Article
Multidisciplinary Sciences
Landen Gozashti, Scott W. Roy, Bryan Thornlow, Alexander Kramer, Manuel Ares, Russell Corbett-Detig
Summary: There is significant variation in intron numbers across eukaryotic genomes, and the major drivers of intron content during evolution remain unclear. This study identified 27,563 introns derived from specialized transposons called Introners in 175 eukaryotic genomes, indicating that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. Species with Introners span diverse phylogenetic backgrounds, and aquatic organisms are more likely to contain Introners. The mechanistic diversity of Introners suggests convergent evolution from nonautonomous transposable elements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tomoki Ueda, Kei-ichiro Nishimura, Yuka Nishiyama, Yuto Tominaga, Katsushi Miyazaki, Hiroyuki Furuta, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Alternative splicing is an important mechanism in eukaryotic cells that allows multiple proteins to be produced from a single gene. Although it is usually associated with group I self-splicing introns, limited examples of alternative splicing have been reported. This study focuses on exon-skipping splicing in genes containing two group I introns and reveals the key structural elements important for this type of splicing through pairwise engineering and biochemical characterization.
Article
Biology
Vojtech Zarsky, Anna Karnkowska, Vittorio Boscaro, Morelia Trznadel, Thomas A. Whelan, Markus Hiltunen-Thoren, Ioana Onut-Brannstrom, Cathryn L. Abbott, Naomi M. Fast, Fabien Burki, Patrick J. Keeling
Summary: Microsporidians and mikrocytids are examples of extreme genome reduction in eukaryotes. While the genome of Mikrocytos mackini is larger and gene-rich compared to microsporidians, much of the genome is composed of transposons. The energy and carbon metabolism of M. mackini share similarities with microsporidians, and both groups have highly reduced spliceosomes.
Article
Biochemistry & Molecular Biology
Chun Shen Lim, Brooke N. Weinstein, Scott W. Roy, Chris M. Brown
Summary: This study used fungal genomes to address questions related to intron evolution, revealing a complex evolutionary history of fungal introns and their underappreciated roles in gene expression. The research showed that intron reduction has occurred in various clades, with some fungi containing as few as zero to 7.6 introns per 1 kb of protein-coding sequence. The study also found conserved introns in ribosome-associated genes, highlighting their potential importance in ribosome biogenesis and gene expression coordination.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Sarah Schleicher, Inka-Rosalia Lottje, Petra Mischnick
Summary: Accurate quantification of isotopologous mixed O-methyl-O-methyl-d(3)-cellooligosaccharides was achieved through investigation into ionization processes with an electrospray ionization ion trap mass spectrometer. By optimizing experimental conditions, potential bias during MS measurement was effectively addressed.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Samantha M. Roberts, Miranda Aldis, Elena T. Wright, Cara B. Gonzales, Zhao Lai, Susan T. Weintraub, Stephen C. Hardies, Philip Serwer
Summary: The diversity of phage propagation, physical properties, and assembly make phages useful in ecological studies and biomedicine, but the known phage diversity is incomplete. The newly described Bacillus thuringiensis siphophage, 0105phi-7-2, expands the known phage diversity significantly. Its unique characteristics include a sharp increase in plaque size as agarose concentration decreases, head-host-cell binding observed through electron microscopy, and the inability to propagate in liquid culture. Genomic sequencing reveals its history as a temperate phage and distant similarity to the prototypical siphophage SPP1 of Bacillus subtilis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Qiqi Chen, Pan Shen, Ralph Bock, Shengchun Li, Jiang Zhang
Summary: A global survey of plastid gene expression during fruit ripening in kiwifruit reveals cis-elements that can potentially trigger high-level transgene expression in edible tissues, providing valuable resources for analyzing plastid gene expression and future efforts to engineer the plastid genome of kiwifruit.
PLANT CELL REPORTS
(2022)
Article
Biochemical Research Methods
Robert L. Schrader, Thomas E. Walker, David H. Russell
Summary: The use of mild collisional activation has been found to remove salts and adducts from large molecules, enhancing measurement accuracy and mass resolution. Adding a short square quadrupole between the ion funnel and transmission quadrupole effectively removes adducts and improves ejection efficiency for ions with low size-to-charge ratio.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Sarah Schleicher, Dominik Horoba, Philip Krafzig, Petra Mischnick
Summary: In this study, the hydroxyethyl substitution in cellulose ethers was analyzed using ESI-IT-MS. The correct quantification of the constituents was achieved through the use of internal standards and optimization of measurement conditions. The study also highlighted potential errors in relative quantification when using internal standards with similar chemistry or for analytes with related structures.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Ryo Kurosawa, Kei Iida, Masahiko Ajiro, Tomonari Awaya, Mamiko Yamada, Kenjiro Kosaki, Masatoshi Hagiwara
Summary: PDIVAS is a tool for detecting disease-causing deep-intronic variants, trained using ensemble machine learning algorithms with high precision and maximum MCC value. In genome sequencing analysis, PDIVAS prioritizes pathogenic variants more efficiently than previous predictors.
