Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects

Wood formation is an excellent model system for quantitative trait analysis due to the strong associations between the transcriptional and metabolic traits that contribute to this complex process. Investigating the genetic architecture and regulatory mechanisms underlying wood formation will enhance our understanding of the quantitative genetics and genomics of complex phenotypic variation. Genome-wide association studies (GWASs) represent an ideal statistical strategy for dissecting the genetic basis of complex quantitative traits. However, elucidating the molecular mechanisms underlying many favorable loci that contribute to wood formation and optimizing GWAS design remain challenging in this omics era. In this review, we summarize the recent progress in GWAS-based functional genomics of wood property traits in major timber species such as Eucalyptus, Populus, and various coniferous species. We discuss several appropriate experimental designs for extensive GWAS in a given undomesticated tree population, such as omics-wide association studies and high-throughput phenotyping technologies. We also explain why more attention should be paid to rare allelic and major structural variation. Finally, we explore the potential use of GWAS for the molecular breeding of trees. Such studies will help provide an integrated understanding of complex quantitative traits and should enable the molecular design of new cultivars

Transcriptome and association mapping revealed functional genes respond to drought stress in Populus

Drought frequency and severity are exacerbated by global climate change, which could compromise forest ecosystems. However, there have been minimal efforts to systematically investigate the genetic basis of the response to drought stress in perennial trees. Here, we implemented a systems genetics approach that combines co-expression analysis, association genetics, and expression quantitative trait nucleotide (eQTN) mapping to construct an allelic genetic regulatory network comprising four key regulators (PtoeIF-2B, PtoABF3, PtoPSB33, and PtoLHCA4) under drought stress conditions. Furthermore, Hap_01PtoeIF-2B, a superior haplotype associated with the net photosynthesis, was revealed through allelic frequency and haplotype analysis. In total, 75 candidate genes related to drought stress were identified through transcriptome analyses of five Populus cultivars (P. tremula × P. alba, P. nigra, P. simonii, P. trichocarpa, and P. tomentosa). Through association mapping, we detected 92 unique SNPs from 38 genes and 104 epistatic gene pairs that were associated with six drought-related traits by association mapping. eQTN mapping unravels drought stress-related gene loci that were significantly associated with the expression levels of candidate genes for drought stress. In summary, we have developed an integrated strategy for dissecting a complex genetic network, which facilitates an integrated population genomics approach that can assess the effects of environmental threats

Novel Myh11 Dual Reporter Mouse Model Provides Definitive Labeling and Identification of Smooth Muscle Cells—Brief Report

Objective: Myh11 encodes a myosin heavy chain protein that is specifically expressed in smooth muscle cells (SMCs) and is important for maintaining vascular wall stability. The goal of this study is to generate a Myh11 dual reporter mouse line for definitive visualization of MYH11+ SMCs in vivo. Approach and Results: We generated a Myh11 knock-in mouse model by inserting LoxP-nlacZ-4XpolyA-LoxP-H2B-GFP-polyA-FRT-Neo-FRT reporter cassette into the Myh11 gene locus. The nuclear (n) lacZ-4XpolyA cassette is flanked by 2 LoxP sites followed by H2B-GFP (histone 2B fused green fluorescent protein). Upon Cre-mediated recombination, nlacZ-stop cassette is removed thereby permitting nucleus localized H2B-GFP expression. Expression of the nuclear localized lacZ or H2B-GFP is under control of the endogenous Myh11 promoter. Nuclear lacZ was expressed specifically in SMCs at embryonic and adult stages. Following germline Cre-mediated deletion of nuclear lacZ, H2B-GFP was specifically expressed in the nuclei of SMCs. Comparison of nuclear lacZ expression with Wnt1Cre and Mef2cCre mediated-H2B-GFP expression revealed heterogenous origins of SMCs from neural crest and second heart field in the great arteries and coronary vessels adjacent to aortic root. Conclusions: The Myh11 knock-in dual reporter mouse model offers an exceptional genetic tool to visualize and trace the origins of SMCs in mice

