Review
Immunology
Ioannis Kienes, Ella L. Johnston, Natalie J. Bitto, Maria Kaparakis-Liaskos, Thomas A. Kufer
Summary: This article summarizes the subversion strategies used by bacterial pathogens to evade host immune detection, focusing on the well-studied NLRs NOD1/2, NLRP3, and NLRC4. The authors discuss how bacterial pathogens activate these NLRs to promote inflammation and disease, as well as mechanisms used by bacteria to attenuate NLR activation and interfere with host immunity. They also highlight the role of NLRs in facilitating immunotolerance and persistence of bacteria in the host, and the therapeutic potential of harnessing bacterial immune subversion strategies for chronic inflammatory conditions.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Pharmacology & Pharmacy
Jincheng Wang, Lulu Zhang, Qi Shi, Bo Yang, Qiaojun He, Jiajia Wang, Qinjie Weng
Summary: Acetaminophen (APAP) hepatotoxicity is a significant cause of acute liver failure, and immune cells play important roles in its pathogenesis by inducing inflammation to exacerbate liver toxicity and promoting liver regeneration by removing dead cells and debris.
BIOCHEMICAL PHARMACOLOGY
(2022)
Article
Entomology
Ashley L. Waring, Joshua Hill, Brooke M. Allen, Nicholas M. Bretz, Nguyen Le, Pooja Kr, Dakota Fuss, Nathan T. Mortimer
Summary: Summary: This study characterizes the gene expression changes in Drosophila fruit flies following infection by different pathogens and identifies a small number of genes that consistently show expression changes. These findings provide new insight into the transcriptional changes that accompany the immune response in fruit flies and may serve as candidate genes for further study.
Article
Microbiology
Simone Dallari, Thomas Heaney, Adriana Rosas-Villegas, Jessica A. Neil, Serre-Yu Wong, Judy J. Brown, Kelly Urbanek, Christin Herrmann, Daniel P. Depledge, Terence S. Dermody, Ken Cadwell
Summary: The study systematically defined the host response in mice to a panel of eukaryotic enteric viruses from six different families, revealing that most infections were asymptomatic in the mice but varied in magnitude and duration based on the microbiota. Flow cytometric and transcriptional profiling uncovered general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine, as well as numerous viral-strain-specific responses. Comparison with bacterial mono-associations identified bacterial species that induce immune responses similar to the viruses examined, emphasizing the importance of viral exposure events in the immune space occupied by the enteric virome.
CELL HOST & MICROBE
(2021)
Article
Neurosciences
Brian T. Kalish, Eunha Kim, Benjamin Finander, Erin E. Duffy, Hyunju Kim, Casey K. Gilman, Yeong Shin Yim, Lilin Tong, Randal J. Kaufman, Eric C. Griffith, Gloria B. Choi, Michael E. Greenberg, Jun R. Huh
Summary: The study found that maternal immune activation in mice induces changes in the mRNA translation machinery in the fetal brain and activates the integrated stress response in male fetuses, which mediates neurobehavioral abnormalities.
NATURE NEUROSCIENCE
(2021)
Article
Microbiology
Katya Frazier, Amal Kambal, Elizabeth A. Zale, Joseph F. Pierre, Nathaniel Hubert, Sawako Miyoshi, Jun Miyoshi, Daina L. Ringus, Dylan Harris, Karen Yang, Katherine Carroll, Jake B. Hermanson, John S. Chlystek, Katherine A. Overmyer, Candace M. Cham, Mark W. Musch, Joshua J. Coon, Eugene B. Chang, Vanessa A. Leone
Summary: The diurnal oscillations of gut microbiota play an important role in maintaining the host’s circadian rhythms and metabolism, ensuring optimal energy balance. This study reveals that the interaction between diet, microbes, and host factors, particularly the C-type lectin antimicrobial peptide Reg3 gamma, is complex and bidirectional. The high-fat diet disrupts the microbial oscillators, leading to dysregulated host Reg3 gamma expression, which subsequently affects the abundance and oscillation of key gut microbes. These findings highlight the coordination of biological rhythms between the host and microbial components, primarily influenced by diet.
