Biology subjects

Larsen, P. A.

Publications and source records attributed to Larsen, P. A..

27 records · Page 2Linked to original sources

bioRxiv2021

RT-QuIC detection of CWD prion seeding activity in white-tailed deer muscle tissues

Chronic wasting disease (CWD) is a prion disease circulating in wild and farmed cervid populations throughout North America (United States and Canada), Europe (Finland, Norway, Sweden), and South Korea. CWD is an immediate threat to cervid heritage and the disease is causing substantial economic losses across multiple sectors. In North America, hunting and farming industries focused on the processing and consumption of white-tailed deer (WTD) venison are particularly vulnerable to CWD, as millions of WTD are consumed annually. Real-time quaking-induced conversion (RT-QuIC) is a highly sensitive assay amplifying misfolded CWD prions in vitro and has facilitated CWD prion detection in a variety of tissues and excreta. To date, no study has comprehensively examined CWD prion content across bulk skeletal muscle tissues harvested from individual CWD infected WTD. Here, we use RT-QuIC to quantify prion-seeding activity in a variety of skeletal muscles from both wild and farmed CWD-positive WTD. We successfully detected CWD prions in muscles commonly used for consumption (e.g., backstrap, tenderloin, etc.) as well as within tongue and neck samples of WTD. Our results help to establish the utility of RT-QuIC for monitoring CWD prions in venison and suggest that the method is useful for preventing CWD prions from entering animal and human food chains. Moreover, our work indicates that CWD prions are more widely distributed across skeletal muscles of infected WTD than previously reported.

molecular biology↗

bioRxiv2021

Comparison of Chronic Wasting Disease Detection Methods and Procedures: implications for free-ranging white-tailed deer (Odocoileus virginianus) surveillance and management

Throughout North America, chronic wasting disease (CWD) has emerged as perhaps the greatest threat to wild cervid populations, including white-tailed deer (Odocoileus virginianus). White-tailed deer are the most sought after big game species across North America with populations of various subspecies in nearly all Canadian provinces, the contiguous USA, and Mexico. Documented CWD cases have dramatically increased across the white-tailed deer range since the mid-1990s, including in Minnesota. CWD surveillance in free-ranging white-tailed deer and other cervid populations mainly depends upon immunodetection methods (e.g., immunohistochemistry [IHC] and enzyme-linked immunosorbent assay [ELISA]) on medial retropharyngeal lymph nodes and obex. More recent technologies centered on prion protein amplification methods of detection have shown promise as more sensitive and rapid CWD diagnostic tools. Here, we used blinded samples to test the efficacy of real time quaking-induced conversion (RT-QuIC) in comparison to ELISA and IHC for screening tissues, blood, and feces collected in 2019 from white-tailed deer in southeastern Minnesota, where CWD has been routinely detected since 2016. Our results support previous findings that RT-QuIC is a more sensitive tool for CWD detection than current antibody-based methods. Additionally, a CWD testing protocol that includes multiple lymphoid tissues (medial retropharyngeal lymph node, parotid lymph node, and palatine tonsil) per animal may effectively identify a greater number of CWD detections in a white-tailed deer population than a single sample type (i.e., medial retropharyngeal lymph nodes). These results reveal that the variability of CWD pathogenesis, sampling protocol, and testing platform must be considered for the effective detection and management of CWD throughout North America.

ecology↗

bioRxiv2020

Integrating indigenous knowledge, ontology, and molecular barcoding to characterize spider monkey (Ateles paniscus) filariasis

Zoonotic disease risk is greatly influenced by cultural practices and belief systems. Yet, few studies have integrated traditional ecological knowledge and ontology with western ways of knowing to better understand potential zoonoses. Here, we integrate molecular phylogenetics, histopathology, and ethnography to characterize a filarial nematode found within the abdominal cavity of spider monkeys (Ateles paniscus). The filarid is recognized as spider monkey cotton by indigenous Waiwai in the Konashen Community Owned Conservation Area, Guyana. Ethnographic data revealed that the Waiwai perceive of spider monkey cotton as a normal characteristic within the spider monkey person. Further, the Waiwai indicated that cotton was ubiquitous with spider monkeys and is not understood to be infectious nor zoonotic. This distinction is in contrast to other internal parasites found within spider monkeys that the Waiwai know to cause disease in both monkeys and humans. Our morphological and molecular characterization support the classification of the filarid as Dipetalonema caudispina, a minimally studied and seemingly non-zoonotic parasite, consistent with Waiwai beliefs. Thus, our findings allow us to establish commensurability between scientific knowledge and indigenous ontology. More broadly, this work highlights the importance of integrating multiple knowledge systems and leveraging advanced genomics to better understand and prevent emerging zoonotic diseases.

evolutionary biology↗

bioRxiv2020

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events

Nucleotide excision repair is the primary DNA repair mechanism that removes bulky DNA adducts such as UV-induced pyrimidine dimers. Correspondingly, genome-wide mapping of nucleotide excision repair with eXcision Repair sequencing (XR-seq), provides comprehensive profiling of DNA damage repair. A number of XR-seq experiments at a variety of conditions for different damage types revealed heterogenous repair in the human genome. Although human repair profiles were extensively studied, how repair maps vary between primates is yet to be investigated. Here, we characterized the genome-wide UV-induced damage repair in gray mouse lemur, Microcebus murinus, in comparison to human. Mouse lemurs are strictly nocturnal, are the worlds smallest living primates, and last shared a common ancestor with humans at least 60 million years ago. We derived fibroblast cell lines from mouse lemur, exposed them to UV irradiation. The following repair events were captured genome-wide through the XR-seq protocol. Mouse lemur repair profiles were analyzed in comparison to the equivalent human fibroblast datasets. We found that overall UV sensitivity, repair efficiency, and transcription-coupled repair levels differ between the two primates. Despite this, comparative analysis of human and mouse lemur fibroblasts revealed that genome-wide repair profiles of the homologous regions are highly correlated. This correlation is stronger for the highly expressed genes. With the inclusion of an additional XR-seq sample derived from another human cell line in the analysis, we found that fibroblasts of the two primates repair UV-induced DNA lesions in a more similar pattern than two distinct human cell lines do. Our results suggest that mouse lemurs and humans, and possibly primates in general, share a homologous repair mechanism as well as genomic variance distribution, albeit with their variable repair efficiency. This result also emphasizes the deep homologies of individual tissue types across the eukaryotic phylogeny.

