Delineating molecular regulatory network of meat quality of longissimus dorsi indicated by transcriptomic, proteomic, and metabolomics analysis in rabbit
This study aims to investigate the potential regulatory network responsible for the meat quality using multi-omics to help developing better varieties. Slaughter performance and meat quality of Shuxing No.1 rabbit outperformed IRA rabbit according to the tested rabbit parameters. Differentially expressed genes (DEGs) and differentially abundance proteins (DAPs) were involved in meat quality-related pathways, such as PI3K - Akt and MAPK signaling pathway. Only SMTNL1 and PM20D2 shared between DEGs and DAPs. Olfactory-sensitive undecanal, a differentially abundant metabolite (DAM) in volatilomics (vDAMs), correlated with all...
Source: Journal of Proteomics - April 24, 2024 Category: Biochemistry Authors: Liangde Kuang Jianhong Zeng Yuying Li Jie Zheng Yongjun Ren Zhiqiang Guo Xiangyu Zhang Cuixia Zhang Chao Yang Xiuli Mei Rui Yang Li Tang Yang Ji Xiaohong Xie Min Lei Congyan Li Source Type: research

Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress
J Proteomics. 2024 Apr 16:105178. doi: 10.1016/j.jprot.2024.105178. Online ahead of print.ABSTRACTEmploying microbial systems for the bioremediation of contaminated waters represent a potential option, however, limited understanding of the underlying mechanisms hampers the implication of microbial-mediated bioremediation. The omics tools offer a promising approach to explore the molecular basis of the bioremediation process. Here, a mass spectrometry-based quantitative proteome profiling approach was conducted to explore the differential protein levels in cadmium-treated Paramecium multimicronucleatum. The Proteome Discove...
Source: Journal of Proteomics - April 18, 2024 Category: Biochemistry Authors: Itrat Zahra Lauren DeVine Robert Cole Hafiza Aroosa Malik Jinke Wu Junneng Wen Amor Hedfi Ayesha Liaqat Roohi Ijaz Uzma Ramzan Abdul Rauf Shakoori Farah Rauf Shakoori Michael J Betenbaugh Source Type: research

Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress
J Proteomics. 2024 Apr 16:105178. doi: 10.1016/j.jprot.2024.105178. Online ahead of print.ABSTRACTEmploying microbial systems for the bioremediation of contaminated waters represent a potential option, however, limited understanding of the underlying mechanisms hampers the implication of microbial-mediated bioremediation. The omics tools offer a promising approach to explore the molecular basis of the bioremediation process. Here, a mass spectrometry-based quantitative proteome profiling approach was conducted to explore the differential protein levels in cadmium-treated Paramecium multimicronucleatum. The Proteome Discove...
Source: Journal of Proteomics - April 18, 2024 Category: Biochemistry Authors: Itrat Zahra Lauren DeVine Robert Cole Hafiza Aroosa Malik Jinke Wu Junneng Wen Amor Hedfi Ayesha Liaqat Roohi Ijaz Uzma Ramzan Abdul Rauf Shakoori Farah Rauf Shakoori Michael J Betenbaugh Source Type: research

Substrate and functional characterization of the lysine acetyltransferase MsKat and deacetylase MsCobB in Mycobacterium smegmatis
In this study, we systematically analyzed the dynamic molecular changes in response to the MsKat/MsCobB overexpression in mycobacteria at proteome and lysine acetylation level by using a TMT-based quantitative proteomic approach. Pathways related with glycolysis, degradation of branched chain amino acids, phosphotransferase system were affected after disturbance of the two regulates enzymes involved in lysine acetylation. We also proved that AMP-dependent synthetase Clp protease, ATP-dependent DNA/RNA helicases and citrate synthase was the substrate of MsKat according to our proteomic data and biological validation. Togeth...
Source: Journal of Proteomics - April 17, 2024 Category: Biochemistry Authors: Yunbo Kan Shuyu Xie Yewen Sun Tong Ye Yunxu Bian Fang Guo Mingya Zhang Tianxian Liu Tianqi Liu Jing Ji Bin Liu Minjia Tan Jun-Yu Xu Source Type: research

