Article
Agronomy
Hsien-Tzu Wang, Yu-Jung Cheng, Jhih-Ting Hsiao, Fuu Sheu, Yen-Chou Kuan
Summary: This study investigated the expression of broccoli HSP and the effect of 17-AAG on broccoli senescence. Through RNA-sequencing, 11 HSP and related genes were identified, with 10 nM 17-AAG treatment significantly alleviating yellowing of broccoli and enhancing stress tolerance. This research highlights the potential of using HSP inducers like 17-AAG to improve shelf life and quality of postharvest crops.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Andrey R. R. Suprun, Konstantin V. V. Kiselev, Alexandra S. S. Dubrovina
Summary: RNA interference (RNAi) is a natural regulatory mechanism that can be induced artificially by applying dsRNA to plant surfaces. This study investigated the effect of exogenous gene-specific dsRNAs on the silencing of tomato genes related to anthocyanin biosynthesis. The results showed that the application of dsRNAs downregulated the mRNA levels of the target genes, upregulated the expression of anthocyanin biosynthesis-related genes, and increased anthocyanin content in tomato leaves. This demonstrates the potential of using exogenous gene-specific dsRNAs to induce gene silencing and enhance plant secondary metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Xinliang Jiang, Junichi Maruyama, Hiroaki Iwasa, Kyoko Arimoto-Matsuzaki, Hiroshi Nishina, Yutaka Hata
Summary: YAP1, a co-transcription activator, serves as a thermosensor in response to heat shock conditions. Its subcellular localization is determined by phosphorylation status, with SRC and HSP90 involved in shuttling between the nucleus and cytoplasm. During heat shock, LATS2 forms aggregates and is dephosphorylated, influencing YAP1 activity in the cellular environment.
EXPERIMENTAL CELL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Phillip A. Frankino, Talha F. Siddiqi, Theodore Bolas, Raz Bar-Ziv, Holly K. Gildea, Hanlin Zhang, Ryo Higuchi-Sanabria, Andrew Dillin
Summary: The transcription factor SKN-1/NRF2 can sense and respond to changes in metabolic state. Knockdown of the amidohydrolase T12A2.1/amdh-1 activates a unique subset of SKN-1 regulated genes, independent of P38-MAPK signaling components. Histidine catabolism genes are required for this activation, possibly through accumulation of a specific catabolite. Activating SKN-1 results in increased oxidative stress resistance but decreased survival to heat stress.
Article
Plant Sciences
Wan-Peng Bai, Hu-Jun Li, Shelley R. Hepworth, Hai-Shuang Liu, Lin-Bo Liu, Gai-Ni Wang, Qing Ma, Ai-Ke Bao, Suo-Min Wang
Summary: This study characterized the acclimation of Zygophyllum xanthoxylum to heat using physiological measurements and transcriptome profiling. Moderate high temperature (40℃) enhanced photosynthetic capacity and plant performance, while severe high temperature (45℃) inhibited growth. Up-regulation of genes related to heat shock factors and heat shock proteins likely contribute to thermotolerance in Z. xanthoxylum.
Article
Engineering, Environmental
Ke Zhang, Joseph Hodge, Anamika Chatterjee, Tae Seok Moon, Kimberly M. Parker
Summary: Double-stranded RNA undergoes alkaline hydrolysis at orders-of-magnitude slower rates compared to single-stranded RNA, and can remain intact for months at neutral pH. Increasing pH effectively attenuates enzymatic degradation of dsRNA without inducing alkaline hydrolysis, which differs significantly from ssRNA. Understanding these unique properties of dsRNA allows for greater control of stability in RNAi technology and provides insights into various applications, including isolation, detection, and inactivation of dsRNA viruses.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xueqing Wang, Quanlong Jiang, Yuanyuan Song, Zhidong He, Hongdao Zhang, Mengjiao Song, Xiaona Zhang, Yumin Dai, Oezlem Karalay, Christoph Dieterich, Adam Antebi, Ligang Wu, Jing-Dong J. Han, Yidong Shen
Summary: Ageing is a complex process with different features in different tissues. This study isolated cells from different tissues in worms and analyzed the transcriptomic changes during ageing, revealing the diversity of ageing across tissues and identifying tissue-specific longevity regulators. Additionally, novel factors controlling intestinal barrier integrity and sarcomere structure during ageing were discovered.
