Article
Biochemical Research Methods
Alienke van Pijkeren, Anna-Sophia Egger, Madlen Hotze, Elisabeth Zimmermann, Tobias Kipura, Julia Grander, Andre Gollowitzer, Andreas Koeberle, Rainer Bischoff, Kathrin Thedieck, Marcel Kwiatkowski
Summary: Proteomics and metabolomics play vital roles in systems biology, and the simultaneous extraction of proteome and metabolome from the same sample is important. This study compared the performance of different surfactants and urea for proteome extraction and found that urea showed the best efficiency for simultaneous proteo-metabolome analysis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Plant Sciences
Xueping Han, Jinzheng Wang, Guiping Wang, Fang Dong, Peixian Nie, Xiaomin Xue
Summary: This study investigated the flavonoid content in different developmental stages of 'Kuijin' and 'Katy' apricots and explored the metabolic basis of flavonol synthesis using metabolome and transcriptome analysis. The results showed a gradual decrease in flavonoid content as fruits developed. Three pairs of significant differences in flavonoid content were identified, and their correlation with structural genes and transcription factors was analyzed. These findings provide new insights into flavonol biosynthesis and can contribute to the improvement of the nutritional and health value of apricots.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Computer Science, Information Systems
Ugur Erkan, Abdurrahim Toktas, Feyza Toktas, Fayadh Alenezi
Summary: This study presents an image encryption algorithm (IEA) using a novel 2D chaotic map called e pi-map, which is based on Euler and Pi numbers. The e pi-map utilizes the infinite diversity attribute of these numbers and a diffusion operation called bit reversion to manipulate pixel values. The algorithm is extensively evaluated through various cryptanalysis techniques and compared with recent literature, demonstrating its superior performance in terms of ergodicity, complexity, and randomness.
INFORMATION SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Timothy K. Sheils, Stephen L. Mathias, Keith J. Kelleher, Vishal B. Siramshetty, Dac-Trung Nguyen, Cristian G. Bologa, Lars Juhl Jensen, Dusica Vidovic, Amar Koleti, Stephan C. Schurer, Anna Waller, Jeremy J. Yang, Jayme Holmes, Giovanni Bocci, Noel Southall, Poorva Dharkar, Ewy Mathe, Anton Simeonov, Tudor Oprea
Summary: The NIH's IDG program aims to study poorly characterized proteins that can be modulated using small molecules or biologics. The program has produced the Target Central Resource Database (TCRD) and Pharos, which aggregate data from multiple sources and rank targets based on data availability, in machine learning ready format. Integrated data include protein interactions, disease associations, and gene signatures, among others, enabling new visualizations and sections to empower users in exploring the druggable genome.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Ina A. Stelzer, Mohammad S. Ghaemi, Xiaoyuan Han, Kazuo Ando, Julien J. Hedou, Dorien Feyaerts, Laura S. Peterson, Kristen K. Rumer, Eileen S. Tsai, Edward A. Ganio, Dyani K. Gaudilliere, Amy S. Tsai, Benjamin Choisy, Lea P. Gaigne, Franck Verdonk, Danielle Jacobsen, Sonia Gavasso, Gavin M. Traber, Mathew Ellenberger, Natalie Stanley, Martin Becker, Anthony Culos, Ramin Fallahzadeh, Ronald J. Wong, Gary L. Darmstadt, Maurice L. Druzin, Virginia D. Winn, Ronald S. Gibbs, Xuefeng B. Ling, Karl Sylvester, Brendan Carvalho, Michael P. Snyder, Gary M. Shaw, David K. Stevenson, Kevin Contrepois, Martin S. Angst, Nima Aghaeepour, Brice Gaudilliere
Summary: This study conducted a longitudinal analysis of blood samples near the end of pregnancy using a multiomic model, revealing coordinated changes in maternal metabolome, proteome, and immunome 2 to 4 weeks before delivery. These changes, including a surge in steroid hormone metabolites and interleukin-1 receptor type 4, marked a shift from pregnancy maintenance to prelabor biology, providing insights for predicting the day of labor.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Chun-Ying Wang, Martin Lempp, Niklas Farke, Stefano Donati, Timo Glatter, Hannes Link
Summary: The study explores how to alleviate the growth burden on E. coli strains caused by synthetic pathways, highlighting the role of misregulated Cra transcription factor in impairing growth during glycerol production. Engineering Cra-binding sites in promoters maintains metabolic balance in the synthetic pathway, demonstrating a successful solution to the growth burden issue.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Long Zhang, Zhengmin Tang, Hao Zheng, Caihong Zhong, Qiong Zhang
