Article
Virology
Igor V. Babkin, Irina N. Babkina, Nina V. Tikunova
Summary: The molecular evolution of orthopoxviruses was analyzed based on data from ancient VARV DNA and DNA of new orthopoxvirus species, estimating their emergence times. It was found that orthopoxviruses of the Old and New Worlds separated around 40,000 years ago, and recently discovered virus species separated around 10,000-20,000 years ago.
Article
Virology
Sundharraman Subramanian, John A. Dover, Kristin N. Parent, Sarah M. Doore
Summary: The first critical step in a virus's infection cycle is attachment to its host. This study focused on the interaction between bacteriophage Sf6 and its host Shigella flexneri. The phage utilizes a two-step process to recognize and bind to its host, first recognizing the lipopolysaccharide (LPS) of the host and then binding to outer membrane proteins. Through experimental evolution, mutations were observed in the receptor-binding tailspike protein that dramatically affected the binding of the receptors, providing flexibility for the phage in identifying host cells and altering its host range.
JOURNAL OF VIROLOGY
(2022)
Article
Microbiology
Aline R. V. Souza, Annika Brinkmann, Jose Esparza, Andreas Nitsche, Clarissa R. Damaso, Rino Rappuoli
Summary: This study investigates the gene content and genomic structure of historical smallpox vaccines used in the late 19th and early 20th centuries. The findings reveal differences between these vaccines, contemporary vaccinia viruses, and horsepox viruses. The study suggests the coexistence of different horsepox-based vaccines and potentially unsampled progenitors of modern vaccinia virus. This research contributes to our understanding of the origins of contemporary vaccinia viruses and the evolution of smallpox vaccines.
Article
Microbiology
Chorong Park, Chen Peng, M. Julhasur Rahman, Sherry L. Haller, Loubna Tazi, Greg Brennan, Stefan Rothenburg
Summary: The study found significant differences in the inhibition of host proteins by viral inhibitors even within the same virus family, cautioning against assumptions based on phylogenetic relatedness. Host sensitivity to virus inhibition and the effectiveness of viral immune antagonists must be experimentally determined rather than inferred from evolutionary relationships.
Review
Virology
Galina A. Shchelkunova, Sergei N. Shchelkunov
Summary: After the global eradication of smallpox in 1980, the discontinuation of smallpox vaccination led to the loss of immunity against other zoonotic orthopoxvirus infections. An increasing number of human infections with orthopoxviruses, particularly monkeypox, raise concerns about the re-emergence of smallpox or similar diseases.
Article
Microbiology
Minetaro Arita
Summary: The study highlights the role of functional coupling and high-order, multitiered recessive epistasis in the evolution of viruses towards independence from an obligatory host pathway. Specific mutations were found to be essential for viral replication, growth, and spread, with certain mutations conferring enhanced replication in PI4KB/OSBP-independent infection. This research provides insights into the evolutionary pathway of viruses in requiring host factors for infection.
MICROBIOLOGY SPECTRUM
(2021)
Article
Plant Sciences
Ho-Hsiung Chang, Deri Gustian, Chung-Jan Chang, Fuh-Jyh Jan
Summary: This study found that mixed infection affects the mechanical transmissibility and host range of nonmechanically transmissible begomoviruses, ToLCNDV and TYLCTHV. These findings provide important insights into the complex virus-virus interactions and have implications for disease management strategies in the field.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemical Research Methods
Bill Lee, David K. Smith, Yi Guan
Summary: The study used machine learning models to predict the reservoir hosts of viruses, combining sequence alignment and gradient boosting machines to improve prediction accuracy.
Article
Ecology
QinQin Yu, Matti Gralka, Marie-Cecilia Duvernoy, Megan Sousa, Arbel Harpak, Oskar Hallatschek
Summary: Demographic noise, driven by random birth and death events, reduces the efficacy of natural selection in evolution. Single gene deletion mutations decrease demographic noise, increasing the establishment probability of beneficial mutations. Demographic noise can be an evolvable trait of a population.
Article
Biochemical Research Methods
Florian Mock, Adrian Viehweger, Emanuel Barth, Manja Marz
Summary: Zoonosis, the transmission of infections from animals to humans, is a global issue that requires accurate prediction of the viral host to prevent further spread. A new deep learning approach based on viral genome sequence shows high accuracy in predicting the host of viruses, even with limited sequences and unbalanced data.
