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
Plant Sciences
Utpal Bose, Angela Juhasz, Ronald Yu, Mahya Bahmani, Keren Byrne, Malcolm Blundell, James A. Broadbent, Crispin A. Howitt, Michelle L. Colgrave
Summary: This study investigated the regulatory effect of the lys3 mutation in barley, revealing its impact on storage protein accumulation and critical processes in cereal seeds. The results provide insights into how the lys3 mutation remodels cellular functions and impacts phenotype, offering potential applications in selective breeding for favorable agronomic traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Agriculture, Multidisciplinary
Mahya Bahmani, Clare E. O'Lone, Angela Juhasz, Mitchell Nye-Wood, Hugh Dunn, Ian B. Edwards, Michelle L. Colgrave
Summary: This article discusses the importance of barley in the world and the application of proteomics technology in barley research, including the response of proteins to environmental conditions and their impact on food processing. Proteomics can be used to guide barley breeding programs to improve its nutritional value and application scope.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
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
Chemistry, Multidisciplinary
Kyle A. Brown, Morgan K. Gugger, David S. Roberts, David Moreno, Pil Seok Chae, Ying Ge, Song Jin
Summary: We synthesized and characterized a new family of maltose-derived nonionic surfactants containing a photocleavable azo-sulfide linker (mAzo). The self-assembly properties of these surfactants were studied using various techniques, including surface tension measurements, dynamic light scattering, and transmission electron microscopy. The photodegradation process of these surfactants was investigated, revealing the formation of a photo-stable surfactant post-degradation. Furthermore, these mAzo surfactants demonstrated potential in solubilizing challenging proteins from heart tissue.
Article
Biochemical Research Methods
Sarah K. Osama, Edward D. Kerr, Adel M. Yousif, Toan K. Phung, Alison M. Kelly, Glen P. Fox, Benjamin L. Schulz
Summary: Germination is a critical process for flowering plant reproduction and industrial malting, while seed dormancy can lead to inefficiencies in malt production. Proteomic analysis identified significant changes during germination, including a rapid decrease in proteins involved in desiccation tolerance and germination inhibition, as well as reductions in lipid, protein, and nutrient reservoir storage. These consistent changes between laboratory and industrial scales demonstrate the utility of laboratory-scale germination as a model system for industrial malt house processes.
JOURNAL OF PROTEOMICS
(2021)
Review
Biochemistry & Molecular Biology
Meletia Kallianta, Eftychia Pappa, Heleni Vastardis, Christos Rahiotis
Summary: Mass Spectrometry (MS) is a highly sensitive and universal analytical technique that has rapidly developed in recent decades. It has various applications in dentistry, including research on dental materials and agents, laboratory analysis of biospecimens, and real-time diagnostics in oral surgery and pathology. MS can provide valuable insights into the clinical behavior, toxicity, antimicrobial properties, and biomarkers of dental materials and agents. It is also effective in detecting biomarkers in saliva and providing a comprehensive understanding of cellular functions through metabolite analysis. Additionally, MS shows promising potential for surgical approaches to oral malignant disorders. Overall, MS has revolutionized dental research and has the potential to advance personalized dentistry.
Article
Chemistry, Applied
Patricia Alonso-Riano, Rodrigo Melgosa, Ester Trigueros, Alba Ester Illera, Sagrario Beltran, M. Teresa Sanz
Summary: This study assessed the double effect of supercritical carbon dioxide (sc-CO2) in a biorefinery concept applied to brewer's spent grain (BSG). The results showed that high pressures and temperatures resulted in higher content of phenolic and flavonoid compounds, as well as higher antioxidant capacity. Additionally, the enzymatic hydrolysis yield of cellulase in the sc-CO2 treated BSG was improved compared to the non-treated BSG, which could be attributed to the removal of the lipid fraction and morphological changes.
Review
Food Science & Technology
Alice Jaeger, Emanuele Zannini, Aylin W. Sahin, Elke K. Arendt
Summary: This review discusses the importance of extracting and applying proteins from barley, particularly those from brewers' spent grain. Brewers' spent grain is a significant by-product in the brewing industry, and there is great interest in valorising and utilising its proteins.
