农学最新文献

{"title":"Detection and counting method of juvenile abalones based on improved SSD network","authors":"","doi":"10.1016/j.inpa.2023.03.002","DOIUrl":"10.1016/j.inpa.2023.03.002","url":null,"abstract":"<div><p>Detection and counting of abalones is one of key technologies of abalones breeding density estimation. The abalones in the breeding stage are small in size, densely distributed, and occluded between individuals, so the existing object detection algorithms have low precision for detecting the abalones in the breeding stage. To solve this problem, a detection and counting method of juvenile abalones based on improved SSD network is proposed in this research. The innovation points of this method are: Firstly, the multi-layer feature dynamic fusion method is proposed to obtain more color and texture information and improve detection precision of juvenile abalones with small size; secondly, the multi-scale attention feature extraction method is proposed to highlight shape and edge feature information of juvenile abalones and increase detection precision of juvenile abalones with dense distribution and individual coverage; finally, the loss feedback training method is used to increase the diversity of data and the pixels of juvenile abalones in the images to get the even higher detection precision of juvenile abalones with small size. The experimental results show that the [email protected] value, [email protected] value and [email protected] value of the detection results of the proposed method are 91.14%, 89.90% and 80.14%, respectively. The precision and recall rates of the counting results are 99.59% and 97.74%, respectively, which are superior to the counting results of SSD, FSSD, MutualGuide, EfficientDet and VarifocalNet models. The proposed method can provide support for real-time monitoring of aquaculture density for juvenile abalones.</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/S221431732300046X/pdfft?md5=0e659a821a078f0956cfc5f7356a7af0&pid=1-s2.0-S221431732300046X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43549565","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":"CRISPR/Gal4BD-Cas donor adapting systems based on miniaturized Cas proteins for improved gene editing.","authors":"Sen Yang, Bao-Xia Ma, Hong-Run Qian, Jie-Yu Cui, Xiao-Jun Zhang, Li-da Li, Ze-Hui Wei, Zhi-Ying Zhang, Jian-Gang Wang, Kun Xu","doi":"10.16288/j.yczz.24-124","DOIUrl":"https://doi.org/10.16288/j.yczz.24-124","url":null,"abstract":"<p><p>Targeted precise point editing and knock-in can be achieved by homology-directed repair(HDR) based gene editing strategies in mammalian cells. However, the inefficiency of HDR strategies seriously restricts their application in precision medicine and molecular design breeding. In view of the problem that exogenous donor DNA cannot be efficiently recruited autonomously at double-stranded breaks(DSBs) when using HDR strategies for gene editing, the concept of donor adapting system(DAS) was proposed and the CRISPR/Cas9-Gal4BD DAS was developed previously. Due to the large size of SpCas9 protein, its fusion with the Gal4BD adaptor is inconvenient for protein expression, virus vector packaging and <i>in vivo</i> delivery. In this study, two novel CRISPR/Gal4BD-SlugCas9 and CRISPR/Gal4BD-AsCas12a DASs were further developed, using two miniaturized Cas proteins, namely SlugCas9-HF derived from <i>Staphylococcus lugdunensis</i> and AsCas12a derived from <i>Acidaminococcus</i> sp<i>.</i> Firstly, the SSA reporter assay was used to assess the targeting activity of different Cas-Gal4BD fusions, and the results showed that the fusion of Gal4BD with SlugCas9 and AsCas12a N-terminals had minimal distraction on their activities. Secondly, the HDR efficiency reporter assay was conducted for the functional verification of the two DASs and the corresponding donor patterns were optimized simultaneously. The results demonstrated that the fusion of the Gal4BD adaptor binding sequence at the 5'-end of intent dsDNA template (BS-dsDNA) was better for the CRISPR/Gal4BD-AsCas12a DAS, while for the CRISPR/Gal4BD-SlugCas9 DAS, the dsDNA-BS donor pattern was recommended. Finally, CRISPR/Gal4BD-SlugCas9 DAS was used to achieve gene editing efficiency of 24%, 37% and 31% respectively for <i>EMX1, NUDT5</i> and <i>AAVS1</i> gene loci in HEK293T cells, which was significantly increased compared with the controls. In conclusion, this study provides a reference for the subsequent optimization of the donor adapting systems, and expands the gene editing technical toolbox for the researches on animal molecular design breeding.