Article
Pharmacology & Pharmacy
Kirk Chan-Tack, Patrick Harrington, Timothy Bensman, Su-Young Choi, Eric Donaldson, Julian O'Rear, David McMillan, Laine Myers, Mark Seaton, Hanan Ghantous, Yu Cao, Thamban Valappil, Debra Birnkrant, Kimberly Struble
Summary: This article summarizes the regulatory pathway for FDA approval of brincidofovir as the second antiviral approved via the MCMi to combat smallpox, highlighting the unique regulatory approach based on the FDA Animal Rule and the collaborative efforts of academic investigators, the pharmaceutical industry and government agencies in the development process.
ANTIVIRAL RESEARCH
(2021)
Article
Virology
Yasuha Arai, Norihito Kawashita, Emad Mohamed Elgendy, Madiha Salah Ibrahim, Tomo Daidoji, Takao Ono, Tatsuya Takagi, Takaaki Nakaya, Kazuhiko Matsumoto, Yohei Watanabe
Summary: This study identified novel clade 2.2.1 virus polymerase mutations that increased viral replication in human cells by analyzing phylogeny-associated PA mutations. These mutations, along with the PB2-E627K substitution, enhanced replication in contemporary clade 2.2.1.2 viruses compared to ancestral clade 2.2.1 viruses, indicating a higher public health risk for humans.
JOURNAL OF VIROLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lucie S. Monticelli, Georgios Koutsovoulos, Anouck Lasserre, Edwige Amiens-Desneux, Anne-Violette Lavoir, James D. Harwood, Nicolas Desneux
Summary: This study evaluated the effect of phylogenetic (and taxonomic) signals of plants and host species on parasitoid host range. The results indicated the importance of phylogenetic (or taxonomic) signals in dictating parasitoid host specificity. Identifying these signals could be useful for biological control programs.
BIOLOGICAL CONTROL
(2021)
Article
Biochemistry & Molecular Biology
Nicholas F. G. Chen, Chrispin Chaguza, Luc Gagne, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie J. Ash, Rachel Harrington, Seana Cofsky, Selina J. Clancy, Curtis J. Kapsak, Joel M. Sevinsky, Kevin M. Libuit, Daniel J. Park, Peera Hemarajata, Jacob M. C. Garrigues, Nicole M. Green, Sean Sierra-Patev, Kristin Carpenter-Azevedo, Richard C. Huard, Claire Pearson, Kutluhan Incekara, Christina Nishimura, Jian Ping Huang, Emily Gagnon, Ethan Reever, Jafar Razeq, Anthony Muyombwe, Vitor Borges, Rita Ferreira, Daniel Sobral, Silvia Duarte, Daniela M. Santos, Luis Vieira, Joao Paulo Gomes, Carly Aquino, Isabella M. Savino, Karinda Felton, Moneeb Bajwa, Nyjil Hayward, Holly Miller, Allison H. Naumann, Ria P. Allman, Neel M. Greer, Amary Fall, Heba H. Mostafa, Martin P. McHugh, Daniel M. Maloney, Rebecca Dewar, Juliet Kenicer, Abby E. Parker, Katharine Mathers, Jonathan A. Wild, Seb Cotton, Kate E. Templeton, George Churchwell, Philip A. R. Lee, Maria Pedrosa, Brenna McGruder, Sarah Schmedes, Matthew R. Plumb, Xiong Wang, Regina Bones I. Barcellos, Fernanda M. S. D. Godinho, Richard Steiner R. Salvato, Aimee Ceniseros, Mallery Breban, Nathan D. Grubaugh, Glen R. Gallagher, Chantal B. F. Vogels
Summary: The multicountry monkeypox outbreak in 2022, alongside the COVID-19 pandemic, emphasized the importance of genomic surveillance and rapid pathogen whole-genome sequencing. Highly multiplexed amplicon-based sequencing provides a cost-effective and flexible approach for pathogen whole-genome sequencing, allowing for rapid response to emerging pathogens.
Article
Ecology
Stefan Kusch, Justine Larrouy, Heba M. M. Ibrahim, Shantala Mounichetty, Noemie Gasset, Olivier Navaud, Malick Mbengue, Catherine Zanchetta, Celine Lopez-Roques, Cecile Donnadieu, Laurence Godiard, Sylvain Raffaele
Summary: This article discusses the importance of the host range of parasites in assessing disease epidemic dynamics, especially the evolutionary adaptation of pathogens to new hosts. It compares the global transcriptome reprogramming of Sclerotinia sclerotiorum and S. trifoliorum on different hosts, as well as gene space conservation in the genome. The results show that there are differences in the regulation of resistance to Brassicaceae plants in S. trifoliorum, which may be related to its genetic adaptation in host range expansion.