Summary: In this study, the differences in metabolite profiles between kiwifruit roots and fruits were compared, and several differentially expressed metabolites were identified. Among them, three flavonols and one dihydrochalcone showed the greatest differences in content between the two tissues. Transcriptome analysis revealed that genes related to flavonols and dihydrochalcones were highly expressed in roots. Furthermore, two transcription factors were highly expressed in roots, while one transcription factor showed extremely low expression, indicating their potential roles in regulating flavonoid accumulation in kiwifruit.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cardiac & Cardiovascular Systems
Michael J. Previs, Thomas S. O'Leary, Michael P. Morley, Bradley M. Palmer, Martin LeWinter, Jaime M. Yob, Francis D. Pagani, Christopher Petucci, Min-Soo Kim, Kenneth B. Margulies, Zoltan Arany, Daniel P. Kelly, Sharlene M. Day
Summary: This study identified metabolic reprogramming in human HCM hearts, characterized by deficits in nucleotide availability, reduced capacity for fatty acid oxidation, and increases in ketone bodies and branched chain amino acids. These findings have important therapeutic implications for the future design of metabolic modulators to treat HCM.
CIRCULATION-HEART FAILURE
(2022)
Article
Biochemical Research Methods
Pieter M. Dekker, Sjef Boeren, Johannes B. van Goudoever, Jacques J. M. Vervoort, Kasper A. Hettinga
Summary: The study found significant interindividual variation in proteins and peptides in human milk, and identified distinct characteristics in different protein and peptide clusters through weighted correlation network analysis. Several associations between different data sets and specific sample characteristics were also discovered.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Horticulture
H. Gomez-Martinez, A. Bermejo, E. Zuriaga, M. L. Badenes
Summary: Apricot is a key fruit in the Mediterranean region, valued in the diets of Asian and Mediterranean countries. Polyphenols, the most abundant antioxidants in apricots, play a crucial role in defining fruit quality. The study identified the PPV resistant cultivar 'Goldrich' as the best for increasing antioxidants in apricot varieties.
SCIENTIA HORTICULTURAE
(2021)
Review
Medicine, General & Internal
K. Suhre, S. Zaghlool
Summary: Epigenome-wide association studies (EWAS) can identify genes related to clinical endpoints, potentially leading to new diagnostic biomarkers and therapy options. Combining EWAS with deep molecular phenotyping allows further exploration of disease pathways. Methylation of certain genes is associated with specific diseases or physiological challenges, offering possibilities for early diagnosis.
JOURNAL OF INTERNAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Han Shi, Xueting Wu, Yan Zhu, Tao Jiang, Zhengwei Wang, Xuetong Li, Jianju Liu, Yingxue Zhang, Feng Chen, Jinshan Gao, Xiaoyan Xu, Guoqing Zhang, Ning Xiao, Xianzhong Feng, Peng Zhang, Yongrui Wu, Aihong Li, Ping Chen, Xuan Li
Summary: Plant metabolites play crucial roles in various aspects of plant biology, but the lack of a reference metabolome and related analytical tools hampers the study of plant phytochemicals. In this study, a reference metabolome for 153 plant species was constructed using an advanced LC-MS platform. The newly developed database, RefMetaPlant, provides a powerful platform for plant genome-scale metabolite analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Keith J. Kelleher, Timothy K. Sheils, Stephen L. Mathias, Jeremy J. Yang, Vincent T. Metzger, Vishal B. Siramshetty, Dac-Trung Nguyen, Lars Juhl Jensen, Dusica Vidovic, Stephan C. Schurer, Jayme Holmes, Karlie R. Sharma, Ajay Pillai, Cristian G. Bologa, Jeremy S. Edwards, Ewy A. Mathe, Tudor Oprea
Summary: The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. The two main products of the IDG effort are the Target Central Resource Database (TCRD), which curates and aggregates information, and Pharos, a web interface for extracting and visualizing data from TCRD. The latest versions of TCRD and Pharos provide visualization and analysis tools that help reveal higher-level patterns in the underlying data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Emma F. Camp, Tim Kahlke, Brandon Signal, Clinton A. Oakley, Adrian Lutz, Simon K. Davy, David J. Suggett, William P. Leggat
Summary: The Symbiodiniaceae are a diverse family of marine dinoflagellates that have a symbiotic relationship with invertebrates. They are sensitive to thermal stress, and research shows that this sensitivity is influenced by both phylogenetic dependent and independent traits. To understand the drivers of Symbiodiniaceae heat stress tolerance, researchers have provided a dataset that includes transcriptome, metabolome, and proteome data.
