The E3 ubiquitin ligase c-IAP1 regulates PCSK9-mediated LDLR degradation: Linking the TNF-α pathway to cholesterol uptake

Proprotein convertase subtilisin/kexin type 9 (PCSK9), in addition to LDLR (low-density lipoprotein receptor) and APOB (apolipoprotein B), is one of three loci implicated in autosomal dominant hypercholesterolaemia (ADH)^1^. A number of PCSK9 gain-of-function mutations and loss-of-function mutations have been identified from families afflicted with ADH with hypercholesterolaemia or hypocholesterolaemia, respectively^1-4^. In humans, the main function of PCSK9 appears to be the post-transcriptional regulation of the number of cell-surface LDL receptors^5-7^. To date, only LDLR and its closest family members VLDLR and ApoER2 have been shown to bind with PCSK9^8,9^. To find new binding partners for PCSK9, we used a shotgun proteomic method to analyse the protein complex pulled down by immunoprecipitation against FLAG-tagged PCSK9 protein. Among 22 potential novel binding proteins identified, we found that the cellular inhibitor of apoptosis protein 1 (c-IAP1^10^) and the TNF receptor-associated factor 2 (TRAF2^11^) complex are regulated differently in different dominant PCSK9 mutations that occur naturally. Further immunoprecipitation analysis showed that c-IAP1 is a direct binding partner for PCSK9. One of the "gain-of-function" mutants, PCSK9-S127R, which has impaired autocatalytic activity, is defective in binding to c-IAP1. The other dominant mutation, PCSK9-D374Y^12^, which is 10-fold more potent in degrading the LDLR protein than wild-type PCSK9, can be significantly ubiquitinated by c-IAP1 in vitro. The ubiquitinated PCSK9-D374Y is unable to degrade LDLR, which is its main cause of hypercholesterolaemia in patients. These results indicate that there is a novel cholesterol uptake regulation pathway linking PCSK9/LDLR to the E3 ubiquitin ligase c-IAP1 in a TNF-[alpha] response pathway. This highlights the possibility of developing new treatments for human cardiovascular diseases through ubiquitin ligase-mediated ubiquitination of target proteins in cholesterol metabolism

Reverse Engineering of Biological Systems

Gene regulatory network (GRN) consists of a set of genes and regulatory relationships between the genes. As outputs of the GRN, gene expression data contain important information that can be used to reconstruct the GRN to a certain degree. However, the reverse engineer of GRNs from gene expression data is a challenging problem in systems biology. Conventional methods fail in inferring GRNs from gene expression data because of the relative less number of observations compared with the large number of the genes. The inherent noises in the data make the inference accuracy relatively low and the combinatorial explosion nature of the problem makes the inference task extremely difficult. This study aims at reconstructing the GRNs from time-course gene expression data based on GRN models using system identification and parameter estimation methods. The main content consists of three parts: (1) a review of the methods for reverse engineering of GRNs, (2) reverse engineering of GRNs based on linear models and (3) reverse engineering of GRNs based on a nonlinear model, specifically S-systems. In the first part, after the necessary background and challenges of the problem are introduced, various methods for the inference of GRNs are comprehensively reviewed from two aspects: models and inference algorithms. The advantages and disadvantages of each method are discussed. The second part focus on inferring GRNs from time-course gene expression data based on linear models. First, the statistical properties of two sparse penalties, adaptive LASSO and SCAD, with an autoregressive model are studied. It shows that the proposed methods using these two penalties can asymptotically reconstruct the underlying networks. This provides a solid foundation for these methods and their extensions. Second, the integration of multiple datasets should be able to improve the accuracy of the GRN inference. A novel method, Huber group LASSO, is developed to infer GRNs from multiple time-course data, which is also robust to large noises and outliers that the data may contain. An efficient algorithm is also developed and its convergence analysis is provided. The third part can be further divided into two phases: estimating the parameters of S-systems with system structure known and inferring the S-systems without knowing the system structure. Two methods, alternating weighted least squares (AWLS) and auxiliary function guided coordinate descent (AFGCD), have been developed to estimate the parameters of S-systems from time-course data. AWLS takes advantage of the special structure of S-systems and significantly outperforms one existing method, alternating regression (AR). AFGCD uses the auxiliary function and coordinate descent techniques to get the smart and efficient iteration formula and its convergence is theoretically guaranteed. Without knowing the system structure, taking advantage of the special structure of the S-system model, a novel method, pruning separable parameter estimation algorithm (PSPEA) is developed to locally infer the S-systems. PSPEA is then combined with continuous genetic algorithm (CGA) to form a hybrid algorithm which can globally reconstruct the S-systems

