Article
Microbiology
Gabriella Trombini Machado, Claudia Ramos de Carvalho Pinto, Luisa Andrea Villanueva da Fonseca, Taissa Cristina dos Santos Ramos, Tuanny Fernanda Pereira Paggi, Beny Spira
Summary: The COVID-19 pandemic has sparked discussions on virus transmission routes and assessment of risks. Research on virus spread in open air showed that transmission rate decreases exponentially with distance, indicating the importance of implementing measures and evaluating risks.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yanhui Hu, Ben Ewen-Campen, Aram Comjean, Jonathan Rodiger, Stephanie E. Mohr, Norbert Perrimon
Summary: Paralogs are genes that arise through gene duplication and pose a challenge to functional genetics research when they retain overlapping or redundant function. We have developed Paralog Explorer, an online resource that enables researchers to identify candidate paralogous genes in model organisms' genomes and provides access to relevant databases for gene co-expression, protein-protein and genetic interactions, as well as gene ontology and phenotype annotations. This tool expands the capabilities of current ortholog prediction resources for the identification and study of paralogous genes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Virology
Sari Maentynen, Meri M. Salomaa, Minna M. Poranen
Summary: Half a century after the discovery of Pseudomonas phage phi6, more dsRNA phages have been identified, indicating their prevalent existence in nature. Most dsRNA phages infect Pseudomonas strains and utilize bacterial receptors for cell entry. Despite high sequence diversity, a common set of genes can typically be found in dsRNA phage genomes, suggesting shared evolutionary trajectories.
Review
Biochemistry & Molecular Biology
Srivani Veeranarayanan, Aa Haeruman Azam, Kotaro Kiga, Shinya Watanabe, Longzhu Cui
Summary: Cancer, especially solid tumors, presents challenges in modern medicine due to its unique characteristics and variations in microenvironments. Traditional treatment options are limited and ineffective, calling for tailored and personalized approaches. Bacteriophage vectors offer potential for improved tumor theragnostics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Camila Mendes Figueiredo, Marilia Silva Malvezzi Karwowski, Romeu Cassiano Pucci da Silva Ramos, Nicoly Subtil de Oliveira, Lorena Caroline Pena, Everdan Carneiro, Renata Ernlund Freitas de Macedo, Edvaldo Antonio Ribeiro Rosa
Summary: Microbial biofilms are challenging to control due to limited accessibility of antimicrobial drugs. This review discusses the advantages, recommendations, and limitations of using bacteriophages as 'biofilm predators', and the feasibility of using phages to control biofilms in different environments.
Article
Chemistry, Analytical
Ying Chen, Honglin Yang, Shuai Luo, Lin Wang, Shuguang Lu, Zhifeng Fu
Summary: As a multidrug-resistant pathogen, Acinetobacter baumannii is a common nosocomial bacteria. Researchers have developed an engineering protein called ETFP Gp50 as a high-performance recognition probe for wide-spectrum detection and efficient diagnosis of A. baumannii. The protein showed 100% recognition rate and can be used for quantification of A. baumannii in complex sample matrix with high flexibility and low false-negative rate.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Magdalena Podlacha, Lukasz Grabowski, Katarzyna Kosznik-Kawsnicka, Karolina Zdrojewska, Malgorzata Stasilojc, Grzegorz Wegrzyn, Alicja Wegrzyn
Summary: Bacteriophages are viruses that infect bacterial cells, but recent studies have shown that they can significantly influence the functions of tissues, organs, and systems of mammals, including humans. They have the ability to penetrate eukaryotic cells and affect multiple organ systems, including the immune system, respiratory system, central nervous system, and digestive system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Virology
Mariana Alves Elois, Raphael da Silva, Giulia Von Tonnemann Pilati, David Rodriguez-Lazaro, Gislaine Fongaro
Summary: Bacteriophages, the most abundant organisms on earth, can specifically infect one or multiple strains of hosts. They can integrate their genome into the host genome and confer immunity against infection by the same type of bacteriophages. They can also transfer antibiotic resistance genes and have the potential to control bacteria in ecological imbalances. Phage therapy is advocated as a promising alternative for controlling pathogens in industrial and healthcare settings due to its unique ability to control microorganisms and biofilm production.
