农学最新文献

{"title":"Advances in high throughput sequencing methods for DNA damage and repair.","authors":"Yu Liang, Wei Wu","doi":"10.16288/j.yczz.24-203","DOIUrl":"https://doi.org/10.16288/j.yczz.24-203","url":null,"abstract":"<p><p>With the rapid development of high-throughput sequencing technology in the past decade, an increasing number of sequencing methods targeting different types of DNA damage have been developed and widely used in the field. These technologies not only help to elucidate the dynamic processes of repair pathways corresponding to different types of lesions, understand the underlying mechanisms of key factors and identify new hotspots prone to damage, but also greatly advanced our knowledge of crucial physiological processes such as meiotic homologous recombination, antibody generation and cytosine demethylation. These advancements hold significant potential for broader applications in exploring disease initiation and drug development. However, understanding and selecting the appropriate techniques have become difficult. This article reviews the main sequencing detection methods for the most common DNA lesions and introduce their principles, thereby providing valuable insights for the selection, application, further development and optimization of these technologies.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut metagenome-derived image augmentation and deep learning improve prediction accuracy of metabolic disease classification.","authors":"Hui-Yi Zheng, Hua-Xuan Wu, Zhi-Qiang Du","doi":"10.16288/j.yczz.24-086","DOIUrl":"https://doi.org/10.16288/j.yczz.24-086","url":null,"abstract":"<p><p>In recent years, statistics and machine learning methods have been widely used to analyze the relationship between human gut microbial metagenome and metabolic diseases, which is of great significance for the functional annotation and development of microbial communities. In this study, we proposed a new and scalable framework for image enhancement and deep learning of gut metagenome, which could be used in the classification of human metabolic diseases. Each data sample in three representative human gut metagenome datasets was transformed into image and enhanced, and put into the machine learning models of logistic regression (LR), support vector machine (SVM), Bayesian network (BN) and random forest (RF), and the deep learning models of multilayer perceptron (MLP) and convolutional neural network (CNN). The accuracy performance of the overall evaluation model for disease prediction was verified by accuracy (A), accuracy (P), recall (R), F1 score (F1), area under ROC curve (AUC) and 10 fold cross-validation. The results showed that the overall performance of MLP model was better than that of CNN, LR, SVM, BN, RF and PopPhy-CNN, and the performance of MLP and CNN models was further improved after data enhancement (random rotation and adding salt-and-pepper noise). The accuracy of MLP model in disease prediction was further improved by 4%-11%, F1 by 1%-6% and AUC by 5%-10%. The above results showed that human gut metagenome image enhancement and deep learning could accurately extract microbial characteristics and effectively predict the host disease phenotype. The source code and datasets used in this study can be publicly accessed in https://github.com/HuaXWu/GM_ML_Classification.git.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing.","authors":"Xin Wen, Jin Mei, Mei-Yu Qian, Yi-Dan Jiang, Juan Wang, Shi-Bo Xu, Cui-Zhe Wang, Jun Zhang","doi":"10.16288/j.yczz.24-221","DOIUrl":"https://doi.org/10.16288/j.yczz.24-221","url":null,"abstract":"<p><p>GULP1 is an engulfment adaptor protein containing a phosphotyrosine-binding (PTB) domain, and existing studies have shown that it can promote glucose uptake in 3T3-L1 adipocytes. To further explore key metabolically related differential genes downstream of GULP1, this study conducted transcriptome analysis on adipocytes and skeletal muscle cells overexpressing GULP1. Subsequently, abnormally expressed genes were subjected to bioinformatic analysis, and real-time fluorescent quantitative PCR (qRT-PCR) was used for mutual validation with transcriptome sequencing. The results indicated that, with a threshold of <i>P</i> < 0.05 and |Log₂FoldChange| ≥ 1 for screening differentially expressed genes, compared with control cells, there were 278 upregulated and 263 downregulated genes in adipocytes overexpressing GULP1. Metabolism-related GO (Gene Ontology) terms included cholesterol biosynthetic process, cholesterol metabolic