Article
Psychiatry
Rohan H. C. Palmer, Chelsie E. Benca-Bachman, Spencer B. Huggett, Jason A. Bubier, John E. McGeary, Nikhil Ramgiri, Jenani Srijeyanthan, Jingjing Yang, Peter M. Visscher, Jian Yang, Valerie S. Knopik, Elissa J. Chesler
Summary: This study utilized cross-species translational approaches to investigate the genetic factors influencing human tobacco consumption. The results showed that model organism genes contributed to a significant portion of the observed SNP-heritability in tobacco consumption, were enriched for genes associated with human tobacco consumption, and predictive of cigarettes per day using a polygenic score.
TRANSLATIONAL PSYCHIATRY
(2021)
Editorial Material
Neurosciences
Nicole Y. Tsai, Derek S. Welsbie, Xin Duan
Summary: In this issue, three studies present new strategies for uncovering mediators of retinal neuroprotection and optic nerve regeneration, including transcriptional regulators and molecular targets.
Article
Multidisciplinary Sciences
Francesca Genova, Simona Nonnis, Elisa Maffioli, Gabriella Tedeschi, Maria Giuseppina Strillacci, Michela Carisetti, Giuseppe Sironi, Francesca Anna Cupaioli, Noemi Di Nanni, Alessandra Mezzelani, Ettore Mosca, Christopher R. Helps, Peter A. J. Leegwater, Laetitia Dorso, Maria Longeri, Reuben M. Buckley, Danielle Aberdein, Paulo C. Alves, Asa Ohlsson Andersson, Gregory S. Barsh, Rebecca R. Bellone, Tomas F. Bergstrom, Adam R. Boyko, Jeffrey A. Brockman, Margret L. Casal, Marta G. Castelhano, Ottmar Distl, Nicholas H. Dodman, N. Matthew Ellinwood, Jonathan E. Fogle, Oliver P. Forman, Dorian J. Garrick, Edward Ginns, Bianca Haase, Jens Haggstrom, Robert J. Harvey, Daisuke Hasegawa, Isabel Hernandez, Marjo K. Hytonen, Maria Kaukonen, Christopher B. Kaelin, Tomoki Kosho, Emilie Leclerc, Teri L. Lear, Tosso Leeb, Ronald H. L. Li, Hannes Lohi, Mark A. Magnuson, Richard Malik, Shrinivasrao P. Mane, John S. Munday, William J. Murphy, Niels C. Pedersen, Simon M. Peterson-Jones, Max F. Rothschild, Clare Rusbridge, Beth Shapiro, Joshua A. Stern, William F. Swanson, Karen A. Terio, Rory J. Todhunter, Wesley C. Warren, Elizabeth A. Wilcox, Julia H. Wildschutte, Yoshihiko Yu, Leslie A. Lyons
Summary: The study utilized multi-omics analyses to explore unknown pathogenetic processes in Abyssinian cats with amyloidosis, revealing genomic variants, protein expression differences, and differential miRNA expression. The familial amyloid renal form is not a simple monogenic trait and amyloid deposition is triggered by a mix of proteins coded by wild-type genes. This form of amyloidosis in Abyssinian cats can be biochemically classified as AA amyloidosis.
SCIENTIFIC REPORTS
(2021)
Review
Biochemical Research Methods
Cristine J. Reitz, Uros Kuzmanov, Anthony O. Gramolini
Summary: Heart disease is still a major cause of death worldwide, and despite treatment advances, hospitalizations and mortality rates remain high due to its chronic nature. Systems biology approaches, such as mapping molecular networks across various omics datasets, have the potential to enhance our understanding of cardiovascular disease and improve diagnostic biomarker discovery and therapeutic development. However, computational workflows and integration of different levels of analysis in systems biology-based research present ongoing challenges.
Article
Biology
Gerardo Alejo-Jacuinde, Hector-Rogelio Najera-Gonzalez, Ricardo A. Chavez A. Montes, Cristian D. Gutierrez D. Reyes, Alfonso Carlos Barragan-Rosillo, Benjamin Perez Sanchez, Yehia Mechref, Damar Lopez-Arredondo, Lenin Yong-Villalobos, Luis Herrera-Estrella
Summary: This study presents a chromosome-level reference genome for chia and analyzes the transcriptome, proteome, and metabolome to uncover the molecular basis of the unique characteristics of chia seeds. Chia is an emerging crop with functional food properties, but the genetic basis for traits like seed mucilage and polyphenol content remains unclear.
