Article
Immunology
Xiaoyuan Bai, Wenxian Yang, Heqiao Li, Yuna Zhao, Wenhui Fan, He Zhang, Wenjun Liu, Lei Sun
Summary: CsA regulates macrophage polarization and attenuates influenza virus-induced inflammatory responses by decreasing pro-inflammatory cytokines expression, increasing anti-inflammatory cytokines expression, and altering the polarization of macrophages from pro-inflammatory M1 phenotype to anti-inflammatory M2 phenotype. These effects depend on the binding of CsA to CypA.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Microbiology
Fanhua Wei, Chengjiang Gao, Yujiong Wang
Summary: Influenza virus infection can lead to cytokine storms, contributing to severe outcomes. Immunomodulatory drugs offer a promising approach for treating hypercytokinemia induced by acute viral infections.
CRITICAL REVIEWS IN MICROBIOLOGY
(2022)
Article
Microbiology
Haori Qiu, Bincai Yang, Yuhai Chen, Qianwen Zhu, Faxin Wen, Min Peng, Guoqing Wang, Guijie Guo, Biao Chen, Mohamed Maarouf, Min Fang, Ji-Long Chen
Summary: This study used RNA sequencing to analyze the differential expression of circRNAs in mouse lung tissues challenged with influenza A virus (IAV). They found that 413 circRNAs exhibited significantly altered levels following IAV infection, with circMerTK being highly induced. CircMerTK enhances IAV replication by suppressing antiviral immunity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Immunology
Keshia S. Hendricks, Eunice E. To, Raymond Luong, Felicia Liong, Jonathan R. Erlich, Ajay M. Shah, Stella Liong, John J. O'Leary, Doug A. Brooks, Ross Vlahos, Stavros Selemidis
Summary: This study found that endothelial NOX4 oxidase is protective against influenza morbidity and reduces lung inflammation. This suggests that it may serve as a potential therapeutic target for limiting the inflammatory response caused by influenza virus.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Zhao-Chen Shen, Yu-Ting Yang, Yu-Zhuo Guo, Ya-Qin Chai, Jia-Li Liu, Ruo Yuan
Summary: In this study, a high-efficiency electrochemiluminescence (ECL) biosensor was constructed using Zn2+-induced gold cluster aggregation (Zn2+-GCA) as the ECL emitter for ultrasensitive detection of microRNA-21 (miRNA-21). The Zn2+-GCA exhibited a high ECL efficiency of 10.54% compared to Au NCs stabilized by bovine serum albumin. The ultrasensitive ECL biosensor achieved a detection limit of 44.7 aM, demonstrating the potential for clinical diagnosis.
ANALYTICAL CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
Ravishankar Chandrasekaran, Carolyn R. Morris, Isabella M. Butzirus, Zoe F. Mark, Amit Kumar, Dhemerson Souza De Lima, Nirav Daphtary, Minara Aliyeva, Matthew E. Poynter, Vikas Anathy, Anne E. Dixon
Summary: Obesity increases disease severity in response to influenza infection through activation of the p38 MAPK signaling pathway in response to altered arachidonic acid signaling. Obese individuals and obese mice exhibited increased inflammation and lung injury in influenza infection, while also having a decreased interferon response. Inhibition of the p38 MAPK pathway attenuated inflammation, injury, and tissue elastance responses, and improved survival.
FRONTIERS IN PHARMACOLOGY
(2023)
Review
Medicine, Research & Experimental
Mengru Yang, Yi Wang, Yimin Yue, Lanyuan Liang, Mingming Peng, Mantong Zhao, Ying Chen, Xia Cao, Wei Li, Chuanqiu Li, Han Zhang, Jieyong Du, Renxing Zhong, Tianyi Xia, Zunpeng Shu
Summary: Influenza virus-induced pneumonia (IVP) is a highly morbid and contagious pulmonary infectious disease caused by invasion of the influenza virus into the lower respiratory tract. While the current treatment options are limited due to virus variability and drug resistance, Traditional Chinese Medicines (TCMs) offer unique advantages and have been widely used in clinical practice in China. This review provides a comprehensive analysis of TCMs used for IVP prevention and treatment, offering a theoretical basis for future drug development and suggesting the potential for new, low-toxicity drugs with multi-target effects.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Immunology
Praveen M. Varghese, Valarmathy Murugaiah, Nazar Beirag, Nigel Temperton, Haseeb A. Khan, Salman H. Alrokayan, Mohammed N. Al-Ahdal, Beatrice Nal, Futwan A. Al-Mohanna, Robert B. Sim, Uday Kishore
Summary: C4BP binds to different subtypes of Influenza A Virus and modulates the inflammatory response, showing differential effects on H1N1 and H3N2. It inhibits viral entry for H1N1 but promotes infection by H3N2, also regulating the expression of pro-inflammatory cytokines in a subtype-dependent manner.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
SangJoon Lee, Jin-Hyeob Ryu