process, response to lipopolysaccharide, lipid metabolic process, etc. A total of 52 metabolically related differentially expressed genes were enriched in 10 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, with lipid metabolism being highly enriched. In skeletal muscle cells overexpressing GULP1, there were 280 upregulated and 302 downregulated genes, with metabolism-related GO terms including hormone metabolic process, response to lipopolysaccharide, one-carbon metabolic process, etc. A total of 86 metabolically related differentially expressed genes were enriched in 10 KEGG pathways, with amino acid metabolism, lipid metabolism, and carbohydrate metabolism being highly enriched. GULP1's biological functions are extensive, including lipid metabolism and oncology. This study, through transcriptomics and bioinformatic analysis, identified key metabolically related differential genes downstream of GULP1, obtained metabolically related differential genes and signaling pathways after GULP1 overexpression, providing important theoretical basis for future research on GULP1 downstream target genes.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancements and prospects in reconstructing the genetic genealogies of ancient and modern human populations using ancestral recombination graphs.","authors":"Qing-Xin Yang, Meng-Ge Wang, Chao Liu, Hui-Jun Yuan, Guang-Lin He","doi":"10.16288/j.yczz.24-150","DOIUrl":"https://doi.org/10.16288/j.yczz.24-150","url":null,"abstract":"<p><p>With the release of large-scale genomic resources from ancient and modern populations, advancements in computational biology tools, and the enhancement of data mining capabilities, the field of genomics is undergoing a revolutionary transformation. These advancements and changes have not only significantly deepened our understanding of the complex evolutionary processes of human origins, migration, and admixture but have also unveiled the impact of these processes on human health and disease. They have accelerated research into the genetic basis of human health and disease and provided new avenues for uncovering the evolutionary trajectories recorded in the human genome related to population history and disease genetics. The ancestral recombination graph (ARG) reconstructs the evolutionary relationships between genomic segments by analyzing recombination events and coalescence patterns across different regions of the genome. An ARG provides a record of all coalescence and recombination events since the divergence of the sequences under study and specifies a complete genealogy at each genomic position, which is the ideal data structure for genomic analysis. Here, we review the theoretical foundations and research advancements of the ARG, and explore its translational applications and future prospects across various disciplines, including forensic genomics, population genetics, evolutionary medicine, and medical genomics. Our goal is to promote the application of this technique in genomic research, thereby deepening our understanding of the human genome.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Progress and challenges in human developmental cell atlas.","authors":"Yi-Chen Que, Qing-Quan Liu, Yi-Chi Xu","doi":"10.16288/j.yczz.24-153","DOIUrl":"https://doi.org/10.16288/j.yczz.24-153","url":null,"abstract":"<p><p>Illustrating molecular mechanisms of human embryonic development has always been one of the most significant challenges in biology. The scarcity of human embryo samples, the difficulty in dissecting embryo samples, and the complex structures of human organs are the major obstacles in studying human embryogenesis. In recent years, with the rapid advancement of single-cell technology, humans can systematically analyze the dynamic changes in differentiation at various stages of the central dogma and achieve observation and research with spatial information. This has accelerated the progress in constructing a human developmental cell atlas, ultimately allowing us to depict the cell ontology, fate trajectories, and three-dimensional dynamic changes of human development. In this review, we first introduce the single-cell technologies used to construct the atlas, then summarize the latest progress in human developmental cell atlas, followed by identifying the main problems and challenges in this field so far. Finally, we discuss how to utilize the human developmental cell atlas to address key biological and medical issues. This review provides guidance for the optimal use of single-cell omics technology in constructing and applying a human developmental cell atlas.