Biological Sciences publications (MU)
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Items in this collection represent publications of the Department of Biological Sciences faculty, staff, and students, either alone or as co-authors, and which may or may not have been published in an alternate format. Items may contain more than one file type.
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Item Studying gap junctions with PARIS : a new genetically encoded system manipulates the ph inside cells to detect whether they are coupled to each other(eLife Sciences Publications Ltd, 2019) Kick, D. R.; Schulz, D. J.; Biological Science[No abstract available]Item Isolation and characterization T4-and T7-like phages that infect the bacterial plant pathogen agrobacterium tumefaciens(MDPI AG, 2019) Attai, H.; Brown, P. J. B.; Biological ScienceIn the rhizosphere, bacteria–phage interactions are likely to have important impacts on the ecology of microbial communities and microbe–plant interactions. To better understand the dynamics of Agrobacteria–phage interactions, we have isolated diverse bacteriophages which infect the bacterial plant pathogen, Agrobacterium tumefaciens. Here, we complete the genomic characterization of Agrobacterium tumefaciens phages Atu_ph04 and Atu_ph08. Atu_ph04--a T4-like phage belonging to the Myoviridae family--was isolated from waste water and has a 143,349 bp genome that encodes 223 predicted open reading frames (ORFs). Based on phylogenetic analysis and whole-genome alignments, Atu_ph04 is a member of a newly described T4 superfamily that contains other Rhizobiales-infecting phages. Atu_ph08, a member of the Podoviridae T7-like family, was isolated from waste water, has a 59,034 bp genome, and encodes 75 ORFs. Based on phylogenetic analysis and whole-genome alignments, Atu_ph08 may form a new T7 superfamily which includes Sinorhizobium phage PCB5 and Ochrobactrum phage POI1126. Atu_ph08 is predicted to have lysogenic activity, as we found evidence of an integrase and several transcriptional repressors with similarity to proteins in transducing phage P22. Together, this data suggests that Agrobacterium phages are diverse in morphology, genomic content, and lifestyle.Item Partitioning detectability components in populations subject to within-season temporary emigration using binomial mixture models(2014) O'Donnell, Katherine M.; Thompson, Frank R., III; Semlitsch, Raymond D.Detectability of individual animals is highly variable and nearly always < 1; imperfect detection must be accounted for to reliably estimate population sizes and trends. Hierarchical models can simultaneously estimate abundance and effective detection probability, but there are several different mechanisms that cause variation in detectability. Neglecting temporary emigration can lead to biased population estimates because availability and conditional detection probability are confounded. In this study, we extend previous binomial mixture models to account for multiple sources of variation in detectability. The state process describes ecological mechanisms that generate spatial and temporal patterns in abundance, while the observation model accounts for the imperfect nature of counting individuals due to temporary emigration and false absences. We illustrate our model’s potential advantages – including the allowance of temporary emigration between sampling periods – with a case study of southern red-backed salamanders Plethodon serratus. We fit our model and a standard binomial mixture model to counts of terrestrial salamanders surveyed at 40 sites during 3-5 surveys each spring and fall 2010-2012. Our models that partition detectability generated similar parameter estimates to standard binomial mixture models. Aspect was the best predictor of salamander abundance in our case study; abundance increased as aspect became more northeasterly. Increased time-since-rainfall strongly decreased salamander surface activity (i.e. availability for sampling), while higher amounts of woody cover objects and rocks increased conditional detection probability (i.e. probability of capture, given an animal is exposed to sampling). By explicitly accounting for both components of detectability, we increased congruence between our statistical modeling and our ecological understanding of the system. We stress the importance of choosing survey locations and protocols that maximize species availability and conditional detection probability to increase population parameter estimate reliability.Item Intermediate Pond Sizes Contain the Highest Density, Richness, and Diversity of Pond-Breeding Amphibians(2014) Semlitsch, Raymond D.; Peterman, William Earl, 1982-; Anderson, Thomas L.; Drake, Dana L.; Ousterhout, Brittany H.Item Pond-Breeding Amphibian Community Composition in Missouri(2013) Drake, Dana L.; Ousterhout, Brittany H.; Shulse, Christopher D.; Hocking, Daniel J.; Peterman, William E.; Anderson, Thomas L.; Lohraff, Kenton L.; Conner, Christopher A; Harper, Elizabeth H.; Johnson, Jarrett Reed, 1977-; Rittenhouse, Tracy A. Green, 1978-; Rothermel, Betsie B.; Eggert, Lori S.; Semlitsch, Raymond D.Description of data: Site location data and amphibian species and numbers per life stage encountered at each research site in Missouri. Collected: 2002, 2005, 2006, 2012. Collection site: Missouri. Method: Collected from drift fences around ponds in 2002, 2005; dipnet and funnel traps in 2006, 2012.