Article
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Alisa Gega, Athar Ansari
Summary: Introns play a conserved role in enhancing gene expression, with proximity to both the promoter and the terminator regions affecting their regulatory potential. While a promoter-proximal intron is most efficient in enhancing gene expression, a terminator-proximal intron can also positively influence transcription by affecting both the assembly of preinitiation complex and promoter directionality.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Microbiology
D. Holtappels, K. J. Fortuna, M. Vallino, R. Lavigne, J. Wagemans
Summary: The increasing interest in using bacteriophages for therapeutic purposes has led to a significant rise in the number of sequenced phage genomes. The International Committee on Taxonomy of Viruses has proposed a comprehensive and data-driven classification system for phages, which facilitates their taxonomy. In this study, we present the taxonomical classification of a novel Xanthomonas phage FoX4, isolated from a Brussels sprouts field in Belgium. The phage has a limited ability to lyse bacteria but efficiently adsorbs to its host. Based on its genome sequence and low similarity to known phages, the phage is classified as a new phage genus called Foxquatrovirus.
Article
Cell Biology
Katja Zappe, Antonio Kopic, Alexandra Scheichel, Ann-Katrin Schier, Lukas Emanuel Schmidt, Yasmin Borutzki, Heidi Miedl, Martin Schreiber, Theresa Mendrina, Christine Pirker, Georg Pfeiler, Stefan Hacker, Werner Haslik, Dietmar Pils, Andrea Bileck, Christopher Gerner, Samuel Meier-Menches, Petra Heffeter, Margit Cichna-Markl
Summary: The expression of ABC transporter ABCA7 is aberrantly regulated in breast cancer. Epigenetic and genetic alterations, as well as alternative splicing variants, were investigated in ABCA7 in breast cancer. CpG methylation abnormalities were observed at the exon 5-intron 5 boundary in a subtype-specific manner. Treatment with chemotherapeutic agents altered ABCA7 intron levels and dysregulated splicing factors.
Article
Virology
Janet T. Lin, Sarah Kirst, Stevan Cucic, Alexandra Klem, Yi-Min She, Andrew M. Kropinski, Hany Anany
Summary: A novel bacteriophage with high specificity and a long latent period was isolated from EHEC-enriched sewage, expanding our understanding of bacteriophage diversity.
Article
Clinical Neurology
Hong-Dong Li, Cory C. Funk, Karen McFarland, Eric B. Dammer, Mariet Allen, Minerva M. Carrasquillo, Yona Levites, Paramita Chakrabarty, Jeremy D. Burgess, Xue Wang, Dennis Dickson, Nicholas T. Seyfried, Duc M. Duong, James J. Lah, Steven G. Younkin, Allan Levey, Gilbert S. Omenn, Nilufer Ertekin-Taner, Todd E. Golde, Nathan D. Price
Summary: In this study, intron retention (IR) was found to play a role in Alzheimer's disease (AD) through genome-wide analysis of genetic, transcriptomic, and proteomic data. Thousands of IR events were identified, along with differentially expressed genes associated with AD and splicing-related genes that may regulate IR. The findings provide a new resource for exploring new AD biomarkers and pathological mechanisms.
ALZHEIMERS & DEMENTIA
(2021)
Article
Virology
Maroua Oueslati, Dominique Holtappels, Kiandro Fortuna, Mohamed Rabeh Hajlaoui, Rob Lavigne, Najla Sadfi-Zouaoui, Jeroen Wagemans
Summary: In this study, a novel lytic bacteriophage SoKa was isolated, which can effectively lyse Pss and related strains, and possesses characteristics of resistance to low temperature, UV radiation, and biofilm. SoKa has the potential for application in disease control in citrus production.