CELL HOST & MICROBE
(2022)
Article
Multidisciplinary Sciences
Aditi Kulkarni, Ashmita Pandey, Patrick Trainor, Samantha Carlisle, Wanqin Yu, Phanidhar Kukutla, Jiannong Xu
Summary: This study identified a transcriptional axis consisting of Aryl hydrocarbon receptor (AhR) and Kruppel-like factor 10 (KLF10) that regulates immune responses in mosquitoes. Manipulating AhR activity with agonists or antagonists affected mosquito antibacterial immunity. KLF10 was identified as a target gene of AhR and played a crucial role in immune modulation.
SCIENTIFIC REPORTS
(2022)
Article
Immunology
Adi Biram, Jingjing Liu, Hadas Hezroni, Natalia Davidzohn, Dominik Schmiedel, Eman Khatib-Massalha, Montaser Haddad, Amalie Grenov, Sacha Lebon, Tomer Meir Salame, Nili Dezorella, Dotan Hoffman, Paula Abou Karam, Moshe Biton, Tsvee Lapidot, Mats Bemark, Roi Avraham, Steffen Jung, Ziv Shulman
Summary: Consecutive exposures to different pathogens can alter the host immune response. This study found that bacterial infection disrupts pre-existing immune responses and recruits Sca-1+ monocytes into lymphoid organs. This disruption is associated with impaired cellular respiration and is dependent on TNF alpha and IFN gamma. This phenomenon is observed in both vaccine supplementation and infection with Listeria monocytogenes.
Review
Medicine, Research & Experimental
Asmat Ali, Abdul Waris, Muhammad Ajmal Khan, Muhammad Asim, Atta Ullah Khan, Sahrish Khan, Jehan Zeb
Summary: Emerging and re-emerging bacterial infections pose a serious threat to human and animal health, especially those caused by intracellular bacteria. Current treatment methods involve narrow-spectrum antibiotics, but FDA-approved vaccines for obligate intracellular bacterial infections are lacking. However, various types of vaccines are currently being tested in clinical trials, including live, attenuated, subunit, killed whole cell, nano-based, and DNA vaccines.
Article
Multidisciplinary Sciences
Alessandra Gurtner, Costanza Borrelli, Ignacio Gonzalez-Perez, Karsten Bach, Ilhan E. Acar, Nicolas G. Nunez, Daniel Crepaz, Kristina Handler, Vivian P. Vu, Atefeh Lafzi, Kristin Stirm, Deeksha Raju, Julia Gschwend, Konrad Basler, Christoph Schneider, Emma Slack, Tomas Valenta, Burkhard Becher, Philippe Krebs, Andreas E. Moor, Isabelle C. Arnold
Summary: In the past decade, single-cell transcriptomics has provided insights into the biology of eosinophils, a difficult-to-sequence cell type, and their roles in intestinal homeostasis, immune regulation, and host defense. The study reveals the heterogeneity of eosinophils and the gene programs that underpin their pleiotropic functions. It also explains the mechanism by which interleukin-33 (IL-33) and interferon-gamma (IFN gamma) induce the accumulation of active eosinophils in the inflamed colon and their association with CD4(+) T cells.