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297199","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":"A low-cost digital 3D insect scanner","authors":"","doi":"10.1016/j.inpa.2023.03.003","DOIUrl":"10.1016/j.inpa.2023.03.003","url":null,"abstract":"<div><p>Collections of biological specimens are essential in entomology laboratories for scientific knowledge and the characterization of natural varieties. It is vital to liberate useful information from physical collections by digitizing specimens, allowing them to be shared, examined, annotated, and compared more readily. As a result, current research has concentrated on developing 3D modeling machine systems to digitize insect specimens. Despite many great outcomes, these systems have certain drawbacks. In this research, a new scanning machine is proposed for creating 3D virtual models of insects. Our method has overcome certain previous constraints by aiding in the automation of the entire imaging process at a low cost, lowering shooting time, and generating 3D models with accurate color, high resolution, and high accuracy of insect samples with small sizes and complicated structures. Because of its ease of installation and modification, our system may be expanded and utilized in a variety of settings and areas.</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/S2214317323000471/pdfft?md5=db78072a9c6e7a9eeba9abb938606551&pid=1-s2.0-S2214317323000471-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45333040","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":"Analysis of expression characteristics and identification of interaction proteins of transcription factor BnaABI5 in <i>Brassica napus</i>.","authors":"Qian-Qian Ao, Fang-Xiao Lu, Liu-Qing Yang, Chun Li, Zeng-Kang Zhai, Dong-Ye Jia, Yuan-Qing Jiang, Bo Yang","doi":"10.16288/j.yczz.24-064","DOIUrl":"10.16288/j.yczz.24-064","url":null,"abstract":"<p><p>Rapeseed is one important oil crop in China. However, its planting benefit is frequently affected by environmental stresses such as drought in the northwest region of China. The abscisic acid(ABA) signaling pathway plays an important role in plant abiotic stress response and tolerance, and ABFs/AREBs(ABA-responsive element binding factors/ABA-responsive element binding proteins) are the core transcription factors that regulate the expression of ABA-responsive genes. To dissect the key transcription factors mediated abiotic stress, we mainly characterized abscisic acid insensitive 5(BnaABI5) in rapeseed, including its subcellular localization, expression pattern in response to various stress and tissue-specific expression analysis, transcriptional activity analysis as well as interaction screening with BnaMPKs(mitogen-activated protein kinases). Our results showed that the BnaABI5-GFP fusion protein was localized in the nucleus, and its transcript level is induced by drought stress and was mainly expressed in the roots of rapeseed. Furthermore, BnaABI5 showed transcriptional activation activity through a yeast transactivation assay and it also activated the promoter activity of <i>EM6</i> target gene in the transient expression system in tobacco leaves. Moreover, BnaABI5 interacted with BnaMPK6 and BnaMPK13 through BiFC and Y2H analysis. This study preliminarily explored the expression characteristics of transcription factor BnaABI5 and its interaction with BnaMPKs, which might help us for further understanding the function of BnaABI5.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297198","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":"Key technologies and applications of rural energy internet in China","authors":"","doi":"10.1016/j.inpa.2022.03.001","DOIUrl":"10.1016/j.inpa.2022.03.001","url":null,"abstract":"<div><p>Rural energy plays an important role in realizing the goals of “carbon peak” and “carbon neutrality” in China. In this paper, the countryside was regarded as the research object, and the rural energy internet was constructed to study the impact of rural energy development on rural carbon emissions. The most advanced energy and informative technologies in the development of rural energy were introduced from three perspectives, including rural living, rural planting and rural breeding. The benefits of rural energy internet in practical application, including energy and carbon benefits, were presented through three application cases. In general, a low-carbon, digital and intelligent rural energy will be developed, and the goals of “carbon peak” and “carbon neutrality” will be achieved by constructing and applying of rural energy internet in China.</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/S2214317322000282/pdfft?md5=64eda4c88ae8eb55c157e27b6bc98064&pid=1-s2.0-S2214317322000282-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46987028","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":"Progress on CRISPR-Cas gene editing technology in sheep production.","authors":"Dong-Xia Pan, Hui Wang, Ben-Hai Xiong, Xiang-Fang Tang","doi":"10.16288/j.yczz.24-155","DOIUrl":"https://doi.org/10.16288/j.yczz.24-155","url":null,"abstract":"<p><p>Gene editing is a kind of genetic engineering technology that can modify the genome. In recent years, with the rapid development of molecular biotechnology, the clustered regularly interspaced short palindromic repeats associated protein system has