Biology subjects

Young, J. K.

Publications and source records attributed to Young, J. K..

4 recordsLinked to original sources

bioRxiv2025

Generalizing animal movement predictions across landscapes: a scalable framework grounded in empirical telemetry data

BackgroundUnderstanding animal movement across broad ecological contexts is essential for guiding management decisions in natural resource and animal disease management. However, most movement studies collect data over small spatial extents, which challenges using the data for landscape-scale management applications. MethodsWe collated relocation data from 564 wild pigs spanning 25 studies across 10 states in the United States. We derived net and daily displacement distributions for individuals in each of 4 seasons. We fit gamma distributions to displacement distributions and derived mean and dispersion parameters as metrics of displacement magnitude and variation. We modeled mean and dispersion variables using gradient-boosted regression, including landscape and weather predictors, and predicted daily and net displacement distributions across the species range. We used integrated step selection analysis to estimate habitat selection for wild pig groups sharing a common composition of habitat availability across the studied populations. ResultsFemale average ({+/-} 95% confidence interval) net displacement means varied by season, peaking in Jul-Sept at 1,152 {+/-} 140 m along with daily displacement mean distances of 650 {+/-} 41 m. Average net displacement means for males peaked in Oct.-Dec. at 1,651 {+/-} 160 m with daily displacement mean distances of 1,092 {+/-} 95 m. Extreme net displacement values ranged up to 9,649 m and 4,080 m for male and female, respectively, and extreme daily displacement distribution means of 6,616 m for males, and 3,855 m for females. Almost half of the individuals included a similar composition of habitat availability, regardless of study site location. Herbaceous wetland was the most consistently favored land type and was available for more than 70% of all individual pigs across all studies. Preference for other land types depended strongly on habitat availability. ConclusionsBy comparing movement and habitat selection across a large geographic extent, our work provides new insights about the environmental drivers and limits of wild pig movement behavior. Our workflow digests variation wild pig movement distributions and habitat selection into parameters that can be used to predict movement on heterogeneous landscapes for downstream applications such as invasive species elimination campaigns or disease management.

ecology↗

bioRxiv2020

Identification and evolution of Cas9 tracrRNAs

Cas9 trans-activating CRISPR RNAs (tracrRNAs) form distinct structures essential for target recognition and cleavage and dictate exchangeability between orthologous proteins. As non-coding RNAs that are often apart from the CRISPR array, their identification can be arduous. In this paper, a new bioinformatic method for the detection of Cas9 tracrRNAs is presented. The approach utilizes a co-variance model (CM) based on both sequence homology and predicted secondary structure to locate tracrRNAs. This method predicts a tracrRNA for 98% of CRISPR-Cas9 systems identified by us. The identified tracrRNAs exhibit wide variation in sequence identity, however, CM analyses allow 94.7% to be categorized into just 10 related groups. Finally, association between Cas9 amino acid sequence-based phylogeny and tracrRNA secondary structure is evaluated, revealing strong evidence that secondary structure is evolutionarily conserved among Cas9 lineages. Altogether, our findings provide insight into Cas9 tracrRNA evolution and efforts to characterize the tracrRNA of new Cas9 systems.

evolutionary biology↗

bioRxiv2020

Biochemically diverse CRISPR-Cas9 orthologs

CRISPR-Cas9 nucleases are abundant in microbes. To explore this largely uncharacterized diversity, we applied cell-free biochemical screens to rapidly assess the protospacer adjacent motif (PAM) and guide RNA (gRNA) requirements of novel Cas9 proteins. This approach permitted the characterization of 79 Cas9 orthologs with at least 7 distinct classes of gRNAs and 50 different PAM sequence requirements. PAM recognition spanned the entire spectrum of T-, A-, C-, and G-rich nucleotides ranging from simple di-nucleotide recognition to complex sequence strings longer than 4. Computational analyses indicated that most of this diversity came from 4 groups of interrelated sequences providing new insight into Cas9 evolution and efforts to engineer PAM recognition. A subset of Cas9 orthologs were purified and their activities examined further exposing additional biochemical diversity. This constituted both narrow and broad ranges of temperature dependence, staggered-end DNA target cleavage, and a requirement for longer stretches of homology between gRNA and DNA target to function robustly. In all, the diverse collection of Cas9 orthologs presented here sheds light on Cas9 evolution and provides a rich source of PAM recognition and other potentially desirable properties that may be mined to expand the genome editing toolbox with new RNA-programmable nucleases.

biochemistry↗

bioRxiv2019

PAM recognition by miniature CRISPR-Cas14 triggers programmable double-stranded DNA cleavage

In recent years, CRISPR-associated (Cas) nucleases have revolutionized the genome editing field. Being guided by an RNA to cleave double-stranded (ds) DNA targets near a short sequence termed a protospacer adjacent motif (PAM), Cas9 and Cas12 offer unprecedented flexibility, however, more compact versions would simplify delivery and extend application. Here, we present a collection of 10 exceptionally compact (422-603 amino acids) CRISPR-Cas nucleases that recognize and cleave dsDNA in PAM dependent manner. Categorized as class 2 type V-F they come from the Cas14 family and distantly related type V-U3 Cas proteins found in bacteria. Using biochemical methods, we demonstrate that a 5 T- or C-rich PAM sequence triggers double stranded (ds) DNA target cleavage. Based on this discovery, we evaluated whether they can protect against invading dsDNA in E. coli and find that some but not all can. Altogether, our findings show that miniature Cas nucleases are functional CRISPR-Cas defense systems and have the potential to be harnessed as programmable nucleases for genome editing.

biochemistry↗