Article
Environmental Sciences
Baoshi Xu, Jiangtao He, Hua Zou, Jingang Zhang, Lu Deng, Meiping Yang, Fei Liu
Summary: This study investigated the response of representative denitrifying bacterial strains to gatifloxacin exposure in groundwater denitrification. The results showed that different strains had varying responses in nitrate and nitrite removal efficiency, denitrifying enzyme activity, and gene expression under gatifloxacin exposure. Additionally, the study analyzed the degradation characteristics of nitrate using the Monod equation and found no significant increase in antibiotic resistance genes with gatifloxacin exposure.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Zaeema Usman, Zakia Kanwal, Asima Tayyeb, Iqra Noshair, Imran Haider, Naushad Ahmad, Suliman Yousef Alomar
Summary: The study investigated the effects of Pseudomonas aeruginosa and Fusarium oxysporum on Cirrhinus mrigala, and found significant changes in cytokine expression, hemato-biochemical parameters, and tissue histology of the infected fish.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Ying Kai Chan, Sean K. Wang, Colin J. Chu, David A. Copland, Alexander J. Letizia, Helena Costa Verdera, Jessica J. Chiang, Meher Sethi, May K. Wang, William J. Neidermyer, Yingleong Chan, Elaine T. Lim, Amanda R. Graveline, Melinda Sanchez, Ryan F. Boyd, Thomas S. Vihtelic, Rolando Gian Carlo O. Inciong, Jared M. Slain, Priscilla J. Alphonse, Yunlu Xue, Lindsey R. Robinson-McCarthy, Jenny M. Tam, Maha H. Jabbar, Bhubanananda Sahu, Janelle F. Adeniran, Manish Muhuri, Phillip W. L. Tai, Jun Xie, Tyler B. Krause, Andyna Vernet, Matthew Pezone, Ru Xiao, Tina Liu, Wei Wang, Henry J. Kaplan, Guangping Gao, Andrew D. Dick, Federico Mingozzi, Maureen A. McCall, Constance L. Cepko, George M. Church
Summary: The study engineered AAV vectors by incorporating short DNA oligonucleotides to antagonize TLR9 activation, reducing innate immune responses and enhancing gene expression in clinically relevant animal models. The engineered vectors can avoid adverse reactions in some models, demonstrating a potential wider therapeutic window for AAV therapies.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Genetics & Heredity
Juliana Cazarin, Rachel E. Derollo, Siti Noor Ain Binti Ahmad Shahidan, Jamison B. Burchett, Daniel Mwangi, Saikumari Krishnaiah, Annie L. Hsieh, Zandra E. Walton, Rebekah Brooks, Stephano S. Mello, Aalim M. Weljie, Chi V. Dang, Brian J. Altman
Summary: MYC disrupts the molecular circadian clock, releasing metabolic and biosynthetic processes from circadian control, which may provide an advantage to cancer cells.
Article
Public, Environmental & Occupational Health
Wilhelmina M. Huston, Amba Lawrence, Bryan A. Wee, Mark Thomas, Peter Timms, Lenka A. Vodstrcil, Anna McNulty, Ruthy McIvor, Karen Worthington, Basil Donovan, Samuel Phillips, Marcus Y. Chen, Christopher K. Fairley, Jane S. Hocking
Summary: Chlamydia trachomatis infection is the most common bacterial sexually transmitted infection worldwide, causing significant health burden. This study found that 11.8% of women experienced repeat infections after azithromycin treatment, and repeat infection was associated with sexual contact. The study also suggests that Chlamydia may have higher transcriptional activity at certain genes early in the infection, and there may be post-treatment immunological alterations that contribute to repeat infections. Regular testing of high-risk women may be important in reducing sequelae risk.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Biochemistry & Molecular Biology
Wen-Biao Jiao, Vipul Patel, Jonas Klasen, Fang Liu, Petra Pecinkova, Marina Ferrand, Isabelle Gy, Christine Camilleri, Sigi Effgen, Maarten Koornneef, Ales Pecinka, Olivier Loudet, Korbinian Schneeberger
Summary: Gene duplications provide genetic backup and allow genomic changes, but may limit gene flow and cause genetic incompatibilities. Despite being observed in artificial crosses, it is unclear if these occur in nature and their impact on natural populations. This study identified genetic incompatibilities in an intercross population and found incompatible alleles in natural populations, suggesting a collective role of additional gene copies in overcoming genetic incompatibilities during population history.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Chunhui Zhao, Yinhua Tang, Junli Wang, Yanhong Zeng, Hequan Sun, Zichao Zheng, Rong Su, Korbinian Schneeberger, Jane E. Parker, Haitao Cui
Summary: The study reveals the critical role of calcium (Ca2+) as a second messenger in plant immunity, with mutations in the CNGC20 gene affecting the cells' disease resistance responses. The research also highlights the mechanism by which CNGC20 influences PTI and ETI responses, emphasizing the importance of tight control of the CNGC20 calcium ion channel in immune regulation.