Article
Oncology
Gang Xue, Ningbo Zheng, Jing Fang, Guangxu Jin, Xiaoyin Li, Gianpietro Dotti, Qing Yi, Yong Lu
Summary: This research demonstrates that tumor-specific Th9 cells have a unique capacity to eliminate advanced tumors containing ALVs, attributed to their enhanced direct tumor cell killing and interferon alpha/beta-induced bystander antitumor effects. This is due to the accumulation of extracellular ATP within the tumor microenvironment, promoting immune cell infiltration and antitumor cytokine production.
Article
Agronomy
Jianghua Liao, Haoling Rong, Lili You, Kai Xia, Minghui Wang, Peng Han, Chao Li, Jiang Zhang
Summary: By targeting the beta-Actin gene of the Colorado potato beetle, transplastomic plants can trigger a strong resistance to CPB. However, there is still dsRNA accumulation in the tubers, which is unnecessary and may pose a potential food exposure issue. In this study, we compared the activities of two promoters (PrbcL and PpsbD) with the Prrn promoter and found that PpsbD is an effective promoter to reduce dsRNA accumulation in potato tubers while maintaining resistance to CPB in the leaves.
PEST MANAGEMENT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Simona Cugusi, Prashanth Kumar Bajpe, Richard Mitter, Harshil Patel, Aengus Stewart, Jesper Q. Svejstrup
Summary: Besides HSF1, RPRD1B has been identified to play a role in regulating gene expression during the heat shock response.
MOLECULAR AND CELLULAR BIOLOGY
(2022)
Article
Biology
Satheeswaran Thangaraj, Jun Sun
Summary: Physiological experiments on Heterosigma akashiwo provide insights into the metabolic changes of algal blooms under future warming and acidification of the ocean. Despite the expected increase in harmful algal species due to ocean warming and acidification, the population of Heterosigma akashiwo has decreased. However, the physical and metabolic modifications of this species in terms of C:N:P ratio and macromolecule accumulation are still unknown.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Van Giap Do, Youngsuk Lee, Hunjoong Kweon, Seonae Kim
Summary: The coloration of apple fruits depends on pigment content, and light stimulus and carotenoids are involved in the coloring process. The pigment content and the expression of carotenoid metabolism genes in apple fruits vary significantly under different light conditions, and the genetic background also plays a role. Additionally, a combination of light and transitory overexpression of carotenogenic genes can enhance fruit coloration and pigment content.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Baizhen Gao, Qing Sun
Summary: Synthetic biology aims to reprogram living systems efficiently, but programming animal physiology remains challenging due to system complexity. By using engineered bacteria, researchers are able to modulate gene expression in Caenorhabditis elegans through genetic circuit controlled RNAi.
NATURE COMMUNICATIONS
(2021)
Article
Food Science & Technology
Shao-Shuai Bi, Hai-Tao Jin, Milton Talukder, Jing Ge, Cong Zhang, Mei-Wei Lv, Mamoon Ali Yaqoob Ismail, Jin-Long Li
Summary: The study demonstrates a potential protective effect of Nano-Se against Cd-induced cerebellar injury in chickens, enhancing the expression of heat shock factors and heat shock proteins and alleviating cerebellar cell degradation caused by Cd treatment.
