Genetic variation and fine-scale population structure in American pikas across a human-modified landscape

Natural resource extraction can represent a major human modification to the landscape. Habitat reclamation is becoming an increasingly important strategy for abating the loss of biodiversity associated with these developments; however, the demographic and genetic consequences of colonizing artificial habitat remain unknown in many species. Here, we investigated the genetic consequences of landscape modifications for the American pika (Ochotona princeps) relative to two major developments in British Columbia, Canada: a large open-pit copper mine (Highland Valley Copper) under partial reclamation and a bisecting major highway (97C). We assessed microsatellite genotypic data for 109 individuals across 15 sites located either within the mine on artificial habitat or on adjacent natural habitat both north and south of the highway. There were no significant differences in levels of heterozygosity, allelic richness or inbreeding between natural (n?=?7) and artificial sites (n?=?8). However, pikas residing on artificial habitat exhibited significantly higher relatedness estimates. Bayesian clustering analyses revealed two distinct genetic units corresponding to north and south of the highway, with further substructure detected in the south. Likewise, high genetic friction was detected in the central region of the area, largely corresponding to the highway and modified landscape associated with the mine. At a finer scale, pairwise estimates of differentiation and migration rates suggest little gene flow may be occurring among sites across the sampling area, with some evidence for directional migration from artificial to natural sites. Overall, artificial habitat has been successful in promoting occupancy for American pikas, however, barriers to gene flow likely associated with resource extraction and road construction limit connectivity across the landscape.     

Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes

Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.     

Taming hyperactive hDNase I: Stable inducible expression of a hyperactive salt‐ and actin‐resistant variant of human deoxyribonuclease I in CHO cells

While the most common causes of clonal instability are DNA copy number loss and silencing, toxicity of the expressed protein(s) may also induce clonal instability. Human DNase I (hDNase I) is used therapeutically for the treatment of cystic fibrosis (CF) and may have potential benefit for use in systemic lupus erythematosus (SLE). hDNase I is an endonuclease that catalyzes degradation of extracellular DNA and is inhibited by both salt and G‐actin. Engineered versions of hDNase I, bearing multiple point mutations, which renders them Hyperactive, Salt‐ and Actin‐Resistant (HSAR‐hDNase I) have been developed previously. However, constitutive expression of HSAR‐hDNase I enzymes has been very challenging and, despite considerable efforts and screening thousands of clones, no stable clone capable of constitutive expression had been obtained. Here, we developed a regulated expression system for stable expression of an HSAR‐hDNase I in Chinese Hamster Ovary (CHO) cells. The HSAR‐hDNase I clones were stable and, upon induction, expressed enzymatically functional protein. Our findings suggest that degradation of host's DNA mediated by HSAR‐hDNase I during cell division is the likely cause of clonal instability observed in cells constitutively expressing this protein. Purified HSAR‐hDNase I was both hyperactive and resistant to inhibition by salt and G‐actin, resulting in an enzyme having ca. 10‐fold greater specific activity and the potential to be a superior therapeutic agent to wild type (WT) hDNase I. Furthermore, the ability to regulate hDNase I expression has enabled process development improvements that achieve higher cell growth and product titers while maintaining product quality. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 32:523–533, 2017     

Dominant Drivers of Seedling Establishment in a Fire-Dependent Obligate Seeder: Climate or Fire Regimes?

Climate change is causing fire regime shifts in ecosystems worldwide. Plant species with regeneration strategies strongly linked to a fire regime, such as obligate seeders, may be particularly threatened by these changes. It is unclear whether changes in fire regimes or the direct effects of climate change will be the dominant threats to obligate seeders in future. We investigated the relative importance of fire-related variables (fire return interval and fire severity) and environmental factors (climate and topography) on seedling establishment in the world’s tallest angiosperm, an obligate seeder, Eucalyptus regnans. Throughout its range, this species dominates the wet montane forests of south-eastern Australia and plays a keystone role in forest structure. Following major wildfires, we investigated seedling establishment in E. regnans within 1 year of fire as this is a critical stage in the regeneration niche of obligate seeders. Seedling presence and abundance were strongly related to the occurrence of fire but not to variation in fire severity (moderate vs. high severity). Seedling abundance increased with increasing fire return interval (range 26–300 years). First-year seedling establishment was also strongly associated with low temperatures and with high elevations, high precipitation and persistent soil water availability. Our results show that both climate and fire regimes are strong drivers of E. regnans seedling establishment. The predicted warming and drying of the climate might reduce the regeneration potential for some obligate seeders in future and these threats are likely to be compounded by changes in fire regimes, particularly increases in fire frequency.     

Weight Bias among Health Professionals Specializing in Obesity

Purpose: To determine the level of anti‐fat bias in health professionals specializing in obesity and identify personal characteristics that correlate with both implicit and explicit bias. Research Methods and Procedures: The Implicit Associations Test (IAT) and a self‐report questionnaire assessing explicit attitudes, personal experiences with obesity, and demographic characteristics was administered to clinicians and researchers attending the opening session of an international obesity conference (N = 389). The IAT was used to assess overall implicit weight bias (associating “obese people” and “thin people” with “good” vs. “bad”) and three ranges of stereotypes: lazy‐motivated, smart‐stupid, and valuable‐worthless. The questionnaire assessed explicit bias on the same dimensions, along with personal and professional experiences with obesity. Results: Health professionals exhibited a significant pro‐thin, anti‐fat implicit bias on the IAT. In addition, the subjects significantly endorsed the implicit stereotypes of lazy, stupid, and worthless using the IAT. Level of bias was associated with several personal characteristics. Characteristics significantly predictive of lower levels of implicit anti‐fat bias include being male, older, having a positive emotional outlook on life, weighing more, having friends who are obese, and indicating an understanding of the experience of obesity. Discussion: Even professionals whose careers emphasize research or the clinical management of obesity show very strong weight bias, indicating pervasive and powerful stigma. Understanding the extent of anti‐fat bias and the personal characteristics associated with it will aid in developing intervention strategies to ameliorate these damaging attitudes.     

The paradox of multiplex DNA melting on a surface

Under equilibrium conditions, there are two regimes of target capture on a surface – target limited and probe limited. In the probe limited regime, the melting curve from multiplex target dissociation from the surface exhibits a single transition due to a reverse displacement mechanism of the low affinity species. The melting curve cannot be used in analytical methods to resolve heteroduplexes; only with the simplex system can proper thermodynamics be obtained.