Article
Multidisciplinary Sciences
Brieuc Van Nieuwenhuyse, Dimitri Van der Linden, Olga Chatzis, Cedric Lood, Jeroen Wagemans, Rob Lavigne, Kaat Schroven, Jan Paeshuyse, Catherine de Magnee, Etienne Sokal, Xavier Stephenne, Isabelle Scheers, Hector Rodriguez-Villalobos, Sarah Djebara, Maya Merabishvili, Patrick Soentjens, Jean-Paul Pirnay
Summary: In this study, the authors use a combination of bacteriophage and antibiotic therapy to treat extensively drug-resistant Pseudomonas aeruginosa infection in a toddler post liver transplantation. They report on the clinical and microbiological improvement and investigate the reasons why bacterial phage resistance did not lead to therapeutic failure.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Hugo Oliveira, Silvio Santos, Diana P. Pires, Dimitri Boeckaerts, Graca Pinto, Rita Domingues, Jennifer Otero, Yves Briers, Rob Lavigne, Mathias Schmelcher, Andreas Doetsch, Joana Azeredo
Summary: In this study, a newly isolated myovirus CkP1 was found to infect Citrobacter koseri, causing urinary tract infections. The phage showed a broad host range and specifically bound to C. koseri cells through the tail fiber protein. It demonstrated high stability and potential for controlling drug-resistant C. koseri infections.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lammens Eveline-Marie, Nathalie Feyaerts, Alison Kerremans, Maarten Boon, Rob Lavigne
Summary: In this study, four non-toxic RNA polymerases from Pseudomonas phages were identified and characterized for improving gene expression systems in non-model bacterial hosts. The researchers confirmed the broad activity range and orthogonality of these RNA polymerases through screening and characterization. Furthermore, they improved the stringency of the RNA polymerase expression systems by introducing and optimizing phage lysozymes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ana C. Brandao, Leena Putzeys, Diana P. Pires, Marleen Voet, Jan Paeshuyse, Joana Azeredo, Rob Lavigne
Summary: Phage therapy shows promise as an effective treatment against multidrug-resistant bacterial infections, such as those caused by Pseudomonas aeruginosa. However, our understanding of phage-bacteria interaction in a human environment remains limited. In this study, we analyzed the transcriptome of phage-infected P. aeruginosa adhered to human epithelium and observed that phage genome transcription remained unaffected by bacterial growth. Phage utilized a core strategy of predation by upregulating prophage-associated genes, shutting down bacterial surface receptors, and inhibiting motility. We also identified specific responses under lung-simulating conditions, including the expression of genes related to various biological processes. These findings highlight the importance of studying phage-bacteria interplay in complex settings that mimic in vivo conditions and demonstrate the versatility of phage in invading bacterial cells.
Article
Virology
Nata Bakuradze, Maia Merabishvili, Ia Kusradze, Pieter-Jan Ceyssens, Jolien Onsea, Willem-Jan Metsemakers, Nino Grdzelishvili, Guliko Natroshvili, Tamar Tatrishvili, Davit Lazvliashvili, Nunu Mitskevich, Jean-Paul Pirnay, Nina Chanishvili
Summary: Bacteroides fragilis is a commensal gut bacterium associated with blood and tissue infections. Cases of refractory infections caused by strains resistant to common antibiotics for B. fragilis have been reported more frequently. Bacteriophages have been found to be a successful alternative to antibiotic therapy for multidrug-resistant bacterial infections.
Article
Virology
Agnieszka Latka, Abram Aertsen, Dimitri Boeckaerts, Bob Blasdel, Pieter-Jan Ceyssens, Abel Garcia-Pino, Annika Gillis, Rob Lavigne, Gipsi Lima-Mendez, Jelle Matthijnssens, Jolien Onsea, Eveline Peeters, Jean-Paul Pirnay, Damien Thiry, Dieter Vandenheuvel, Els Van Mechelen, Jolien Venneman, Gilbert Verbeken, Jeroen Wagemans, Yves Briers
Summary: The Belgian Society for Viruses of Microbes (BSVoM) was established on June 9, 2022 to promote collaboration among microbial virus researchers in Belgium. Comprising sixteen founders from academia, industry, and government, the society held its inaugural symposium on September 23, 2022 with three thematic sessions, keynote speeches, talks, and poster presentations.
