Cold Spring Harbor protocols最新文献_第2页

Clonal Lineage and Gene Diversity Analysis of Paired Antibody Heavy and Light Chains. 成对抗体重链和轻链的克隆谱系和基因多样性分析

Cold Spring Harbor protocols Pub Date : 2025-01-02 DOI: 10.1101/pdb.prot108628

Ahmed S Fahad, Matías F Gutiérrez-Gonzalez, Bharat Madan, Brandon J DeKosky

引用次数: 0

Sample Preparation for Chromatin Immunoprecipitation (ChIP) from Drosophila Antennal and Brain Samples. 果蝇触角和大脑样本的染色质免疫沉淀 (ChIP) 样品制备。

Cold Spring Harbor protocols Pub Date : 2025-01-02 DOI: 10.1101/pdb.prot108140

Chengcheng Du, Pelin Volkan

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Beyond Single Clones: High-Throughput Sequencing in Antibody Discovery. 超越单克隆：抗体发现中的高通量测序。

Cold Spring Harbor protocols Pub Date : 2025-01-02 DOI: 10.1101/pdb.top107772

Ahmed S Fahad, Matías F Gutiérrez-Gonzalez, Bharat Madan, Brandon J DeKosky

引用次数: 0

Chromatin Immunoprecipitation (ChIP) Using Drosophila Antennal and Brain Samples. 利用果蝇触角和大脑样本进行染色质免疫沉淀（ChIP）

Cold Spring Harbor protocols Pub Date : 2025-01-02 DOI: 10.1101/pdb.prot108142

Chengcheng Du, Pelin Volkan

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Using Chromatin Immunoprecipitation (ChIP) to Study the Chromatin State in Drosophila. 利用染色质免疫沉淀 (ChIP) 研究果蝇的染色质状态。

Cold Spring Harbor protocols Pub Date : 2025-01-02 DOI: 10.1101/pdb.top108139

Chengcheng Du, Pelin Volkan

引用次数: 0

High-Throughput Free Amino Acid Quantification from Maize Tissues. 玉米组织中游离氨基酸的高通量定量分析。

Cold Spring Harbor protocols Pub Date : 2024-12-23 DOI: 10.1101/pdb.prot108631

Huda Ansaf, Abou Yobi, Ruthie Angelovici

{"title":"High-Throughput Free Amino Acid Quantification from Maize Tissues.","authors":"Huda Ansaf, Abou Yobi, Ruthie Angelovici","doi":"10.1101/pdb.prot108631","DOIUrl":"https://doi.org/10.1101/pdb.prot108631","url":null,"abstract":"Amino acids in maize can exist in both a free and protein-bound state. While most amino acids are part of a protein backbone, a small percentage of them remain free and play important biological roles, serving as signaling molecules, nitrogen transporters, osmolytes, and precursors for multiple primary and secondary metabolites. Their levels vary widely especially in maize leaves, depending on the developmental stage and in response to environmental conditions. Therefore, accurate and reliable quantification of free amino acids (FAAs) is vital in any effort aimed at studying their response to developmental and environmental cues. In this protocol, we describe a robust, high-throughput method that quantifies the 20 proteogenic amino acids (i.e., those that can be incorporated into proteins) that are found in the free form in maize tissue. This method consists of three major parts: first, aqueous extraction of FAAs from maize tissue; second, separation, detection, and quantification of all 20 proteogenic amino acids using ultraperformance liquid chromatography-tandem mass spectrometry; and third, data analysis and processing using the MassLynx data analysis software, TargetLynx.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881534","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}

引用次数: 0

High-Throughput Protein-Bound Amino Acid Quantification from Maize Kernels. 玉米籽粒蛋白结合氨基酸的高通量定量分析。

