Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, James Broadbent, Utpal Bose, Mitchell G. Nye-Wood, Ian B. Edwards, Michelle L. Colgrave
Summary: This study analyzed the proteome and malt characteristics of three barley lines grown in different locations in Western Australia using LC-MS. The results showed a correlation between genetics, growing locations, proteins, and traits such as malt yield.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Lukasz Pawel Kozlowski
Summary: Proteome-pI 2.0 is an online database that predicts the isoelectric points and pKa values of proteins and peptides, catering to analytical biochemistry and proteomics techniques. The database includes over 61 million protein sequences and utilizes 21 methods to predict the isoelectric point of proteins and one method for inferring pKa values, facilitating bottom-up proteomics analysis.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Food Science & Technology
Qingqing Qin, Jia Liu, Shumin Hu, Jianjun Dong, Junhong Yu, Li Fang, Shuxia Huang, Lushan Wang
Summary: This study analyzed the mechanisms of malting performance variance among different barley cultivars, especially Chinese barley Gan-7. Differential expression proteins play crucial roles in genetic information processing and carbohydrate metabolism pathways, with the low alpha-amylase abundance being related to poor alpha-amylase activity in Gan-7. The findings provide insights for optimizing the malting process for Chinese domestic barley cultivars, particularly Gan-7.
JOURNAL OF CEREAL SCIENCE
(2021)
Article
Chemistry, Analytical
Runsheng Zheng, Natalia Govorukhina, Tabiwang N. Arrey, Christopher Pynn, Ate van der Zee, Gyorgy Marko-Varga, Rainer Bischoff, Alexander Boychenko
Summary: This study compares 1D-nanoLC-MS with an automated online-2D high-pH RP x low pH RP separation method for deep proteome profiling, demonstrating that the new method can increase peptide and protein identifications without the need for extra sample handling. Serum sample preparation related changes were revealed, which should be taken into account when planning multicentric biomarker discovery and validation studies.
ANALYTICAL CHEMISTRY
(2021)
Article
Plant Sciences
Zdenek Perutka, Katerina Kaduchova, Ivo Chamrad, Jana Beinhauer, Rene Lenobel, Beata Petrovska, Veronique Bergougnoux, Jan Vrana, Ales Pecinka, Jaroslav Dolezel, Marek Sebela
Summary: Proteins play a crucial role in the structure and function of the nuclear genome, but our knowledge of their functions, especially in plant chromosomes, remains incomplete. A study using flow cytometry purified barley mitotic metaphase chromosomes and characterized their proteins, identifying various chromosomal proteins including histones and topoisomerase. This research enhances our understanding of plant chromosomal proteins and provides a basis for further functional characterization and comparative phylogenetic analyses.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, Utpal Bose, Mitchell G. Nye-Wood, Malcolm Blundell, Crispin A. Howitt, Michelle L. Colgrave
Summary: In this study, the proteome profile of barley grain and malt samples was investigated using SWATH-MS proteomics. The results showed that the C-hordein-reduced lines had a more significant impact on proteome level changes during malting. Upregulated proteins in C-hordein-reduced lines were mainly involved in the tricarboxylic acid cycle and fatty acid peroxidation processes. Proteomics approaches in hordein-reduced barley lines after malting also revealed additional changes in the proteome driven by the genetic background. These findings provide valuable insights for barley breeders and maltsters to optimize gluten-free grains in malt products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Food Science & Technology
Jiyoung Park, Hyun-Jung Chung, Hye Young Park, Hyun-Jin Park, Sea-Kwan Oh
Summary: Malt production and conditioning were carried out using three different barley cultivars in South Korea. The quality and starch characteristics of the malts were compared, with a significant reduction in starch content observed. Heugho and Hopum barley exhibited higher coleoptile elongation compared to Kwangmaeg barley. After malting, the mono- and di-saccharide contents increased, with Hopum barley showing the highest fermentable sugar level.
FOOD SCIENCE AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Shakila H. Peli Thanthri, Thomas H. Linz
Summary: This report presents a microfluidic thermal gel transient isotachophoresis (TG-tITP) method for rapid and high-resolution separation of native proteins. By utilizing the viscosity response of thermal gels and temperature gradients, this method achieves a wide mass range separation with 15,000-fold less protein loading and five-fold faster analysis times.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Agriculture, Dairy & Animal Science
Mohan Kiran, Naveena B. Maheswarappa, Rituparna Banerjee, Venkatesh Ch, Srikanth Rapole
Summary: The study showed that slaughtering of sheep without stunning resulted in changes in protein abundance related to various physiological processes. These protein alterations have the potential to serve as indicators for assessing animal welfare.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Agata Piasecka, Andrea Baier
Summary: This study investigated the impact of three trophic modes on the growth parameters and biochemical composition of Chlorella species. The results showed that mixotrophic cultivation using an agro-industrial by-product stimulated the growth of all species, yielding high amounts of protein-rich biomass. The study also provided insights into the proteome of Chlorella cells cultured under molasses supplementation conditions.