Article
Biochemistry & Molecular Biology
Sumaiya Nazli, Kip D. Zimmerman, Angelica M. Riojas, Laura A. Cox, Michael Olivier
Summary: The proteomic analysis of plasma has great potential for precision medicine and biomarker identification. However, detecting and quantifying low abundance proteins in plasma is challenging. This study developed a mass spectrometry approach using tandem mass tags (TMT) and a tissue reference sample, which successfully identified and quantified numerous proteins in nonhuman primate plasma samples. The methodology promises to increase the number of putative disease biomarkers by efficiently quantifying plasma proteins released from specific tissues.
Review
Biochemistry & Molecular Biology
Ekaterina Mikhailovna Stakhneva, Evgeniia Vitalievna Striukova, Yulia Igorevna Ragino
Summary: Proteomic studies play a crucial role in investigating atherosclerotic cardiovascular diseases, identifying potential biomarkers, and offering novel diagnostic approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Larissa van der Maas, Maarten Danial, Gideon F. A. Kersten, Bernard Metz, Hugo D. Meiring
Summary: A mass spectrometric method was developed to identify and quantify antigens in DTaP vaccines. The method can be used for both final batch release and in-process control monitoring, potentially reducing the need for animal testing.
Article
Agricultural Engineering
Evelynar Wagner, Mara Eugenia Peria, Gaston Ezequiel Ortiz, Natalia Lorena Rojas, Pablo Daniel Ghiringhelli
Summary: The valorization of brewer's spent grain (BSG), the main solid waste from this industry, is important for reducing environmental impact. Efficient enzymatic sugar release was observed after pretreatment with H2O2, showing potential for high-value utilization.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Multidisciplinary Sciences
John P. McGee, Pei Su, Kenneth R. Durbin, Michael A. R. Hollas, Nicholas W. Bateman, G. Larry Maxwell, Thomas P. Conrads, Ryan T. Fellers, Rafael D. Melani, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
Summary: This study introduces a semi-automated single-ion mass spectrometry workflow for top-down tandem mass spectrometry analysis directly from tissue microenvironments. The results demonstrate that this method can identify multiple proteoforms in tumor samples within a short period of time, and effectively identify proteoform signatures in tumor and stromal regions.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Nicolai Bjodstrup Palstrom, Rune Matthiesen, Lars Melholt Rasmussen, Hans Christian Beck
Summary: The human plasma proteome reflects the physiological state of the cardiovascular system and has been used to analyze plasma biomarkers for cardiovascular diseases for decades. However, current plasma biomarkers only address a limited subset of cardiovascular diseases, and there is an urgent need for biomarkers for diseases with increasing incidence like heart failure and abdominal aortic aneurysm. Recent advancements in technologies for analyzing the human plasma proteome are addressing the complexity and facilitating the discovery of novel biomarkers for cardiovascular diseases.
Article
Multidisciplinary Sciences
Kae Hwan Sim, Lillian Chia-Yi Liu, Hwee Tong Tan, Kelly Tan, Daniel Ng, Wei Zhang, Yuansheng Yang, Stephen Tate, Xuezhi Bi
Article
Endocrinology & Metabolism
Man Mohan Shrestha, Chun-Yan Lim, Xuezhi Bi, Robert C. Robinson, Weiping Han
Summary: This study identifies Tmod3 as a novel AMPK effector in regulating GLUT4 translocation and glucose uptake, revealing its crucial role in F-actin remodeling and GLUT4 insertion into the PM.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Multidisciplinary Sciences
Eun Myoung Shin, Vinh Thang Huynh, Sultan Abda Neja, Chia Yi Liu, Anandhkumar Raju, Kelly Tan, Nguan Soon Tan, Jayantha Gunaratne, Xuezhi Bi, Lakshminarayan M. Iyer, L. Aravind, Vinay Tergaonkar
Summary: GREB1 catalyzes O-GlcNAcylation of ER alpha at residues T553/S554, stabilizing ER alpha protein by inhibiting its association with the ubiquitin ligase ZNF598. Loss of GREB1-mediated glycosylation of ER alpha results in reduced cellular ER alpha levels and insensitivity to estrogen, while higher GREB1 expression in ER alpha(+) breast cancer is associated with greater survival in response to tamoxifen.