Article
Microbiology
Marianne Nicolas, Angelina Trotereau, Antoine Culot, Arshnee Moodley, Robert Atterbury, Jeroen Wagemans, Rob Lavigne, Philippe Velge, Catherine Schouler
Summary: Colibacillosis, the most common bacterial disease affecting poultry, is primarily treated with antibiotics. However, the rise of multidrug-resistant avian-pathogenic Escherichia coli (APEC) necessitates the exploration of alternative treatments, such as phage therapy. This study isolates and characterizes 19 genetically diverse coliphages, and demonstrates their efficacy in controlling APEC infections in ovo.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Laure Verstraete, Juliana Aizawa, Matthias Govaerts, Linda De Vooght, Rob Lavigne, Jan Michiels, Bram van den Bergh, Paul Cos
Summary: The importance of targeting persister cells in antibiotic therapies is increasingly evident as they contribute to relapsing infections and the development of antibiotic resistance. This study focused on persistence in the clinically relevant pathogen Pseudomonas aeruginosa, which is associated with chronic lung infections in cystic fibrosis patients. The researchers optimized a mouse model to simulate these lung infections and found that the survival levels of P. aeruginosa in the model correlated with survival levels measured in traditional persistence assays. These findings validate current techniques for studying persistence and provide opportunities to explore new persistence mechanisms and antipersister strategies in vivo.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Niels Vander Elst, Joni Bert, Herman Favoreel, Rob Lavigne, Evelyne Meyer, Yves Briers
Summary: Engineered endolysins have shown potential as add-on treatments for bovine streptococcal mastitis, with high bacteriolytic activity against antibiotic-resistant strains and the ability to eradicate biofilms and exhibit intracellular activity.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Microbiology
Jessica Duarte da Silva, Lene Bens, Adriele J. do Carmo Santos, Rob Lavigne, Jose Soares, Luis D. R. Melo, Marta Vallino, Roberto Sousa Dias, Zuzanna Drulis-Kawa, Sergio Oliveira de Paula, Jeroen Wagemans
Summary: Proteus mirabilis is a significant pathogen causing catheter-associated urinary tract infections (CAUTIs). Two phages, BigMira and MidiMira, were studied and found to have similarities with four missense mutations impacting their depolymerase activity. Analysis of clinical P. mirabilis strains revealed differences in antibiotic resistance profiles and lipopolysaccharide locus, explaining phages' host range. The presence of antimicrobial resistance genes poses challenges for treating infections caused by multidrug-resistant bacteria.
Article
Microbiology
Eveline-Marie Lammens, Daniel Christophe Volke, Kaat Schroven, Marleen Voet, Alison Kerremans, Rob Lavigne, Hanne Hendrix
Summary: The development of CRISPR-Cas-based engineering technologies has revolutionized the microbial biotechnology field. The alternative Class I Type I-C CRISPR-Cas3 system has been utilized as a highly efficient genome editing tool for Pseudomonas hosts.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Pilar Garcia, Rafael Tabla, Hany Anany, Roberto Bastias, Lone Brondsted, Susana Casado, Pablo Cifuentes, John Deaton, Thomas G. Denes, Mohammad Aminul Islam, Rob Lavigne, Andrea I. Moreno-Switt, Natsuko Nakayama, Cristina Munoz Madero, Alexander Sulakvelidze, Antonet M. Svircev, Jeroen Wagemans, Elena G. Biosca, Dacil Rivera
Summary: This meeting discussed the suitability of using bacteriophages as alternative antimicrobials in the agrifood sector. It brought together researchers, industry delegates, and policymakers to debate the advantages, potential shortcomings, and regulatory aspects of phage application strategies.
Article
Microbiology
Kaat Schroven, Leena Putzeys, Alison Kerremans, Pieter-Jan Ceyssens, Marta Vallino, Jan Paeshuyse, Farhana Haque, Ahmed Yusuf, Matthias D. Koch, Rob Lavigne
Summary: This study elucidates the molecular mechanism of the phage-encoded protein PIT4, which interacts with multiple histidine kinases to regulate key virulence factors in Pseudomonas aeruginosa. This finding highlights the potential of phage-derived proteins as targets for anti-virulence compounds.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Saartje Uyttebroek, Laura Bessems, Willem-Jan Metsemakers, Yves Debaveye, Laura Van Gerven, Lieven Dupont, Melissa Depypere, Jeroen Wagemans, Rob Lavigne, Maya Merabishvili, Jean-Paul Pirnay, David Devolder, Isabel Spriet, Jolien Onsea
Summary: This study investigated the stability of bacteriophage preparations used in the treatment of various infections. The results showed that the titer of bacteriophages decreased after storage, indicating the importance of maintaining therapeutic concentrations. The study also found that storing bacteriophage solutions in polypropylene syringes helped maintain stability. Nasal irrigation or infusion through a catheter did not affect the titer of bacteriophages.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Naiqing Xu, Xinen Tang, Xin Wang, Miao Cai, Xiaowen Liu, Xiaolong Lu, Shunlin Hu, Min Gu, Jiao Hu, Ruyi Gao, Kaituo Liu, Yu Chen, Xiufan Liu, Xiaoquan Wang
Summary: This study found that the H9N2 subtype avian influenza virus has a high airborne transmissibility, while the H7N9 virus does not. The Hemagglutinin protein of the H9N2 virus was found to play a key role in replication, stability, and airborne transmission.
