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

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

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

On Flow Maldistribution in PEMFC Stacks

Polymer electrolyte membrane fuel cell (PEMFC) stacks are widely studied for their own advantages. The flow maldistribution in unit cells may severely influence the fuel cell stack performance, mainly including the uniformity of current density and the voltage. Investigations of flow maldistribution in PEMFC stacks are rarely found, and presented results are unsystematic, scattered, and even contradictory. Thus, it is necessary to review and summarize the previous concerned papers, and to get some methods or guidelines for reducing the flow maldistribution in PEMFC stacks. In this paper, the existing literature concerning flow maldistributions in PEMFC stacks is reviewed. The effects of the arrangement of flow configurations, design parameters, and operating conditions on the flow maldistribution are discussed. Some suggestions are outlined to reduce the flow maldistribution in PEMFC stacks. The need for further research is also discussed

Integrative analysis of miRNA–mRNA network in idiopathic membranous nephropathy by bioinformatics analysis

Background Currently, several specific antigens, M-type receptor for secretory phospholipase A2(PLA2R1), thrombospondin type-1 domain-containing 7A(THSD7A), and neural epidermal growth factor-like 1 protein (NELL-1), are discovered associated with the onset of idiopathic membranous nephropathy (IMN). But the pathomechanisms of IMN still need to be further claried. Understanding the mechanisms of IMN is required to improve its diagnosis and treatment. Methods In this study, we constructed miRNA regulatory networks to investigate IMN development. Moreover, miRNAs and mRNAs that were differentially expressed between Idiopathic Membranous Nephropathy (IMN) patients and normal controls were examined using the GSE115857 dataset and our previous sequence study. DE miRNA target genes were determined based on the FUNRICH software, starBase, miRDB, and miRWalk, and an miRNA-mRNA network was designed using DE-mRNAs that were negatively correlated with DE-miRNAs. The miRNA-mRNA network contained 228 miRNA-mRNA pairs. Thereafter, we conducted KEGG pathway, GO functional annotation, immune-related gene screening, protein interaction networks, and potential hub gene analyses. Furthermore, 10 miRNAs and 10 genes were determined and preliminarily validated using the validation dataset from GEO. Finally, we identified which pair may offer more accurate diagnosis and therapeutic targets for IMN. Results Two miRNA-mRNA pairs, miR-155-5p-FOS and miR-146a-5p-BTG2, were differentially expressed in IMN, indicating that these genes may affect IMN through immune processes. These findings may offer more accurate diagnoses and therapeutic targets for IMN

A Promising Process to Remove Nitrate from Solar Panel Production Wastewater and Meanwhile Generating Electricity

For traditional heterotrophic denitrification technology, organics are usually added as the electron donor for nitrate removal, which increases the operation cost for wastewater treatment. Solar panel production wastewater contains a large amount of nitrate. To decrease the operation cost and reduce CO2 emissions, an iron anode microbial fuel cell (Fe-MFC) was constructed to treat solar panel production wastewater by sequencing batch operation. The results showed that the maximum nitrate removal efficiency reached 99.98% and the maximum removal rate was 0.049 kg·m−3·d−1. The output voltages rose rapidly to 560 ± 10 mV within 2 h and then stabilized at 520 ± 50 mV for about 40 h. Combining the detection of coulombic efficiency, CV curve, q* value and internal resistance; the decrease in denitrification efficiency and electricity generation efficiency probably resulted from the passivation of iron anode and the aging of the cathode biofilm resulted in the efficiency decrease. From the microbial analysis, Chryseobacterium, Thermomonas and Thauera predominated at the end of Fe-MFC operation. Microorganisms that cannot adapt to the autotrophic environment in Fe-MFC died out finally. Periodic replacement of the iron anode and domestication of the bio-cathode were essential to maintain the Fe-MFC efficiency. The Fe-MFC technology was feasible to be used to remove nitrate and generate electricity from solar panel production wastewater. Without organics addition, the Fe-MFC technology was cost-efficient and environmentally friendly, endowing itself with a broad prospect of application

