Article
Biochemistry & Molecular Biology
Hsin-Mei Huang, Philipp Stephan, Hajo Kries
Summary: By incorporating zinc-finger tags into split NRPS modules to create DNA-templated NRPS (DT-NRPS), researchers have demonstrated that covalent intermediate channeling is possible along the DNA template for the biosynthesis of non-ribosomal peptides and other polymers. This innovative catalytic strategy outperforms previously reported DNA-templated enzyme cascades in terms of DNA acceleration, indicating its potential for sequence-controlled biosynthesis.
CELL CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Bo-Siyuan Jian, Shao-Lun Chiou, Chun-Chia Hsu, Josh Ho, Yu-Wei Wu, John Chu
Summary: The traditional natural product discovery approach has only explored a small portion of nature's chemical diversity. By using bioinformatic tools, we can interpret the instructions encoded in microbial biosynthetic genes and overcome methodological limitations, thus expanding the scope of discovery. The evaluation of prediction algorithms for nonribosomal peptides (NRPs) synthesis shows that there is still a vast unexplored biosynthetic diversity in nature, suggesting the possibility of discovering unknown NRPs with functional roles other than siderophores.
ACS CHEMICAL BIOLOGY
(2023)
Article
Genetics & Heredity
Daren W. Brown, Hye-Seon Kim, Amy E. McGovern, Crystal E. Probyn, Robert H. Proctor
Summary: The genus Fusarium includes pathogens that are of global concern to animal and plant health. Analysis of PKS genes in the genomes of Fusarium species revealed the potential of different clades of PKSs to produce structurally distinct polyketide-derived natural products. This highlights the diverse natural product potential of Fusarium and its ability to produce metabolites with medical and other applications.
FUNGAL GENETICS AND BIOLOGY
(2022)
Article
Genetics & Heredity
Adriana Rego, Antonio Fernandez-Guerra, Pedro Duarte, Philipp Assmy, Pedro N. Leao, Catarina Magalhaes
Summary: This study assessed the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. The recovery of complete or near-complete biosynthetic gene clusters from bacterial metagenome-assembled genomes highlights the potential for discovering novel secondary metabolites in Arctic Ocean planktonic microbiomes. The strategy employed in this study will facilitate future bioprospection efforts by identifying promising samples for bacterial isolation and providing full-length BGCs for heterologous expression.
MICROBIAL GENOMICS
(2021)
Article
Immunology
Karthick Raja Arulprakasam, Dhanasekaran Dharumadurai
Summary: The evolution of genome sequencing technology and advancement of computational genome mining tools have improved the prediction of secondary metabolites. This study explored the diversity and distribution of Biosynthetic Gene Clusters (BGCs) among different species of actinobacteria genera, revealing the conservation of genus-specific gene clusters and highly conserved bioactive compounds with pharmacological activity against bacterial and fungal pathogens. Large-scale analysis of natural products, including different genera of actinobacteria, is necessary to address antibiotic resistance.
MICROBIAL PATHOGENESIS
(2021)
Article
Food Science & Technology
Lizeth Guardado-Valdivia, Alejandra Chacon-Lopez, Jesus Murillo, Jorge Poveda, Jose Luis Hernandez-Flores, Luis Xoca-Orozco, Selene Aguilera
Summary: The bean pathogen Pseudomonas syringae pv. phaseolicola NPS3121 synthesizes phaseolotoxin at 18 degrees C, with gene PSPPH_4550 playing a crucial role in regulation. The Pbo cluster, consisting of 16 genes, is found to be unrelated to phaseolotoxin biosynthesis cluster and may participate in the regulation of toxin production. Operons pboA and pboO are essential for phaseolotoxin biosynthesis, while pboK and pboJ only influence toxin amount.
Article
Biochemical Research Methods
Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel, Eivind Almaas
Summary: A pipeline for automated reconstruction of BGC associated metabolic pathways was developed, successfully predicting 72.8% of metabolic reactions. The reconstructed pathways were introduced into a genome-scale metabolic model, showing the potential for reliable in silico predictions. Application of the pipeline to a large BGC database identified 17 enzymatic reactions for increasing compound production, but with limited impact. These results suggest more sophisticated strain-engineering strategies are needed for efficient BGC expression hosts.
