Review
Biotechnology & Applied Microbiology
Tanner R. Treece, Jake N. Gonzales, Joseph R. Pressley, Shota Atsumi
Summary: Biological chemical production has become a promising renewable alternative to traditional petrochemical synthesis. Photosynthetic microorganisms capable of sequestering atmospheric carbon dioxide have gained significant attention in the field of metabolic engineering. However, the intrinsic limitations of carbon fixation and photosynthesis have led to slower growth and lower product titers compared to heterotrophic organisms. Efforts to improve photosynthetic microorganisms as renewable chemical production hosts have focused on rewiring carbon fixation and photosynthesis, investigating alternative carbon fixation pathways, installing sugar catabolism, exploring fast-growing photosynthetic species, and using synthetic biology tools such as CRISPR to alter metabolism.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Natalie Stewart, Simon Wisnovsky
Summary: Carbohydrate molecules called glycans coat living cells and play crucial roles in cell behavior and disease. Recent advancements in functional genomics technologies have allowed for a better understanding of how glycosylation is regulated and altered in various cell types. These technologies also present opportunities for further research in cellular glycobiology.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Hye Kyung Lee, Ludwig Knabl, Mary Walter, Priscilla A. Furth, Lothar Hennighausen
Summary: The study suggests that prior infection status significantly impacts the immune response following BA.2 infection, with significantly increased neutralizing antibody levels in patients with a previous history of COVID-19.
Article
Plant Sciences
Ryo Kariyazono, Takashi Osanai
Summary: This study identified the binding sites of SigE and SigA using ChIP-seq analysis and found that they shared most of their binding sites, but SigE exclusively occupied the promoters of the SigE regulon.
Article
Cell Biology
Han Liu, Jingyue Xu, Yu Lan, Hee-Woong Lim, Rulang Jiang
Summary: This study investigated the molecular mechanisms of tendon development by generating a Scx(Flag) knockin mouse strain and identifying Scx direct target genes in developing tendon tissues. The results provide novel insights into the role of Scx in tendon development and homeostasis, offering valuable resources for further research on tendon cell differentiation and tissue regeneration. The Scx(Flag) mice present a useful tool for unraveling the molecular mechanisms underlying developmental and disease processes involving Scx.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Jose M. Uribe-Salazar, Gulhan Kaya, Aadithya Sekar, KaeChandra Weyenberg, Cole Ingamells, Megan Y. Dennis
Summary: Our study systematically assessed the accuracy of CRISPR/Cas9 tool predictions for on- and off-target gene editing in zebrafish embryos, revealing large discrepancies between experimentally observed editing efficiencies and predictions made by commonly used gRNA design tools. We also investigated potential confounders of G(0)-based CRISPR screens by analyzing control embryos, identifying potentially lasting effects from the microinjection process. This research provides a valuable resource for the zebrafish community to enhance the design and implementation of CRISPR/Cas9 experiments.
Article
Biotechnology & Applied Microbiology
Xinlei Wang, Lei Yu, Angela Ruohao Wu
Summary: This study demonstrates that methanol fixation can faithfully preserve biological signals in scRNA-seq, with the effects of fixation being subtle and related to library construction methods. Transcript length and GC content play a role in how fixation affects transcripts in full-length sequencing data, while this effect is alleviated in Drop-seq results.
Article
Microbiology
Shanmugam Solaiyappan Mani, Barbara Reinhold-Hurek
Summary: The study found that Azoarcus olearius BH72 can induce nitrogen fixation by activating genes related to carbon metabolism and motility, while simultaneously reducing energy expenditure by suppressing translation and vitamin biosynthesis. Additionally, the strain is primed for alternative nitrogen sources such as nitrate, urea, and amino acids.
Article
Cardiac & Cardiovascular Systems
Alba Alvarez-Franco, Raquel Rouco, Rafael J. Ramirez, Guadalupe Guerrero-Serna, Maria Tiana, Sara Cogliati, Kuljeet Kaur, Mohammed Saeed, Ricardo Magni, Jose Antonio Enriquez, Fatima Sanchez-Cabo, Jose Jalife, Miguel Manzanares
Summary: Transcriptomic and proteomic analysis of AF progression in a large animal model shows significant changes occurring at early stages, including previously undescribed increase in mitochondria, changes to the chromatin of atrial CMs, and genes related to neural function and cell proliferation.
