ratios (HR) 0.79, 95% confidence intervals (CI) 0.71–0.88], CVD (HR 0.80, 95% CI 0.64–1.00), respiratory disease (HR 0.66, 95% CI 0.48–0.92), and other causes (HR 0.77, 95% CI 0.68–0.88) than those without dentures. Joint analysis revealed that older adults with fewer natural teeth and no dentures had higher mortality. Additionally, interaction analyses showed that the effects of the number of natural teeth on all-cause mortality were more pronounced in older adults aged <80  years (p-value for interaction = 0.03).ConclusionHaving fewer natural teeth, particularly less than 10 teeth, is linked to an increased risk of mortality from all causes, including CVD, cancer, and other causes, but not respiratory disease. The use of dentures would mitigate the adverse impact of tooth loss on all-cause and some cause-specific mortality

Endocytosis of the seven-transmembrane RGS1 protein activates G-protein-coupled signalling in Arabidopsis

Signal transduction typically begins by ligand-dependent activation of a concomitant partner which is otherwise in its resting state. However, in cases where signal activation is constitutive by default, the mechanism of regulation is unknown. The Arabidopsis thaliana heterotrimeric Gα protein self-activates without accessory proteins, and is kept in its resting state by the negative regulator, AtRGS1 (Regulator of G protein Signaling 1), which is the prototype of a seven transmembrane receptor fused with an RGS domain. Endocytosis of AtRGS1 by ligand-dependent endocytosis physically uncouples the GTPase accelerating activity of AtRGS1 from the Gα protein, permitting sustained activation. Phosphorylation of AtRGS1 by AtWNK8 kinase causes AtRGS1 endocytosis, required both for G protein-mediated sugar signaling and cell proliferation. In animals, receptor endocytosis results in signal desensitization, whereas in plants, endocytosis results in signal activation. These findings reveal how different organisms rearrange a regulatory system to result in opposite outcomes using similar phosphorylation-dependent endocytosis

Simulation Studies for the First Pathfinder of the CATCH Space Mission

The Chasing All Transients Constellation Hunters (CATCH) space mission is an intelligent constellation consisting of 126 micro-satellites in three types (A, B, and C), designed for X-ray observation with the objective of studying the dynamic universe. Currently, we are actively developing the first Pathfinder (CATCH-1) for the CATCH mission, specifically for type-A satellites. CATCH-1 is equipped with Micro Pore Optics (MPO) and a 4-pixel Silicon Drift Detector (SDD) array. To assess its scientific performance, including the effective area of the optical system, on-orbit background, and telescope sensitivity, we employ the Monte Carlo software Geant4 for simulation in this study. The MPO optics exhibit an effective area of $41$ cm$^2$ at the focal spot for 1 keV X-rays, while the entire telescope system achieves an effective area of $29$ cm$^2$ at 1 keV when taking into account the SDD detector's detection efficiency. The primary contribution to the background is found to be from the Cosmic X-ray Background. Assuming a 625 km orbit with an inclination of $29^\circ$, the total background for CATCH-1 is estimated to be $8.13\times10^{-2}$ counts s$^{-1}$ in the energy range of 0.5--4 keV. Based on the background within the central detector and assuming a Crab-like source spectrum, the estimated ideal sensitivity could achieve $1.9\times10^{-12}$ erg cm$^{-2}$ s$^{-1}$ for an exposure of 10$^4$ s in the energy band of 0.5--4 keV. Furthermore, after simulating the background caused by low-energy charged particles near the geomagnetic equator, we have determined that there is no need to install a magnetic deflector

Identification of a Functional Genetic Variant at 16q12.1 for Breast Cancer Risk: Results from the Asia Breast Cancer Consortium

Genetic factors play an important role in the etiology of breast cancer. We carried out a multi-stage genome-wide association (GWA) study in over 28,000 cases and controls recruited from 12 studies conducted in Asian and European American women to identify genetic susceptibility loci for breast cancer. After analyzing 684,457 SNPs in 2,073 cases and 2,084 controls in Chinese women, we evaluated 53 SNPs for fast-track replication in an independent set of 4,425 cases and 1,915 controls of Chinese origin. Four replicated SNPs were further investigated in an independent set of 6,173 cases and 6,340 controls from seven other studies conducted in Asian women. SNP rs4784227 was consistently associated with breast cancer risk across all studies with adjusted odds ratios (95% confidence intervals) of 1.25 (1.20−1.31) per allele (P = 3.2×10−25) in the pooled analysis of samples from all Asian samples. This SNP was also associated with breast cancer risk among European Americans (per allele OR  = 1.19, 95% CI  = 1.09−1.31, P = 1.3×10−4, 2,797 cases and 2,662 controls). SNP rs4784227 is located at 16q12.1, a region identified previously for breast cancer risk among Europeans. The association of this SNP with breast cancer risk remained highly statistically significant in Asians after adjusting for previously-reported SNPs in this region. In vitro experiments using both luciferase reporter and electrophoretic mobility shift assays demonstrated functional significance of this SNP. These results provide strong evidence implicating rs4784227 as a functional causal variant for breast cancer in the locus 16q12.1 and demonstrate the utility of conducting genetic association studies in populations with different genetic architectures

FTO genetic variants, dietary intake and body mass index: insights from 177 330 individuals

FTO is the strongest known genetic susceptibility locus for obesity. Experimental studies in animals suggest the potential roles of FTO in regulating food intake. The interactive relation among FTO variants, dietary intake and body mass index (BMI) is complex and results from previous often small-scale studies in humans are highly inconsistent. We performed large-scale analyses based on data from 177 330 adults (154 439 Whites, 5776 African Americans and 17 115 Asians) from 40 studies to examine: (i) the association between the FTO-rs9939609 variant (or a proxy single-nucleotide polymorphism) and total energy and macronutrient intake and (ii) the interaction between the FTO variant and dietary intake on BMI. The minor allele (A-allele) of the FTO-rs9939609 variant was associated with higher BMI in Whites (effect per allele = 0.34 [0.31, 0.37] kg/m2, P = 1.9 × 10−105), and all participants (0.30 [0.30, 0.35] kg/m2, P = 3.6 × 10−107). The BMI-increasing allele of the FTO variant showed a significant association with higher dietary protein intake (effect per allele = 0.08 [0.06, 0.10] %, P = 2.4 × 10−16), and relative weak associations with lower total energy intake (−6.4 [−10.1, −2.6] kcal/day, P = 0.001) and lower dietary carbohydrate intake (−0.07 [−0.11, −0.02] %, P = 0.004). The associations with protein (P = 7.5 × 10−9) and total energy (P = 0.002) were attenuated but remained significant after adjustment for BMI. We did not find significant interactions between the FTO variant and dietary intake of total energy, protein, carbohydrate or fat on BMI. Our findings suggest a positive association between the BMI-increasing allele of FTO variant and higher dietary protein intake and offer insight into potential link between FTO, dietary protein intake and adiposit