BMC BIOINFORMATICS
(2021)
Article
Microbiology
Pallabi Saha, Atrayee Sarkar, Nazmiara Sabnam, Meghana D. Shirke, H. B. Mahesh, Aman Nikhil, Anantharamanan Rajamani, Malali Gowda, Subhankar Roy-Barman
Summary: Rice blast caused by Magnaporthe oryzae is a major constraint in rice production, especially in India where it causes significant economic losses. India is the center of origin and diversity for rice as well as the Magnaporthe species complex. Analysis of the genome assemblies of M. oryzae strains from different parts of India revealed key genes for secondary metabolism and their role in functional adaptation across strains. This study is the first to investigate secondary metabolism genes and their evolutionary implications in multiple strains of M. oryzae.
FEMS MICROBIOLOGY LETTERS
(2021)
Article
Hematology
Thomas Lewis, David B. Corcoran, David E. Thurston, Peter J. Giles, Kevin Ashelford, Elisabeth J. Walsby, Christopher D. Fegan, Andrea G. S. Pepper, Khondaker Miraz Rahman, Chris Pepper
Summary: Novel C8-linked benzofused pyrrolo[2,1c][1,4]benzodiazepine monomeric hybrids have been identified as potent inhibitors of NF-KB in CLL and multiple myeloma cells, showing promising therapeutic potential for NF-KB-driven cancers.
Article
Plant Sciences
Kevin M. King, Gavin J. Eyres, Jonathan S. West, Clara Siraf, Pavel Matusinsky, Jana Palicova, Gail G. M. Canning, Geoff L. Bateman, Bart A. Fraaije, Paul S. Dyer
Summary: Eyespot, caused by fungal pathogens Oculimacula acuformis and O. yallundae, is a significant cereal stem-base disease in temperate regions. Differentiating between the two pathogens is important for effective disease management, and the development of two molecular methods for species-specific and mating-type discrimination helps in this regard. The study also reveals the role of sexual reproduction in the dispersal of eyespot disease.
Article
Agronomy
Kevin M. King, Diana E. Bucur, Faye Ritchie, Nichola J. Hawkins, Agata M. Kaczmarek, Yabing Duan, Steven Kildea, Jonathan S. West, Bart A. Fraaije
Summary: Pyrenopeziza brassicae causes leaf spot disease in Europe/Oceania (lineage 1) and North America (lineage 2), with European populations showing decreased azole sensitivity and prevalence of CYP51 substitutions, while North American populations remain highly sensitive. UK field trials revealed high G460S levels in European populations before treatment, indicating unclear further selection during trials; European populations showed resistance to MBC carbendazim. Recommendations include mixing azoles with QoI/SDHI for robust disease control.
Article
Cardiac & Cardiovascular Systems
Ling Li, Zhifen Chen, Moritz von Scheidt, Shuangyue Li, Andrea Steiner, Ulrich Gueldener, Simon Koplev, Angela Ma, Ke Hao, Calvin Pan, Aldons J. Lusis, Shichao Pang, Thorsten Kessler, Raili Ermel, Katyayani Sukhavasi, Arno Ruusalepp, Julien Gagneur, Jeanette Erdmann, Jason C. Kovacic, Johan L. M. Bjorkegren, Heribert Schunkert
Summary: This study systematically identified susceptibility genes for coronary artery disease (CAD) using transcriptome-wide association studies (TWAS). The study prioritized candidate causal genes at known GWAS loci, identified 18 novel genes associated with CAD, and suggested potential tissues and pathways of action for these TWAS CAD genes.
BASIC RESEARCH IN CARDIOLOGY
(2022)
Article
Agronomy
Kevin M. King, Jonathan S. West
Summary: In Spring 2021, Phoma-like disease symptoms were observed on wasabi crops in three UK sites, with fungal isolates identified as P. biglobosus subclade 'canadensis' and 'brassicae'. Pathogenicity testing showed these isolates were pathogenic to wasabi, oilseed rape, cabbage, and pak choi, completing Koch's postulates and representing new discoveries in Europe.
