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1.
ChemSusChem ; : e202400481, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38571332

ABSTRACT

All-solid-state sodium metal batteries face the challenges of low ionic conductivity of solid electrolytes and poor wettability towards metallic Na anode. Herein, Na3Zr2Si2PO12 solid electrolyte is doped with Ca2+, obtaining a high ionic conductivity of 2.09×10-3 S cm-1 with low electronic conductivity of 1.43×10-8 S cm-1 at room temperature, which could accelerate Na+ transportation and suppress sodium dendrite growth. Meanwhile, a graphite-based interface layer is coated on Na3.4Zr1.8Ca0.2Si2PO12 (Na3.4Zr1.8Ca0.2Si2PO12-G) in order to improve the solid-solid contact between solid electrolyte and Na anode, realizing a uniform current distribution and smooth Na metal plating/stripping, and thus achieving a triple higher critical current density of 3.5 mA cm-2 compared with that of Na3.4Zr1.8Ca0.2Si2PO12. In addition, the assembled Na3V2(PO4)3/Na3.4Zr1.8Ca0.2Si2PO12-G/Na all-solid-state battery exhibits excellent electrochemical performances with a reversible capacity of 81.47 mAh g-1 at 1 C and capacity retention of 97.75 % after 500 cycles.

2.
Heliyon ; 10(3): e24437, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38322894

ABSTRACT

Background: Traditional Chinese Medicine (TCM), has been used for hepatocellular carcinoma (HCC) at every therapeutic stage, even before tumor formation. However, the efficacy of TCM in reducing the incidence of HCC in patients with chronic hepatitis B-related cirrhosis remains unclear. This study aims to address this gap. Methods: Publications were collected from PubMed, EMBASE, Cochrane Library, Web of Science, CNKI, Sino Med, VIP, and Wan Fang Databases. Relative risk (RR) was calculated with a 95 % confidence interval (CI). Heterogeneity was assessed. The Cochrane Collaboration's tool was used to assess the risk of bias. Results: 10 studies with 2702 patients showed that the combination therapy significantly reduced the incidence of HCC in patients with post-hepatitis B cirrhosis at 1, 3, and 5 years. However, the preventive effects of TCM were in compensated cirrhosis, but not the decompensated cirrhosis. Furthermore, TCM correlated with improved liver function and enhanced virological response. Conclusion: Combination therapy with TCM demonstrated the certain potential in reducing the incidence of HCC in patients with hepatitis B cirrhosis. This is attrinuted to the improvement of liver function and enhancement of the viral response. However, the efficacy of TCM in the field still needs more high-quality RCTs to provide stronger evidence in the future.

3.
Food Res Int ; 174(Pt 1): 113502, 2023 12.
Article in English | MEDLINE | ID: mdl-37986417

ABSTRACT

Viruses are major pathogens that cause food poisoning when ingested via contaminated food and water. Therefore, the development of foodborne virus detection technologies that can be applied throughout the food distribution chain is essential for food safety. A common nucleic acid-based detection method is polymerase chain reaction (PCR), which has become the gold standard for monitoring food contamination by viruses due to its high sensitivity, and availability of commercial kits. However, PCR-based methods are labor intensive and time consuming, and are vulnerable to inhibitors that may be present in food samples. In addition, the methods are restricted with regard to site of analysis due to the requirement of expensive and large equipment for sophisticated temperature regulation and signal analysis procedures. To overcome these limitations, optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives for nucleic acid-based detection of foodborne viruses. Biosensors are promising portable detection tools owing to their easy integration into compact platforms and ability to be operated on-site. However, the complexity of food components necessitates the inclusion of tedious preprocessing steps, and the lack of stability studies on residual food components further restricts the practical application of biosensors as a universal detection method. Here, we summarize the latest advances in nucleic acid-based strategies for the detection of foodborne viruses, including PCR-based and isothermal amplification-based methods, gene amplification-free methods, as well as food pretreatment methods. The principles, strengths/disadvantages, and performance of each method, problems to be solved, and future prospects for the development of a universal detection method are discussed.


