Natural selection and functional diversification of the epidermal growth factor receptorEGFR family in vertebrates

AbstractBackgroundGenes that have been subject to adaptive evolution can produce varying degrees of pathology or differing symptomatology. ErbB family receptor activation will initiate a number of downstream signaling pathways, such as mitogen-activated protein kinase (MAPK), activator of transcription (STAT), the modulation of calcium channels, and so on, all of which lead to aggressive tumor behavior. However, the evolutionary mechanisms operating in the retention of ErbB family genes and the changes in selection pressures are not clear.ResultsSixty-two full-length cDNA sequences from 27 vertebrate species were extracted from the UniProt protein database, NCBI's GenBank and the Ensembl database. The result of phylogenetic analysis showed that the four ErbB family members in vertebrates might be formed by gene duplication. In order to determine the mode of evolution in vertebrates, selection analysis and functional divergence analysis were combined to explain the relationship of the site-specific evolution and functional divergence in the vertebrate ErbB family. Our results indicate that the acceleration of asymmetric evolutionary rates and purifying selection together were the main force for the production of ErbBs, and positive selections were detected in the ErbB family.ConclusionAn evolutional phylogeny of 27 vertebrates was presented in our study; the tree showed that the genes have evolved through duplications followed by purifying selection, except for seven sites, which evolved by positive selection. There was one common site with positive selection and functional divergence. In the process of functional differentiation evolving through gene duplication, relaxed selection may play an important part

PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http://pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.National Natural Science Foundation of China [32022078]; National Key R&D Program of China [2022YFF1000900]; Local Innovative and Research Teams Project of Guangdong Province [2019BT02N630]; China Agriculture Research System [CARS-35]. Funding for open access charge: National Natural Science Foundation of China [32022078].info:eu-repo/semantics/publishedVersio

A compendium of genetic regulatory effects across pig tissues

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.</p

PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http://pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.National Natural Science Foundation of China [32022078]; National Key R&D Program of China [2022YFF1000900]; Local Innovative and Research Teams Project of Guangdong Province [2019BT02N630]; China Agriculture Research System [CARS-35]. Funding for open access charge: National Natural Science Foundation of China [32022078].Peer reviewe

Optimal trajectory planning of robot energy consumption based on improved sparrow search algorithm

In order to reduce the energy consumption of the welding robot and ensure the cooperative movement of the robot joints, a trajectory planning method with optimal energy consumption based on improved sparrow search algorithm is proposed. Firstly, the trajectory planning model with optimal energy consumption is established based on the joint torque and angular velocity of the robot. To make the velocity, acceleration and jerk of each joint of the robot be bounded and continuous, the joint space trajectory is constructed with seventh degree B-spline curve. The total energy consumption of the robot is calculated by combining kinematic and dynamic parameters. On the basis of improved sparrow search algorithm, the time series corresponding to the optimal energy consumption is solved by using elite reverse learning, non-dominated sorting and Gaussian-Cauchy variation strategy, and then the optimal continuous motion trajectory of energy consumption is planned. The simulation results show that the proposed method can not only achieve continuous smooth control objective, but also effectively reduce energy consumption

Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and Enzymes Involved in Triterpenoid Biosynthesis

G. pentaphyllum (Gynostemma pentaphyllum), a creeping herbaceous perennial with many important medicinal properties, is widely distributed in Asia. Gypenosides (triterpenoid saponins), the main effective components of G. pentaphyllum, are well studied. FPS (farnesyl pyrophosphate synthase), SS (squalene synthase), and SE (squalene epoxidase) are the main enzymes involved in the synthesis of triterpenoid saponins. Considering the important medicinal functions of G. pentaphyllum, it is necessary to investigate the transcriptomic information of G. pentaphyllum to facilitate future studies of transcriptional regulation. After sequencing G. pentaphyllum, we obtained 50,654,708 unigenes. Next, we used RPKM (reads per kilobases per million reads) to calculate expression of the unigenes and we performed comparison of our data to that contained in five common databases to annotate different aspects of the unigenes. Finally, we noticed that FPS, SS, and SE showed differential expression of enzymes in DESeq. Leaves showed the highest expression of FPS, SS, and SE relative to the other two tissues. Our research provides transcriptomic information of G. pentaphyllum in its natural environment and we found consistency in unigene expression, enzymes expression (FPS, SS, and SE), and the distribution of gypenosides content in G. pentaphyllum. Our results will enable future related studies of G. pentaphyllum

Genetic Algorithm-Optimized Extreme Learning Machine Model for Estimating Daily Reference Evapotranspiration in Southwest China