Review
Microbiology
Scott C. Weaver, Naomi L. Forrester, Jianying Liu, Nikos Vasilakis
Summary: Transmission of arthropod-borne viruses involves infection and replication in both arthropod vectors and vertebrate hosts, with population bottlenecks and founder effects playing important roles in arboviral evolution and spread, as well as the emergence of human disease.
NATURE REVIEWS MICROBIOLOGY
(2021)
Review
Geosciences, Multidisciplinary
Mohamad Nor Azra, Mohd Iqbal Mohd Noor, Min Pau Tan, Mahmoud Dawood, Muhammad Amin, Ivar Zekker, Muhammad Fuad Abdullah, Zulkiflee Abd Latif, Faezah Pardi
Summary: Determining the impact of climate change on aquatic organisms is crucial for analyzing food and protein sources important for human nutrition. This study aimed to review the current development and frontiers of climate change model organisms. Results showed that Zebrafish and Medaka are important model organisms for climate change research, with Zebrafish gaining increasing importance due to its simple anatomy and established studies.
FRONTIERS IN EARTH SCIENCE
(2022)
Article
Multidisciplinary Sciences
Bernard Conrad, Christian Iseli, Magnus Pirovino, Jordi Villa-Freixa
Summary: All life forms on earth can be traced back to a common ancestor called LUCA through Darwinian evolution. These life forms share two important features - a metabolism for extracting and converting energy, and a genetic system for heredity. However, genome replication often leads to the emergence of genetic parasites. In this study, we propose a model that simulates the energetic and replicative conditions of LUCA-like organisms and their parasites, and investigate the problem-solving abilities of host-parasite pairs. Our findings suggest that a nested parasitism model involving three host-parasite pairs can achieve robust and stable homeostasis, forming a complete life cycle. This model, which includes competition and habitat restriction, efficiently captures, channels, and transforms energy, enabling dynamic host survival and adaptation.
Article
Multidisciplinary Sciences
Wei Zong, Tanbin Rahman, Li Zhu, Xiangrui Zeng, Yingjin Zhang, Jian Zou, Song Liu, Zhao Ren, Jingyi Jessica Li, Etienne Sibille, Adrian V. Lee, Steffi Oesterreich, Tianzhou Ma, George C. Tseng
Summary: Model organisms serve as substitutes for human studies and play an important role in accelerating research. However, the molecular congruence between model organisms and humans has been debated. This study proposes a framework called Congruence Analysis for Model Organisms (CAMO) to objectively quantify the resemblance of model organisms to humans in terms of molecular response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Iwona Gierlicka, Suresh I. S. Rattan, Maciej Wnuk
Summary: With the development of materials engineering, research on new tools for gerontology-related diagnostic and therapeutic applications, such as precision and personalised medicine, has expanded significantly. Nanotechnology allows for precise delivery of drugs to specific organs and cells, enhancing their therapeutic effects. This article discusses the potential use of bacteriophages as nanocarriers to improve the safety and efficacy of conventional medical therapies. Furthermore, bacteriophages can be modified to acquire novel properties and improve their ability to detect and deliver treatments to senescent cells.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Multidisciplinary Sciences
Samuel J. Hobbs, Tanita Wein, Allen Lu, Benjamin R. Morehouse, Julia Schnabel, Azita Leavitt, Erez Yirmiya, Rotem Sorek, Philip J. Kranzusch
Summary: CBASS and Pycsar are bacterial defense systems against phages, and phages have developed anti-CBASS and anti-Pycsar proteins to counteract these defenses. These proteins degrade cyclic nucleotide signals that activate host immunity. Acb1 and Apyc1 are identified as founding members of distinct families of immune evasion proteins, and they block downstream effector activation, protecting phages from CBASS and Pycsar defense.