been widely used as a powerful gene editing tool due to its high efficiency, accuracy and flexibility. The CRISPR-Cas system makes a significant contribution to different aspects of livestock production by introducing site-specific modifications such as insertions, deletions or single base replacements at specific genomic sites. In terms of sheep production applications, by establishing animal models that improve production economic traits and disease resistance, the function of key genes can be studied to accelerate the improvement of traits, thereby accelerating the improvement of traits. In this review, we summarize the mechanism and function of CRISPR-Cas system and its application in the production of reproductive traits, meat use traits, wool production traits, lactation traits and disease resistance traits of sheep and the establishment of sheep animal models.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297204","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":"Pig face recognition based on improved YOLOv4 lightweight neural network","authors":"","doi":"10.1016/j.inpa.2023.03.004","DOIUrl":"10.1016/j.inpa.2023.03.004","url":null,"abstract":"<div><p>With the vigorous development of intelligence agriculture, the progress of automated large-scale and intensive pig farming has accelerated significantly. As a biological feature, the pig face has important research significance for precise breeding of pigs and traceability of health. In the management of live pigs, many managers adopt traditional methods, including color marking and RFID identification, but there will be problems such as off-label, mixed-label and waste of manpower. This work proposes a non-invasive way to study the identification of multiple individuals in pigs. The model was to first replace the original backbone network of YOLOv4 with MobileNet-v3, a popular lightweight network. Then depth-wise separable convolution was adopted in YOLOv4′s feature extraction network SPP and PANet to further reduce network parameters. Moreover, CBAM attention mechanism formed by the concatenation of CAM and SAM was added to PANet to ensure the network accuracy while reducing the model weight. The introduction of multi-attention mechanism selectively strengthened key areas of pig face and filtered out weak correlation features, so as to improve the overall model effect. Finally, an improved MobileNetv3-YOLOv4-PACNet (M-YOLOv4-C) network model was proposed to identify individual sows. The mAP were 98.15 %, the detection speed FPS were 106.3frames/s, and the model parameter size was only 44.74 MB, which can be well implanted into the small-volume pig house management sensors and applied to the pig management system in a lightweight, fast and accurate manner. This model will provide model support for subsequent pig behavior recognition and posture analysis.</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/S2214317323000483/pdfft?md5=15cedd90f8b826def2e4ca0a3a7b3834&pid=1-s2.0-S2214317323000483-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46956825","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":"Identification of a pathogenic variant and pre-implantation genetic testing for a Chinese family affected with split-hand/foot malformation.","authors":"Li-Bin Mei, Yi-Yuan Zhang, Xian-Jing Huang, Hong Ji, Ping-Ping Qiu, Lu Ding, Xuemei He, Ping Li","doi":"10.16288/j.yczz.24-141","DOIUrl":"https://doi.org/10.16288/j.yczz.24-141","url":null,"abstract":"<p><p>Split-hand/foot malformation is a serious congenital limb malformation characterized by syndactyly and underdevelopment of the phalanges and metatarsals. In this study, we reported a case of a fetus with hand-foot cleft deformity. Whole exome and Sanger sequencing were used to filter out candidate gene mutation sites and provide pre-implantation genetic testing(PGT) for family members. Genetic testing results showed that there was a homozygous mutation c.786G>A (p.Trp262*) in the fetal <i>WNT10B</i>, and both parents were carriers of heterozygous mutations. PGT results showed that out of the two blastocysts, one was a heterozygous mutant and the other was a homozygous mutant. All the embryos had diploid chromosomes. The heterozygous embryo was transferred, and a singleton pregnancy was successfully achieved. This study suggests that homozygous mutations in <i>WNT10B</i> are the likely cause of hand-foot clefts in this family. For families with monogenic diseases, preimplantation genetic testing can effectively prevent the birth of an affected child only after identifying the pathogenic mutation.