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research progress on single-cell expression quantitative trait loci.","authors":"Xiao-Peng Xu, Xiao-Ying Fan","doi":"10.16288/j.yczz.24-162","DOIUrl":"https://doi.org/10.16288/j.yczz.24-162","url":null,"abstract":"<p><p>Expression quantitative trait loci (eQTL) represent genetic variants that regulate gene expression levels. eQTL analysis has become a crucial method for identifying the functional roles of disease-associated genetic variants in the post-genome-wide association study (GWAS) era, yielding numerous significant discoveries. Traditional eQTL analysis relies on whole-genome sequencing combined with bulk RNA-seq, which obscures gene expression differences between cells and thus fails to identify cell type- or state-dependent eQTL. This limitation makes it challenging to elucidate the roles of disease-associated genetic variants under specific conditions. In recent years, with the development and widespread application of single-cell RNA sequencing (scRNA-seq) technology, scRNA-seq-based eQTL (sc-eQTL) research has emerged as a focal point. The advantage of this approach lies in its ability to leverage the resolution and granularity of single-cell sequencing to uncover eQTL that are dependent on cell type, cell state, and cellular dynamics. This significantly enhances our ability to analyze genetic variants associated with gene expression. Consequently, it holds substantial significance for advancing our understanding of the formation of complex organs and the mechanisms underlying disease onset, progression, intervention, and treatment. This review comprehensively examines the recent advancements in sc-eQTL studies, focusing on their development, experimental design strategies, modeling approaches, and current challenges. The aim is to offer researchers novel perspectives for identifying disease-associated loci and elucidating gene regulatory mechanisms.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid determination of oil content of single peanut seed by near-infrared hyperspectral imaging","authors":"Shunting Zhang ,&nbsp;Xue Li ,&nbsp;Du Wang ,&nbsp;Li Yu ,&nbsp;Fei Ma ,&nbsp;Xuefang Wang ,&nbsp;Mengxue Fang ,&nbsp;Huiying Lyu ,&nbsp;Liangxiao Zhang ,&nbsp;Zhiyong Gong ,&nbsp;Peiwu Li","doi":"10.1016/j.ocsci.2024.05.002","DOIUrl":"10.1016/j.ocsci.2024.05.002","url":null,"abstract":"<div><div>Oil content is a crucial indicator for evaluating the quality of peanuts. A rapid and non-destructive method to determine oil content of individual peanut seed can provide robust technical support for breeding high-oil-content peanut varieties. In this study, we established a rapid determination method using near-infrared hyperspectral imaging and chemometrics to assess the oil content of single peanut seed. After selecting key wavelengths through competitive adaptive reweighted sampling (CARS), uninformative variable elimination (UVE), and random frog (RF), we constructed an oil content calibration model based on partial least squares regression for single peanut seed. Validation results demonstrated that the correlation coefficient was 0.8393 with a root mean square error of 1.7771 in the calibration set, while it was 0.7915 with a root mean square error of 2.2943 in the independent prediction set. Most samples exhibited relative errors below 5%, confirming the reliability of this model in predicting oil content of single peanut seed.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Solvent-free synthesis of diacylglycerols via enzymatic glycerolysis between edible oils and glycerol catalyzed by self-made immobilized lipase PS@LXTE-1000","authors":"Yuhao Li ,&nbsp;Yi Zhang ,&nbsp;Run Liu ,&nbsp;Zhonghui Liu ,&nbsp;Kheng-Lim Goh ,&nbsp;Vladimir Zivkovic ,&nbsp;Mingming Zheng","doi":"10.1016/j.ocsci.2024.05.003","DOIUrl":"10.1016/j.ocsci.2024.05.003","url":null,"abstract":"<div><div>Diglycerol (DAG) is a structural lipid with the functions to lower body fat accumulation and decrease serum triglyceride level. However, the enzymatic synthesis of DAG is limited by the high-efficient and economic lipases. In this paper, the immobilized lipase PS@LXTE-1000 was self-made by immobilizing the <em>Pseudomomas cepacian</em> lipase on to the hydrophobic microporous resin LXTE-1000. The results indicate that LXTE-1000 was a uniform mesoporous sphere with the mean diameter of 400 ​μm, pore size of 14.6 ​nm, pore volume of 0.5 ​cm³/g and surface area of 126.0 ​m²/g, showing superior structural