Reference evapotranspiration (ET0) is an essential component in hydrological and ecological processes. The Penman–Monteith (PM) model of Food and Agriculture Organization of the United Nations (FAO) model requires a number of meteorological parameters; it is urgent to develop high-precision and computationally efficient ET0 models with fewer parameter inputs. This study proposed the genetic algorithm (GA) to optimize extreme learning machine (ELM), and evaluated the performances of ELM, GA-ELM, and empirical models for estimating daily ET0 in Southwest China. Daily meteorological data including maximum temperature (Tmax), minimum temperature (Tmin), wind speed (u2), relative humidity (RH), net radiation (Rn), and global solar radiation (Rs) during 1992–2016 from meteorological stations were used for model training and testing. The results from the FAO-56 Penman–Monteith formula were used as a control group. The results showed that GA-ELM models (with R2 ranging 0.71–0.99, RMSE ranging 0.036–0.77 mm·d−1) outperformed the standalone ELM models (with R2 ranging 0.716–0.99, RMSE ranging 0.08–0.77 mm·d−1) during training and testing, both of which were superior to empirical models (with R2 ranging 0.36–0.91, RMSE ranging 0.69–2.64 mm·d−1). ET0 prediction accuracy varies with different input combination models. The machine learning models using Tmax, Tmin, u2, RH, and Rn/Rs (GA-ELM5/GA-ELM4 and ELM5/ELM4) obtained the best ET0 estimates, with R2 ranging 0.98–0.99, RMSE ranging 0.03–0.21 mm·d−1, followed by models with Tmax, Tmin, and Rn/Rs (GA-ELM3/GA-ELM2 and ELM3/ELM2) as inputs. The machine learning models involved with Rn outperformed those with Rs when the quantity of input parameters was the same. Overall, GA-ELM5 (Tmax, Tmin, u2, RH and Rn as inputs) outperformed the other models during training and testing, and was thus recommended for daily ET0 estimation. With the estimation accuracy, computational costs, and availability of input parameters accounted, GA-ELM2 (Tmax, Tmin, and Rs as inputs) was determined to be the most effective model for estimating daily ET0 with limited meteorological data in Southwest China

The Impact of Colonoscopy Quality Control Table on Adenoma Detection Rates

Objective. This study aims to investigate the effects of reporting colonoscopy findings and the regular review of outcomes on adenoma detection rates. Methods. Patients who underwent colonoscopy from August 2013 to February 2014 were selected as the intervention group. The preintervention group included patients who underwent colonoscopy from January 2013 to July 2013, in which the procedure sheet for this group of patients was not accomplished. The primary outcome was adenoma detection rate (ADR), and secondary outcomes included the success rate of intubation and withdrawal time. Results. This study included 2,467 cases: 1,302 cases in the intervention group and 1,165 cases in the preintervention group. There was no significant difference in demographic characteristics between the two groups. In the intervention group, withdrawal time of colonoscopy was longer (P<0.01), and the success rate of intubation (92.5% versus 89.1%, P<0.05) and detection rate of polyps (32.6% versus 27.6%, P<0.05) and adenomas (20.0% versus 16.1%, P<0.05) were higher. Significantly high detection rates for proximal adenomas, flat adenomas, and adenomas with a diameter <5 mm were observed in the intervention group (all P<0.01). Conclusion. The reporting and review of procedure details help to improve quality indicators of colonoscopy

Deficit drip irrigation improves kiwifruit quality and water productivity under rain-shelter cultivation in the humid area of South China

Comprehending crop responses to water deficit at different growth stages is crucial for developing effective irrigation strategies. Different water deficit treatments (WDTs) were applied to the kiwifruit vines to investigate the effect of water deficit during different growth stages on the fruit quality, yield, and water productivity (WP); subsequently, the technique for order preference by similarity to an ideal solution method (TOPSIS) was employed to determine optimal treatments for kiwifruit cultivation. A total of 17 irrigation treatments were applied, including one control treatment (CTL, full irrigation) and four WDTs (denoted as D15%, D25%, D35%, and D45% respectively) during the bud burst to leafing (I), flowering to fruit set (II), fruit expansion (III), and fruit maturation (IV) stages. Results showed that WDTs during I, II, III, and IV decreased evapotranspiration (ET) over the whole growth period of kiwifruit vines by 1.2–3.8, 1.5–4.4, 4.7–14.3, and 6.9–21.3% compared with CTL, respectively. WDTs during stages I and II increased fruit volume (Vf) and fruit weight (FW), while exhibiting no significant impact on yield, WP, and chemical quality of kiwifruit. WDTs during stage III improved fruit firmness (Fn), total soluble solids (TSS), and titratable acidity (TA); however, it also caused severe reduction in Vf, FW, yield, and WP. Appropriate WDTs during stage IV significantly improved Fn, TSS, TA, vitamin C (Vc), and WP without compromising Vf, FW, and yield of kiwifruit. The IV-D25% treatment was determined to be the optimal treatment for improving fruit quality and WP of kiwifruit while maintaining yield, which increased TSS, TA, Vc, and WP by 9.1, 6.1, 19.2, 4.6%, respectively; the combination of D25%, D25%, full irrigation, and D25% treatments during stages I, II, III, and IV should be a viable irrigation strategy to simultaneously achieve high yield, quality, and WP of kiwifruit

Method for Determining the Fracture Parameters of Fully Graded Dam Concrete

This paper describes a method for determining the initiation and unstable toughness of fully graded concrete of arbitrary specimen size. The method first predicts the initiation and peak loads of concrete specimens of any size, as well as crack length-to-height ratios based on the fracture test results of concrete specimens with limited sizes or crack length-to-height ratios. Then, combined with the fracture extreme theory, the fracture toughness of concrete with varying size or crack length-to-height ratios is determined. Finally, in order to verify the applicability of the method, it is used to calculate the fracture toughness of small aggregate concrete and fully graded concrete with different sizes or crack length-to-height ratios, and its prediction accuracy is evaluated through indices such as mean absolute percentage error, root mean square error and reliability index a15. The results show that the proposed method can meet the needs of practical engineering applications and can provide theoretical basis for the optimization of the fracture test method of fully graded concrete and the determination of fracture parameters in crack stability or propagation analysis