Interactions between Graphene and Ionic Liquid Electrolyte in Supercapacitors

The graphene material prepared by the chemical reduction method usually has oxygenic functional groups in it and such functional groups often result in interactions between the graphene electrode and the electrolyte in supercapacitors. We have examined the existential form of interactions between graphene as the electrode and three kinds of ionic liquid, 1-ethyl-3-methylimidazolium bis (trifluoromethylsulfonyl) imide (EMI-TFSI), 1-ethyl-3-methylimidazolium tetrafluoroborate (EMI-BF4), and 1-methyl-1-propylpiperidinium bis (trifluoromethyl sulfonyl) imide (MPPp-TFSI), as the electrolyte of a supercapacitor. Mass spectroscopy (MS) and Fourier transform infrared spectroscopy (FT-IR) analyses confirmed that the residual hydroxyl groups in graphene were transferred to EMI+ and TFSI lost oxygen atoms to graphene, while little reaction took place in BF4 or MPPp(+), during the process of charging. The chemical reactions are suggested to contribute to the device capacitance while it is also one of the reasons for the decreased electrochemical stability window. In this study the highest energy density achieved using the graphene electrode is 169 Wh kg (1) in MPPp-TFSI electrolyte charged to 4.4 V. (C) 2016 Elsevier Ltd. All rights reserved

Synthesis of Magnetic α-Fe2O3/Rutile TiO2 Hollow Spheres for Visible-Light Photocatalytic Activity

The high recombination rate of the electron-hole pair on the surface of rutile TiO2 (RT) reduces its photocatalytic performance, although it has high thermodynamic stability and few internal grain defects. Therefore, it is necessary for RT to develop effective methods to reduce electron-hole pair recombination. In this study, magnetic α-Fe2O3/Rutile TiO2 self-assembled hollow spheres were fabricated via a facile hydrothermal reaction and template-free method. Based on the experimental result, phosphate concentration was found to play a crucial role in controlling the shape of these hollow α-Fe2O3/RT nanospheres, and the optimal concentration is 0.025 mM. Due to a heterojunction between α-Fe2O3 and RT, the electron-hole pair recombination rate was reduced, the as-synthesized hollow α-Fe2O3/RT nanospheres exhibited excellent photocatalysis in rhodamine B (RhB) photodegradation compared to α-Fe2O3 and RT under visible-light irradiation, and the degradation rate was about 16% (RT), 60% (α-Fe2O3), and 93% (α-Fe2O3/RT) after 100 min. Moreover, α-Fe2O3/RT showed paramagnetism and can be recycled to avoid secondary environmental pollution

Exploring the high-quality ingredients and mechanisms of Da Chuanxiong Formula in the treatment of neuropathic pain based on network pharmacology, molecular docking, and molecular dynamics simulation

Da Chuanxiong Formula (DCXF) is a traditional herbal prescription used for pain management. It consists of Chuanxiong Rhizoma (CR) and Gastrodiae Rhizoma (GR). Despite its long history of use, the underlying therapeutic mechanism of DCXF remains insufficiently understood. Therefore, in this study, key target genes were obtained through network pharmacology research methods and molecular docking techniques, including transient receptor potential vanilloid 1 (TRPV1), adenosine A2a receptor (ADORA2A), nuclear receptor subfamily 3 group C member 1 (NR3C1), and protein kinase C beta (PRKCB). Molecular dynamics simulations demonstrated the favorable binding between all four key genes and their corresponding compounds. Notably, chronic constriction injury (CCI) treatment resulted in a significant decrease in mechanical threshold and thermal latency period for rat foot contraction, which was ameliorated upon administration of DCXF. Furthermore, real-time quantitative reverse transcription PCR (RT-qPCR) and western blot (WB) analyses indicated an upregulation of TRPV1, ADORA2A, NR3C1, and PRKCB expression in the rat dorsal root ganglion following CCI, which was attenuated by treatment with DCXF. The expressions of inflammatory factors, including tumor necrosis factor-α (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6), in the rat dorsal root ganglion were assessed using ELISA, confirming consistent trends with the aforementioned findings. The results of this study offer a promising theoretical foundation for the utilization of DCXF in the treatment of neuropathic pain (NP)

Ionic liquid modified graphene for supercapacitors with high rate capability

Ionic liquids (ILs) with large electrochemical windows up to 4 V have been employed as the electrolyte to boost the energy density of graphene-based supercapacitors. However, due to the larger molecular size, lower conductivity, and higher viscosity of the IL electrolyte, graphene-based supercapacitors in IL electrolyte usually exhibit low rate capability. To make graphene-based electrodes more compatible with the IL electrolyte, we functionalized chemically reduced graphene oxide with the same IL which is also used as the electrolyte. Electrochemical test results show that the relaxation time and charge transfer resistance at electrode-electrolyte interface for IL modified electrode is one third and one fourth of that for the pristine graphene electrode, respectively, indicating the improved compatibility between the IL modified electrode and the electrolyte. Furthermore, the capacitance retention of the IL modified electrode from current density of 0.5 to 20 A g(-1) is 85%, which is much higher than that of the pristine electrode (53%). (C) 2015 Elsevier Ltd. All rights reserved