Article
Plant Sciences
Johanna Krahmer, Ammad Abbas, Virginie Mengin, Hirofumi Ishihara, Andres Romanowski, James J. Furniss, Thiago Alexandre Moraes, Nicole Krohn, Maria Grazia Annunziata, Regina Feil, Saleh Alseekh, Toshihiro Obata, Alisdair R. Fernie, Mark Stitt, Karen J. Halliday
Summary: Phytochrome photoreceptors play a crucial role in regulating plant growth responses to shade, as well as in carbon resource management, metabolism, and growth. Studies show that phytochrome influences metabolic fluxes, stress metabolite synthesis, sugar accumulation, and vacuolar sugar transport, ultimately impacting biomass production. Despite modified metabolism and altered architecture, growth rates in adult phy mutants resemble those of wild-type plants, with delayed seedling growth and smaller cotyledon size identified as the cause of the biomass defect in adult-stage mutants.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Multidisciplinary Sciences
Ejaz Hussain, Andres Romanowski, Karen J. Halliday
Summary: Plants are capable of adapting to changing circumstances, including responding to red light wavelengths from nearby vegetation. This study discovered the role of PHYTOCHROME-INTERACTING FACTOR 7 in constraining leaf blade cell division, and identified ANGUSTIFOLIA3 as a potential target. The research also found that PIF7 and AN3 exert antagonistic control over gene expression through common promoter motifs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Manish Goel, Korbinian Schneeberger
Summary: Third-generation genome sequencing technologies have significantly increased the number of high-quality genome assemblies. Plotsr is an efficient tool for visualizing structural similarities and rearrangements between genomes, capable of comparing on chromosome level or selected regions, and enhancing visualization with regional identifiers or histogram tracks.
Article
Genetics & Heredity
Hequan Sun, Wen-Biao Jiao, Jose A. Campoy, Kristin Krause, Manish Goel, Kat Folz-Donahue, Christian Kukat, Bruno Huettel, Korbinian Schneeberger
Summary: This study reports the reconstruction of the autotetraploid genome of potato based on high-quality long reads, single-cell sequencing, and Hi-C data, revealing the characteristics of genome similarity and structural rearrangements caused by recent inbreeding. Only a portion of the genes were present in all four haplotypes, and some genes may be regulated through allele-specific DNA methylation.
Article
Plant Sciences
Natanael Vinegra de la Torre, Alice Vayssieres, Evelyn Obeng-Hinneh, Ulla Neumann, Yanhao Zhou, Ana Lazaro, Adrian Roggen, Hequan Sun, Sara C. Stolze, Hirofumi Nakagami, Korbinian Schneeberger, Ton Timmers, Maria C. Albani
Summary: This study characterized three allelic enhancers of pep1 in Arabis alpina, which lead to early flowering. It identified an AAA(+) ATPase gene, AaFRAT1, with unknown function, as the causal mutation for these enhancers. The study also investigated the expression patterns and subcellular localization of AaFRAT1, and found that it contributes to flowering time regulation and the perennial growth habit in A. alpina.