Article
Biotechnology & Applied Microbiology
Alison P. Lee, Yee Jiun Kok, Meiyappan Lakshmanan, Dawn Leong, Lu Zheng, Hsueh Lee Lim, Shuwen Chen, Shi Ya Mak, Kok Siong Ang, Neil Templeton, Taha Salim, Xiaona Wei, Eric Gifford, Andy Hee-Meng Tan, Xuezhi Bi, Say Kong Ng, Dong-Yup Lee, Wai Lam W. Ling, Ying Swan Ho
Summary: This study investigated the impact of different pH set points on mAb production using longitudinal multi-omics profiling, revealing differential regulation of intracellular pathways, resulting in variations in productivity, titer, and quality profiles. Additionally, a time-dependent change in mAb N-glycosylation profiles, independent of pH, was identified due to protein accumulation in the endoplasmic reticulum disrupting cellular homeostasis over time. The findings provide a deeper understanding of intracellular processes in mAb-producing CHO cell line and can serve as a baseline for quality optimization and control in mAb production.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Microbiology
Christophe Lay, Collins Wenhan Chu, Rikky Wenang Purbojati, Enzo Acerbi, Daniela Drautz-Moses, Paola Florez de Sessions, Song Jie, Eliza Ho, Yee Jiun Kok, Xuezhi Bi, Shuwen Chen, Shi Ya Mak, Mei Chien Chua, Anne E. N. Goh, Wen Chin Chiang, Rajeshwar Rao, Surasith Chaithongwongwatthana, Nipon Khemapech, Voranush Chongsrisawat, Rocio Martin, Guus Roeselers, Ying Swan Ho, Martin L. Hibberd, Stephan C. Schuster, Jan Knol
Summary: The study revealed significant differences in the gut microbiome of infants born via C-section and vaginal delivery in early stages, with C-section infants showing compromised microbiome features. The addition of synbiotics may help prevent the formation of a compromised microbiome.
Article
Oncology
Amrita M. Nargund, Chang Xu, Amit Mandoli, Atsushi Okabe, Gao Bin Chen, Kie Kyon Huang, Taotao Sheng, Xiaosai Yao, Jia Ming Nickolas Teo, Raghav Sundar, Yee Jiun Kok, Yi Xiang See, Manjie Xing, Zhimei Li, Chern Han Yong, Aparna Anand, A. I. Zul Fazreen, Lai Fong Poon, Michelle Shu Wen Ng, Javier Yu Peng Koh, Wen Fong Ooi, Su Ting Tay, Xuewen Ong, Angie Lay Keng Tan, Heike Grabsch, Melissa J. Fullwood, Tean Bin Teh, Xuezhi Bi, Atsushi Kaneda, Shang Li, Patrick Tan
Summary: Mutations in the MSH2 gene are causative in gastric cancer, and MSH2 has a novel epigenomic function in regulating gene expression. MSH2 binds to tumor-associated superenhancers in early-stage gastric cancer, playing a role in chromatin rewiring and cell adhesion pathway expression. Loss of MSH2 in advanced gastric cancer leads to deficient cell adhesion pathway expression and enhanced tumorigenesis. Additionally, MSH2-deficient gastric cancer cells show addiction to BET inhibition.
