Article
Oncology
Longlong Liu, Pradeep Kumar Patnana, Xiaoqing Xie, Daria Frank, Subbaiah Chary Nimmagadda, Annegret Rosemann, Marie Liebmann, Luisa Klotz, Bertram Opalka, Cyrus Khandanpour
Summary: This study demonstrates that AML cells with an MLL/AF9 genotype have a high dependency on oxidative phosphorylation and could be targeted for therapy using metformin.
Review
Oncology
Geraldine Gentric, Fatima Mechta-Grigoriou
Summary: Tumors exhibit metabolic heterogeneity with utilization of carbon sources other than glucose, such as amino acids, fatty acids, and lactate. This diversity in metabolic pathways influences cancer cell invasion capabilities and is also present in Cancer-Associated Fibroblasts (CAF).
Article
Microbiology
Nicole Pearcy, Yue Hu, Michelle Baker, Alexandre Maciel-Guerra, Ning Xue, Wei Wang, Jasmeet Kaler, Zixin Peng, Fengqin Li, Tania Dottorini
Summary: The study focuses on the identification of genetic determinants associated with antimicrobial resistance in E. coli using a computational approach that integrates machine learning with metabolic modeling. The findings reveal key genetic determinants linked to growth and metabolic adaptations, providing insights into the complex interplay between antibiotic resistance and metabolic rewiring in bacteria. This computational solution has the potential to be applied to other human and animal pathogens for further studies on antimicrobial resistance.
Article
Agricultural Engineering
Han Sun, Yuanyuan Ren, Yuwei Fan, Xue Lu, Weiyang Zhao, Feng Chen
Summary: This study investigated the mechanism of fed-batch culture on product biosynthesis in Chromochloris zofingiensis through dynamic modeling, metabolite determination, enzyme activity analysis, and metabolic flux analysis. Results showed that fed-batch culture significantly increased biomass concentration, biodiesel, and protein production potentials while promoting carotenoid and lipid biosynthesis. Economic analysis indicated that fed-batch culture reduced biomass costs, making it a cost-effective strategy for improving the economic viability of microalgal production.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemical Research Methods
Luca Rappez, Mira Stadler, Sergio Triana, Rose Muthoni Gathungu, Katja Ovchinnikova, Prasad Phapale, Mathias Heikenwalder, Theodore Alexandrov
Summary: SpaceM is an open-source method for in situ single-cell metabolomics that can detect a large number of metabolites per hour and predict and validate the cell types and metabolic states. By simulating different stimuli, SpaceM reveals the coexistence of different cellular metabolic states and the mechanisms of balance disruption.
Article
Chemistry, Multidisciplinary
Yan Zhao, Zhi-Xuan Li, Yan-Jing Zhu, Jing Fu, Xiao-Fang Zhao, Ya-Ni Zhang, Shan Wang, Jian-Min Wu, Kai-Ting Wang, Rui Wu, Cheng-Jun Sui, Si-Yun Shen, Xuan Wu, Hong-Yang Wang, Dong Gao, Lei Chen
Summary: This study investigates the molecular heterogeneity and evolution of hepatobiliary tumors using single-cell RNA sequencing, revealing that certain tumor subpopulations exhibit broad-spectrum drug resistance. The CD44-positive population may play a key role in drug resistance. Shared metabolism advantage clusters across organoids and the combination of GAPDH and NDRG1 are proposed as independent predictors for patient survival.
Article
Medicine, Research & Experimental
Zhiping Liu, Huidong Shi, Jiean Xu, Qiuhua Yang, Qian Ma, Xiaoxiao Mao, Zhimin Xu, Yaqi Zhou, Qingen Da, Yongfeng Cai, David J. R. Fulton, Zheng Dong, Akrit Sodhi, Ruth B. Caldwell, Yuqing Huo
Summary: Pathological angiogenesis leading to irreversible blindness is closely related to the abnormal retinal angiogenesis caused by microglia cells within neovascular areas. The study explores the heterogeneity of microglia associated with neovascularization and characterizes the transcriptional profiles and metabolic pathways of proangiogenic microglia in the mouse model of oxygen-induced proliferative retinopathy (PR). Several unique types of microglia associated with PR were identified and found to potentially promote retinal angiogenesis, which may have implications for the future treatment of PR and other pathological ocular angiogenesis-related diseases.
