Article
Chemistry, Applied
Rocio Galindo-Lujan, Laura Pont, Zoran Minic, Maxim V. Berezovski, Victoria Sanz-Nebot, Fernando Benavente
Summary: This study analyzed the proteins from different varieties of quinoa seeds from Peru and Bolivia using advanced LC-MS/MS technology, identifying protein similarities and differences in the proteome. The comprehensive experimental quinoa seed proteome map presented in this study serves as a valuable starting point for further characterization and nutritional studies of quinoa and quinoa-containing food products.
Article
Biochemical Research Methods
Huu-Quang Nguyen, Dabin Lee, Yeoseon Kim, Geul Bang, Kun Cho, Young-Sun Lee, Jong Eun Yeon, David M. Lubman, Jeongkwon Kim
Summary: This study utilized LC-MS/MS to analyze the protein expression profiles of extracellular vesicles from serum samples of patients with various fatty liver diseases, revealing significant differences in protein expression levels of apolipoproteins, immunoglobulins, and other markers. Through principal component analysis, a clear differentiation between ALD and NAFLD was achieved. The up-regulation of alpha-2-macroglobulin in alcoholic hepatitis and apolipoprotein C3 in NAFLD were identified as significant findings.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Joanna Bons, Gauthier Husson, Marie Chion, Muriel Bonnet, Myriam Maumy-Bertrand, Francois Delalande, Sarah Cianferani, Frederic Bertrand, Brigitte Picard, Christine Carapito
Summary: Mass spectrometry is a valuable tool for protein quantification, with SWATH-MS outperforming SRM in sensitivity and dynamic range, while PRM remains the best performer. An original label-free quantification method on SWATH-MS provided a comprehensive analysis of muscle proteomes and further insights into the effects of muscle type on candidate biomarkers of beef qualities and muscle metabolism.
Article
Plant Sciences
Muhammad Afzal, Malte Sielaff, Valentina Curella, Manjusha Neerukonda, Khaoula El Hassouni, Detlef Schuppan, Stefan Tenzer, C. Friedrich H. Longin
Summary: The study analyzed the expression of 756 proteins across 150 wheat cultivars using proteomics and found that environmental conditions have a significant impact on protein expression. Wheat cultivars varied greatly in their protein profiles, with 114 proteins being crucial for bread quality and human health.
Article
Biochemistry & Molecular Biology
Nor Hafiza Sayuti, Nabilah Zulkefli, Jen Kit Tan, Norazalina Saad, Syarul Nataqain Baharum, Hamizah Shahirah Hamezah, Hamidun Bunawan, Qamar Uddin Ahmed, Humaira Parveen, Sayeed Mukhtar, Meshari A. Alsharif, Murni Nazira Sarian
Summary: This study found that PMEE can provide neuroprotection against H2O2-induced oxidative stress by activating multiple signaling pathways, and PMEE may serve as a preventative therapy for neurodegenerative diseases.
Article
Parasitology
Ricardo Perez-Sanchez, Angel Carnero-Moran, M. Luz Valero, Ana Oleaga
Summary: Using a proteomics informed by transcriptomics (PIT) approach, the researchers successfully obtained and characterized the proteome of the saliva of Ornithodoros erraticus adult ticks. They identified novel salivary proteins and functions, and found significant differences between sexes in the saliva proteome of O. erraticus ticks. These findings improve our understanding of feeding physiology in O. erraticus ticks and will contribute to the development of vaccines for controlling O. erraticus infestations and the diseases it transmits.
PARASITES & VECTORS
(2022)
Article
Biochemistry & Molecular Biology
Aleksandra E. Lewandowska, Anna Fel, Marcel Thiel, Paulina Czaplewska, Krzysztof Lukaszuk, Jacek R. Wisniewski, Stanislaw Oldziej
Summary: Two label-free quantitative workflows based on different high-resolution mass spectrometers and LC setups were presented for the analysis of human follicular fluid proteome, with around 1000 proteins identified in each workflow. The concentration values obtained from both workflows showed significant correlation, leading to unified lists of proteins linked to oocyte maturity and blastocyst development. The Quad-Orbitrap workflow is suitable for in-depth analysis of low abundant proteome without extensive fractionation, while the Triple Quad-TOF workflow offers a more robust approach with potential for effectiveness with increasing number of analyzed samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Agriculture, Dairy & Animal Science
Alessio Di Luca, Francesca Bennato, Andrea Ianni, Lisa Grotta, Michael Henry, Paula Meleady, Giuseppe Martino
Summary: In this study, proteomic technologies were used to compare the milk proteome of two goat breeds, Teramana and Saanen. The analysis identified 29 proteins that could discriminate between the two breeds. This research contributes to our understanding of the goat milk proteome and provides important information for future studies on goat milk proteins.