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Agronomy
Michelle T. Hulin, Andrea Vadillo Dieguez, Francesca Cossu, Samantha Lynn, Karen Russell, Helen C. Neale, Robert W. Jackson, Dawn L. Arnold, John W. Mansfield, Richard J. Harrison
Summary: The study identified resistant accessions to the major bacterial canker pathogens using a rapid leaf pathogenicity test, and found that this resistance extended to several Prunus species and hybrids. This resistance trait was associated with reduced bacterial growth after inoculation and showed potential for introducing into commercial germplasm.
Article
Plant Sciences
Amanda Karlstrom, Antonio Gomez-Cortecero, Charlotte F. Nellist, Matthew Ordidge, Jim M. Dunwell, Richard J. Harrison
Summary: This study identifies the first QTL associated with resistance to Neonectria ditissima in apple scion germplasm. The results show that the QTL present in commonly used apple breeding germplasm have a low to medium effect on resistance to N. ditissima. Therefore, multiple QTL need to be considered to improve resistance through breeding.
Article
Plant Sciences
Michelle T. Hulin, Mojgan Rabiey, Ziyue Zeng, Andrea Vadillo Dieguez, Sophia Bellamy, Phoebe Swift, John W. Mansfield, Robert W. Jackson, Richard J. Harrison
Summary: Through examining the genomic diversity of Pseudomonas syringae in the cherry phyllosphere, it was found that nonpathogenic strains contain reservoirs of T3SE genes and there may be horizontal gene transfer of different T3SE genes in cherry pathogens. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the emergence of new pathotypes. Genome-based epidemiological surveillance can be used to apply timely control measures to prevent disease.
Article
Genetics & Heredity
Krishna G. Aragam, Tao Jiang, Anuj Goel, Stavroula Kanoni, Brooke N. Wolford, Deepak S. Atri, Elle M. Weeks, Minxian Wang, George Hindy, Wei Zhou, Christopher Grace, Carolina Roselli, Nicholas A. Marston, Frederick K. Kamanu, Ida Surakka, Loreto Munoz Venegas, Paul Sherliker, Satoshi Koyama, Kazuyoshi Ishigaki, Bjorn O. Asvold, Michael R. Brown, Ben Brumpton, Paul S. de Vries, Olga Giannakopoulou, Panagiota Giardoglou, Daniel F. Gudbjartsson, Ulrich Gueldener, Syed M. Ijlal Haider, Anna Helgadottir, Maysson Ibrahim, Adnan Kastrati, Thorsten Kessler, Theodosios Kyriakou, Tomasz Konopka, Ling Li, Lijiang Ma, Thomas Meitinger, Soeren Mucha, Matthias Munz, Federico Murgia, Jonas B. Nielsen, Markus M. Noethen, Shichao Pang, Tobias Reinberger, Gavin Schnitzler, Damian Smedley, Gudmar Thorleifsson, Moritz von Scheidt, Jacob C. Ulirsch, David O. Arnar, Noel P. Burtt, Maria C. Costanzo, Jason Flannick, Kaoru Ito, Dong-Keun Jang, Yoichiro Kamatani, Amit V. Khera, Issei Komuro, Iftikhar J. Kullo, Luca A. Lotta, Christopher P. Nelson, Robert Roberts, Gudmundur Thorgeirsson, Unnur Thorsteinsdottir, Thomas R. Webb, Aris Baras, Johan L. M. Bjoerkegren, Eric Boerwinkle, George Dedoussis, Hilma Holm, Kristian Hveem, Olle Melander, Alanna C. Morrison, Marju Orho-Melander, Loukianos S. Rallidis, Arno Ruusalepp, Marc S. Sabatine, Kari Stefansson, Pierre Zalloua, Patrick T. Ellinor, Martin Farrall, John Danesh, Christian T. Ruff, Hilary K. Finucane, Jemma C. Hopewell, Robert Clarke, Rajat M. Gupta, Jeanette Erdmann, Nilesh J. Samani, Heribert Schunkert, Hugh Watkins, Cristen J. Willer, Panos Deloukas, Sekar Kathiresan, Adam S. Butterworth
Summary: This study identified and characterized over 250 risk loci for coronary artery disease (CAD) through a genome-wide association study, shedding light on the potential causal mechanisms for CAD. The research findings revealed the involvement of early developmental processes, cell cycle signaling, and vascular cell migration and proliferation in the pathogenesis of CAD.