Article
Multidisciplinary Sciences
Peyton J. Tebon, Bowen Wang, Alexander L. Markowitz, Ardalan Davarifar, Brandon L. Tsai, Patrycja Krawczuk, Alfredo E. Gonzalez, Sara Sartini, Graeme F. Murray, Huyen Thi Lam Nguyen, Nasrin Tavanaie, Thang L. Nguyen, Paul C. Boutros, Michael A. Teitell, Alice Soragni
Summary: High throughput drug screening is an important approach to study tumor biology and identify therapeutic directions. Traditional platforms cannot accurately reflect the biology of human tumors, but bioprinted tumor organoids coupled with time-resolved imaging and machine learning methods can provide more effective information and guide therapy selection.
NATURE COMMUNICATIONS
(2023)
Review
Microbiology
Abhyudai Singh, Michael Saint-Antoine
Summary: The stochasticity of gene product levels can cause individual cells in a population to have different phenotypic states. The dynamic nature of this intercellular variation makes it challenging to characterize. This review focuses on the use of the Luria-Delbruck experiment to understand the transient heritability of cellular states and discusses modeling approaches for capturing dynamic state transitions in cell populations.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Parthiv Patel, Nir Drayman, Ping Liu, Mustafa Bilgic, Savas Tay
Summary: The study investigates the heterogeneity of individual cells in response to environmental cues, revealing underlying mechanisms using computer vision technology. Results demonstrate that the ratio of NF-kappa B to inhibitor of NF-kappa B determines the activation probability of cells, highlighting the importance of minute leaky amounts of NF-kappa B in cell activation predictability.
Article
Multidisciplinary Sciences
Smruthy Sivakumar, Dexter X. Jin, Hanna Tukachinsky, Karthikeyan Murugesan, Kimberly McGregor, Natalie Danziger, Dean Pavlick, Ole Gjoerup, Jeffrey S. Ross, Robert Harmon, Jon Chung, Brennan Decker, Lucas Dennis, Garrett M. Frampton, Luciana Molinero, Steffi Oesterreich, Jeffrey M. Venstrom, Geoffrey R. Oxnard, Priti S. Hegde, Ethan S. Sokol
Summary: Liquid biopsies are valuable tools for monitoring breast cancer progression and acquired mutations. This study investigates genomic profiling of tissue and liquid biopsies in breast cancer patients to characterize tumor evolution and identify potential vulnerabilities. The findings highlight the importance of liquid biopsies in understanding treatment-driven tumor evolution and identifying new treatment options for advanced breast cancer.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Mohammad A. Iqbal, Shumaila Siddiqui, Kirk Smith, Prithvi Singh, Bhupender Kumar, Salem Chouaib, Sriram Chandrasekaran
Summary: Extensive metabolic heterogeneity in breast cancers can be classified into three subtypes based on metabolic pathways, which are strongly correlated with tumor aggressiveness and patient outcome. Machine-learning can be used to identify metabolic subtypes and guide precision therapies for breast cancers.