Subject(s)
Nucleic Acids , Viruses , Nucleic Acid Amplification Techniques/methods , Polymerase Chain Reaction/methods , Food Safety , Viruses/genetics , Nucleic Acids/analysis
4.
J Agric Food Chem ; 71(43): 15942-15953, 2023 Nov 01.
Article in English | MEDLINE | ID: mdl-37862248

ABSTRACT

Viral foodborne diseases cause serious harm to human health and the economy. Rapid, accurate, and convenient approaches for detecting foodborne viruses are crucial for preventing diseases. Biosensors integrating electrochemical and optical properties of nanomaterials have emerged as effective tools for the detection of viruses in foods. However, they still face several challenges, including substantial sample preparation and relatively poor sensitivity due to complex food matrices, which limit their field applications. Hence, the purpose of this review is to provide an overview of recent advances in biosensing techniques, including electrochemical, SERS-based, and colorimetric biosensors, for detecting viral particles in food samples, with emerging techniques for extraction/concentration of virus particles from food samples. Moreover, the principle, design, and advantages/disadvantages of each biosensing method are comprehensively described. This review covers the recent development of rapid and sensitive biosensors that can be used as new standards for monitoring food safety and food quality in the food industry.


Subject(s)
Biosensing Techniques , Foodborne Diseases , Nanostructures , Humans , Biosensing Techniques/methods , Food Safety , Nanostructures/chemistry , Virion , Electrochemical Techniques/methods
5.
Heliyon ; 9(8): e18591, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37554780

ABSTRACT

Background & aims: Traditional Chinese medicine and radiofrequency ablation are becoming increasingly important in the treatment of primary liver cancer. However, the clinical outcome of traditional Chinese medicine plus radiofrequency ablation is contentious. This study aimed to conduct a meta-analysis of randomized controlled clinical trials to address this gap. Methods: Short-term efficacy, alpha-fetoprotein level, immune function, liver function, and quality of life outcomes in patients with primary liver cancer treated with Chinese herbal medicine adjuvant radiofrequency ablation were systematically reviewed. Results: Eighteen randomized controlled clinical trials with 1488 patients with primary liver cancer were included. The combination treatment significantly increased the objective remission rate and quality of patient survival compared to the control group. Combination treatment significantly improved immunity and liver function factors, including CD3, CD4, CD4/CD8, alanine aminotransferase, aspartate aminotransferase, total bilirubin, and albumin levels. However, there were no statistical differences in CD8 levels across treatments. Trial sequential analysis showed that the cumulative Z-curve of the Objective response rate crossed the conventional and test sequence monitoring boundaries; however, it did not cross the required information size line. Conclusions: Traditional Chinese medicine combined with radiofrequency ablation for primary liver cancer can effectively reduce alpha-fetoprotein and improve clinical efficacy, immune function, liver function, as well as the quality of life.

6.
Carbohydr Polym ; 318: 121140, 2023 Oct 15.
Article in English | MEDLINE | ID: mdl-37479447

ABSTRACT

Short-chain glucan (SCG) is a linear homopolymer containing 10 to 50 glucose units linked with α(1,4) glycosidic bonds. With its abundant, low-cost, nontoxic, biodegradable/biocompatible nature, self-assembled SCG particles (SSC) have emerged as functional biomaterials, which have recently attracted tremendous attentions in various fields. SCG self-assembly occurs through the spontaneous association of molecules under equilibrium conditions into stable and structurally well-defined nanoscale or micrometer-scale aggregates, which is governed by various intermolecular non-covalent interactions, including hydrogen-bonding, electrostatic, hydrophobic, and van der Waals. With precise and effective control of the self-assembly process of SSC, its structural modulation and function integration can be expected. Thus, we convinced that SCG self-assembly could provide an effective means of developing starch-based functional biomaterials with beneficial health properties and wide application in food industries. In this review, we provide an overview of recent advances in the green approach for the self-assembly of SSC, as well as the influence of thermodynamic and kinetic factors on its morphology and physicochemical properties. We highlight recent contributions to developing strategies for the construction of SSC with increasing complexity and functionality that are suitable for a variety of food applications. Finally, we briefly outline our perspectives and discuss the challenges in the field.


Subject(s)
Glucans , Starch , Thermodynamics , Biocompatible Materials , Kinetics
7.
J Anim Sci Biotechnol ; 14(1): 69, 2023 May 04.
Article in English | MEDLINE | ID: mdl-37138301

ABSTRACT

BACKGROUND: Chickens provide globally important livestock products. Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding. Influenced by a combination of genetic and environmental factors, metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits. However, the serum metabolite profile and genetic architecture of the metabolome in chickens have not been well studied. RESULTS: Here, comprehensive metabolome detection was performed using non-targeted LC-MS/MS on serum from a chicken advanced intercross line (AIL). In total, 7,191 metabolites were used to construct a chicken serum metabolomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population. Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. Many functional genes affect metabolite synthesis, metabolism, and regulation. We highlight the key roles of TDH and AASS in amino acids, and ABCB1 and CD36 in lipids. CONCLUSIONS: We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a reference for future chicken metabolome characterization work. Meanwhile, we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.