Substrate and functional characterization of the lysine acetyltransferase MsKat and deacetylase MsCobB in Mycobacterium smegmatis
In this study, we systematically analyzed the dynamic molecular changes in response to the MsKat/MsCobB overexpression in mycobacteria at proteome and lysine acetylation level by using a TMT-based quantitative proteomic approach. Pathways related with glycolysis, degradation of branched chain amino acids, phosphotransferase system were affected after disturbance of the two regulates enzymes involved in lysine acetylation. We also proved that AMP-dependent synthetase Clp protease, ATP-dependent DNA/RNA helicases and citrate synthase was the substrate of MsKat according to our proteomic data and biological validation. Togeth...
Source: Journal of Proteomics - April 17, 2024 Category: Biochemistry Authors: Yunbo Kan Shuyu Xie Yewen Sun Tong Ye Yunxu Bian Fang Guo Mingya Zhang Tianxian Liu Tianqi Liu Jing Ji Bin Liu Minjia Tan Jun-Yu Xu Source Type: research

Proteomic and metabolomic insights into seed germination of Ferula assa-foetida
J Proteomics. 2024 Apr 9;300:105176. doi: 10.1016/j.jprot.2024.105176. Online ahead of print.ABSTRACTCold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory ...
Source: Journal of Proteomics - April 11, 2024 Category: Biochemistry Authors: Ashwani Punia Manglesh Kumari Monika Chouhan Vishal Saini Robin Joshi Ashok Kumar Rajiv Kumar Source Type: research

Proteomic and metabolomic insights into seed germination of Ferula assa-foetida
J Proteomics. 2024 Apr 9;300:105176. doi: 10.1016/j.jprot.2024.105176. Online ahead of print.ABSTRACTCold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory ...
Source: Journal of Proteomics - April 11, 2024 Category: Biochemistry Authors: Ashwani Punia Manglesh Kumari Monika Chouhan Vishal Saini Robin Joshi Ashok Kumar Rajiv Kumar Source Type: research

Proteomic and metabolomic insights into seed germination of Ferula assa-foetida
J Proteomics. 2024 Apr 9;300:105176. doi: 10.1016/j.jprot.2024.105176. Online ahead of print.ABSTRACTCold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory ...
Source: Journal of Proteomics - April 11, 2024 Category: Biochemistry Authors: Ashwani Punia Manglesh Kumari Monika Chouhan Vishal Saini Robin Joshi Ashok Kumar Rajiv Kumar Source Type: research

Proteomic and metabolomic insights into seed germination of Ferula assa-foetida
J Proteomics. 2024 Apr 9:105176. doi: 10.1016/j.jprot.2024.105176. Online ahead of print.ABSTRACTCold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in Ferula assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory ...
Source: Journal of Proteomics - April 11, 2024 Category: Biochemistry Authors: Ashwani Punia Manglesh Kumari Monika Chouhan Vishal Saini Robin Joshi Ashok Kumar Rajiv Kumar Source Type: research

Proteomic and metabolomic insights into seed germination of Ferula assa-foetida
J Proteomics. 2024 Apr 9:105176. doi: 10.1016/j.jprot.2024.105176. Online ahead of print.ABSTRACTCold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in Ferula assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory ...
Source: Journal of Proteomics - April 11, 2024 Category: Biochemistry Authors: Ashwani Punia Manglesh Kumari Monika Chouhan Vishal Saini Robin Joshi Ashok Kumar Rajiv Kumar Source Type: research

A candidate panel of eight urinary proteins shows potential of early diagnosis and risk assessment for diabetic kidney disease in type 1 diabetes
J Proteomics. 2024 Apr 2;300:105167. doi: 10.1016/j.jprot.2024.105167. Online ahead of print.ABSTRACTDiabetic kidney disease (DKD) poses a significant health challenge for individuals with diabetes. At its initial stages, DKD often presents asymptomatically, and the standard for non-invasive diagnosis, the albumin-creatinine ratio (ACR), employs discrete categorizations (normal, microalbuminuria, macroalbuminuria) with limitations in sensitivity and specificity across diverse population cohorts. Single biomarker reliance further restricts the predictive value in clinical settings. Given the escalating prevalence of diabete...
Source: Journal of Proteomics - April 4, 2024 Category: Biochemistry Authors: Jeremy Altman Shan Bai Sharad Purohit John White Dennis Steed Su Liu Diane Hopkins Jin-Xiong She Ashok Sharma Wenbo Zhi Source Type: research

