Showing items related by title, author, creator and subject.

• Metagenomic Insights Into the Diversity of Halophilic Microorganisms Indigenous to the Karak Salt Mine, Pakistan

  Cycil, Leena Mavis; DasSarma, Shiladitya; Pecher, Wolf; McDonald, Ryan; AbdulSalam, Maria; Hasan, Fariha (Frontiers Media S.A., 2020-07-14)

  Hypersaline regions are terrestrial analogs of the Earth’s primitive ecosystem and extraterrestrial environment. The salt range in Pakistan is considered among a few of the ancient salt deposits in the subcontinent. Karak salt mine is situated at the Northwest end in Pakistan. Despite the fact that halophiles initiated the formation of terrestrial ecosystems, their products and identities remain hidden. Some preliminary studies limited to culture-dependent isolations have been reported. Characterizing the microbiome that spans over centuries of ecosystem development is crucial, given their role in shaping landscape succession and biogeochemical cycles. Here, we used metagenomics techniques to explore the microbial diversity of the Karak salt mine. We used 16S rRNA Illumina amplicon sequencing to characterize the halophilic communities entrapped in Karak mine. The results were interpreted using Illumina Basespace, QIIME, and Cytoscape. Cultures were isolated at 16–25% salinity. Metagenomics data was consistent with our preliminary culturing data, indicating remarkable species to strain-level diversity of unique halophiles. A total of 107,099 (brine) and 122,679 (salt) reads were obtained. 16S rRNA based sequencing revealed a microbiome with bacteria (66% brine and 72% salt) dominated by Bacteroidetes and Proteobacteria with a strikingly high abundance of Archaea (18% brine and 13% salt). Alpha diversity has higher values in salt than in the brine. The study of the halophiles in the Karak salt mine provides clues for species contributing to the maintenance of biogeochemical cycles of the ecosystem. This is the first report of a metagenomic study of any hypersaline region of Pakistan. © Copyright © 2020 Cycil, DasSarma, Pecher, McDonald, AbdulSalam and Hasan.
• Combining actigraph link and petpace collar data to measure activity, proximity, and physiological responses in freely moving dogs in a natural environment

  Ortmeyer, H.K.; Robey, L.; McDonald, T. (MDPI AG, 2018)

  Although several studies have examined the effects of an owner's absence and presence on a dog's physiological responses under experimental conditions over short periods of time (minutes), little is known about the effects of proximity between humans and freely moving dogs under natural conditions over longer periods of time (days). The first aim of our study was to determine whether the combined data generated from the PetPace Collar and Actigraph Link accelerometer provide reliable pulse, respiration, and heart rate variability results during sedentary, light-moderate, and vigorous bouts in 11 freely moving dogs in a foster caretaker environment over 10-15 days. The second aim was to determine the effects of proximity (absence and presence of caretaker) and distance (caretaker and dog within 0-2 m) on the dogs' physiological responses. Aim 1 results: Pulse and respiration were higher during light-moderate bouts compared to sedentary bouts, and higher at rest while the dogs were standing and sitting vs. lying. Heart rate variability (HRV) was not different between activity levels or position. Aim 2 results: During sedentary bouts, pulse and respiration were higher, and HRV lower, when there was a proximity signal (caretaker present) compared to no proximity signal (caretaker absent). Using multiple regression models, we found that activity, position, distance, and signal presence were predictors of physiological response in individual dogs during sedentary bouts. Our results suggest that combining data collected from Actigraph GT9X and PetPace monitors will provide useful information, both collectively and individually, on dogs' physiological responses during activity, in various positions, and in proximity to their human caretaker. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.
• Optimal COVID-19 quarantine and testing strategies.

  Wells, Chad R; Townsend, Jeffrey P; Pandey, Abhishek; Moghadas, Seyed M; Krieger, Gary; Singer, Burton; McDonald, Robert H; Fitzpatrick, Meagan C; Galvani, Alison P (Springer Nature, 2021-01-07)

  For COVID-19, it is vital to understand if quarantines shorter than 14 days can be equally effective with judiciously deployed testing. Here, we develop a mathematical model that quantifies the probability of post-quarantine transmission incorporating testing into travel quarantine, quarantine of traced contacts with an unknown time of infection, and quarantine of cases with a known time of exposure. We find that testing on exit (or entry and exit) can reduce the duration of a 14-day quarantine by 50%, while testing on entry shortens quarantine by at most one day. In a real-world test of our theory applied to offshore oil rig employees, 47 positives were obtained with testing on entry and exit to quarantine, of which 16 had tested negative at entry; preventing an expected nine offshore transmission events that each could have led to outbreaks. We show that appropriately timed testing can make shorter quarantines effective. © 2021, The Author(s).