COMMUNICATIONS BIOLOGY
(2023)
Review
Cell Biology
Martijn Cordes, Karin Pike-Overzet, Erik B. B. Van Den Akker, Frank J. T. Staal, Kirsten Cante-Barrett
Summary: Flow cytometry has traditionally been used to characterize immune cells and their markers. Single-cell RNA-sequencing has revolutionized the study of immune development, allowing for the analysis of heterogenous tissues and the integration of omics data at the single-cell level. This integration contributes to our understanding of the immune system by revealing the heterogeneity within cell populations identified by surface markers and the correlation between RNA and protein data.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lisette J. A. Kogelman, Katrine Falkenberg, Filip Ottosson, Madeleine Ernst, Francesco Russo, Valdemar Stentoft-Hansen, Samuel Demharter, Peer Tfelt-Hansen, Arieh S. Cohen, Jes Olesen, Thomas Folkmann Hansen
Summary: This study aimed to uncover the mechanisms of triptan using metabolomics and transcriptomics in spontaneous migraine attacks. It found three differential metabolites associated with triptan treatment: cortisol, sumatriptan, and glutamine. The change in sumatriptan levels correlated with a change in the expression of GNAI1 and VIPR2 genes, which are known to regulate cAMP levels. Additionally, the study revealed the effect of triptans on fatty acid oxidation, a mechanism previously not associated with triptans but known to be involved in migraine.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Yujin Jeong, Seong-Joo Hong, Sang-Hyeok Cho, Seonghoon Yoon, Hookeun Lee, Hyung-Kyoon Choi, Dong-Myung Kim, Choul-Gyun Lee, Suhyung Cho, Byung-Kwan Cho
Summary: The marine cyanobacterium Synechocystis sp. PCC 7338, which has the advantage of growing in seawater, was studied to determine its complete genome sequence and transcriptional changes under high salt stress. The analysis revealed the use of cyclic electron transport through photosystem I by the strain to meet the ATP demand in a high-salt environment.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agronomy
Yu Fu, Hao Tan, Bo Wang, Weihong Peng, Qun Sun, Yang Yu
Summary: This study investigates the factors causing browning in yellow cultivars of Flammulina filiformis. It reveals that oxygen plays an essential role in the browning process. Integrated multi-omic analyses are used to identify genes and metabolic pathways involved in oxidative deterioration. The study identifies laccase 4 as a crucial polyphenol oxidase catalyzing the browning reaction. These findings lay the foundations for postharvest preservation and genetic breeding of F. filiformis.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Biology
Priyanka Baloni, Matthias Arnold, Luna Buitrago, Kwangsik Nho, Herman Moreno, Kevin Huynh, Barbara Brauner, Gregory Louie, Alexandra Kueider-Paisley, Karsten Suhre, Andrew J. Saykin, Kim Ekroos, Peter J. Meikle, Leroy Hood, Nathan D. Price, P. Murali Doraiswamy, Cory C. Funk, A. Ivan Hernandez, Gabi Kastenmueller, Rebecca Baillie, Xianlin Han, Rima Kaddurah-Daouk
Summary: This study investigates the role of sphingomyelin and ceramide metabolism in Alzheimer's disease through multi-omics analyses and imaging features. The findings suggest potential therapeutic targets in the sphingomyelin pathway and demonstrate the efficacy of modulators of S1P metabolism in treating Alzheimer's disease, as validated in mouse models.
COMMUNICATIONS BIOLOGY
(2022)
Review
Pharmacology & Pharmacy
Rebecca L. Murdaugh, Jamie N. Anastas
Summary: Despite improvements in cancer patient outcomes, tumor resistance to therapy remains a major problem. The variability between cancer cells has been identified as a driver of therapeutic resistance. Single cell profiling technologies can assess this heterogeneity and provide insights into the characteristics of resistant sub-populations. Studies have shown the advantages of single cell analysis in treating certain cancers, but the potential in pediatric high grade glioma and other brain tumors remains unknown. By using single cell multi-omic analyses, we may discover novel strategies to overcome treatment resistance in these tumors with limited options.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Microbiology
Susheel Bhanu Busi, Zhentian Lei, Lloyd W. Sumner, James M. Amos-Landgraf
Summary: The onset of colon cancer is strongly associated with differences in microbial taxa in the gastrointestinal tract. Utilizing a multi-omics approach, this study reveals the impact of the gut microbiome on the susceptibility to adenoma development and identifies metabolic and transcriptomic pathways involved. The findings enhance our understanding of the role of the gut microbiome in colon cancer and provide insights for potential biomarkers and therapeutic targets.
Article
Biotechnology & Applied Microbiology
Xiaoni Zhang, Shengnan Lin, Dan Peng, Quanshu Wu, Xuezhu Liao, Kunli Xiang, Zehao Wang, Luke R. Tembrock, Mohammed Bendahmane, Manzhu Bao, Zhiqiang Wu, Xiaopeng Fu
Summary: This study used an integrated multi-omics approach to investigate the genetic and biochemical pathways underlying the important ornamental features of carnation flowers. Through assembling a high-quality genome, generating metabolomic and transcriptomic datasets, the study revealed spatial and temporal differences in pigment and volatile compound accumulation in carnation flowers and proposed key genes and pathways involved.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Applied
Tingting Li, Qin Wang, Yan Yang, Dingka Song
Summary: In this study, the molecular structure of a novel polysaccharide in the mutant S. sanghuang strain A130 was characterized, and the potential mechanism of polysaccharide synthesis in S. sanghuang was investigated through comparative transcriptomic and proteomic analysis. The genes/proteins involved in glycolysis/gluconeogenesis, such as CBH1 and MSH6, were found to be differentially expressed between A130 and SH-1, suggesting their potential role in regulating polysaccharide production. Proteomic analysis also revealed significant differences in the abundance of TYR and TREH between A130 and SH-1, and their involvement in polysaccharide production was confirmed through integrated transcriptomic-proteomic analysis and feedback inhibition experiments. Overall, this study provides critical insights into the genes/pathways regulating polysaccharide synthesis and high yield in S. sanghuang.
CARBOHYDRATE POLYMERS
(2023)
Article
Plant Sciences
Hong Zhang, Mao-Fa Yang, Qian Zhang, Bin Yan, Yu-Lan Jiang
Summary: In this study, endophytic fungi were isolated from Rosa roxburghii plants and screened for antimicrobial activity. The strain Epicoccum latusicollum HGUP191049 showed excellent antagonistic activity with low minimum inhibitory concentration. Metabolomic analysis revealed that HGUP191049 produced a diverse range of antimicrobial secondary metabolites.
FRONTIERS IN PLANT SCIENCE
(2022)
