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1. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages

   https://doi.org/10.1093/g3journal/jkac244  

   Howell, Abigail A; Versoza, Cyril J; Cerna, Gabriella; Johnston, Tyler; Kakde, Shriya; Karuku, Keith; Kowal, Maria; Monahan, Jasmine; Murray, Jillian; Nguyen, Teresa; et al (September 2022, G3 Genes|Genomes|Genetics)

   Reyes-Lamothe, R (Ed.)

   Abstract Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages—and thus one of the selective pressures acting on complex microbial systems in nature—remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from 6 subclusters (P1–P6). A series of comparative genomic analyses revealed that mycobacteriophages of subcluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of subclusters P2–P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles—a temperate characteristic that impedes their usage in antibacterial applications. 

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2. Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages

   https://doi.org/10.1093/g3journal/jkab291  

   Crane, Adele; Versoza, Cyril J; Hua, Tiana; Kapoor, Rohan; Lloyd, Lillian; Mehta, Rithik; Menolascino, Jueliet; Morais, Abraham; Munig, Saige; Patel, Zeel; et al (August 2021, G3 Genes|Genomes|Genetics)

   Wong, A (Ed.)

   Abstract Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections but also offering novel insights into pathogen genetics and evolution. A prominent example is cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative nonpathogenic relatives, such as Mycobacterium smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate subcluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with Mycobacterium leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, subcluster K1 mycobacteriophages are able to integrate into the genomes of Mycobacterium abscessus and Mycobacterium marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance. 

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3. Complete Genome Sequences of Mycobacteriophages OKaNui and DroogsArmy

   https://doi.org/10.1128/MRA.00791-20  

   Fast, Kayla M.; Johnson, Kadaisha G.; Mayfield, Kaitlyn N.; Stephens, Leah A.; Reid, T. Hunter; Ryan, Emma D.; Keener, Tracy W.; Sandel, Michael W. (August 2020, Microbiology Resource Announcements)

   Roux, Simon (Ed.)

   ABSTRACT Mycobacteriophages OKaNui and DroogsArmy were isolated from soil using the bacterial host Mycobacterium smegmatis mc 2 155, which belongs to the phylum Actinobacteria . OKaNui was discovered in east Mississippi and DroogsArmy in west Alabama in the United States. The genomes of OKaNui and DroogsArmy were 51,424 bp and 53,254 bp long, respectively. 

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4. Evaluation of Genome Sequences of the Bacteriophages JeTaime and Luna22

   https://doi.org/10.1128/MRA.00746-21  

   Flota, Maximiliano F.; Moss, Caitlyn R.; Balish, Mitchell F.; Chen, Nikki; Cherry, Kristen C.; Cornely, Kathleen A.; D’Alessandro, Hayley M.; DiBenedetto, Mouna S.; DeGiorgis, Joseph A.; Dixon, Steven Grant; et al (October 2021, Microbiology Resource Announcements)

   Stedman, Kenneth M. (Ed.)

   ABSTRACT The mycobacteriophages JeTaime (E cluster) and Luna22 (Q cluster) were isolated from soil in Providence, Rhode Island, and Charleston, South Carolina, respectively, using a Mycobacterium smegmatis mc 2 155 host. The genome of JeTaime is 75,099 bp (142 predicted genes), and that of Luna22 is 53,730 bp (87 predicted genes). Both phages exhibit Siphoviridae morphology. 

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5. Evolving Tropical Cyclone Tracks in the North Atlantic in a Warming Climate

   https://doi.org/10.1029/2021EF002326  

   Garner, Andra J.; Kopp, Robert E.; Horton, Benjamin P. (December 2021, Earth's Future)

   Abstract Tropical cyclone (TC) track characteristics in a changing climate remain uncertain. Here, we investigate the genesis, tracks, and termination of >35,000 synthetic TCs traveling within 250 km of New York City (NYC) from the pre‐industrial era (850–1800 CE) to the modern era (1970–2005 CE) to the future (2080–2100 CE). Under a very high‐emissions scenario (RCP8.5), TCs are more likely to form closer to the United States (U.S.) southeast coast (>15% increase), terminate in the northeastern Atlantic (>6% increase), and move most slowly along the U.S. Atlantic coast (>15% increase) from the pre‐industrial to future. Under our modeled scenarios, TCs are more likely to travel within 100 km of Boston, MA, USA (p = 0.01) and Norfolk, VA, USA (p = 0.05) than within 100 km of NYC in the future. We identify reductions in the time between genesis and the time when TCs come within 100 km of NYC, Boston, or Norfolk, as well as increased duration of TC impacts from individual storms at all three cities in the future. 

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