Article
Plant Sciences
Johanna Acevedo-Garcia, Kim Walden, Franz Leissing, Kira Baumgarten, Katarzyna Drwiega, Mark Kwaaitaal, Anja Reinstadler, Matthias Freh, Xue Dong, Geo Velikkakam James, Lisa C. Baus, Martin Mascher, Nils Stein, Korbinian Schneeberger, Nahal Brocke-Ahmadinejad, Martin Kollmar, Paul Schulze-Lefert, Ralph Panstruga
Summary: Loss-of-function alleles of plant MLO genes confer broad-spectrum resistance to powdery mildews. In barley, mutations in Ror genes, including Ror1 encoding a myosin motor protein, partially impair the immunity conferred by mlo mutants. The myosin accumulates transiently during powdery mildew infection and is involved in intracellular transport processes critical for extracellular immunity.
Article
Multidisciplinary Sciences
Qichao Lian, Victor Solier, Birgit Walkemeier, Stephanie Durand, Bruno Huettel, Korbinian Schneeberger, Raphael Mercier
Summary: This study reveals the recombination landscape in the genome of Arabidopsis and its relationship with polymorphisms. The results show that the recombination frequency varies along different chromosomal regions and is highly correlated with sequence divergence. However, polymorphisms are not the main determinant of the shape of the recombination landscape. Instead, it is predominantly influenced by chromatin accessibility and DNA methylation. In inbred lines with minimal polymorphisms, the megabase-scale recombination landscape is similar to that in hybrids, except for cases where heterozygous large rearrangements prevent recombination locally. These findings provide new insights into the relationship between recombination landscape and polymorphisms.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Vidya Oruganti, Helena Toegelova, Ales Pecinka, Andreas Madlung, Korbinian Schneeberger
Summary: Gene flow between species in the genus Arabidopsis is significant and may be achieved through polyploidization. However, polyploidization poses challenges due to genomic instabilities. In this study, an autoallohexaploid population was created by crossing diploid Arabidopsis thaliana with allotetraploid Arabidopsis suecica. Genome resequencing revealed two major mechanisms promoting stable genomic exchange in this population. Legitimate meiotic recombination and chromosome segregation between autopolyploid chromosomes of A. thaliana genomes occurred without a bias for parental origin, while occasional exchanges between homoeologous chromosomes were tolerated. These mechanisms may facilitate gene flow and stable introgression in natural populations.
Article
Plant Sciences
Rafael Campos-Martin, Sophia Schmickler, Manish Goel, Korbinian Schneeberger, Achim Tresch
Summary: Genotyping by low-coverage whole-genome DNA sequencing is improved by a hidden Markov model that imposes an optimal minimum length constraint on genomic segments.
Article
Plant Sciences
Maria L. Sorkin, Shin-Cheng Tzeng, Stefanie King, Andres Romanowski, Nikolai Kahle, Rebecca Bindbeutel, Andreas Hiltbrunner, Marcelo J. Yanovsky, Bradley S. Evans, Dmitri A. Nusinow
Summary: Many molecular and physiological processes in plants occur at a specific time of day, regulated by the circadian clock. The MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its coactivators LNK1 and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. Affinity purification coupled with mass spectrometry (APMS) identified time-of-day-specific protein interactors of the RVE8-LNK1/LNK2 complex, including COR27 and COR28, which bind and antagonize the ability of the complex to induce target gene expression in the evening.
Editorial Material
Biochemistry & Molecular Biology
Shahram Shokrian Hajibehzad, Andres Romanowski, Ronald Pierik
Summary: A recent study reveals that photosynthetically produced sucrose functions as a key regulator of root growth and development in plants, dependent on shoot-derived auxin.
Correction
Biochemical Research Methods
Manish Goel, Korbinian Schneeberger
Article
Biochemical Research Methods
Tomasz Zielinski, Johnny Hay, Andrew Romanowski, Anja Nenninger, Alistair McCormick, Andrew J. Millar
Summary: Practical delivery of Findable, Accessible, Reusable and Interoperable principles for research data management requires expertise, time resource, (meta)data standards and formats, software tools and public repositories. SynBio2Easy, a tool presented in this paper, streamlines and automates operations on Synthetic Biology Open Language (SBOL) designs using Microsoft Excel(R) tables as metadata inputs.