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)
Review
Food Science & Technology
Priyanka Chopra, Himanshu Chhillar, Yu-Jin Kim, Ick Hyun Jo, Sun Tae Kim, Ravi Gupta
Summary: This review summarizes the distribution, structural diversity, biotransformation, and functional attributes of ginsenosides in both plants and animals. It also discusses the biosynthesis of ginsenosides and their metabolism in the human body, along with the major regulators and stimulators. Moreover, it consolidates the biotechnological interventions to enhance ginsenoside biosynthesis and advancements in synthetic biosystems for efficient ginsenoside production.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Correction
Agronomy
Riyazuddin Riyazuddin, Kalpita Singh, Nadeem Iqbal, Nisha Nisha, Anita Rani, Manu Kumar, Nisha Khatri, Manzer H. Siddiqui, Yasheshwar, Sun Tae Kim, Feher Attila, Ravi Gupta
Article
Biochemistry & Molecular Biology
Junko Shibato, Fumiko Takenoya, Michio Yamashita, Ravi Gupta, Cheol Woo Min, Sun Tae Kim, Ai Kimura, Ichiro Takasaki, Motohide Hori, Seiji Shioda, Randeep Rakwal
Summary: This study aimed to understand the mechanism of neuronal outgrowth in PC12 cells treated with PACAP. Transcriptomic and proteomic analyses revealed several key regulators involved in neurite outgrowth, potentially involving cAMP signaling, PI3K-Akt signaling, and calcium signaling pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Junko Shibato, Fumiko Takenoya, Ai Kimura, Cheol Woo Min, Michio Yamashita, Ravi Gupta, Sun Tae Kim, Randeep Rakwal, Seiji Shioda
Summary: This study investigated the hair-growing effects of a cell extract obtained from cactus Notocactus ottonis. The extract was found to be more effective than the control groups in promoting hair growth. Further analysis revealed the presence of growth-promoting factors and provided insights into the molecular mechanisms underlying the hair-promoting effects. This study suggests the potential use of the cactus extract as a hair-growth-promoting agent.
Article
Plant Sciences
Priya Gahlowt, Durgesh Kumar Tripathi, Ravi Gupta, Vijay Pratap Singh
PLANT CELL REPORTS
(2023)
Article
Plant Sciences
Ravi Gupta
Summary: Plant immune response is controlled by various phytohormones and plant growth regulators. Salicylic acid, jasmonic acid, and ethylene have established roles, while nitric oxide, polyamines, and hydrogen sulfide are emerging as key regulators. Melatonin has shown promise in enhancing plant resistance, but its molecular mechanism is still unknown. Evidence suggests that melatonin regulates plant immunity by maintaining ROS homeostasis, interacting with other hormones, and inducing the accumulation of defense molecules. Engineering crops with increased melatonin production could improve crop productivity under stress conditions.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Plant Sciences
Pooja Singh, Saumya Jaiswal, Ajayraj Kushwaha, Priya Gahlowt, Vipul Mishra, Durgesh Kumar Tripathi, Surendra Pratap Singh, Ravi Gupta, Vijay Pratap Singh
Summary: In this study, it was found that peroxynitrite is necessary for ethylene-mediated aerenchyma formation in rice roots under waterlogging conditions. Aerenchyma formation is crucial for the survival of plants under waterlogging stress, and the involvement of peroxynitrite in this process has been elusive. The findings highlight the role of peroxynitrite in ethylene-mediated aerenchyma formation and its potential for the development of waterlogging stress-tolerant rice varieties.