Use of data-independent acquisition mass spectrometry to identify an objective serum indicator of the need for osteoporotic therapeutic intervention
This study aimed to identify objective serum indicators of the need for therapeutic intervention in individuals at risk of osteoporotic fracture. Comprehensive proteome analyses of serum collected from patients with osteoporosis but no fractures, patients with osteopenia and fragility fractures, and controls were performed by data-independent acquisition mass spectrometry. Collective evaluation of the proteome analysis data and ELISA-based assays identified serum ECM1 as a potential objective marker of the risk of fragility fractures in patients with osteoporosis or osteopenia. The findings are an important step toward the...
Source: Journal of Proteomics - April 4, 2024 Category: Biochemistry Authors: Yusuke Nakai Ken Kumagai Yoko Ino Tomoko Akiyama Kayano Moriyama Yuriko Takeda Kenji Egashira Takashi Ohira Akihide Ryo Tomoyuki Saito Yutaka Inaba Hisashi Hirano Yayoi Kimura Source Type: research

A candidate panel of eight urinary proteins shows potential of early diagnosis and risk assessment for diabetic kidney disease in type 1 diabetes
J Proteomics. 2024 Apr 2;300:105167. doi: 10.1016/j.jprot.2024.105167. Online ahead of print.ABSTRACTDiabetic kidney disease (DKD) poses a significant health challenge for individuals with diabetes. At its initial stages, DKD often presents asymptomatically, and the standard for non-invasive diagnosis, the albumin-creatinine ratio (ACR), employs discrete categorizations (normal, microalbuminuria, macroalbuminuria) with limitations in sensitivity and specificity across diverse population cohorts. Single biomarker reliance further restricts the predictive value in clinical settings. Given the escalating prevalence of diabete...
Source: Journal of Proteomics - April 4, 2024 Category: Biochemistry Authors: Jeremy Altman Shan Bai Sharad Purohit John White Dennis Steed Su Liu Diane Hopkins Jin-Xiong She Ashok Sharma Wenbo Zhi Source Type: research

Use of data-independent acquisition mass spectrometry to identify an objective serum indicator of the need for osteoporotic therapeutic intervention
This study aimed to identify objective serum indicators of the need for therapeutic intervention in individuals at risk of osteoporotic fracture. Comprehensive proteome analyses of serum collected from patients with osteoporosis but no fractures, patients with osteopenia and fragility fractures, and controls were performed by data-independent acquisition mass spectrometry. Collective evaluation of the proteome analysis data and ELISA-based assays identified serum ECM1 as a potential objective marker of the risk of fragility fractures in patients with osteoporosis or osteopenia. The findings are an important step toward the...
Source: Journal of Proteomics - April 4, 2024 Category: Biochemistry Authors: Yusuke Nakai Ken Kumagai Yoko Ino Tomoko Akiyama Kayano Moriyama Yuriko Takeda Kenji Egashira Takashi Ohira Akihide Ryo Tomoyuki Saito Yutaka Inaba Hisashi Hirano Yayoi Kimura Source Type: research

A candidate panel of eight urinary proteins shows potential of early diagnosis and risk assessment for diabetic kidney disease in type 1 diabetes
J Proteomics. 2024 Apr 2:105167. doi: 10.1016/j.jprot.2024.105167. Online ahead of print.ABSTRACTDiabetic kidney disease (DKD) poses a significant health challenge for individuals with diabetes. At its initial stages, DKD often presents asymptomatically, and the standard for non-invasive diagnosis, the albumin-creatinine ratio (ACR), employs discrete categorizations (normal, microalbuminuria, macroalbuminuria) with limitations in sensitivity and specificity across diverse population cohorts. Single biomarker reliance further restricts the predictive value in clinical settings. Given the escalating prevalence of diabetes, o...
Source: Journal of Proteomics - April 4, 2024 Category: Biochemistry Authors: Jeremy Altman Shan Bai Sharad Purohit John White Dennis Steed Su Liu Diane Hopkins Jin-Xiong She Ashok Sharma Wenbo Zhi Source Type: research