Territoriality and habitat selection of feral pigs on Fort Benning, Georgia, USA

Feral pigs are one of the most successful, widespread, economically and environmentally damaging invasive mammalian species worldwide. I conducted a study of feral pig sounders (female social groups) on Fort Benning, Georgia to test our hypotheses that feral pigs were territorial at the sounder level and that territoriality was a key factor influencing habitat selection of feral pigs. I used Global Positioning System (GPS) location data from 24 individuals representing 18 sounders combined with mark-recapture and camera trap data to evaluate evidence of territorial behavior at the individual and sounder levels by comparing the degree of overlap between home ranges. I categorized the landscape into five land cover types (open grassy areas, upland hardwood forest, pine forest, pine-hardwood forest, and hardwood bottomland forest) based on differences in the food and cover resources they provided feral pigs and used Ivlev\u27s index to evaluate habitat use within sounder home ranges. Sounders had nearly exclusive home ranges and had completely exclusive core areas, suggesting that female feral pigs on Fort Benning were territorial at the sounder level but not at the individual level. Sounders used the majority of forested cover types in proportion to availability and this supports our hypothesis that territorial behavior is a key factor influencing habitat selection by feral pigs on Fort Benning. Furthermore, the need for territory maintenance (patrolling, scent-marking) may mask changes in habitat selection based solely on resource availability. Territorial behavior in feral pigs could influence population density by limiting access to reproductive space. Removal strategies that: 1) match distribution of removal efforts to distribution of territories, 2) remove entire sounders instead of individuals, and 3) focus efforts where high quality food resources strongly influence territorial behaviors may be best for long-term control of feral pigs. Since feral pigs use the majority of forest cover types in proportion to availability, feral pig management actions need to address potential impacts across Fort Benning instead of limiting management actions to hardwood bottoms where pig activity is more apparent

tracrRNA regulation of CRISPR-Cas immunity

All immune systems must distinguish self from non-self to carry out immunity against foreign agents while avoiding potentially lethal auto-immunity. Bacterial immune systems are no exception, and must, on a cell-autonomous level, molecularly delineate between foreign and host matter to achieve maximum immunity at minimal costs. The prokaryotic adaptive immune system CRISPR-Cas can obtain, store, and deploy molecular memories of previous bacterial virus (bacteriophage, phage) infection to eliminate future invasions from the same or genetically similar invaders. However, molecular memories can also be acquired from the host genome, leading to the question of how hosts are able to mitigate these costs to support the retention of beneficial CRISPR-Cas systems. One strategy employed to minimize harmful off-target effects of immune systems is the tight regulation of expression or activity of the immune components. However, before our work, nothing was known about how the type II-A CRISPR-Cas system from Streptococcus pyogenes was regulated. This thesis explores the discovery, characterization, and biological significance of a novel regulator of the bacterial immune system CRISPR-Cas, tracr-L. We find that tracr-L, a non-coding RNA encoded within the CRISPR locus, is able to utilize Cas9 to repress transcription from its own promoter. We provide evidence that while tracr-L is a strong repressor of CRISPR-Cas immunity, tracr-L repression is also a protective mechanism shielding host cells from the negative consequences of Cas overexpression. We explore the evolutionary conservation of tracr-L and speculate on its role in shaping bacterial genome evolution and in facilitating horizontal gene transfer. We also explore the regulation of tracr-L by phage-encoded anti-CRISPR (Acr) proteins, and how Acr-phage infections can lead to a burst of Cas expression which can serve to increase host survival against phage lysis. Our work demonstrates a novel and direct mechanistic link between phage infection and CRISPR-Cas expression and highlights a strategy hosts can employ to maximize CRISPR-Cas immunity while minimizing auto-immune costs. As such, the tracr-L auto-regulatory circuit represents a weapon in the bacteria-phage arms race that serves as a counter-measure for CRISPR-Cas hosts against the emergence of phage-encoded Acrs

tracrRNA regulation of CRISPR-Cas immunity

All immune systems must distinguish self from non-self to carry out immunity against foreign agents while avoiding potentially lethal auto-immunity. Bacterial immune systems are no exception, and must, on a cell-autonomous level, molecularly delineate between foreign and host matter to achieve maximum immunity at minimal costs. The prokaryotic adaptive immune system CRISPR-Cas can obtain, store, and deploy molecular memories of previous bacterial virus (bacteriophage, phage) infection to eliminate future invasions from the same or genetically similar invaders. However, molecular memories can also be acquired from the host genome, leading to the question of how hosts are able to mitigate these costs to support the retention of beneficial CRISPR-Cas systems. One strategy employed to minimize harmful off-target effects of immune systems is the tight regulation of expression or activity of the immune components. However, before our work, nothing was known about how the type II-A CRISPR-Cas system from Streptococcus pyogenes was regulated. This thesis explores the discovery, characterization, and biological significance of a novel regulator of the bacterial immune system CRISPR-Cas, tracr-L. We find that tracr-L, a non-coding RNA encoded within the CRISPR locus, is able to utilize Cas9 to repress transcription from its own promoter. We provide evidence that while tracr-L is a strong repressor of CRISPR-Cas immunity, tracr-L repression is also a protective mechanism shielding host cells from the negative consequences of Cas overexpression. We explore the evolutionary conservation of tracr-L and speculate on its role in shaping bacterial genome evolution and in facilitating horizontal gene transfer. We also explore the regulation of tracr-L by phage-encoded anti-CRISPR (Acr) proteins, and how Acr-phage infections can lead to a burst of Cas expression which can serve to increase host survival against phage lysis. Our work demonstrates a novel and direct mechanistic link between phage infection and CRISPR-Cas expression and highlights a strategy hosts can employ to maximize CRISPR-Cas immunity while minimizing auto-immune costs. As such, the tracr-L auto-regulatory circuit represents a weapon in the bacteria-phage arms race that serves as a counter-measure for CRISPR-Cas hosts against the emergence of phage-encoded Acrs