Review
Virology
Xi Yu, Gong Cheng
Summary: Mosquito-borne viral diseases are a significant burden on global public health due to their ability to adapt and mutate, leading to widespread epidemics.
Article
Virology
Irene Hoxie, John J. Dennehy
Summary: The reassortment of Rotavirus A (RVA) may generate new genome constellations with different segments showing varying degrees of co-segregation and host-species associations. The genetic diversity of all segments decreased dramatically around 2007, coinciding with the introduction of RVA vaccines. Additionally, codon usage patterns varied among segments, with some exhibiting higher adaptation to host genomes.
Review
Microbiology
Fabrizio Spagnolo, Monica Trujillo, John J. Dennehy
Summary: The issue of antibiotic resistance is becoming increasingly severe, with new antibiotics having a short lifespan before resistance emerges. Resistance genes are prevalent in nature, and the key to understanding the development of resistance lies in the context of how microbes produce and use antibiotics.
Article
Multidisciplinary Sciences
Davida S. Smyth, Monica Trujillo, Devon A. Gregory, Kristen Cheung, Anna Gao, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Terri D. Lyddon, Michelle Markman, Clayton Rushford, Kaung Myat San, Geena Sompanya, Fabrizio Spagnolo, Reinier Suarez, Emma Teixeiro, Mark Daniels, Marc C. Johnson, John J. Dennehy
Summary: Tracking the genetic diversity of SARS-CoV-2 is important to monitor the emergence of novel variants resistant to immunity. The researchers detected increasing frequencies of novel cryptic SARS-CoV-2 lineages in the New York City wastewater, containing mutations rarely observed in clinical samples. These lineages share mutations with the Omicron variant and have expanded tropism and resistance to neutralizing antibodies.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Sherin Kannoly, Abhyudai Singh, John J. Dennehy
Summary: Optimality models have had a complex history in evolutionary biology. In this study, researchers revisit evolutionary optimization by examining the lysis time of a bacteriophage. The results show that natural selection has led to an optimal lysis time that maximizes progeny production. This finding is important for understanding the genetic constraints and tradeoffs in organismal evolution.
Correction
Multidisciplinary Sciences
Davida S. Smyth, Monica Trujillo, Devon A. Gregory, Kristen Cheung, Anna Gao, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Terri D. Lyddon, Michelle Markman, Clayton Rushford, Kaung Myat San, Geena Sompanya, Fabrizio Spagnolo, Reinier Suarez, Emma Teixeiro, Mark Daniels, Marc C. Johnson, John J. Dennehy
NATURE COMMUNICATIONS
(2022)
Article
Engineering, Environmental
Antun Skanata, Fabrizio Spagnolo, Molly Metz, Davida S. Smyth, John J. Dennehy
Summary: Airborne transmission is the main route for various respiratory diseases to infect hosts. A new method has been developed to detect long-range transmission of viable virus particles in closed spaces. By using aerosolized virus and host combinations, the method quantifies airborne transmission and determines the impact of humidity on dispersal.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2022)
Editorial Material
Microbiology
John J. Dennehy
Summary: Improving awareness and advanced technology contribute to a brighter future for scientists who are deaf or hard of hearing.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Devon A. Gregory, Monica Trujillo, Clayton Rushford, Anna Flury, Sherin Kannoly, Kaung Myat San, Dustin T. Lyfoung, Roger W. Wiseman, Karen Bromert, Ming-Yi Zhou, Ellen Kesler, Nathan J. Bivens, Jay Hoskins, Chung-Ho Lin, David H. O'Connor, Chris Wieberg, Jeff Wenzel, Rose S. Kantor, John J. Dennehy, Marc C. Johnson
Summary: Wastewater-based epidemiology is an effective method for tracking the appearance and spread of SARS-COV-2 lineages in communities. In 2021, novel SARS-COV-2 RBD lineages were consistently detected in wastewater samples from 9 sewersheds in the US, containing multiple amino acid substitutions and sharing similarities with the Omicron variant. These lineages, potentially originating from long-term patient infections or animal reservoirs, demonstrate greater genetic diversity than commonly observed.