Article
Biochemical Research Methods
Ravi Gupta, Cheol Woo Min, Ju-Young Jung, Tae-Ho Ham, Jong-Seong Jeon, Lae-Hyeon Cho, Soon Wook Kwon, Sun Tae Kim
Summary: This study analyzed the proteomes of red and black rice seeds and compared them with white rice seeds. The results showed that red rice seeds are rich in β-carotene, while black rice seeds are rich in anthocyanins. Additionally, proteins associated with lignin and tocopherol biosynthesis were significantly increased in both red and black rice seeds. These findings provide insights into the molecular mechanisms underlying pigment accumulation in rice.
Editorial Material
Plant Sciences
Priya Gahlowt, Durgesh Kumar Tripathi, Francisco J. Corpas, Ravi Gupta, Vijay Pratap Singh
Summary: This study reveals that nitric oxide plays multifaceted roles in plants. It was found that NO produced in the shoot apex leads to S-nitrosation of transcription factor GT-1, which subsequently regulates the expression of the HSFA2 gene, resulting in thermotolerance in Arabidopsis thaliana.
TRENDS IN PLANT SCIENCE
(2023)
Review
Plant Sciences
Lirong Wei, Dacheng Wang, Ravi Gupta, Sun Tae Kim, Yiming Wang
Summary: Rice, as one of the most consumed foods globally, faces challenges in productivity and quality due to pathogenic microbes. Proteomics tools have been used to study protein level changes in rice-microbe interactions, leading to the identification of disease resistance-related proteins. Targeting proteins and pathways associated with the host's immune response is an efficient strategy for developing stress-resistant crops.
Article
Plant Sciences
Priya Gahlowt, Durgesh Kumar Tripathi, Samiksha Singh, Ravi Gupta, Vijay Pratap Singh
Summary: A recent discovery of a protein called HT1 has been found to cause continuous opening of stomata due to its kinase activity. However, the reversible interaction between MAP4/12 and HT1 protein acts as a CO2/bicarbonate sensor and inhibits HT1 kinase activity, resulting in the closing of stomata.
PLANT CELL REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Samiksha Singh, Nawal Kishore Dubey, Durgesh Kumar Tripathi, Ravi Gupta, Vijay Pratap Singh
Summary: The study found that nitric oxide (NO) and hydrogen peroxide (H2O2) can alleviate the toxicity of hexavalent chromium (Cr(VI)) in wheat seedlings by regulating antioxidant enzymes and metabolites, as well as up-regulating high affinity sulfate transporter. They collectively controlled the occurrence of oxidative stress.
Article
Plant Sciences
Jinmi Yoon, Cheol Woo Min, Jiyoung Kim, Gibeom Baek, Dohyeon Kim, Jeong Woo Jang, Ravi Gupta, Sun Tae Kim, Lae-Hyeon Cho
Summary: Understanding the molecular mechanisms underlying early seed development is crucial for improving crop yield and quality. In this study, a comparative proteomic analysis of WT and osctps1-2 mutant rice seeds was conducted to investigate the molecular mechanism of early seed development. The results revealed that OsCTPS1 abundance increased at 1 DAP, and phosphorylation inhibition increased its stability. Additionally, reduced MCM protein levels and defects in seed development were observed in the mutant. These findings highlight the importance of post-transcriptional regulation in early seed development in rice.
Review
Biochemistry & Molecular Biology
Tanashvi Seth, Sejal Asija, Shahid Umar, Ravi Gupta
Summary: Plants activate a sophisticated signaling cascade in response to pests and pathogens, with lipids playing a crucial role in mediating these defense responses. Different types of lipids are involved in cell signaling during plant-pathogen interaction and each lipid has specific relevance and contributes to specific signaling cascades. Lipid biosynthetic enzymes, including phospholipases, are involved in the production of defense signaling molecules. Lipids participate in stress signaling by mediating signal transduction, acting as precursors for bioactive molecules, regulating ROS formation, and interacting with phytohormones.
Article
Chemistry, Applied
Ravi Gupta, Neha Kaushik, Manorma Negi, Nagendra Kumar Kaushik, Eun Ha Choi
Summary: This study explored the impact of plasma-activated water (PAW) on radish roots, revealing that PAW treatment can enhance antioxidant enzyme activity and the accumulation of functional compounds. The integration of proteomics and metabolomics analysis provided novel insights into the molecular mechanism underlying the growth and accumulation of these compounds in radish plants induced by PAW treatment.