Article
Developmental Biology
Hao Chen, Katherine E. Williams, Elaine Y. Kwan, Mirhan Kapidzic, Kenisha A. Puckett, Rayyan K. Aburajab, Joshua F. Robinson, Susan J. Fisher
Summary: During pregnancy, cytotrophoblasts from the placenta differentiate into specialized subpopulations, with some following an invasive pathway crucial for proper fetal development. The ability of these cells to migrate, invade and remodel arteries is essential for ensuring adequate blood flow to nourish the fetus. Advances in understanding the molecular features regulating the differentiation of these cells are ongoing, with a mass spectrometry-based approach providing new insights into their differentiation dynamics.
Article
Medical Laboratory Technology
Jing Ye, Pengcheng Liu, Renming Li, Hui Liu, Wenjing Pei, Changxiu Ma, Bing Shen, Dahai Zhao, Xiaoyu Chen
Summary: This study identified differentially expressed proteins (DEPs) in connective tissue disease-associated interstitial lung disease (CTD-ILD) using label-free mass spectrometry. The results showed that these DEPs may play important roles in the development of CTD-ILD and can be potential new biomarkers for early diagnosis of CTD-ILD.
JOURNAL OF CLINICAL LABORATORY ANALYSIS
(2022)
Article
Chemistry, Analytical
Xue Wang, Liang Jin, Chenqi Hu, Shichen Shen, Shuo Qian, Min Ma, Xiaoyu Zhu, Fengzhi Li, Jianmin Wang, Yu Tian, Jun Qu
Summary: Quantitative proteomics in large cohorts faces challenges in reliability, accuracy, and reproducibility. The ultra-high-resolution IonStar method described in this study achieves reproducible protein measurement in large cohorts while minimizing ratio compression. Compared to the state-of-the-art SWATH-MS method, IonStar shows superior quantitative accuracy, precision, and reproducibility for lower-abundance proteins and significantly altered proteins.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Daniel G. Delafield, Hannah N. Miles, William A. Ricke, Lingjun Li
Summary: The ubiquity of mass spectrometry-based bottom-up proteomic analyses highlights the importance of validating methodologies for increased efficiency, coverage, and profiling depth. This study demonstrates the potential of porous graphitic carbon chromatography (PGC) as a means to enhance proteomic coverage without altering sample preparation, instrument configuration, or acquisition methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Parasitology
Ana Oleaga, Angel Carnero-Moran, M. Luz Valero, Ricardo Perez-Sanchez
Summary: This study aimed to increase data on the composition of the saliva proteome of adult Ornithodoros moubata ticks, with a focus on females, to aid in the selection of salivary antigens for tick vaccines. Using mass spectrometry approaches, SWATH-MS proved superior in identifying proteins in female saliva and revealed significant quantitative differences between male and female saliva proteomes. This new knowledge can inform the rational selection of salivary candidates as antigen targets for tick vaccine development.
PARASITES & VECTORS
(2021)
Article
Plant Sciences
Yi-Fan Duan, Cheng Zhang, Min Zhang, Yu Ye, Kai-Lu Zhang, Mo-Xian Chen, Lin Chen, Xian-Rong Wang, Fu-Yuan Zhu
Summary: The study using proteomic approach revealed significant protein changes in pistils of male and hermaphroditic Osmanthus fragrans flowers, indicating the contributions of carbohydrate metabolism, secondary metabolism, and post-transcriptional regulation to the androdioecy breeding system. This sheds new light on the genetic basis and industrial development of Osmanthus fragrans.