Article
Microbiology
Sherin Kannoly, Gabriella Oken, Jonathan Shadan, David Musheyev, Kevin Singh, Abhyudai Singh, John J. Dennehy
Summary: Bacteriophage burst size, which is the number of phage virions released from infected bacterial cells, depends on the duration of an intracellular progeny accumulation phase. In this study, the burst size mean and variance of the lambda phage were estimated at the single-cell level using lysogens bearing lysis-deficient lambda prophages. The results showed that burst size initially increased exponentially with lysis time and then saturated at longer lysis times. Cell-to-cell variation in lysis timing did not significantly contribute to burst size noise, and differences in burst size originated from intercellular heterogeneity in cellular capacities to produce phages.
MICROBIOLOGY SPECTRUM
(2023)
Editorial Material
Biology
John J. Dennehy
Summary: A deaf virologist reflects on how the pandemic has affected his access to academic spaces, presenting both challenges and opportunities.
Article
Medicine, Research & Experimental
Saba A. Qasmieh, McKaylee M. Robertson, Chloe A. Teasdale, Sarah G. Kulkarni, Heidi E. Jones, David A. Larsen, John J. Dennehy, Margaret McNairy, Luisa N. Borrell, Denis Nash
Summary: A survey conducted in New York City revealed that 22.1% of adult residents had been infected with SARS-CoV-2 in the previous two weeks. The study also found that hybrid immunity, resulting from both vaccination and prior infection, likely played a role in limiting the spread of the virus.
COMMUNICATIONS MEDICINE
(2023)
Letter
Medicine, General & Internal
John J. Dennehy, Ravindra K. Gupta, William P. Hanage, Marc C. Johnson, Thomas P. Peacock
Article
Engineering, Environmental
Catherine Hoar, Francoise Chauvin, Alexander Clare, Hope McGibbon, Esmeraldo Castro, Samantha Patinella, Dimitrios Katehis, John J. Dennehy, Monica Trujillo, Davida S. Smyth, Andrea I. Silverman
Summary: New York City's wastewater monitoring program tracked the viral loads of SARS-CoV-2 in sewershed-level and found a significant positive correlation between viral loads in wastewater and new COVID-19 cases. This study provides insights for future wastewater-based epidemiology efforts.
ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY
(2022)
Article
Public, Environmental & Occupational Health
Amy E. Kirby, Rory M. Welsh, Zachary A. Marsh, Alexander T. Yu, Duc J. Vugia, Alexandria B. Boehm, Marlene K. Wolfe, Bradley J. White, Shannon R. Matzinger, Allison Wheeler, Laura Bankers, Kevin Andresen, Cristal Salatas, Devon A. Gregory, Marc C. Johnson, Monica Trujillo, Sherin Kannoly, Davida S. Smyth, John J. Dennehy, Nicolae Sapoval, Katherine Ensor, Todd Treangen, Lauren B. Stadler, Loren Hopkins
MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT
(2022)
Article
Engineering, Environmental
Brian M. Pecson, Emily Darby, Charles N. Haas, Yamrot M. Amha, Mitchel Bartolo, Richard Danielson, Yeggie Dearborn, George Di Giovanni, Christobel Ferguson, Stephanie Fevig, Erica Gaddis, Donald Gray, George Lukasik, Bonnie Mull, Liana Olivas, Adam Olivieri, Yan Qu
Summary: In response to COVID-19, the international water community developed methods to quantify the SARS-CoV-2 genetic signal in untreated wastewater. An interlaboratory assessment evaluated the reproducibility and sensitivity of 36 standard operating procedures (SOPs), showing that a variety of methods are capable of producing reproducible results and emphasizing the importance of selecting the same SOP or laboratory to track SARS-CoV-2 trends.
ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY
(2021)