8.
Sci Adv ; 9(18): eade1204, 2023 05 03.
Article in English | MEDLINE | ID: mdl-37134160

ABSTRACT

A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements in the chicken genome by integrating 377 genome-wide sequencing datasets from 23 adult tissues. In total, we annotated 1.57 million regulatory elements, representing 15 distinct chromatin states, and predicted about 1.2 million enhancer-gene pairs and 7662 super-enhancers. This functional annotation of the chicken genome should have wide utility on identifying regulatory elements accounting for gene regulation underlying domestication, selection, and complex trait regulation, which we explored. In short, this comprehensive atlas of regulatory elements provides the scientific community with a valuable resource for chicken genetics and genomics.


Subject(s)
Chickens , Regulatory Sequences, Nucleic Acid , Animals , Chickens/genetics , Regulatory Sequences, Nucleic Acid/genetics , Genomics , Chromatin , Genome , Enhancer Elements, Genetic
9.
Pharm Biol ; 61(1): 520-530, 2023 Dec.
Article in English | MEDLINE | ID: mdl-36908041

ABSTRACT

CONTEXT: Qutan Huoxue decoction (QTHX) is used to treat non-alcoholic steatohepatitis (NASH) with good efficacy in the clinic. However, the mechanism is not clear yet. OBJECTIVE: This study investigates the mechanism of QTHX in the treatment of NASH. MATERIALS AND METHODS: Potential pathways of QTHX were predicted by network pharmacology. Fourty Sprague Dawley (SD) rats (half normal diet, half high-fat diet) were fed six to eight weeks, primary hepatocytes and Kupffer cells were extracted and co-cultured by the 0.4-micron trans well culture system. Then, the normal co-cultured cells were treated by normal serum, the NASH co-cultured cells were treated with various concentrations of QTHX-containing serum (0, 5, 7.5 or 10 µg/mL) for 24 h. The expression of targets were measured with Activity Fluorometric Assay, Western blot and PCR assay. RESULTS: Network pharmacology indicated that liver-protective effect of QTHX was associated with its anti-inflammation response, oxidative stress, and lipid receptor signalling. 10 µg/mL QTHX significantly reduced the inflammation response and lipid levels in primary hepatocytes (ALT: 46.43 ± 2.76 U/L, AST: 13.96 ± 1.08 U/L, TG: 0.25 ± 0.01 mmol/L, TC: 0.14 ± 0.05 mmol/L), comparing with 0 µg/mL NASH group (ALT: 148 ± 9.22 U/L, AST: 53.02 ± 2.30 U/L, TG: 0.74 ± 0.07 mmol/L, TC: 0.91 ± 0.07 mmol/L) (p < 0.01). Meanwhile, QTHX increased expression of SOCS1 and decreased expression of TLR4, Myd88, NF-κB. CONCLUSIONS: The study suggested that QTHX treats NASH in rats by activating the SCOS1/NF-κB/TLR4 pathway, suggesting QTHX could be further developed as a potential liver-protecting agent.


Subject(s)
Non-alcoholic Fatty Liver Disease , Rats , Animals , Non-alcoholic Fatty Liver Disease/drug therapy , Rats, Sprague-Dawley , NF-kappa B/metabolism , Toll-Like Receptor 4/metabolism , Network Pharmacology , Liver , Diet, High-Fat , Lipids
10.
Food Chem ; 418: 135942, 2023 Aug 30.
Article in English | MEDLINE | ID: mdl-36963138

ABSTRACT

Resistant starch particles (RSP) formed by antisolvent precipitation method has attracted much attention as a functional food ingredient having beneficial effects on obesity and diabetes. However, the effect of solvent polarity on the physicochemical properties and digestibility of RSP remains unclear. Here, n-propanol, isopropanol, acetone, and ethanol were employed as antisolvents to prepare RSP. The width and length of the resulting RSP decreased from 0.87 µm to 0.59 µm and from 2.56 µm to 1.31 µm, respectively, upon increasing the solvent polarity, while dramatically decreasing their crystallinity and the gelatinization enthalpy from 80.5% to 62.3% and from 67.9 ± 14.4 J/g to 41.5 ± 8.3 J/g, respectively, suggesting that solvent polarity is critical factor determining morphology, crystallinity, and thermostability of RSP. Furthermore, the level of resistant starch in RSP was found to be inversely proportional to the degree of solvent polarity, which would provide a useful means for modulating the digestibility of RSP.