Article
Genetics & Heredity
Chad Smithson, Nick Tang, Scott Sammons, Mike Frace, Dhwani Batra, Yu Li, Ginny L. Emerson, Darin S. Carroll, Chris Upton
Article
Genetics & Heredity
Shin-Lin Tu, Yoshinori Nakazawa, Jinxin Gao, Kimberly Wilkins, Nadia Gallardo-Romero, Yu Li, Ginny L. Emerson, Darin S. Carroll, Chris Upton
Article
Genetics & Heredity
Chad Smithson, Hermann Meyer, Crystal M. Gigante, Jinxin Gao, Hui Zhao, Dhwani Batra, Inger Damon, Chris Upton, Yu Li
Article
Virology
Chad Smithson, Jacob Imbery, Chris Upton
Article
Genetics & Heredity
Adrian J. Verster, Erin B. Styles, Abigail Mateo, W. Brent Derry, Brenda J. Andrews, Andrew G. Fraser
G3-GENES GENOMES GENETICS
(2017)
Article
Biology
John C. Whitney, S. Brook Peterson, Jungyun Kim, Manuel Pazos, Adrian J. Verster, Matthew C. Radey, Hemantha D. Kulasekara, Mary Q. Ching, Nathan P. Bullen, Diane Bryant, Young Ah Goo, Michael G. Surette, Elhanan Borenstein, Waldemar Vollmer, Joseph D. Mougous
Article
Virology
Shin-Lin Tu, Jeannette P. Staheli, Colum McClay, Kathleen McLeod, Timothy M. Rose, Chris Upton
Article
Microbiology
Adrian J. Verster, Elhanan Borenstein
Article
Multidisciplinary Sciences
Benjamin D. Ross, Adrian J. Verster, Matthew C. Radey, Danica T. Schmidtke, Christopher E. Pope, Lucas R. Hoffman, Adeline M. Hajjar, S. Brook Peterson, Elhanan Borenstein, Joseph D. Mougous
Article
Biotechnology & Applied Microbiology
Ana Victoria C. Pilar, Nicholas Petronella, Forest M. Dussault, Adrian J. Verster, Sadjia Bekal, Roger C. Levesque, Lawrence Goodridge, Sandeep Tamber
Article
Biochemical Research Methods
Alexander Eng, Adrian J. Verster, Elhanan Borenstein
BMC BIOINFORMATICS
(2020)
Article
Ecology
Maayan Kreitzman, Harold Eyster, Matthew Mitchell, Aldona Czajewska, Keefe Keeley, Sean Smukler, Noah Sullivan, Adrian Verster, Kai M. A. Chan
Summary: Given the environmental impacts of conventional agriculture, new methods for growing food that support biodiversity and ecosystem functions are needed. A study of woody perennial polyculture fields in the U.S. Midwest found higher biodiversity and ecosystem functions compared to conventional fields, with food production increasing with field age.
Article
Biochemical Research Methods
Adrian Verster, Nicholas Petronella, Judy Green, Fernando Matias, Stephen P. J. Brooks
Summary: We developed a Bayesian regression model (BRACoD) to determine associations between intestinal bacteria and physiological measurements. The algorithm corrects for the compositional nature of the data and provides a list of associations. Simulation experiments showed that adopting a cut point value of >= 0.3 optimized the true positive rate.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Food Science & Technology
L. E. Carter, S. Bugiel, A. Nunnikhoven, A. J. Verster, G. S. Bondy, I. H. A. Curran
Summary: This study investigates the toxicity of low doses of OTA in rats exposed in utero and throughout development using transcriptomics and previous data. The findings suggest that male rats show activation of innate and adaptive immune responses to OTA exposure, while this response is not observed in female rats. Differentially expressed genes related to karyomegaly, MAPK activity, and immune activation are found in both male and female rats, indicating the developmental effects of OTA exposure. The study confirms that OTA causes renal toxicity and alters liver and reproductive pathways in rats.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Microbiology
Adrian J. Verster, Benjamin D. Ross, Matthew C. Radey, Yiqiao Bao, Andrew L. Goodman, Joseph D. Mougous, Elhanan Borenstein
CELL HOST & MICROBE
(2017)