Article
Microbiology
Kevin M. King, Gail Canning, Kang Zhou, Zekuan Liu, Mingde Wu, Jonathan S. West
Summary: This study indirectly investigates the potential role of sexual reproduction in the pathogenic fungus Plenodomus biglobosus, which causes blackleg disease in oilseed rape. The mating types of P. biglobosus in China are unbalanced, indicating predominantly asexual reproduction. These findings are important for improving the understanding of blackleg disease, particularly in China.
Article
Medicine, General & Internal
Ulrich Gueldener, Thorsten Kessler, Moritz von Scheidt, Johann S. Hawe, Beatrix Gerhard, Dieter Maier, Mark Lachmann, Karl-Ludwig Laugwitz, Salvatore Cassese, Albert W. Schoemig, Adnan Kastrati, Heribert Schunkert
Summary: This study applied self-organizing maps (SOMs) to detect regular patterns in multi-layered data for better prediction of in-stent restenosis (ISR) after percutaneous coronary intervention with stenting. The SOM approach identified known and novel predictors for restenosis risk, but did not significantly improve the prediction of ISR compared to conventional multivariable models.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Agronomy
Samara Nunes Campos Vicentini, Nichola J. Hawkins, Kevin M. King, Silvino Intra Moreira, Adriano Augusto de Paiva Custodio, Rui Pereira Leite Junior, Diego Portalanza, Felipe Rafael Garces-Fiallos, Loane Dantas Krug, Jonathan S. West, Bart A. Fraaije, Waldir Cintra De Jesus Junior, Paulo Cezar Ceresini
Summary: We developed a new monitoring tool for managing wheat blast, which provides quantitative measurement of pathogen inoculum levels and detection of fungicide resistance alleles. The results showed significant variations in pathogen inoculum levels and widespread distribution of fungicide resistance alleles in aerosol populations. However, the impact of weather variables on pathogen dynamics was not significant.
Review
Computer Science, Artificial Intelligence
Johannes Krefting, Partho Sen, Diana David-Rus, Ulrich Gueldener, Johann S. Hawe, Salvatore Cassese, Moritz von Scheidt, Heribert Schunkert
Summary: Outcome research supporting guideline recommendations for primary and secondary preventions relies heavily on data from clinical trials and selected hospital populations. The increasing volume of real-world medical data could significantly enhance the prediction, prevention, and care of cardiovascular disease (CVD). This review highlights the potential of health insurance claims (HIC) data to improve healthcare provision and discusses the challenges faced by patients, physicians, health insurers, and policy makers in utilizing such data.
FRONTIERS IN ARTIFICIAL INTELLIGENCE
(2023)
Article
Agronomy
Joanna Kaczmarek, Jonathan S. West, Kevin M. King, Gail G. M. Canning, Akinwunmi O. Latunde-Dada, Yong-Ju Huang, Bruce D. L. Fitt, Malgorzata Jedryczka
Summary: The study used SYBR-Green qPCR technology to successfully detect the abundance of airborne ascospores. Different primer pairs showed variations in specificity and sensitivity.
PEST MANAGEMENT SCIENCE
(2023)
Article
Biodiversity Conservation
Helen Maria Cockerton, Charlotte Florence Nellist, Timo Hytonen, Suzanne Litthauer, Katie Hopson, Adam Whitehouse, Maria Sobczyk, Richard Jonathan Harrison
Summary: This study identified three loci, including one known major locus and two epistatic modifiers, that affect the flowering habit of strawberries through a genome-wide association study. These findings are crucial for improving the genetic improvement of strawberries.
PLANTS PEOPLE PLANET
(2023)