Review
Chemistry, Analytical
Liujuan Zhan, Huimin Liu, Zhuanghao Hou, Yiwen Gao, Baoyou Chu, Guangming Huang
Summary: Heterogeneity is a common phenomenon in individual bacterium of bacterial populations even with the same gene and environment. Metabolites, as the basis for maintaining biological activities, provide a more direct and dynamic picture of cell function. Single bacterium metabolic analysis techniques, including RNA sequencing, fluorescent probes, Raman spectroscopy, and mass spectrometry, have been summarized in this review.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Fan Wu, Yao Zhou, Yingying Shen, Zhengxi Sun, Lei Li, Tao Li
Summary: Fusarium head blight (FHB) caused by Fusarium graminearum is a destructive disease for wheat production, and the resistance mechanism is complex with different types of resistances. Studying the resistance mechanism of FHB in wheat using multi-omics methods can help identify critical genes or pathways and improve FHB resistance in wheat breeding programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Food Science & Technology
Liyi Wang, Xueyan Zhao, Shiqi Liu, Wenjing You, Yuqin Huang, Yanbing Zhou, Wentao Chen, Shu Zhang, Jiying Wang, Qiankun Zheng, Yizhen Wang, Tizhong Shan
Summary: This study investigated the cellular and transcriptional mechanisms underlying lipid deposition in highly-marbled pork using single-nucleus RNA sequencing and bulk RNA sequencing. The results revealed that the high marbled group had higher intramuscular fat (IMF) contents and lower drip loss compared to the low marbled group. Single-nucleus RNA sequencing showed a higher percentage of adipocytes in the high marbled group. Additionally, bulk RNA sequencing identified different genes involved in lipid metabolism and fatty acid elongation. The findings provide new insights into the cellular and molecular signatures of marbling formation in pork.
NPJ SCIENCE OF FOOD
(2023)
Article
Biochemistry & Molecular Biology
Sharanjeet Atwal, Suparat Giengkam, Suwittra Chaemchuen, Jack Dorling, Nont Kosaisawe, Michael VanNieuwenhze, Somponnat Sampattavanich, Peter Schumann, Jeanne Salje
MOLECULAR MICROBIOLOGY
(2017)
Article
Biology
Yin P. Hung, Carolyn Teragawa, Nont Kosaisawe, Taryn E. Gillies, Michael Pargett, Marta Minguet, Kevin Distor, Briana L. Rocha-Gregg, Jonathan L. Coloff, Mark A. Keibler, Gregory Stephanopoulos, Gary Yellen, Joan S. Brugge, John G. Albeck
Correction
Multidisciplinary Sciences
Nattapol Attatippaholkun, Nont Kosaisawe, Yaowalak U-Pratya, Panthipa Supraditaporn, Chanchao Lorthongpanich, Kovit Pattanapanyasat, Surapol Issaragrisil
SCIENTIFIC REPORTS
(2018)
Article
Multidisciplinary Sciences
Nattapol Attatippaholkun, Nont Kosaisawe, Yaowalak U-Pratya, Panthipa Supraditaporn, Chanchao Lorthongpanich, Kovit Pattanapanyasat, Surapol Issaragrisil
SCIENTIFIC REPORTS
(2018)
Article
Genetics & Heredity
Jirat Chenbhanich, Ivy Riano, Shreya Madhavaram, Cagney Cristancho, Alekya Poloju, Victor Alejandro Zavala Gonzalez, Nont Kosaisawe, Thomas Treadwell
Summary: Resident-led structured genetic education effectively increased family history documentation in the EMR of an internal medicine resident continuity clinic, showing clinical utility. Time constraint was identified as the most reported barrier, and positive family history could potentially alter medical management in 13% of patients with documented FH.
JOURNAL OF COMMUNITY GENETICS
(2022)
Article
Oncology
Anastasia L. Berg, Megan R. Showalter, Nont Kosaisawe, Michelle Hu, Nathanial C. Stephens, Michael Sa, Hailey Heil, Noemi Castro, Jenny J. Chen, Kacey VanderVorst, Madelyn R. Wheeler, Zachary Rabow, Tomas Cajka, John Albeck, Oliver Fiehn, Kermit L. Carraway
Summary: Bis(monoacylglycero)phosphates (BMPs), lipid components within endolysosomal organelles, have been associated with pathological states such as neurodegenerative diseases and lysosomal storage disorders. This study identified lower BMP levels in transformed cells compared to normal cells, and observed an enrichment of 22:6 BMP species in breast cancer models. Functional analysis suggests that 22:6 BMPs serve as reactive oxygen species scavengers, protecting lysosomes from oxidant-induced damage. These findings highlight the potential therapeutic target of BMP-mediated lysosomal protection in breast tumor cells.