Cold Spring Harbor protocols Pub Date : 2024-12-23 DOI: 10.1101/pdb.prot108632

Huda Ansaf, Abou Yobi, Ruthie Angelovici

{"title":"High-Throughput Protein-Bound Amino Acid Quantification from Maize Kernels.","authors":"Huda Ansaf, Abou Yobi, Ruthie Angelovici","doi":"10.1101/pdb.prot108632","DOIUrl":"https://doi.org/10.1101/pdb.prot108632","url":null,"abstract":"In cereal crops, seed quality is determined by the composition and levels of protein-bound amino acids, which account for ∼90% of the seed total amino acid content. In maize particularly, seed quality is affected by the low levels of lysine and tryptophan, two amino acids that humans and animals cannot synthesize and must obtain from the diet. The low levels of these two amino acids in seeds is due to the dominance of seed storage proteins, namely zeins, which are deficient in these two amino acids. Many efforts have been deployed to improve the nutritional composition of maize kernels (i.e., seeds). Still, the lack of high-throughput and inexpensive methods for the quantification of amino acids that are found within proteins has limited those efforts, especially when large populations are targeted. In this protocol, we describe a robust, efficient, and high-throughput method for the quantification of all 20 proteogenic (protein-forming) amino acids from a crude protein extract. The method consists of four major parts: first, release of the 20 proteogenic amino acids from the protein backbone through hydrolysis; second, aqueous extraction of the released amino acids; third, separation, detection, and quantification of the released amino acids using a multiple reaction monitoring-based ultraperformance liquid chromatography-tandem mass spectrometry detection; and fourth, data analysis and processing using the MassLynx data analysis software, TargetLynx.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881554","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}

引用次数: 0

Amino Acid Quantification from Maize Tissues. 玉米组织氨基酸定量分析。

Cold Spring Harbor protocols Pub Date : 2024-12-23 DOI: 10.1101/pdb.top108440

Huda Ansaf, Abou Yobi, Ruthie Angelovici

{"title":"Amino Acid Quantification from Maize Tissues.","authors":"Huda Ansaf, Abou Yobi, Ruthie Angelovici","doi":"10.1101/pdb.top108440","DOIUrl":"https://doi.org/10.1101/pdb.top108440","url":null,"abstract":"Amino acid analysis is a vital part of analytical biochemistry. The increasing demand for low nitrogen fertilization and for plant-based diets with balanced amino acid levels and composition have made it crucial to develop reliable, fast, and affordable methods for analyzing amino acids in plants. As maize accounts for 43% of global cereal production, improving the amino acid composition of its kernels (i.e., seeds) is critically important for meeting the dietary requirements of humans and livestock. Moreover, amino acid quantification in maize leaves is necessary for improving yield prediction, stress sensing, and nitrogen use efficiency. Many amino acid quantification methods use reverse-phase high-pressure liquid chromatography and gas chromatography approaches to assess the amino acid content of maize tissues. Historically, these techniques involved the use of chemical derivatization, a chemical reaction that alters the properties of a compound to make it detectable or more sensitive to detection. Although accurate, these methods are time-consuming, expensive, and unsuitable for large populations. Here, we introduce two high-throughput methods for quantifying amino acids from large maize populations, such as those used for quantitative trait locus mapping, genome-wide association studies, and large mutant populations. Both methods use an ultraperformance liquid chromatography-tandem mass spectrometry instrument to quantify all 20 proteogenic amino acids in a maize tissue in a short run time. A dependable, affordable, and high-throughput method for quantifying amino acids in maize has important implications for assessing kernel quality, yield, and management efficacy, such as fertilizer usage and watering.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881474","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}

引用次数: 0

Examining Cell-Specific Localization in Aedes aegypti Tissues with Fluorescence In Situ Hybridization. 利用荧光原位杂交技术检查埃及伊蚊组织中的特异性细胞定位。

Cold Spring Harbor protocols Pub Date : 2024-12-02 DOI: 10.1101/pdb.prot108280

Farwa Sajadi, Jean-Paul V Paluzzi

引用次数: 0

Filleting and Immunostaining of Larvae to Visualize Drosophila Dendritic Arborization Neuron Dendrite Arbors. 对幼虫进行切片和免疫染色以观察果蝇的树突分化神经元树突节。

Cold Spring Harbor protocols Pub Date : 2024-12-02 DOI: 10.1101/pdb.prot108148

Fangke Xu, Jason Y Tann, Oliver R Wilkes, Adrian W Moore

引用次数: 0