Subject(s)
Resistant Starch , Starch , Starch/chemistry , Solvents , Thermodynamics , 2-Propanol
11.
J Mol Cell Biol ; 15(2)2023 06 13.
Article in English | MEDLINE | ID: mdl-36822625

ABSTRACT

RNA base editing is a promising tool in precise molecular therapy. Currently, there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions. Thus, RESCUE can generate twice the number of mutations compared to REPAIR. However, transcription-wide impact due to RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully appreciated. Therefore, to determine the off-target effects of RESCUE-mediated editing, we employed transcription-wide sequencing on cells edited by RESCUE. The SNVs showed different off-target effects on mRNA, circRNA, lncRNA, and miRNA expression patterns and their interacting networks. Our results illustrate the transcription-wide impact of RESCUE-induced off-target SNVs and highlight the need for careful characterization of the off-target impact by this editing platform.


Subject(s)
Gene Editing , MicroRNAs , Animals , Gene Editing/methods , Mutation , MicroRNAs/genetics , RNA, Messenger , Nucleotides , CRISPR-Cas Systems , Mammals
12.
Zool Res ; 44(1): 53-62, 2023 Jan 18.
Article in English | MEDLINE | ID: mdl-36317479

ABSTRACT

The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However, epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described. The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50 796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L (active in the duodenum), RCBTB1 (muscle and liver), and novel long non-coding RNA ENSGALG00000053256 (bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.


Subject(s)
Chickens , Chromatin , Epigenesis, Genetic , Animals , Body Weight/genetics , Chickens/genetics , Chromatin/genetics , Genome-Wide Association Study/veterinary , Mammals/genetics
13.
Exp Ther Med ; 25(1): 4, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36561627

ABSTRACT

The present study describes the clinical profile and ankyrin 1 (ANK1) mutation status of a Chinese family with hereditary spherocytosis (HS). A young male patient (proband) was diagnosed with HS after presenting with anaemia and jaundice. The Coombs test was negative and spherocytes were found in peripheral blood smears. Magnetic resonance imaging showed splenomegaly and splenic iron depositions. The red blood cell osmotic fragility test was positive. The eosin-5'-maleimide binding test showed reduced mean channel fluorescence. Whole-exome sequencing revealed a novel ANK1 mutation (c.4707G>A), resulting in a nonsense mutation (p.Trp1569*). The patient's father, paternal aunt and paternal grandmother exhibited comparable clinical symptoms and Sanger sequencing confirmed the same mutation in these family members. To the best of our knowledge, an HS pedigree with this novel ANK1 nonsense mutation has not been previously reported. At the same time, the unique clinical presentation of this pedigree helps our understanding of the heterogeneity of clinical manifestations of HS.

14.
Zhongguo Ying Yong Sheng Li Xue Za Zhi ; 38(2): 187-192, 2022 Mar.
Article in Chinese | MEDLINE | ID: mdl-36031580

ABSTRACT

Objective: By isolating and purifying primary hepatocytes and primary Kupffer cells from rats with nonalcoholic steatohepatitis (NASH), and establishing the primary cell model of NASH in vitro, to provide reliable technical support for cell experiment in the study of NASH. Methods: Forty SD rats were selected and randomly divided into the control group and the NASH group. The rats in the control group were fed with common feed, and the rats in the NASH group were fed with a high-fat diet (88% basal feed + 10% lard + 2% cholesterol). After 6-8 weeks, using the NASH score table, the liver tissue section steatosis + intralobular inflammation + ballooning degeneration score ≥ 4 points under pathological observation, indicating that the rat NASH model was successfully established. And the primary hepatocytes of NASH rats were isolated and purified by collagenase in situ perfusion. Cells were identified by CK-18 and CD68 immunofluorescence and ink swallowing test. The lipid accumulation was tested by Oil red O staining, and the contents of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were determined to evaluate the liver function in primary hepatocytes of NASH rats. The expressions of inflammatory factors of primary Kupffer cells were detected by Western blot. Finally, primary hepatocytes and primary Kupffer cells were co cultured at the ratio of 6:1 and observed under microscope. Results: NASH primary hepatocytes and primary Kupffer cells were successfully isolated and purified. Compared with the control group, Oil red O staining showed that the primary hepatocytes of the NASH group had obvious fat deposition, and the AST and ALT levels in the primary hepatocytes of the NASH group were significantly higher than those of the control group, indicating obvious liver damage (P< 0.05). The Western blot result showed that the levels of TNF-α, IL-1ß and MCP-1 in primary Kupffer cells was significantly higher than the control group (P<0.05). Conclusion: The primary hepatocytes and primary Kupffer cells of NASH rats were isolated successfully by collagenase in situ perfusion. At the same time, a proportional co-culture rat in vitro primary cell NASH model was successfully established.