Dnmt3a is essential for hematopoietic stem cell differentiation

Loss of the de novo DNA methyltransferases Dnmt3a and Dnmt3b in embryonic stem cells obstructs differentiation; however, the role of these enzymes in somatic stem cells is largely unknown. Using conditional ablation, we show that Dnmt3a loss progressively impairs hematopoietic stem cell (HSC) differentiation over serial transplantation, while simultaneously expanding HSC numbers in the bone marrow. Dnmt3a-null HSCs show both increased and decreased methylation at distinct loci, including substantial CpG island hypermethylation. Dnmt3a-null HSCs upregulate HSC multipotency genes and downregulate differentiation factors, and their progeny exhibit global hypomethylation and incomplete repression of HSC-specific genes. These data establish Dnmt3a as a critical participant in the epigenetic silencing of HSC regulatory genes, thereby enabling efficient differentiation

Energy-Saving Optimization Method of Urban Rail Transit Based on Improved Differential Evolution Algorithm

The transformation of railway infrastructure and traction equipment is an ideal way to realize energy savings of urban rail transit trains. However, upgrading railway infrastructure and traction equipment is a high investment and difficult process. To produce energy-savings in the urban rail transit system without changing the existing infrastructure, we propose an energy-saving optimization method by optimizing the traction curve of the train. Firstly, after analyzing the relationship between the idle distance and running energy-savings, an optimization method of traction energy-savings based on the combination of the inertia motion and energy optimization is established by taking the maximum idle distance as the objective; and the maximum allowable running speed, passenger comfort, train timetable, maximum allowable acceleration and kinematics equation as constraints. Secondly, a solution method based on the combination of the adaptive dynamic multimodal differential evolution algorithm and the Q learning algorithm is applied to solve the optimization model of energy-savings. Finally, numeric experiments are conducted to verify the proposed method. Extensive experiments demonstrate the effectiveness of the proposed method. The results show that the method has significant energy-saving properties, saving energy by about 11.2%

Computation of electrostatic forces between solvated molecules determined by the Poisson–Boltzmann equation using a boundary element method

A rigorous approach is proposed to calculate the electrostatic forces among an arbitrary number of solvated molecules in ionic solution determined by the linearized Poisson-Boltzmann equation. The variational principle is used and implemented in the frame of a boundary element method (BEM). This approach does not require the calculation of the Maxwell stress tensor on the molecular surface, therefore it totally avoids the hypersingularity problem in the direct BEM whenever one needs to calculate the gradient of the surface potential or the stress tensor. This method provides an accurate and efficient way to calculate the full intermolecular electrostatic interaction energy and force, which could potentially be used in Brownian dynamics simulation of biomolecular association. The method has been tested on some simple cases to demonstrate its reliability and efficiency, and parts of the results are compared with analytical results and with those obtained by some known methods such as adaptive Poisson-Boltzmann solver

Biological tribology properties of the modified polyether ether ketone composite materials

Modification of poly-ether-ether-ketone (PEEK) to adapt to the biological properties of materials is currently the key point in the research of medical materials. The tribological properties and biocompatibility of the PEEK composites modified by carbon fiber (CF), potassium titanate whisker(PTW) and nano-particles were discussed in this paper. The results show the modified PEEK composites by a certain length to diameter ratio of CF show the best using effect in vivo experiments in good blood compatibility, which is suitable for orthopaedic implant materials. A large number of experiments show that the PEEK composites would be modified with a certain ratio of CF (about 30%wt.), whisker (about 15%wt.) and HA (about 5%wt.) particle with better biological tribological properties, more important value in medical research

MLK3 phophorylates AMPK independently of LKB1.

Emerging evidence has shown that cellular energy metabolism is regulated by the AMPK and MLK3-JNK signaling pathways, but the functional link between them remains to be determined. The present study aimed to explore the crosstalk between MLK3 and AMPK. We found that both JNK and AMPK were phosphorylated at their activation sites by TNF-α, Anisomycin, H2O2 and sorbitol. Interestingly, sorbitol stimulated phosphorylation of AMPK at T172 in LKB1-deficient cells. Following the screening of more than 100 kinases, we identified that MLK3 induced phosphorylation of AMPK at T172. Our in vitro analysis further revealed that MLK3-mediated phosphorylation of AMPK at T172 was independent of AMP, but addition of AMP caused a mobility shift of AMPK, an indication of autophosphorylation, suggesting that AMP binding and phosphorylation of T172 leads to maximal activation of AMPK. GST-pull down assays showed a direct interaction between AMPKα1 subunit and MLK3. Altogether, our results indicate that MLK3 serves as a common upstream kinase of AMPK and JNK and functions as a direct upstream kinase for AMPK independent of LKB1