FOOD AND CHEMICAL TOXICOLOGY
(2021)
Article
Plant Sciences
Wen-Ya Ma, Qiu-Yun Qin, Ying-Ning Zou, Kamil Kuca, Bhoopander Giri, Qiang-Sheng Wu, Abeer Hashem, Al-Bandari Fahad Al-Arjani, Khalid F. Almutairi, Elsayed Fathi Abd Allah, Yong-Jie Xu
Summary: AMF enhances drought tolerance in walnut by activating antioxidant defense systems and Hsfs transcription levels, reducing oxidative damage.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Daniel T. Youmans, Anne R. Gooding, Robin D. Dowell, Thomas R. Cech
Summary: Mutations in the SUZ12 subunit of PRC2 can drive it into PRC2.1 or PRC2.2 subcomplexes, affecting the expression of certain genes in pluripotent stem cells, particularly homeobox transcription factors.
Article
Medicine, Research & Experimental
Fabienne Gally, Sarah K. Sasse, Jonathan S. Kurche, Margaret A. Gruca, Jonathan H. Cardwell, Tsukasa Okamoto, Hong W. Chu, Xiaomeng Hou, Olivier B. Poirion, Justin Buchanan, Sebastian Preissl, Bing Ren, Sean P. Colgan, Robin D. Dowell, Ivana Yang, David A. Schwartz, Anthony N. Gerber
Summary: The G/T transversion rs35705950, located 3 kb upstream of the MUC5B start site, is identified as a key risk factor for idiopathic pulmonary fibrosis. Through analysis of accessible chromatin and nuclease sensitivity data, it is shown that this region affects the expression of MUC5B and is subject to epigenetic remodeling in IPF patients' lung tissue.
Article
Multidisciplinary Sciences
Qing Yang, Tassa K. Saldi, Patrick K. Gonzales, Erika Lasda, Carolyn J. Decker, Kimngan L. Tat, Morgan R. Fink, Cole R. Hager, Jack C. Davis, Christopher D. Ozeroff, Denise Muhlrad, Stephen K. Clark, Will T. Fattor, Nicholas R. Meyerson, Camille L. Paige, Alison R. Gilchrist, Arturo Barbachano-Guerrero, Emma R. Worden-Sapper, Sharon S. Wu, Gloria R. Brisson, Matthew B. McQueen, Robin D. Dowell, Leslie Leinwand, Roy Parker, Sara L. Sawyer
Summary: The study found that even asymptomatic individuals with SARS-CoV-2 may have low viral loads that are not infectious. Moreover, only 2% of individuals are responsible for carrying 90% of the virions circulating within communities, potentially acting as viral supercarriers and superspreaders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Marko Melnick, Patrick Gonzales, Thomas J. LaRocca, Yuping Song, Joanne Wuu, Michael Benatar, Bjorn Oskarsson, Leonard Petrucelli, Robin D. Dowell, Christopher D. Link, Mercedes Prudencio
Summary: This study developed a bioinformatic pipeline to identify potential etiological agents in RNA-seq data, successfully confirming the presence of known and novel viral sequences through testing and application in practical cases.
G3-GENES GENOMES GENETICS
(2021)
Article
Microbiology
Joseph M. Cabral, Camille H. Cushman, Catherine N. Sodroski, David M. Knipe
Summary: Histones are rapidly loaded onto the HSV genome upon entry into human fibroblast nuclei. ATRX, along with other histone H3 chaperones, plays a role in restricting viral replication by altering the structure of histone H3-loaded viral chromatin. ATRX is unique in its ability to significantly reduce HSV replication compared to other factors, likely by promoting reduced accessibility of viral DNA during infection.
Article
Engineering, Biomedical
Cierra J. Walker, Claudia Crocini, Daniel Ramirez, Anouk R. Killaars, Joseph C. Grim, Brian A. Aguado, Kyle Clark, Mary A. Allen, Robin D. Dowell, Leslie A. Leinwand, Kristi S. Anseth
Summary: Increased extracellular stiffness activates fibroblasts, leading to the transformation of transiently activated fibroblasts into myofibroblasts with condensed chromatin. The condensed chromatin structure of myofibroblasts is associated with cytoskeletal stability, and nuclear mechanosensing plays a key role in driving distinct chromatin signatures in persistently activated fibroblasts.