Box Traps for Feral Swine Capture: A Comparison of Gate Styles in Texas

Many different types of traps have been developed to increase feral swine (Sus scrofa) capture efficiency. Though not previously compared, gate styles may influence capture success. Our objectives were to report feral swine capture data from 31 trapping campaigns conducted in 17 counties from 2005 to 2011 in Texas, USA, compare capture rates by demographic category between side-swing and rooter gates, and evaluate influences of moisture, using the Palmer Drought Severity Index (PDSI), on juvenile capture rates. We trapped feral swine during all months of the year. Our trap configurations were identical with the exception of gate style. Traps had either side-swing or rooter gates. We captured 1,310 feral swine during 2,424 trap-nights. We found no differences in capture rates between gate styles for adults, adult males, or adult females. However, we found juvenile capture rates and total capture rates to differ between gate styles. Box traps with rooter gates captured more juveniles, resulting in more total captures than in box traps with side-swing gates. Partitioned rooter gates are constructed to allow for continual entry after the gate has been tripped; whereas with single-panel side-swine gates, continual entry may be more challenging for juvenile animals that lack the size and strength to push through the spring tension. Rooter gates should be considered over side-swing gates in management programs aimed at overall damage reduction. However, in management or research programs that seek to capture adult feral swine, side-swing gates may be more appropriate because fewer non-target juvenile feral swine are captured

Preemptive optimization of a clinical antibody for broad neutralization of SARS-CoV-2 variants and robustness against viral escape

Most previously authorized clinical antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lost neutralizing activity to recent variants due to rapid viral evolution. To mitigate such escape, we preemptively enhance AZD3152, an antibody authorized for prophylaxis in immunocompromised individuals. Using deep mutational scanning (DMS) on the SARS-CoV-2 antigen, we identify AZD3152 vulnerabilities at antigen positions F456 and D420. Through two iterations of computational antibody design that integrates structure-based modeling, machine-learning, and experimental validation, we co-optimize AZD3152 against 24 contemporary and previous SARS-CoV-2 variants, as well as 20 potential future escape variants. Our top candidate, 3152-1142, restores full potency (100-fold improvement) against the more recently emerged XBB.1.5+F456L variant that escaped AZD3152, maintains potency against previous variants of concern, and shows no additional vulnerability as assessed by DMS. This preemptive mitigation demonstrates a generalizable approach for optimizing existing antibodies against potential future viral escape

X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes

The sequence diversity of natural and laboratory populations of Brugia pahangi and Brugia malayi was assessed with Illumina resequencing followed by mapping to identify single nucleotide variants and insertions/deletions. In natural and laboratory Brugia populations, there is a lack of sequence diversity on chromosome X relative to the autosomes (πX/πA = 0.2), which is lower than the expected πX/πA = 0.75). A reduction in diversity is also observed in other filarial nematodes with neo-X chromosome fusions in the genera Onchocerca and Wuchereria, but not those without neo-X chromosome fusions in the genera Loa and Dirofilaria. In the species with neo-X chromosome fusions, chromosome X is abnormally large, containing a third of the genetic material such that a sizable portion of the genome is lacking sequence diversity. Such profound differences in genetic diversity can be consequential, having been associated with drug resistance and adaptability, with the potential to affect filarial eradication

Ground-based rodent control in a remote Hawaiian rainforest on Maui.

Effective control of introduced mammalian predators is essential to the recovery of native bird species in Hawai‘i. Between August 1996 and December 2004, introduced rodents were controlled within three home ranges of the Po‘ouli Melamprosops phaeosoma, a critically endangered Hawaiian honeycreeper. Rats were controlled using a combination of ground-based rodenticide (0.005% diphacinone) application and snap traps. Beginning in August 2001, we monitored the effectiveness of these rodent control efforts. Relative abundances of Black Rats Rattus rattus and Polynesian Rats R. exulans were measured in each of five snap-trapping grids seven times over a 35-month period. Rat populations decreased inside of the rodent control areas, but control effectiveness differed between rat species. During the first year of monitoring, target control levels for R. rattus were consistently achieved in only one of the rodent control areas. Control techniques were refined in areas failing to meet targets. Subsequently, we achieved target control levels for R. rattus more consistently in all three rodent control areas. However, relative abundances of R. exulans did not differ between rodent control and reference areas, indicating that our rodent control techniques were insufficient to reduce population levels of this species. These findings signify a need for further improvement of rodent control methods in Hawai‘i, especially for Polynesian Rats, and demonstrate the critical importance of periodic monitoring of the response of rodent populations to management. In the future, managers may need to design rodent control operations targeting R. rattus and R. exulans independently to achieve best results