Summary: The innate immune system serves as the first line of defense against influenza viruses, and mRNA vaccines are being explored as a promising alternative to traditional approaches due to their safety, cost-effectiveness, rapid development capabilities, and high efficacy. This review provides insights into the innate immune response to mRNA vaccination, as well as discusses the future directions and challenges in advancing this promising therapeutic approach.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yekaterina Kovalyova, Daniel W. Bak, Elizabeth M. Gordon, Connie Fung, Jennifer H. B. Shuman, Timothy L. Cover, Manuel R. Amieva, Eranthie Weerapana, Stavroula K. Hatzios
Summary: Oxidative stress, a prominent characteristic of most cancers, is involved in tumor formation. However, the molecular events of oxidation contributing to tumorigenesis remain largely unknown. This study demonstrates that inactivation of a redox-sensitive cysteine in the host protease legumain, which is oxidized during infection with the gastric cancer-causing bacterium Helicobacter pylori, accelerates tumor growth. These findings establish a connection between infection-induced oxidation and tumorigenesis, highlighting the significance of cysteine reactivity in tumor growth.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Virology
Rashid Manzoor, Nao Eguchi, Reiko Yoshida, Hiroichi Ozaki, Tatsunari Kondoh, Kosuke Okuya, Hiroko Miyamoto, Ayato Takada
Summary: Protective immunity against influenza A viruses mainly relies on antibodies to hemagglutinin (HA), but the conserved M2 protein has been studied as a vaccine antigen for cross-protective immunity. This study reveals that an M2-specific antibody can interfere with the HA-M2 association, providing a novel mechanism for the antiviral activity of M2-specific antibodies.
JOURNAL OF VIROLOGY
(2021)
Article
Immunology
Florian Krammer, Stacey Schultz-Cherry
Summary: Recent evidence of avian H5N1 virus transmission among mammals raises concerns about its potential for a pandemic. We need to increase awareness, preparedness, and adopt safe farming practices to prevent the emergence of concerning pathogens in the future.
NATURE REVIEWS IMMUNOLOGY
(2023)
Article
Immunology
Yan Guo, You-Hui Tu, Xu Wu, Shuang Ji, Ji-Long Shen, Hui-Mei Wu, Guang-He Fei
Summary: The study showed that RvD1 can play dual beneficial roles in protecting airway epithelium barrier function and reducing inflammation via the Nrf2 pathway, providing a promising treatment option for influenza A virus infection.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Pharmacology & Pharmacy
Lirun Zhou, Lei Bao, Yaxin Wang, Mengping Chen, Yingying Zhang, Zihan Geng, Ronghua Zhao, Jing Sun, Yanyan Bao, Yujing Shi, Rongmei Yao, Shanshan Guo, Xiaolan Cui
Summary: Geniposide, extracted from Gardenia jasminoides J.Ellis, has been found to possess pleiotropic activity against various diseases, particularly showing good therapeutic effects on different strains of influenza virus. The study explored the mechanism of geniposide on influenza A virus (IAV) through network pharmacology analysis, revealing a multi-target inhibitory effect on influenza, with one of the mechanisms being the calcium signaling pathway. Experimental data demonstrated that geniposide alleviates extracellular Ca2+ influx, decreases neuraminidase activity, and suppresses IAV replication in vitro by disrupting the interplay between IAV RNA polymerase and CAMKII.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemical Research Methods
Yue Yin, Jia Li, Jin Li, Minjung Lee, Sibo Zhao, Linlang Guo, Jianfang Li, Mutian Zhang, Yun Huang, Xiao-Nan Li, Zhenzhong Deng, Deqiang Sun
Summary: LiBis is a novel method that improves the alignment efficiency of low-input WGBS data by dynamically clipping initially unmapped reads and remapping them. This method significantly enhances the quantity of CpG sites and the precision in quantifying the methylation status, while also improving the cost effectiveness of low-input WGBS experiments.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Cell Biology
Hugh D. Mitchell, Amie J. Eisfeld, Kelly G. Stratton, Natalie C. Heller, Lisa M. Bremer, Ji Wen, Jason E. McDermott, Lisa E. Gralinski, Amy C. Sims, Mai Q. Le, Ralph S. Baric, Yoshihiro Kawaoka, Katrina M. Waters
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2019)
Article
Immunology
Satoshi Fukuyama, Kiyoko Iwatsuki-Horimoto, Maki Kiso, Noriko Nakajima, Robert W. Gregg, Hiroaki Katsura, Yuriko Tomita, Tadashi Maemura, Tiago Jose da Silva Lopes, Tokiko Watanabe, Jason E. Shoemaker, Hideki Hasegawa, Seiya Yamayoshi, Yoshihiro Kawaoka
JOURNAL OF INFECTIOUS DISEASES
(2020)
Article
Engineering, Chemical
Jordan J. A. Weaver, Jason E. Shoemaker
Article
Virology
Emily E. Ackerman, Jason E. Shoemaker
Article
Biochemical Research Methods
Robert W. Gregg, Fathima Shabnam, Jason E. Shoemaker
Summary: The study revealed that cell heterogeneity can enhance IFN beta responses during infection. Only 20-30% of cells need to respond during infection, beyond which no additional protection against cell death or reduction of viral load is provided.