NATURE BIOMEDICAL ENGINEERING
(2021)
Article
Immunology
Lara N. Janiszewski, Michael Minson, Mary A. Allen, Robin D. Dowell, Amy E. Palmer
Summary: The study shows that host cells undergoing Salmonella infection undergo widespread changes in metal transport, metal-dependent genes, and metal homeostasis genes to remodel iron, copper, and zinc availability. Infection increases cytosolic zinc levels while limiting zinc within phagosomes. Manipulation of zinc at the host-pathogen interface is more nuanced than that of iron or copper.
INFECTION AND IMMUNITY
(2021)
Article
Biochemistry & Molecular Biology
Arnav Gupta, Sarah K. Sasse, Margaret A. Gruca, Lynn Sanford, Robin D. Dowell, Anthony N. Gerber
Summary: This study employed precision nuclear run-on sequencing and assay for transposase-accessible chromatin sequencing to investigate the effects of wood smoke particles on airway epithelial cells. It found a primary role for AHR in mediating the response to WSP in airway epithelial cells, as well as crosstalk between AHR and NF kappa B signaling in controlling proinflammatory gene expression.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Cecilia B. Levandowski, Taylor Jones, Margaret Gruca, Sivapriya Ramamoorthy, Robin D. Dowell, Dylan J. Taatjes
Summary: This study investigated the impact of the interaction between Delta 40p53 and WTp53 on growth arrest and mRNA biogenesis. The results showed that Delta 40p53:WTp53 can influence cellular response to Nutlin-induced p53 activation, as well as specific changes in mRNA induction in response to other stimuli.
Correction
Engineering, Biomedical
Cierra J. Walker, Claudia Crocini, Daniel Ramirez, Anouk R. Killaars, Joseph C. Grim, Brian A. Aguado, Kyle Clark, Mary A. Allen, Robin D. Dowell, Leslie A. Leinwand, Kristi S. Anseth
NATURE BIOMEDICAL ENGINEERING
(2021)
Article
Biology
Jonathan D. Rubin, Jacob T. Stanley, Rutendo F. Sigauke, Cecilia B. Levandowski, Zachary L. Maas, Jessica Westfall, Dylan J. Taatjes, Robin D. Dowell
Summary: Transcription Factor Enrichment Analysis (TFEA) is a computational method that detects positional motif enrichment associated with changes in transcription, providing insights into cellular processes. TFEA is applicable to various types of transcriptional regulation data, identifying key regulators and unraveling temporal regulatory networks.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Samuel Hunter, Rutendo F. Sigauke, Jacob T. Stanley, Mary A. Allen, Robin D. Dowell
Summary: Variations in run-on sequencing protocols leave identifiable features in the resulting datasets, affecting differences in quality control metrics and signal distribution at transcribed regions. However, these variations have limited impact on the analysis of key regulators underlying transcriptional changes.
Article
Biotechnology & Applied Microbiology
Cierra J. Walker, Dilara Batan, Carrie T. Bishop, Daniel Ramirez, Brian A. Aguado, Megan E. Schroeder, Claudia Crocini, Jessica Schwisow, Karen Moulton, Laura Macdougall, Robert M. Weiss, Mary A. Allen, Robin Dowell, Leslie A. Leinwand, Kristi S. Anseth
Summary: Aortic valve stenosis (AVS) is a fibrotic disease characterized by thickened valve leaflets. The activation of valve interstitial cells (VICs) to myofibroblasts (aVICs) plays a crucial role in AVS. This study reveals the importance of epigenetic mechanisms and mechanical regulation in VIC activation, and identifies CREBBP as a potential therapeutic target for AVS.
BIOENGINEERING & TRANSLATIONAL MEDICINE
(2022)