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297202","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 on deep learning in genomics.","authors":"Yan-Chun Bao, Cai-Xia Shi, Chuan-Qiang Zhang, Ming-Juan Gu, Lin Zhu, Zai-Xia Liu, Le Zhou, Feng-Ying Ma, Ri-Su Na, Wen-Guang Zhang","doi":"10.16288/j.yczz.24-151","DOIUrl":"https://doi.org/10.16288/j.yczz.24-151","url":null,"abstract":"<p><p>With the rapid growth of data driven by high-throughput sequencing technologies, genomics has entered an era characterized by big data, which presents significant challenges for traditional bioinformatics methods in handling complex data patterns. At this critical juncture of technological progress, deep learning-an advanced artificial intelligence technology-offers powerful capabilities for data analysis and pattern recognition, revitalizing genomic research. In this review, we focus on four major deep learning models: Convolutional Neural Network(CNN), Recurrent Neural Network(RNN), Long Short-Term Memory(LSTM), and Generative Adversarial Network(GAN). We outline their core principles and provide a comprehensive review of their applications in DNA, RNA, and protein research over the past five years. Additionally, we also explore the use of deep learning in livestock genomics, highlighting its potential benefits and challenges in genetic trait analysis, disease prevention, and genetic enhancement. By delivering a thorough analysis, we aim to enhance precision and efficiency in genomic research through deep learning and offer a framework for developing and applying livestock genomic strategies, thereby advancing precision livestock farming and genetic breeding technologies.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297205","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":"Spectroscopic measurement and dielectric relaxation study of vegetable oils","authors":"","doi":"10.1016/j.inpa.2023.04.002","DOIUrl":"10.1016/j.inpa.2023.04.002","url":null,"abstract":"&lt;div&gt;&lt;p&gt;The purpose of the current study is to investigate the qualitative characterization of nine different pure vegetable oil samples using dielectric spectroscopy which is a vastly resourceful and reasoned technique in the temperature range 0 ℃ to 25 ℃. Time-domain reflectometry technique is applied up to the microwave frequencies of 50 GHz for the first time for qualitative characterization of the selected vegetable oil samples with a special focus on the variances of dielectric properties like dielectric permittivity (&lt;em&gt;ε&lt;/em&gt;′), dielectric loss (&lt;em&gt;ε″&lt;/em&gt;), relaxation time concerning temperature and other physiochemical properties of the vegetable oil specimens.&lt;/p&gt;&lt;p&gt;The experimental methodology involves the use of time-domain reflectometry (TDR) measurements up to the scale of 50 GHz done to analyse the aspects like lower and higher scales of values towards the static dielectric permittivity (&lt;em&gt;ε&lt;sub&gt;s&lt;/sub&gt;&lt;/em&gt;) and relaxation time (&lt;em&gt;τ&lt;/em&gt;) (ps) to further meaningfully compare and correlate this values with the fatty acid profiles of each of the nine vegetable oil samples to reason and draw comparative inferences about the quality aspects of vegetable oils. Microwave TDR studies provide an effective, alternate, simple, rapid, and viable way to exercise quality control and actuate data regarding the quality status of vegetable oils. Variances of dielectric permittivity (&lt;em&gt;ε′&lt;/em&gt;) concerning dielectric loss (&lt;em&gt;ε″&lt;/em&gt;) are graphically interpreted using the Cole Davidson model. The static dielectric permittivity (&lt;em&gt;ε&lt;sub&gt;s&lt;/sub&gt;&lt;/em&gt;) was further recertified and measured accurately by using a precision LCR meter. Thermodynamic properties of all the nine vegetable oil samples like enthalpy (ΔH) (kJ/mol) and entropy of activation (ΔS) (J/mol ∙ K) are also calculated to further insight the dependence of dielectric properties of these oil samples concerning temperature.&lt;/p&gt;&lt;p&gt;This dielectric spectroscopic study affirms the association of the quality aspects of these nine vegetable oil samples with their dielectric properties by providing meaningful correlations, comparatives and concurrencies of dielectric properties concerning the physiochemical properties which are a part of fatty acid profiles of these samples, which is a novel aspect of this study. The Cole-Cole plot underlines the tendency of realignment of dipoles as per the applied field. The complex permittivity spectra indicate the dwindling nature of molecular alignment including a slow decline to average coinciding values depending on the molecular bonding pattern of vegetable oil samples. The activation energy (ΔH) in (kJ/mol) is calculated for all the samples which are indicative of endothermic nature which experimentally proves that high energy is required for rotation of unsaturated oil sample molecules with low relaxation times.&lt;/p&gt;&lt;p&gt;The highlight of the current dielectric spectroscopic study is that it conclusively divides the nine vegetable oil samples into","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/S2214317323000513/pdfft?md5=dd5c937752933ef085859c3a768dbf14&pid=1-s2.0-S2214317323000513-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46607529","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}