Article
Biophysics
Muying Wang, Lauren L. Luciani, Heeju Noh, Ericka Mochan, Jason E. Shoemaker
BIOPHYSICAL JOURNAL
(2020)
Article
Biochemical Research Methods
Heeju Noh, Ziyi Hua, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
Summary: Understanding the molecular targets of diseases and drugs is crucial for drug discovery and treatment formulation. High-throughput gene transcription profiling technology provides whole-genome data, but identifying direct gene targets can be challenging due to the complexity of gene regulatory networks. DeltaNeTS+ is a powerful network analysis tool that can infer direct gene targets from gene expression profiles, combining steady-state and time-course data and leveraging gene network structure information.
BMC BIOINFORMATICS
(2021)
Correction
Biochemistry & Molecular Biology
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristobal Monraz Gomez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Drager, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Bornigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason E. Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gokce Yagmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. A. B. Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Groues, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Pena-Chilet, Kinza Rian, Tomas Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Auge, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Willighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristobal Monraz Gomez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Draeger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Boernigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason E. Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gokce Yagmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Groues, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Pena-Chilet, Kinza Rian, Tomas Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Auge, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider
Summary: The C19DMap is an open, interoperable and computable repository of COVID-19 molecular mechanisms, serving as a computational resource for network analysis and disease modeling. This framework provides tools, platforms and guidelines for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemical Research Methods
Josua O. Aponte-Serrano, Jordan J. A. Weaver, T. J. Sego, James A. Glazier, Jason E. Shoemaker
Summary: Respiratory viruses pose significant public health challenges, and understanding the immune response mechanisms and developing effective treatments are crucial. A spatialized multicellular computational model of RNA virus infection and antiviral response mediated by type-I interferon was presented, showing that modifying signaling molecules or diffusion lengths could affect viral plaque growth. The model suggests that cytokine assay measurements may be most informative under conditions leading to arrested plaque growth.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Virology
Emily E. Ackerman, Jordan J. A. Weaver, Jason E. Shoemaker
Summary: The timing and magnitude of the innate immune response to viral infection vary across different influenza A virus subtypes. This study uses computational modeling and immunologic data to identify the immune interactions that differ in mice infected with low-pathogenic H1N1 or high-pathogenic H5N1 influenza viruses. The production rate of interferon is found to be the major driver of strain-specific immune responses.
Article
Multidisciplinary Sciences
Lisa M. Bramer, Robert D. Hontz, Amie J. Eisfeld, Amy C. Sims, Young-Mo Kim, Kelly G. Stratton, Carrie D. Nicora, Marina A. Gritsenko, Athena A. Schepmoes, Osamu Akasaka, Michiko Koga, Takeya Tsutsumi, Morio Nakamura, Ichiro Nakachi, Rie Baba, Hiroki Tateno, Shoji Suzuki, Hideaki Nakajima, Hideaki Kato, Kazunari Ishida, Makoto Ishii, Yoshifumi Uwamino, Keiko Mitamura, Vanessa L. Paurus, Ernesto S. Nakayasu, Isaac K. Attah, Andrew G. Letizia, Katrina M. Waters, Thomas O. Metz, Karen Corson, Yoshihiro Kawaoka, Vincent R. Gerbasi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto
Summary: To better understand the pathology of COVID-19, a multi-omics and correla-tive analysis was conducted on a clinical cohort. Severe patients exhibited elevated levels of pulmonary surfactant, while mild patients showed an increase in the carnosine dipeptidase modifying enzyme (CNDP1). Both mild and severe patients had elevated L-cystine and enzymes related to glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both patient groups, with higher formation in severe cases. CNDP1 may play a protective role in suppressing PSPB release, while NET formation is correlated with increased PSPB levels and disease severity, potentially leading to pulmonary occlusions.
Article
Immunology
Ryota Sato, Chieko Makino-Okamura, Quingshun Lin, Muying Wang, Jason E. Shoemaker, Tomohiro Kurosaki, Hidehiro Fukuyama
INTERNATIONAL IMMUNOLOGY
(2020)
Proceedings Paper
Automation & Control Systems
Emily E. Ackerman, Ericka Mochan, Jason E. Shoemaker
Article
Medicine, Research & Experimental
Edward J. Perkins, Kalyan Gayen, Jason E. Shoemaker, Philipp Antczak, Lyle Burgoon, Francesco Falciani, Steve Gutsell, Geoff Hodges, Aude Kienzler, Dries Knapen, Mary McBride, Catherine Willett, Francis J. Doyle, Natalia Garcia-Reyero
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION
(2019)