CARDIOVASCULAR RESEARCH
(2021)
Article
Biology
Alex L. Yenkin, John C. Bramley, Colin L. Kremitzki, Jason E. Waligorski, Mariel J. Liebeskind, Xinyuan E. Xu, Vinay D. Chandrasekaran, Maria A. Vakaki, Graham W. Bachman, Robi D. Mitra, Jeffrey D. Milbrandt, William J. Buchser
Summary: In this paper, the authors present a functional genomics platform called Raft-Seq, which combines high-content imaging, machine learning, and microraft isolation to identify cellular phenotypes underlying human diseases. The platform demonstrates its efficacy in distinguishing pathogenic mutations, even when the cellular phenotype is subtle, and utilizes multiple cellular features that can be configured on-the-fly.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yurie Soejima, Miho Takeuchi, Nao Miyamoto, Motoji Sawabe, Toshio Fukusato
Summary: In this study, ITGB6-ko CCA cell clones were successfully generated, showing decreased migration and invasion as well as downregulation of PODXL2. These findings suggest integrin beta 6 as a potential therapeutic target or diagnostic marker candidate in iCCA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Developmental Biology
Yingzhang Huang, Limeng Zhou, Chunhui Hou, Dianjing Guo
Summary: This study reveals the proteome landscape of Arabidopsis early embryogenesis through nanoproteomic analysis, and identifies gene enrichment related to ribosome biogenesis and auxin signaling. The positive correlation between mRNA and protein is confirmed by integrating RNA-sequencing data. This work provides valuable insights for further investigation into plant embryo development.
Article
Immunology
Neftali Ramirez, Sara Posadas-Cantera, Niko Langer, Andres Caballero Garcia de Oteyza, Michele Proietti, Baerbel Keller, Fangwen Zhao, Victoria Gernedl, Matteo Pecoraro, Hermann Eibel, Klaus Warnatz, Esteban Ballestar, Roger Geiger, Claudia Bossen, Bodo Grimbacher
Summary: This study investigated the disturbances of transcription factor binding and transcriptome profiles in naive B cells from CVID patients with TACI mutations. The findings suggest decreased chromatin accessibility and dysregulation of NF-kappa B and MAPK pathways in affected individuals. The study also reveals increased cell death pathways and reduced cell metabolism pathways in steady state, and enhanced immune responses and decreased cell survival after stimulation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Joris Van Houtven, Bart Cuypers, Pieter Meysman, Jef Hooyberghs, Kris Laukens, Dirk Valkenborg
Summary: This study investigated the application of a normalization method called CONSTANd in transcriptomics and proposed an adjustment for joint analysis. The results showed that CONSTANd can efficiently process large datasets, reduce systematic bias, and quickly reveal the underlying biological structure.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Virology
Angelene M. Cantwell, Harinder Singh, Maryann Platt, Yanbao Yu, Yi-Han Lin, Yuji Ikeno, Gene Hubbard, Yan Xiang, Norberto Gonzalez-Juarbe, Peter H. Dube
Summary: The study reports a Syrian hamster model that develops severe COVID-19-like disease, showing dynamic innate immune responses and immune pathologies consistent with severe human disease. Using an integrated multiorgan analysis, changes in gene transcription and protein expression over the course of infection were evaluated to provide a kinetic overview of host responses to infection. The model will be valuable for understanding the pathogenesis of severe COVID-19 and testing interventions.
JOURNAL OF VIROLOGY
(2021)
Article
Cell Biology
Ernesto S. Nakayasu, Farooq Syed, Sarah A. Tersey, Marina A. Gritsenko, Hugh D. Mitchell, Chi Yuet Chan, Ercument Dirice, Jean-Valery Turatsinze, Yi Cui, Rohit N. Kulkarni, Decio L. Eizirik, Wei-Jun Qian, Bobbie-Jo M. Webb-Robertson, Carmella Evans-Molina, Raghavendra G. Mirmira, Thomas O. Metz
Article
Microbiology
Paul Daly, Mao Peng, Hugh D. Mitchell, Young-Mo Kim, Charles Ansong, Heather Brewer, Peter de Gijsel, Mary S. Lipton, Lye Meng Markillie, Carrie D. Nicora, Galya Orr, Ad Wiebenga, Kristiina S. Hilden, Mirjam A. Kabel, Scott E. Baker, Miia R. Makela, Ronald P. de Vries
ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Biochemical Research Methods
Chia-Feng Tsai, Rui Zhao, Sarah M. Williams, Ronald J. Moore, Kendall Schultz, William B. Chrisler, Ljiljana Pasa-Tolic, Karin D. Rodland, Richard D. Smith, Tujin Shi, Ying Zhu, Tao Liu
MOLECULAR & CELLULAR PROTEOMICS
(2020)
Article
Multidisciplinary Sciences
Paul D. Piehowski, Ying Zhu, Lisa M. Bramer, Kelly G. Stratton, Rui Zhao, Daniel J. Orton, Ronald J. Moore, Jia Yuan, Hugh D. Mitchell, Yuqian Gao, Bobbie-Jo M. Webb-Robertson, Sudhansu K. Dey, Ryan T. Kelly, Kristin E. Burnum-Johnson
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Analytical
Gabe Nagy, Isaac K. Attah, Christopher R. Conant, Weijing Liu, Sandilya V. B. Garimella, Harsha P. Gunawardena, Jared B. Shaw, Richard D. Smith, Yehia M. Ibrahim
ANALYTICAL CHEMISTRY
(2020)
Article
Chemistry, Analytical
Piliang Xiang, Ying Zhu, Yu Yang, Zhitao Zhao, Sarah M. Williams, Ronald J. Moore, Ryan T. Kelly, Richard D. Smith, Shaorong Liu
ANALYTICAL CHEMISTRY
(2020)
Article
Biochemical Research Methods
Jacob Kagan, Robert L. Moritz, Richard Mazurchuk, Je Hyuk Lee, Peter Vasili Kharchenko, Orit Rozenblatt-Rosen, Eytan Ruppin, Fredrik Edfors, Fiona Ginty, Yury Goltsev, James A. Wells, John LaCava, Jessica L. Riesterer, Ronald N. Germain, Tujin Shi, Mark S. Chee, Bogdan A. Budnik, John R. Yates, Brian T. Chait, Jeffery R. Moffitt, Richard D. Smith, Sudhir Srivastava
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Oncology
Yuqian Gao, Yi-Ting Wang, Yongmei Chen, Hui Wang, Denise Young, Tujin Shi, Yingjie Song, Athena A. Schepmoes, Claire Kuo, Thomas L. Fillmore, Wei-Jun Qian, Richard D. Smith, Sudhir Srivastava, Jacob Kagan, Albert Dobi, Isabell A. Sesterhenn, Inger L. Rosner, Gyorgy Petrovics, Karin D. Rodland, Shiv Srivastava, Jennifer Cullen, Tao Liu
Article
Chemistry, Analytical
Sarah M. Williams, Andrey Liyu, Chia-Feng Tsai, Ronald J. Moore, Daniel J. Orton, William B. Chrisler, Matthew J. Gaffrey, Tao Liu, Richard D. Smith, Ryan T. Kelly, Ljiljana Pasa-Tolic, Ying Zhu
ANALYTICAL CHEMISTRY
(2020)
Article
Cell Biology
Eric S. Orwoll, Jack Wiedrick, Carrie M. Nielson, Jon Jacobs, Erin S. Baker, Paul Piehowski, Vladislav Petyuk, Yuqian Gao, Tujin Shi, Richard D. Smith, Douglas C. Bauer, Steven R. Cummings, Jodi Lapidus
Article
Biochemical Research Methods
Christopher R. Conant, Isaac K. Attah, Sandilya V. B. Garimella, Gabe Nagy, Aivett Bilbao, Richard D. Smith, Yehia M. Ibrahim
Summary: In this study, five different waveforms were characterized in terms of their transmission efficiency, IMS resolution, and resolving power, with triangle and asymmetric ramp profiles found to offer modestly greater resolution and resolving power compared to others. The research also revealed that separations were generally improved with higher TW amplitudes, moderately improved by lower speeds, but experienced decreases in signal intensity under extreme operating conditions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Ailin Li, Gabe Nagy, Christopher R. Conant, Randolph Norheim, Joon Yong Lee, Cameron Giberson, Adam L. Hollerbach, Venkateshkumar Prabhakaran, Isaac K. Attah, Christopher D. Chouinard, Aneesh Prabhakaran, Richard D. Smith, Yehia M. Ibrahim, Sandilya V. B. Garimella
ANALYTICAL CHEMISTRY
(2020)
Article
Chemistry, Analytical
Ailin Li, Christopher R. Conant, Xueyun Zheng, Kent J. Bloodsworth, Daniel J. Orton, Sandilya V. B. Garimella, Isaac K. Attah, Gabe Nagy, Richard D. Smith, Yehia M. Ibrahim
ANALYTICAL CHEMISTRY
(2020)
Article
Multidisciplinary Sciences
Kendall Martin, Tong Zhang, Pengfei Zhang, William B. Chrisler, Fillmore L. Thomas, Fen Liu, Tao Liu, Wei-Jun Qian, Richard D. Smith, Tujin Shi
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2020)
Article
Mathematical & Computational Biology
Yuping Zhang, Zhengqing Ouyang, Wei-Jun Qian, Richard D. Smith, Wing Hung Wong, Ronald W. Davis
STATISTICS AND ITS INTERFACE
(2020)