Article
Biochemistry & Molecular Biology
Tushar Warrier, Chadi El Farran, Yingying Zeng, Benedict Shao Quan Ho, Qiuye Bao, Zi Hao Zheng, Xuezhi Bi, Huck Hui Ng, Derrick Sek Tong Ong, Justin Jang Hann Chu, Amartya Sanyal, Melissa Jane Fullwood, James J. Collins, Hu Li, Jian Xu, Yuin-Han Loh
Summary: SETDB1 regulates lineage-specific genes and endogenous retroviral elements through H3K9me3 deposition. In addition, it co-regulates target gene expression and genome topology with the topological regulator Cohesin at DiSCs, which are regions proximal to gene promoters involved in embryonic stem cell pluripotency and lineage development. This discovery is important for understanding the maintenance and differentiation of embryonic stem cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Chee Fan Tan, Soon Hong Kwan, Chun Shing Lee, Yan Ni Annie Soh, Ying Swan Ho, Xuezhi Bi
Summary: We have developed a protein extraction process to produce cottonseed meal protein isolate (CSMPI) with ultra-low gossypol content. The CSMPI has better functional properties and digestibility compared to pea protein isolate. The results suggest that CSMPI has potential applications as an alternative protein source in human food.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Yixin Zhang, Wei Wei, Huamei Wen, Zhongle Cheng, Zhongwen Mi, Jing Zhang, Xiaolong Liu, Xinjiong Fan
Summary: This study introduces a novel biofilm-targeted strategy using combined enzymes to prevent biofilm formation and break down preformed biofilms. By modifying the quorum-sensing inhibitor AidH and combining it with the glycosyl hydrolase PslG, the combined-enzyme intervention effectively disrupts biofilms of Pseudomonas aeruginosa. The strategy also helps reverse antibiotic resistance in multidrug-resistant clinical strains. This research highlights the potential clinical application of the combined-enzyme approach for P. aeruginosa infection.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biotechnology & Applied Microbiology
Yangyang Zhan, Haixia Xu, Hween Tong Tan, Ying Swan Ho, Dongxiao Yang, Shuwen Chen, Dave Siak-Wei Ow, Xin Lv, Fang Wei, Xuezhi Bi, Shouwen Chen
Summary: This study investigates the mechanisms of B. licheniformis DW2 resistance to 2-PE using multi-omics technology. The tolerant strain displays multifactorial mechanisms, including global stress response activation, repair system activation, NADPH supply increase, cell morphology and membrane composition changes, and metabolic pathway remodeling. The findings provide novel insights for improving 2-PE resistance and achieving industrial-scale production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Chemistry, Applied
Lin Zhao, Ming-Hsu Chen, Xuezhi Bi, Juan Du
Summary: The study aimed to modify the physicochemical properties of plant-based proteins using microbial transglutaminase (MTG) and investigate its effects on protein structure and digestion. MTG treatment significantly increased water holding capacity and decreased oil holding capacity of the protein blend. It also resulted in stronger and more elastic gels with lower gel point temperature. The application of MTG led to protein-protein interactions and the formation of a more ordered structure with better thermal stability. In vitro digestion showed changes in amino acid release in the digests of the MTG-treated protein blend. Overall, MTG can be used to develop innovative food products with modified functionalities and unique digestion characteristics.
FOOD HYDROCOLLOIDS
(2023)
Review
Biochemistry & Molecular Biology
Jin Hao Tan, Anqi Chen, Jiawu Bi, Yee Hwee Lim, Fong Tian Wong, Dave Siak-Wei Ow
Summary: This review discusses the potential use of three newly identified D-allulose 3-epimerases for the industrial-scale manufacturing of D-allulose. It also highlights other methods to enhance the process efficiency, such as improving the thermotolerance and acid resistance of D-allulose enzymes, utilizing Bacillus subtilis for the biosynthesis of D-allulose, and immobilizing D-allulose enzymes to enhance their activity, half-life, and stability. These research advancements have led to increased yields of D-allulose, bridging the gap between small-scale production and industrial-scale manufacturing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Naoki Miyamoto, Young-Hyun Go, Larissa Miasiro Ciaramicoli, Haw-Young Kwon, Heon Seok Kim, Xuezhi Bi, Young Hyun Yu, Beomsue Kim, Hyung-Ho Ha, Nam-Young Kang, Seong-Wook Yun, Jin-Soo Kim, Hyuk-Jin Cha, Young-Tae Chang
Summary: The molecular targets of CDy1, ALDH2 and ABCB1, were identified through live-cell affinity-matrix and ABC transporter CRISPRa library screening, revealing the potential for multi-dimensional cellular distinction of specific cell types.
RSC CHEMICAL BIOLOGY
(2021)