genomics↗

bioRxiv2019

Complex processes of cryptic speciation in mouse lemurs from a micro-endemism hotspot in Madagascar

AO_SCPLOWBSTRACTC_SCPLOWMouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic explosion has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we take an integrative approach to investigate species diversity in two pairs of sister lineages that occur in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among them. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the species-level distinction of two previously described species, M. mittermeieri and M. lehilahytsara is not supported - a result that is particularly striking when using the genealogical discordance index (gdi). Non-sister lineages occur sympatrically in two of the localities sampled for this study, despite an estimated divergence time of less than 1 Ma. This suggests rapid evolution of reproductive isolation in the focal lineages, and in the mouse lemur clade generally. The divergence time estimates reported here are based on the MSC and calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated concatenated likelihood estimates, however. We discuss the possible explanations for this discrepancy, noting that there are theoretical justifications for preferring the MSC estimates in this case.

evolutionary biology↗

bioRxiv2019

Pedigree-based measurement of the de novo mutation rate in the gray mouse lemur reveals a high mutation rate, few mutations in CpG sites, and a weak sex bias

Spontaneous germline mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in only a few lineages. It is therefore critical to expand the phylogenetic scope of these studies to gain a more general understanding of observed mutation rate patterns. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (Microcebus murinus), we estimated the mutation rate to be 1.64 x 10-8 (95% credible interval: 1.41 x 10-8 to 1.98 x 10-8) mutations/site/generation. This estimate is higher than those measured for most previously characterized mammals. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG-sites. Given the surprising nature of these observations, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species. This analysis yielded patterns consistent with the mutation spectrum from the pedigree mutation-rate analysis, which provides confidence in our ability to accurately identify de novo mutations with our data and bioinformatic filters.

evolutionary biology↗

bioRxiv2019

Next-generation in situ conservation and capacity building in Madagascar using a mobile genetics lab

Madagascar is a biodiversity hotspot that is facing rapid rates of deforestation, habitat destruction and poverty. Urgent action is required to document the status of biodiversity to facilitate efficacious conservation plans. Within country, new generations of Malagasy scientists and conservationists are taking on leadership roles, although many lack access to modern genetic sequencing and are underrepresented in academic publications, when compared to international counterparts.\n\nWith the recent advent of portable and affordable genetic technologies, it is now possible to tackle logistical considerations. Mobile genetics labs, with the capacity for in situ DNA extraction, amplification and sequencing, can produce scientifically reproducible data under field conditions, minimizing the time between sample collection and data analysis. Additionally, mobile labs offer powerful training opportunities for in-country scientists that enable local students and researchers to actively participate and contribute fully to the research enterprise, and that further empower these communities to contribute to the conservation dialog.\n\nHere, we show \"proof of concept\" by deploying a miniaturized thermal cycler alongside the Oxford Nanopore MinION DNA sequencer in Madagascar, including in the newly established Anjajavy Protected Area in northwestern Madagascar. We successfully extracted DNA from tissue samples collected using minimally-invasive techniques, amplified and sequenced a phylogenetically informative mitochondrial gene (cytochrome-b; cytb), and thereby confirmed the presence of Danfoss mouse lemur (M. danfossi) within the Anjajavy Reserve.\n\nTo demonstrate the reproducibility of our methods, we successfully performed our established molecular and analytical pipeline at two additional locations in Madagascar, where we also conducted two-day workshops at local higher-education Institutions to demonstrate the process from tissue samples to DNA sequencing. Ultimately, we show that a mobile genetics lab can provide reliable and expeditious results, become a powerful educational tool, and allow scientists to conduct genetic analyses, potentially allowing for rapid interventions under emergency conditions in situ.

genetics↗

bioRxiv2019

Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and chromosomal hotspots across mammals

Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera Microcebus and Cheirogaleus, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly-speciose and morphologically-cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, as might be expected if they have each evolved to respond to specific stimuli. Further, a detailed syntenic comparison of mouse lemurs with mouse (genus Mus) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as V1R \"hotspots.\"

genomics↗

bioRxiv2017

Alu elements, evolution of the human brain, and the spectrum of neurological disease

Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the positive aspects of Alus, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potentially vulnerable to the epigenetic dysregulation of Alu elements operating across the suite of nuclear-encoded mitochondrial genes that are critical for both mitochondrial and CNS function. Here, we highlight the beneficial neurological aspects of Alu elements as well as their potential to cause disease by disrupting key cellular processes across the CNS. We identify at least 37 neurological and neurodegenerative disorders wherein deleterious Alu activity has been implicated as a contributing factor for the manifestation of disease and, for many of these disorders, this activity is operating on genes that are essential for proper mitochondrial function. We conclude that the epigenetic dysregulation of Alu elements can ultimately disrupt mitochondrial homeostasis within the CNS. This mechanism is a plausible source for the incipient neuronal stress that is consistently observed across a spectrum of sporadic neurological and neurodegenerative disorders.

neuroscience↗