Article
Chemistry, Analytical
Carolina Rojas Ramirez, Jessica A. Espino, Lisa M. Jones, Daniel A. Polasky, Alexey I. Nesvizhskii
Summary: Monitoring protein structure before and after environmental alterations can provide insights into protein function. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry allows for monitoring of structural rearrangements by exposing proteins to radicals. However, the challenges of processing FPOP data have limited its proteome-scale uses. In this study, a computational workflow was developed to analyze FPOP data sets more efficiently, enabling the identification of modified peptide spectra at a faster rate than previous methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Rijul Bhimwal, Richard R. Rustandi, Anne Payne, Mohamed Dawod
Summary: This review highlights the noteworthy advancements in capillary gel electrophoresis for protein separation and analysis from 2015 to 2021. It provides an overview of the technique's historical perspective, principles, challenges, and limitations, and discusses the advancements made to overcome these issues and expand our understanding of the method. The review also presents applications of capillary gel electrophoresis and future directions for the technique.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Sharifah Zakiah Syed Sulaiman, Wei Miao Tan, Rozanaliza Radzi, Intan Nur Fatiha Shafie, Mokrish Ajat, Rozaihan Mansor, Suhaila Mohamed, Norasfaliza Rahmad, Angela Min Hwei Ng, Seng Fong Lau
Summary: This study compared the proteomic changes in the synovial fluid of surgically and chemically induced osteoarthritis (OA) models. The surgical model showed a wider range of protein changes, while the chemical model had slower OA progression.
Article
Chemistry, Multidisciplinary
Henock M. Deberneh, Doaa R. Abdelrahman, Sunil K. Verma, Jennifer J. Linares, Andrew J. Murton, William K. Russell, Muge N. Kuyumcu-Martinez, Benjamin F. Miller, Rovshan G. Sadygov
Summary: Heavy water metabolic labeling combined with liquid chromatography coupled with mass spectrometry is a high throughput technique for measuring protein turnover rates in vivo. The authors provide theoretical formulas for the dynamics of six mass isotopomers and propose a method that utilizes partial isotope profiles to compute protein turnover rate. This approach improves proteome coverage and accuracy of label enrichment estimation.
COMMUNICATIONS CHEMISTRY
(2023)
Editorial Material
Plant Sciences
J. Liu, L. Yang, J. Zhou, G. Cai, X. Li, J. Lu
Editorial Material
Plant Sciences
J. Liu, W. Feng, L. Yang, X. Li, J. Lu
Editorial Material
Plant Sciences
J. Liu, L. Yang, P. Miao, D. Wu, G. Cai, X. Li, J. Lu
Article
Agriculture, Multidisciplinary
Guolin Cai, Yifan Liu, Xiaomin Li, Jian Lu
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Hua Yang, Junyong Sun, Tiantian Tian, Hong Gu, Xiaomin Li, Guolin Cai, Jian Lu
JOURNAL OF FOOD BIOCHEMISTRY
(2019)
Editorial Material
Plant Sciences
J. Liu, J. Xiao, J. Zhou, G. Cai, X. Li, J. Lu
Article
Chemistry, Applied
Xiaomin Li, Xizhu Xie, Jun Liu, Dianhui Wu, Guolin Cai, Jian Lu
Article
Chemistry, Applied
Hua Yang, Tiantian Tian, Hong Gu, Xiaomin Li, Guolin Cai, Junyong Sun, Dianhui Wu, Jian Lu
Article
Biotechnology & Applied Microbiology
Dianhui Wu, Wenjuan Xie, Xiaomin Li, Guolin Cai, Jian Lu, Guangfa Xie
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Article
Food Science & Technology
Wei Yu, Guangfa Xie, Dianhui Wu, Xiaomin Li, Jian Lu
Article
Agriculture, Multidisciplinary
Hua Yang, Ying Xie, Xiaomin Li, Dianhui Wu, Guolin Cai, Jian Lu
Summary: Untargeted metabolomics analysis using HILIC LC-MS identified 22 key differential metabolites associated with browning of Dangshan pear wine, including glucose, phenylalanine, aloin, etc. Maillard reaction and oxidation were critical pathways in the browning process.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Food Science & Technology
Hua Yang, Xuexue Chen, Xiaomin Li, Dianhui Wu, Guolin Cai, Jian Lu
Summary: Sulfur dioxide and reduced glutathione are the most effective inhibitors for preventing browning in Dangshan pear wine, reducing the degree of browning and increasing brightness.
JOURNAL OF FOOD PROCESSING AND PRESERVATION
(2022)
Article
Food Science & Technology
Yueling Shang, Xiaomin Li, Guolin Cai, Dujun Wang, Fengwei Li, Jian Lu, Xiaohong Yu
Summary: The xylanase inhibitor from barley has the potential to inhibit microbial enzymes and mitigate premature yeast flocculation during fermentation.
JOURNAL OF THE INSTITUTE OF BREWING
(2022)
Article
Microbiology
Jun Liu, Xiaomin Li, Yueqin Liu, Chengyu Xing, Ying Xie, Guolin Cai, Jian Lu
Summary: This study analyzed the genetic diversity of 35 industrial brewing yeasts using ISSR markers, and established three core collections to improve germplasm resource preservation, management, and utilization efficiency. Core1 was considered the best core collection based on loci retention ratio and trait coverage efficiency.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Guolin Cai, Dianhui Wu, Xiaomin Li, Jian Lu
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2020)