Label-free based comparative proteomic analysis of whey proteins between different milk yields of Dezhou donkey

2019 ◽  
Vol 508 (1) ◽  
pp. 237-242 ◽  
Author(s):  
Xinhao Zhang ◽  
Haijing Li ◽  
Jie Yu ◽  
Xiangshan Zhou ◽  
Chuanliang Ji ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Whey Proteins ◽  
Label Free ◽  
Comparative Proteomic Analysis

scholarly journals MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis

2008 ◽  
Vol 24 (22) ◽  
pp. 2641-2642 ◽  
Author(s):  
D. Hwang ◽  
N. Zhang ◽  
H. Lee ◽  
E. Yi ◽  
H. Zhang ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Label Free ◽  
Comparative Proteomic Analysis

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Comparative proteomic analysis of four biotechnological strainsLactococcus lactisthrough label-free quantitative proteomics

2018 ◽  
Vol 12 (2) ◽  
pp. 265-274 ◽  
Author(s):  
Wanderson M. Silva ◽  
Cassiana S. Sousa ◽  
Leticia C. Oliveira ◽  
Siomar C. Soares ◽  
Gustavo F.M.H. Souza ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Quantitative Proteomics ◽  
Label Free ◽  
Comparative Proteomic Analysis

scholarly journals Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids. Results Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Production ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract BackgroundMaize is a major crop worldwide and heterotic hybrids play important roles in global maize production. Heterosis refers hybrid progeny of species or varieties exhibiting superior traits compared with those of their parents and much attention has been paid to heterosis associated genes recently. The hybridization between parents can change the expression pattern of some proteins such as non-additive proteins which might lead to heterosis, so that comparative proteomic analysis of maize hybrid and its parents is helpful for understanding the mechanism of heterosis.ResultsSecond seedling leaves of maize hybrids "Zhongdan 808" and "Zhongdan 909" and their parents were collected at three-leaf stage for protein extractions. Over 2,000 protein groups were accurately assessed in the two hybrids and their parents by label-free quantification. Quantitative data analyses of the proteomes revealed that the two hybrids were more similar to their female parents. Additionally, pathway enrichment analysis showed that most non-additive proteins in Zhongdan 808 were mainly enriched in stress-related pathways, while those in Zhongdan 909 were mainly enriched in photosynthesis. ConclusionsIn comparison with their parents, the excellent agronomic traits of hybrid Zhongdan 808 was correlated with the high expression levels of some proteins related to stress responses and and metabolic functions, while those of Zhongdan 909 was correlated with photosynthesis. Our proteomics results supported previous physiological and morphological research. This work may provide useful information for understanding of the molecular mechanisms involved in the heterosis of hybrid maize.

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

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