Subject(s)
Non-alcoholic Fatty Liver Disease , Animals , Coculture Techniques , Collagenases , Hepatocytes , Kupffer Cells , Liver , Rats , Rats, Sprague-Dawley
15.
Front Psychol ; 13: 946570, 2022.
Article in English | MEDLINE | ID: mdl-35859842

ABSTRACT

Exploring the impact of corporate social responsibility (CSR) fulfillment and disclosure on enterprises' sustainable innovation capacity can not only expand the research boundary of factors of sustainable innovation and the impact of CSR, but it can also serve as a reference for the decision-making of listed companies in increasing pollution problems. Using a sample of 224 Chinese A-share businesses in the heavy pollution industry listed between 2016 and 2020 and employing an ordinary least square regression, the results provide empirical evidence that CSR is positively associated with sustainable innovation. Second, the business environment can serve as a moderator of the relationship between CSR and sustainable innovation, and the positive relationship between CSR and sustainable innovation is more pronounced in regions with better macroeconomic conditions. Additionally, the improvement of CSR for sustainable innovation is more clear in state-owned firms than in non-state-owned enterprises. After a series of robustness tests that eliminate marketization, law enforcement, and macro-political unpredictability, the results still hold. This study broadens the scope of CSR and sustainable innovation research. In addition, the theoretical and practical significance of this study's findings is referenced in this paper.

16.
Hepatol Int ; 16(4): 858-867, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35729469

ABSTRACT

BACKGROUND: The optimal locoregional treatment for hepatocellular carcinoma (HCC) patients with portal vein tumor thrombus (PVTT) is unclear. This study aimed to investigate the efficacy of Gamma knife radiosurgery (GKR) versus transcatheter arterial chemoembolization (TACE) in HCC patients with PVTT. METHODS: This retrospective study included 544 HCC patients with PVTT (GKR, 202; TACE, 342). Propensity score matching (PSM) analysis identified 171 matched pairs of patients. The primary endpoint was overall survival (OS). RESULTS: Before PSM, the GKR group exhibited longer median OS (mOS) than the TACE group (17.2 vs. 8.0 months, p < 0.001). We followed the Cheng's classification for PVTT. In the subgroup analysis, GKR was associated with significantly longer mOS for patients with PVTT II-IV (17.5 vs. 8.7 months, p < 0.001; 17.2 vs. 7.8 months, p = 0.001; 14.5 vs. 6.5 months, p = 0.001, respectively) and comparable OS for patients with PVTT I. After PSM, the GKR group had also a longer mOS than the TACE group (15.8 vs. 10.4 months, p < 0.001). In the subgroup analysis, the GKR group demonstrated superior mOS for patients with PVTT II-IV (all p < 0.05) and comparable OS for patients with PVTT I. CONCLUSIONS: GKR was associated better OS than TACE in HCC patients with PVTT, especially for patients with PVTT II-IV. CLINICAL TRIALS REGISTRATION: The study was registered in the Chinese Clinical Trials Registry under the registration number ChiCTR2100051057.


Subject(s)
Carcinoma, Hepatocellular , Chemoembolization, Therapeutic , Liver Neoplasms , Radiosurgery , Thrombosis , Carcinoma, Hepatocellular/complications , Carcinoma, Hepatocellular/pathology , Carcinoma, Hepatocellular/therapy , Humans , Liver Neoplasms/complications , Liver Neoplasms/pathology , Liver Neoplasms/therapy , Portal Vein/pathology , Propensity Score , Retrospective Studies , Thrombosis/surgery , Treatment Outcome
17.
Nucleic Acids Res ; 50(D1): D471-D479, 2022 01 07.
Article in English | MEDLINE | ID: mdl-34788852

ABSTRACT

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.