properties for lipase immobilization. Under the optimal reaction conditions with the molar ratio of rapeseed oil to glycerol being 1:1, adding amount of immobilized lipase being 4%, reaction at 50 ​°C, the highest DAG content of 46.7% was achieved in 3 ​h via enzymatic glycerolysis catalyzed by LXTE-1000. After 7 cycles of reuse, the self-made LXTE-1000 could still retain 78.3% of its initial catalytic ability. Besides, LXTE-1000 was observed to facilitate the DAG production via glycerolysis reaction between glycerol with other seven edible oils including corn oil, sesame oil, peony seed oil, rice bran oil, peanut oil, soybean oil and flaxseed oil. Specifically, the glycerolysis reaction with sesame oil, peony seed oil and rice bran oil even led to the DAG content of 52.1%, 53.3% and 51.2%, respectively, Hence, this paper provide a novel strategy to produce high-efficient and economic immobilized lipases, which shows great potential in the green synthesis of functional lipids such as DAG.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142535347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of adding flaxseed milk coproduct and okara on the quality and glycemic response of Chinese steamed bread","authors":"Yan Tang ,&nbsp;Yaqiong Pei ,&nbsp;Jiahui Wang ,&nbsp;Haichao He ,&nbsp;Mingkai Sun ,&nbsp;Yashu Chen ,&nbsp;He Liu ,&nbsp;Hu Tang ,&nbsp;Qianchun Deng","doi":"10.1016/j.ocsci.2024.06.007","DOIUrl":"10.1016/j.ocsci.2024.06.007","url":null,"abstract":"<div><div>Flaxseed milk coproduct (FMC) is a by-product of flaxseed milk. Okara is a by-product of processed soybean products. In this study, we investigated the quality of dough and Chinese steamed bread (CSB) with the addition of FMC and okara. We also examined the in vitro starch digestibility, expected glycemic index (eGI), starch crystallinity, and short-range order structure of CSB. The results showed that FMC and okara decreased the dough fluidity, formed a dense structure, and enhanced the mechanical properties of the dough. FMC and okara increased the hardness, gumminess, and chewiness of the CSB, while decreasing its cohesion and elasticity. The addition of FMC and okara improved the nutrient content of CSB and reduced the eGI from 75.86 to 51.56. FMC and okara altered the multiscale structure of starch, effectively shielding the amylase site of action, and limited the interaction between amylase and starch. This study provides a reference for the high-value utilization of oilseed processing by-products.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Artificial intelligence solutions to reduce information asymmetry for Colombian cocoa small-scale farmers","authors":"","doi":"10.1016/j.inpa.2023.03.001","DOIUrl":"10.1016/j.inpa.2023.03.001","url":null,"abstract":"<div><p>The lack of information creates problems for Colombian small-scale farmers, as it impedes them from selling at fair prices and knowing efficient production techniques. Around the world, many technological interventions have proven helpful in reducing information asymmetries. Therefore, we proposed a technological scheme based on a genetic algorithm and a natural language processor (NLP) that enables producers to obtain knowledge through information processing. Also, we ran fieldwork in twenty municipalities and a survey among 500 Colombian cocoa small-scale farmers in different regions in Colombia. This fieldwork helps us determine small-scale farmers' necessities, market conditions, and the relevance of an Artificial Intelligence (AI) tool. The results have shown that AI methodologies could improve the economic conditions of small farmers by providing access to information on prices, weather, and production techniques. The fieldwork evidence that a technological tool is a good option only if there are dynamic trade cycles. AI tools could transmit and process information to become producers' knowledge and help them evolve into collective strategies. The methodology, which combines genetic algorithms, NLP, and fieldwork for cocoa farming, is a novelty that contributes to information asymmetry reduction. We contributed to the literature about adopting AI tools to develop cocoa small-scale farming better.</p></div>","PeriodicalId":53443,"journal":{"name":"Information Processing in Agriculture","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214317323000458/pdfft?md5=fc59c81b0d445fce4bff213f690d8056&pid=1-s2.0-S2214317323000458-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41628896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}