Search for: All records

Mobile genetic elements (MGEs), including plasmids, phages and genome islands, are major sources of bacterial genetic diversity. The small plasmid pT181 confers tetracycline resistance in bacterial pathogen Staphylococcus aureus via an efflux pump, TetK. pT181 was one of the earliest sequenced S. aureus plasmids, and has been isolated in both clinical and livestock-associated strains for decades, both as an independent replicon and integrated in the chromosome as part of staphylococcal cassette chromosome mec (SCCmec). Bacterial genome analysis tools and high-quality sequences with metadata are publicly available, but these resources remain underleveraged for examining historical data, especially when studying the spread of MGEs across a species and over time. Using publicly available reads and metadata, we explored the evolution of pT181 over almost seven decades of samples to identify temporal trends in sequence evolution, copy number changes, and spread across S. aureus and beyond. pT181 was prevalent across S. aureus (found in 9.5% of 83,366 genomes tested), with a conserved sequence outside of three hypervariable regions. The history of pT181 since 1954 is characterized by spread across strains, significant variation in plasmid copy number of the independent replicon, and increasing frequency of integration of the plasmid into the S. aureus chromosome. We have identified multiple chromosomal integration locations of the plasmid, including outside of the previously characterized SCCmec. We find that pT181 has been transferred across staphylococcaceae and into a Gram-negative species. The repeated integration of pT181 into the chromosome may indicate co-evolution of the plasmid and the host, potentially to facilitate increased antibiotic resistance. 

{"Abstract":["This data product contains physical, chemical, and biological data ranging from the minute to daily to weekly scale in six artificial ponds (400 square meter surface area, 2m depth) in central Iowa (USA) 2020. Ponds were paired into three sets of treatment and reference with treatment ponds receiving two nutrient pulses designed to increase ambient phosphorus concentrations ~ 3 - 5%. Nitrogen and phosphorus were added as NH4NO3 and H3PO4, respectively, at a 24:1 molar ratio. The first nutrient pulse occurred on Julian day of year (DOY) 176 corresponding to a 3% increase and the second nutrient pulse occurred on DOY 211 to a 5% increase. Each treatment-reference set had a different food web structure established ranging between low, intermediate, and high complexity based on trophic connectivity and food chain length. \n \n Added to this data package is a document titled "2020 Iowa State University Horticultural Farm Experimental Ponds Nutrient Addition Experiment". For experimental set up, context, and a summary table of the data tables archived herein with available variables please review this document. It is added to aid in successful interpretation and to increase ease-of-use. Please email Tyler Butts (tyler.james.butts@gmail.com) for any and all questions regarding context or use of this dataset!"]} 

Instabilities of fluid-fluid interfaces occur in many forms within passive soft matter. Adding activity to one of the fluids can dramatically change the stability of the interface. Triggering active flows externally offers a unique opportunity to study the linear growth of the instability and quantitatively compare experiment and theory. We investigate the interfacial instability of a deformable three-dimensional active nematic liquid crystal droplet confined between two parallel plates. Spontaneous active flows drive the growth of undulations along the active/passive interface, with the mode number of the fastest-growing mode increasing with droplet radius and decreasing with gap height. Applying the lubrication approximation to a minimal nematohydrodynamic model reveals that the growth rates of the interfacial modes are determined by the active timescale and the relaxation timescales associated with liquid crystalline order as well as capillary and viscous stresses. We find multiple points of agreement between experiment and theory, including the shape evolution of individual droplets, the growth rates of unstable modes averaged across many droplets, and the extensional shear flows observed within droplets. 

Abstract BackgroundPrescribed fires play a critical role in reducing the intensity and severity of future wildfires by systematically and widely consuming accumulated vegetation fuel. While the current probability of prescribed fire escape in the United States stands very low, their consequential impact, particularly the large wildfires they cause, raises substantial concerns. The most direct way of understanding this trade-off between wildfire risk reduction and prescribed fire escapes is to explore patterns in the historical prescribed fire records. This study investigates the spatiotemporal patterns of escaped prescribed fires in California from 1991 to 2020, offering insights for resource managers in developing effective forest management and fuel treatment strategies. ResultsThe results reveal that the months close to the beginning and end of the wildfire season, namely May, June, September, and November, have the highest frequency of escaped fires. Under similar environmental conditions, areas with more records of prescribed fire implementation tend to experience fewer escapes. The findings revealed the vegetation types most susceptible to escaped prescribed fires. Areas with tree cover ranging from 20 to 60% exhibited the highest incidence of escapes compared to shrubs and grasslands. Among all the environmental conditions analyzed, wind speed stands out as the predominant factor that affects the risk of prescribed fire escaping. ConclusionsThese findings mark an initial step in identifying high-risk areas and periods for prescribed fire escapes. Understanding these patterns and the challenges of quantifying escape rates can inform more effective landscape management practices. 