Subject(s)
Databases, Protein , Gene Regulatory Networks , Protein Processing, Post-Translational , Proteins/metabolism , Software , Animals , Arabidopsis/genetics , Arabidopsis/metabolism , Bacteria/genetics , Bacteria/metabolism , Humans , Internet , Mice , Models, Molecular , Molecular Sequence Annotation , Protein Binding , Protein Conformation , Protein Interaction Mapping , Proteins/chemistry , Proteins/genetics , Rats , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism
18.
Nucleic Acids Res ; 50(D1): D460-D470, 2022 01 07.
Article in English | MEDLINE | ID: mdl-34850155

ABSTRACT

The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of >4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.


Subject(s)
Antimicrobial Peptides , Databases, Factual , Software , Antimicrobial Peptides/chemistry , Antimicrobial Peptides/pharmacology , Genomics , Open Reading Frames , Protein Conformation , Proteomics
19.
Genet Sel Evol ; 53(1): 82, 2021 Oct 27.
Article in English | MEDLINE | ID: mdl-34706641

ABSTRACT

BACKGROUND: Growth traits are of great importance for poultry breeding and production and have been the topic of extensive investigation, with many quantitative trait loci (QTL) detected. However, due to their complex genetic background, few causative genes have been confirmed and the underlying molecular mechanisms remain unclear, thus limiting our understanding of QTL and their potential use for the genetic improvement of poultry. Therefore, deciphering the genetic architecture is a promising avenue for optimising genomic prediction strategies and exploiting genomic information for commercial breeding. The objectives of this study were to: (1) conduct a genome-wide association study to identify key genetic factors and explore the polygenicity of chicken growth traits; (2) investigate the efficiency of genomic prediction in broilers; and (3) evaluate genomic predictions that harness genomic features. RESULTS: We identified five significant QTL, including one on chromosome 4 with major effects and four on chromosomes 1, 2, 17, and 27 with minor effects, accounting for 14.5 to 34.1% and 0.2 to 2.6% of the genomic additive genetic variance, respectively, and 23.3 to 46.7% and 0.6 to 4.5% of the observed predictive accuracy of breeding values, respectively. Further analysis showed that the QTL with minor effects collectively had a considerable influence, reflecting the polygenicity of the genetic background. The accuracy of genomic best linear unbiased predictions (BLUP) was improved by 22.0 to 70.3% compared to that of the conventional pedigree-based BLUP model. The genomic feature BLUP model further improved the observed prediction accuracy by 13.8 to 15.2% compared to the genomic BLUP model. CONCLUSIONS: A major QTL and four minor QTL were identified for growth traits; the remaining variance was due to QTL effects that were too small to be detected. The genomic BLUP and genomic feature BLUP models yielded considerably higher prediction accuracy compared to the pedigree-based BLUP model. This study revealed the polygenicity of growth traits in yellow-plumage chickens and demonstrated that the predictive ability can be greatly improved by using genomic information and related features.


Subject(s)
Chickens , Genome-Wide Association Study , Animals , Chickens/genetics , Genomics , Genotype , Models, Genetic , Phenotype , Polymorphism, Single Nucleotide , Quantitative Trait Loci
20.
Sensors (Basel) ; 21(16)2021 Aug 20.
Article in English | MEDLINE | ID: mdl-34451049

ABSTRACT

This paper presents a new model for multi-object tracking (MOT) with a transformer. MOT is a spatiotemporal correlation task among interest objects and one of the crucial technologies of multi-unmanned aerial vehicles (Multi-UAV). The transformer is a self-attentional codec architecture that has been successfully used in natural language processing and is emerging in computer vision. This study proposes the Vision Transformer Tracker (ViTT), which uses a transformer encoder as the backbone and takes images directly as input. Compared with convolution networks, it can model global context at every encoder layer from the beginning, which addresses the challenges of occlusion and complex scenarios. The model simultaneously outputs object locations and corresponding appearance embeddings in a shared network through multi-task learning. Our work demonstrates the superiority and effectiveness of transformer-based networks in complex computer vision tasks and paves the way for applying the pure transformer in MOT. We evaluated the proposed model on the MOT16 dataset, achieving 65.7% MOTA, and obtained a competitive result compared with other typical multi-object trackers.

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