Article
Virology
Samar S. Ewies, Sabry M. Tamam, Ahmed S. Abdel-Moneim, Sherin R. Rouby
Summary: Contagious ecthyma (CE) is a highly contagious viral disease of sheep and goats worldwide. The study provided a clinical description of CE and screened for genetic variation in the B2L gene. Infected sheep exhibited anorexia and oral lesions, while inoculated chicken embryos showed pock lesions. The B2L gene was successfully amplified and found to be highly conserved.
Article
Virology
Yigal Farnoushi, Dan Heller, Avishai Lublin
Summary: In recent years, new variants of avian reovirus (ARV) have caused a variety of symptoms in chickens worldwide, including viral arthritis/tenosynovitis. This study analyzed emerging ARV variants in Israel and found significant genetic diversity. Most ARV isolates in Israel belonged to genotypic cluster 5 (GC5). The study suggests that Israel has not experienced the emergence of new ARV variants since the introduction of the live vaccine (ISR-7585), but ongoing monitoring is needed due to the continuous emergence of ARV variants.
Article
Virology
Shigeru Tajima, Michiyo Kataoka, Yuki Takamatsu, Hideki Ebihara, Chang-Kweng Lim
Summary: Yokose virus (YOKV), a bat-associated flavivirus, was found to replicate at a slower rate in mosquito cells compared to other mosquito-borne flaviviruses. Specific nucleotide mutations in the virus were identified to enhance its proliferation ability in mosquito cells.
Article
Virology
Alejandra Borjabad, Baojun Dong, Wei Chao, David J. Volsky, Mary Jane Potash
Summary: This study investigated HIV brain disease using a mouse model, and found that poly I:C can reverse associated cognitive impairment and reduce virus burden. The results also revealed transcriptional changes related to neuronal function and innate immune responses.
Article
Virology
Ching-Hung Lin, Feng-Cheng Hsieh, Meilin Wang, Chieh Hsu, Hsuan-Wei Hsu, Chun-Chun Yang, Cheng-Yao Yang, Hung-Yi Wu
Summary: This study demonstrates that the synthesis of coronavirus subgenomic mRNA is not solely determined by the sequence homology between the leader TRS and TRS-B, but also by the disassociation of the coronavirus polymerase from the viral genome. This finding provides a new insight into the transcription mechanism of coronaviruses.
Article
Virology
Nicholas S. Kron, Benjamin W. Neuman, Sathish Kumar, Patricia L. Blackwelder, Dayana Vidal, Delphina Z. Walker-Phelan, Patrick D. I. Gibbs, Lynne A. Fieber, Michael C. Schmale
Summary: Two recent studies documented the genome of a novel virus in marine animals, finding that the virus is widespread in apparently healthy animals but not highly expressed in neurons. The studies also identified viral replication factories and high levels of defective genomes in chronically infected animals.
Article
Virology
Andrew M. Ramey, Laura C. Scott, Christina A. Ahlstrom, Evan J. Buck, Alison R. Williams, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson
Summary: We successfully detected and characterized highly pathogenic avian influenza viruses in hunter-harvested wild waterfowl samples from western Alaska. Genomic analysis revealed three independent viral introductions into Alaska. Our findings demonstrate the utility and potential limitations of using molecular processing approaches directly on original swab samples for viral research and monitoring.
Article
Virology
Ting Gong, Dongdong Wu, Yongzhi Feng, Xing Liu, Qi Gao, Xiaoyu Zheng, Zebu Song, Heng Wang, Guihong Zhang, Lang Gong
Summary: This study discovered that quercetin can inhibit PEDV replication both in vivo and in vitro, and alleviate the clinical symptoms and intestinal injury caused by the virus. This provides a new direction for the development of PED antiviral drugs.
Article
Virology
Min Zhu, Hao Zeng, Jianqiao He, Yaohui Zhu, Pingping Wang, Jianing Guo, Jinfan Guo, Huabo Zhou, Yifeng Qin, Kang Ouyang, Zuzhang Wei, Weijian Huang, Ying Chen
Summary: The reassortment between avian H9N2 and Eurasian avian-like (EA) H1N1 viruses may have potentially changed from avian-to-mammals adaptation. This study found that the introduction of EA H1N1 internal genes into H9N2 virus restored the replication capability and resulted in extreme virulence in some cases. This raises new concerns for public health due to the possible coexistence of H9N2 and EA H1N1 viruses in dogs.