Emergence of epidemic viruses in new hosts threatens both human and other animal populations, and often involves virus evolution to overcome barriers that normally prevent efficient infection and spread in that host. After transfer the separated viruses will evolve in parallel as they spread within the original and new hosts. Here we examine the details of a virus involved in such a host-jumping event, where we define the natural evolution of feline panleukopenia virus (FPV) over 60 y, clarify the origins of the new pandemic canine parvovirus (CPV) that arose in the 1970s, and compare the separate evolution of those viruses over 47 y in cats or dogs. Several live-attenuated FPV vaccine viruses originated from early-1960s isolates or were a recombinant of an early virus, and many sequences in databases proved to be vaccine-derived. The sequences of wild viruses showed that FPV-like strains evolved at less than one-third the rate observed for CPV in dogs, and the higher rate of CPV evolution has been consistent since 1979, when a genetic variant became widespread. The common ancestor of the CPV lineage was related to FPVs from Europe and contained several unique host-adaptive capsid changes associated with canine transferrin receptor type-1 binding. Although the FPV vaccine strains are around 60 y old, little selection for antigenic variation was observed. The distinct evolutionary patterns of these closely related viruses circulating for decades in different hosts emphasize the complex evolution associated with viral epidemic emergence and spread in endemic and new hosts. 

The emerald ash borer (EAB), Agrilus planipennis, is a destructive invasive insect of North American ash (Fraxinus). While microorganisms associated with the beetle may contribute to tree decline and death, the microbial community succession during an EAB attack is unknown. We repeatedly sampled the bottom two meters of green ash (Fraxinus pennsylvanica) and black ash (Fraxinus nigra) in seven stands across an infestation gradient over four years. Amplicon libraries were sequenced from control phloem tissue of trees showing no symptoms of infestation, uninfested phloem of trees with EAB, infested phloem (galleries), frass, and larvae to determine if there are shifts in the fungal and bacterial communities as trees succumb to EAB attack. We found that the control phloem communities significantly differed from the beetle-infested phloem in both tree species. Furthermore, as EAB progressed in its attack from the top limbs to the tree’s base, the microbial communities in uninfested phloem outside the galleries shifted away from communities in phloem of control trees. In infested phloem, more than 80% of the detected taxa were absent from control trees (i.e., most taxa were non-latent). However, the relative abundance of latent taxa in infested phloem was higher than the relative abundance of the non-latent taxa, especially for potential canker-causing fungi, which increased 21-fold and 32-fold in black ash and green ash trees, respectively. These findings provide valuable insight into how a woodboring beetle shapes the microbial environment within trees over time, influencing the overall microbial diversity, such as canker-causing and wood decay taxa. 

Polymer science holds a pivotal role in areas such as advanced materials design, drug delivery systems, and biological systems, where being able to efficiently predict polymer thermodynamics and self-assembly is crucial. Self-consistent field theory (SCFT) offers a theoretical framework with many successful predictions that have guided experiments. However, there are classes of systems that are challenging to describe with SCFT due to their computational expense, such as anisotropic systems and worm-like chain models. In this study, we take a first step toward alleviating these challenges by developing a machine-learning approach that can predict density fields directly from the potential fields without the need for computing chain propagators, which is typically the computationally demanding step of a field theory. By integrating different types of neural network models into SCFT, we compared the performance of the models and developed a robust and computationally efficient model for Gaussian chain models that form disordered, inhomogeneous (microphase separated) structures. Our model is able to achieve a speedup of more than three times for the same size systems and up to 100 times for larger systems in our tested systems. The results of this work demonstrate one strategy for how deep learning can be leveraged to improve the efficiency of large-scale SCFT simulations, and the methods herein could be readily extended to other, more computationally demanding models. 

ABSTRACT AimThe harvester ant genusPogonomyrmexhas an amphitropical desert distribution, with high species diversity in arid regions of North America, South America and Hispaniola, and low species diversity in mesic regions. Here, we examine the historical biogeography ofPogonomyrmexto understand how the genus established its current distribution, with a focus on the origins of its amphitropical desert distribution and its spread to Hispaniola. LocationNorth America, South America and Hispaniola. MethodsWe inferred a new phylogeny ofPogonomyrmexusing ultraconserved elements (UCEs); we included duplicate samples of several species to test for species monophyly and evolutionary relationships within the genus. We used this phylogeny and geographic range data of extantPogonomyrmexto reconstruct the ancestral ranges and transcontinental dispersals of the genus. Additionally, we used a time‐stratified ancestral range reconstruction to test ifPogonomyrmexmay have utilized the hypothesized GAARlandia land bridge for dispersals to Hispaniola and North America. ResultsOur ancestral range reconstruction infers that the last common ancestor ofPogonomyrmexlived in northern South America during the middle Eocene. We infer thatPogonomyrmexdispersed from South America to North America twice, first in the Eocene and again in the Eocene or Oligocene. Results of our time‐stratified ancestral range reconstruction suggested thatPogonomyrmexdid not disperse over the GAARlandia land bridge; we instead infer thatPogonomyrmexdispersed over the Central American Seaway to North America on both occasions and was potentially aided by the pre‐isthmus Panama Arc. Further, we infer thatPogonomyrmexdispersed to Hispaniola from North America or Central America during the Oligocene or Miocene. Main ConclusionThis work adds to the growing body of literature that suggests that invertebrates were dispersing between North America and South America well before complete closure of the Isthmus of Panama, and that long‐distance dispersal played a significant role in the origins of desert biodiversity in North and South America.