Parameter sensitivity and economic analyses of an interchange-fracture enhanced geothermal system

Previous research has shown that interchange-fracture enhanced geothermal systems show desirable heat extraction performance. However, their parameter sensitivity has not been systematically investigated. In this study, a three-dimensional, unsteady flow and heat transfer model for an enhanced geothermal system with an interchange-fracture structure was established. The influences of pivotal parameters, including stimulated reservoir volume permeability, fracture spacing, fracture aperture, and injection flow rate on the thermal extraction performance of the interchange-fracture enhanced geothermal system were systematically researched. In addition, the economics of this system were evaluated. The results show that the heat extraction performance of the interchange-fracture system is significantly affected by a change of stimulated reservoir volume permeability and injection flow rate. Increasing permeability reduces electricity costs and improves economic income, while increasing the injection flow rate increases output power but hinders the long-term running stability of the system. Our research provides guidance for the optimal design of an interchange-fracture enhanced geothermal system.Cited as: Yu, G., Liu, C., Zhang, L., Fang, L. Parameter sensitivity and economic analyses of an interchange-fracture enhanced geothermal system. Advances in Geo-Energy Research, 2021, 5(2): 166-180, doi: 10.46690/ager.2021.02.0

Long terminal repeat retrotransposons of Oryza sativa

BACKGROUND: Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes. RESULTS: Using a new data-mining program, LTR_STRUC, (LTR retrotransposon structure program), we have mined the GenBank rice (Oryza sativa) database as well as the more extensive (259 Mb) Monsanto rice dataset for LTR retrotransposons. Almost two-thirds (37) of the 59 families identified consist of copia-like elements, but gypsy-like elements outnumber copia-like elements by a ratio of approximately 2:1. At least 17% of the rice genome consists of LTR retrotransposons. In addition to the ubiquitous gypsy- and copia-like classes of LTR retrotransposons, the rice genome contains at least two novel families of unusually small, non-coding (non-autonomous) LTR retrotransposons. CONCLUSIONS: Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred over the evolutionary history of rice LTR retrotransposons. Like LTR retrotransposons in other species with relatively small genomes, many rice LTR retrotransposons are relatively young, indicating a high rate of turnover

Understanding the Factors That Control theFormation and Morphology of Zn5(OH)8(NO3)2⋅2H2Othrough Hydrothermal Route

The influence of the choice of ethanol-water volume ratio, concentration of zinc salt, and ZnO buffer layer on the formation andmorphology of Zn5(OH)8(NO3)2⋅2H2O grown from the hydrothermal route was systematically discussed. Experimental resultssuggested that Zn5(OH)8(NO3)2⋅2H2O rectangle sheets and Zn5(OH)8(NO3)2⋅2H2O upright-standing plates were obtained bylimiting ethanol-water volume ratio. The concentration of zinc salt was crucial for getting phase-pure Zn5(OH)8(NO3)2⋅2H2O. Thepresence of ZnO buffer layer could lead to the that chemical composition of product grown on the substrate was totally differentfrom the product grown in the solution. Possible formation mechanism of Zn5(OH)8(NO3)2⋅2H2O was also studied. Ramanspectrum of Zn5(OH)8(NO3)2⋅2H2O displays a complex behavior with four modes, which can be assigned to the vibrationalmodes of Zn–H–O, Zn–O, H2O-nitrate, and nitrate. Porously ZnO rectangle sheets were obtained by thermal treatment ofZn5(OH)8(NO3)2⋅2H2O rectangle sheets

Genomic imprinting defect in Zfp57 mutant iPS cell lines

AbstractZFP57 maintains genomic imprinting in mouse embryos and ES cells. To test its roles during iPS reprogramming, we derived iPS clones by utilizing retroviral infection to express reprogramming factors in mouse MEF cells. After analyzing four imprinted regions, we found that parentally derived DNA methylation imprint was largely maintained in the iPS clones with Zfp57 but missing in those without maternal or zygotic Zfp57. Intriguingly, DNA methylation imprint was lost at the Peg1 and Peg3 but retained at the Snrpn and Dlk1-Dio3 imprinted regions in the iPS clones without zygotic Zfp57. This finding will be pursued in future studies