Article
Medicine, General & Internal
Zohaib Iqbal, Helene A. Fachim, J. Martin Gibson, Ivona Baricevic-Jones, Amy E. Campbell, Bethany Geary, Rachelle P. Donn, Dashne Hamarashid, Akheel Syed, Anthony D. Whetton, Handrean Soran, Adrian H. Heald
Summary: Bariatric surgery induces metabolic pathway recalibration, potentially contributing to the remission of type 2 diabetes mellitus. Analysis of plasma samples identified several proteins that may serve as biomarkers for T2DM remission after surgery.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Plant Sciences
Muhammad Asyraf Mohd Amnan, Wan Mohd Aizat, Fiqri Dizar Khaidizar, Boon Chin Tan
Summary: Drought poses a significant threat to the agricultural sector, with limited knowledge on plant responses to drought stress and recovery. Pandanus amaryllifolius, a moderate drought-tolerant plant, displayed changes in morpho-physiological, biochemical, and protein levels in response to drought stress. The study revealed alterations in leaf relative water content, chlorophyll content, electrolyte leakage, proline and malondialdehyde contents, and antioxidant enzyme activities in drought-stressed and recovered P. amaryllifolius plants, with significant protein changes related to carbon metabolism, photosynthesis, stress response, and antioxidant activity.
Review
Plant Sciences
Juwairiah Remali, Idin Sahidin, Wan Mohd Aizat
Summary: This review provides a detailed overview of the biosynthesis of plant xanthones, highlighting the intricacies and differences between species. The pathway involves the shikimate pathway and oxidative coupling reactions to form xanthone ring compounds. The review also covers the biosynthesis of various downstream xanthone derivatives. The information collected here will be a valuable resource for further molecular research and synthetic biology applications in xanthone-producing plants.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Pharmacology & Pharmacy
Ummi Kalthum Azlan, Nur Aisyah Khairul Annuar, Ahmed Mediani, Wan Mohd Aizat, Hanafi Ahmad Damanhuri, Xiaohui Tong, Daijiro Yanagisawa, Ikuo Tooyama, Wan Zurinah Wan Ngah, Ibrahim Jantan, Hamizah Shahirah Hamezah
Summary: Neurodegenerative diseases (NDs) significantly impact patients' lives with progressive neurological disabilities. Neuroinflammation and oxidative reactions contribute to the progression of NDs. Moringa oleifera has been found to possess neuroprotective and anti-neuroinflammatory effects due to its phytochemicals with antioxidant and anti-inflammatory properties. However, further studies, including in vivo animal models and preclinical investigations, are needed to develop M. oleifera constituents into neuroprotective agents before clinical trials can be conducted.
FRONTIERS IN PHARMACOLOGY
(2023)
Review
Plant Sciences
Syed Muhammad Iqbal Syed Othman, Arif Faisal Mustaffa, M. Hafiz Che-Othman, Abdul Fatah A. Samad, Hoe-Han Goh, Zamri Zainal, Ismanizan Ismail
Summary: The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. Various mimic tools have been developed, with STTM being the most-developed due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA in diverse plant species and explores a modified STTM approach for studying miRNA function with spatial-temporal expression.
Review
Biotechnology & Applied Microbiology
Tiew-Yik Ting, YaDong Li, Hamidun Bunawan, Ahmad Bazli Ramzi, Hoe-Han Goh
Summary: Saccharomyces cerevisiae, a long-standing biotechnological application, has seen accelerated advancement through systems and synthetic biology approaches. Omics studies of S. cerevisiae have been used to investigate its stress tolerance in different industries. The development of genome-scale metabolic models and molecular tools like genome editing tools and metabolic engineering, along with omics data analysis, has facilitated the establishment of heterologous compound productions in cell factories.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Fatin Lyana Azman Shah, Syarul Nataqain Baharum, Hoe-Han Goh, Thean Chor Leow, Ahmad Bazli Ramzi, Siti Nurbaya Oslan, Suriana Sabri
Summary: In this study, the CHI gene was isolated from the cDNA of Polygonum minus and characterized. The protein sequence of PmCHI was classified as type I based on the presence of conserved residues in the active site. The 3D structure of PmCHI was predicted through homology modeling and validated, providing valuable insights for further research on its functional properties.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Multidisciplinary Sciences
Rubashiny Veeramohan, Arief Izzairy Zamani, Kamalrul Azlan Azizan, Hoe-Han Goh, Wan Mohd Aizat, Mohd Fauzi Abd Razak, Nur Sabrina Mohd Yusof, Sharif Mahsufi Mansor, Syarul Nataqain Baharum, Chyan Leong Ng
Summary: This study investigated the secondary metabolite composition of Mitragyna speciosa leaves in different maturity stages using LC-ESI-TOF-MS. The results identified 86 putatively annotated metabolite features, including alkaloids, flavonoids, terpenoids, phenylpropanoids, carboxylic acids, glucosides, phenols, and phenolic aldehydes. The multivariate analysis showed a significant difference in metabolite levels between young and mature leaves. Several new alkaloids were tentatively identified, highlighting the diverse biological activities of M. speciosa. These findings contribute to a better understanding of its pharmaceutical potential.
Article
Agronomy
Ili Nadhirah Jamil, Azhani Abdul-Rahman, Hoe-Han Goh, Wan Mohd Aizat
Summary: Mangosteen exhibits unique ripening behavior and transcriptomic analysis reveals differentially expressed transcripts at different ripening stages. The fruit conserves carbon skeleton rather than energy production at the early ripening stage and upregulates transcripts related to anthocyanin and xanthone biosynthesis. This study provides insights into the regulation of ripening in mangosteen and could contribute to its commercial utilization and preservation.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Review
Horticulture
Ching-Ching Wee, Vijay Kumar Subbiah, Masanori Arita, Hoe-Han Goh
Summary: Fruit ripening is a complex process involving the coordination of genes, hormones, and environmental factors. Understanding this mechanism is crucial for improving shelf life and storage duration. However, our current understanding is limited to model organisms, and the mechanism for non-model fruits remains largely unknown.
SCIENTIA HORTICULTURAE
(2023)
Article
Entomology
Vinothienii Vengatharajuloo, Hoe-Han Goh, Maizom Hassan, Nisha Govender, Suhaila Sulaiman, Nor Afiqah-Aleng, Sarahani Harun, Zeti-Azura Mohamed-Hussein
Summary: This study identifies key regulatory genes involved in hormone pathways in the larvae stage of Metisa plana through gene co-expression network analysis. These findings provide potential targets for gene silencing technologies and contribute to understanding the function of M. plana genes.
Article
Plant Sciences
Ching-Ching Wee, Nor Azlan Nor Muhammad, Vijay Kumar Subbiah, Masanori Arita, Yasukazu Nakamura, Hoe-Han Goh
Summary: This study reports the complete plastome of the Mesta variety of mangosteen cultivated in Malaysia, which is known for its flavor, texture, and seedlessness. Comparative analysis with other Garcinia plastomes found that the gene content, order, and orientation were highly conserved among the Garcinia species. These findings provide future references for species identification and phylogenomic analysis of the Garcinia genus.
Article
Plant Sciences
Muhammad Asyraf Mohd Amnan, Wee Fei Aaron Teo, Wan Mohd Aizat, Fiqri Dizar Khaidizar, Boon Chin Tan
Summary: Wood vinegar, a sustainable alternative, has been shown to promote plant growth and enhance stress tolerance. This study evaluated the efficacy of oil palm wood vinegar (OPWV) in mitigating the adverse effects of drought stress on Pandanus amaryllifolius. The results demonstrated that applying OPWV at a specific concentration and frequency increased the plant's tolerance to drought stress.
Review
Agronomy
Noor Hanini Che Lah, Hesham Ali El Enshasy, Ahmed Mediani, Kamalrul Azlan Azizan, Wan Mohd Aizat, Jen Kit Tan, Adlin Afzan, Normah Mohd Noor, Emelda Rosseleena Rohani
Summary: Systems biology is an interdisciplinary field that combines expertise in biology, chemistry, mathematics, physics, and engineering to study complex living systems using mathematical models and quantitative molecular computations. This approach can be used to investigate molecular and metabolic changes in difficult-to-store plant seeds. This review discusses how omics analyses can help uncover the molecular responses and metabolic changes in recalcitrant seeds.