Emergence of Ixodes scapularis (Acari: Ixodidae) in a Small Mammal Population in a Coastal Oak-Pine Forest, Maine, USA

In the United States, surveillance has been key to tracking spatiotemporal emergence of blacklegged ticks [Ixodes scapularis Say (Ixodida:Ixodidae)] and their pathogens such as Borrelia burgdorferi Johnson, Schmid, Hyde, Steigerwalt & Brenner (Spirochaetales: Spirochaetaceae), the agent of Lyme disease. On the Holt Research Forest in midcoastal Maine, collection of feeding ticks from live-trapped small mammal hosts allowed us to track the emergence and establishment of I. scapularis, 1989–2019. From 1989–1995, we collected only I. angustus Neumann (Ixodida: Ixodidae)(vole tick), Dermacentor variabilis Say (Ixodida: Ixodidae) (American dog tick), and I. marxi Banks (Ixodida: Ixodidae) (squirrel tick) from seven species of small mammals. The most abundant tick host was the white-footed mouse [Peromyscus leucopus Rafinesque (Rodentia:Cricetidae)] followed by the red-backed vole (Myodes gapperi Vigors (Rodentia: Cricetidae)). Emergence of I. scapularis was signaled via the appearance of subadult I. scapularis in 1996. Emergence of B. burgdorferi was signaled through its appearance in I. scapularis feeding on mice in 2005. There was a substantial increase in I. scapularis prevalence (proportion of hosts parasitized) and burdens (ticks/host) on white-footed mice and red-backed voles in 2007. The ~11-yr time-to-establishment for I. scapularis was consistent with that seen in other studies. White-footed mice comprised 65.9% of all captures and hosted 94.1% of the total I. scapularis burden. The white-footed mouse population fluctuated interannually, but did not trend up as did I. scapularis prevalence and burdens. There were concurrent declines in I. angustus and D. variabilis. We discuss these results in the broader context of regional I. scapularis range expansion.

Systems genetics uncovers microbe-lipid-host connections in the murine gut

The molecular bases of how host genetic variation impact gut microbiome remain largely unknown. Here, we used a genetically diverse mouse population and systems genetics strategies to identify interactions between molecular phenotypes, including microbial functions, intestinal transcripts and cecal lipids that influence microbe-host dynamics. Quantitative trait loci (QTL) analysis identified genomic regions associated with variations in bacterial taxa, bacterial functions, including motility, sporulation and lipopolysaccharide production, and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and cecal levels of ornithine lipids (OL). Follow-up studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that OL have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits. Collectively, these results suggest that OL are key players in A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.

Hantavirus outbreaks in the American Southwest: Propagation and retraction of rodent and virus diffusion waves from sky-island refugia

Hantavirus outbreaks in the American Southwest are hypothesized to be driven by episodic seasonal events of high precipitation, promoting rapid increases in virus-reservoir rodent species that then move across the landscape from high quality montane forested habitats (refugia), eventually over-running human residences and increasing disease risk. In this study, the velocities of rodents and virus diffusion wave propagation and retraction were documented and quantified in the sky-islands of northern New Mexico and related to rodent-virus relationships in refugia versus nonrefugia habitats. Deer mouse (Peromyscus maniculatus) refugia populations exhibited higher Sin Nombre Virus (SNV) infection prevalence than nonrefugia populations. The velocity of propagating diffusion waves of Peromyscus from montane to lower grassland habitats was measured at [Formula: see text] m/day (SE), with wave retraction velocities of [Formula: see text] m/day. SNV infection diffusion wave propagation velocity within a deer mouse population averaged [Formula: see text] m/day, with a faster retraction wave velocity of [Formula: see text] m/day. A spatio-temporal analysis of human Hantavirus Pulmonary Syndrome (HPS) cases during the initial 1993 epidemic revealed a positive linear relationship between the time during the epidemic and the distance of human cases from the nearest deer mouse refugium, with a landscape diffusion wave velocity of [Formula: see text] m/day ([Formula: see text]). These consistent diffusion propagation wave velocity results support the traveling wave component of the HPS outbreak theory and can provide information on space–time constraints for future outbreak forecasts.

Whole-genome sequencing analysis reveals the population history of Mus musculus in Madagascar

In Madagascar, the house mouse (Mus musculus) is thought to have colonized along with humans and is now one of the most successfully colonized rodents on the island. In this study, we determined the whole-genome sequences of the Madagascar house mouse captured from the wild. We examined the evolutionary history of its population regarding the mitochondrial and autosomal genomes. We confirmed that in the mitochondrial genomes of Madagascar house mice, a monophyletic clade forms a basal origin within the species. An analysis of autosomal genomic sequences indicates that the Madagascar house mouse population is genetically a member of M. m. castaneus (CAS). It also contains genetic elements of M. m. domesticus (DOM) resulting from ancient hybridization. The signature of a strong population bottleneck 1000–3000 years ago was observed in the mitochondrial and autosomal genomic data. We also show that the divergence of the Madagascar population from the CAS population occurred approximately 50,000–99,000 years ago. Madagascar house mice show strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal regions. However, our results suggest that they would not have originated directly from the Indonesian islands, where Austronesian-speaking people in Madagascar originated. Because the ancient hybridization signature with DOM did not appear in the Indonesian and other CAS samples, we propose that Madagascar house mice were not directly brought by Austronesian-speaking people but came from somewhere around the Middle East or South Asia soon after the colonization of initial farmers.

Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population

BackgroundA strong predictor for the development of alcohol use disorders (AUDs) is altered sensitivity to the intoxicating effects of alcohol. Individual differences in the initial sensitivity to alcohol are controlled in part by genetic factors. Mice offer a powerful tool for elucidating the genetic basis of behavioral and physiological traits relevant to AUDs; but conventional experimental crosses have only been able to identify large chromosomal regions rather than specific genes. Genetically diverse, highly recombinant mouse populations allow for the opportunity to observe a wider range of phenotypic variation, offer greater mapping precision, and thus increase the potential for efficient gene identification.MethodsWe have taken advantage of the Diversity Outbred (DO) mouse population to identify and precisely map quantitative trait loci (QTL) associated with ethanol sensitivity. We phenotyped 798 male J:DO mice for three measures of ethanol sensitivity: ataxia, hypothermia, and loss of the righting response. We used high density MEGAMuga and GIGAMuga arrays to obtain genotypes ranging from 77,808 – 143,259 SNPs. In addition, we performed RNA sequencing in striatum to map expression QTLs and to identify gene expression-trait correlations.ResultsWe then applied a systems genetic strategy to identify narrow QTLs and construct the network of correlations that exist between DNA sequence, gene expression values and ethanol-related phenotypes to prioritize our list of positional candidate genes.ConclusionsOur results can be used to identify alleles that contribute to AUDs in humans, elucidate causative biological mechanisms, or assist in the development of novel therapeutic interventions.

Abstract MP252: Genetic Architecture Of Heart Mitochondrial Proteome Influencing Cardiac Hypertrophy

Our lab studies how natural genetic variations affect common diseases using a mouse population called hybrid mouse diversity panel (HMDP). In this study, we have explored the genetic regulation of mitochondrial pathways and their contribution to heart function using an integrative proteomics approach. We first performed a whole heart proteomic analysis in the HMDP (72 strains, n=2-3 mice) and surveyed mitochondrial localization using MitoCarta2.0. We retrieved 840 of these proteins (quantified in ≥50 strains) and performed high-resolution association mapping on their respective abundance levels to the HMDP genotypes. Our analyses identified three genetic loci, located on chromosome (chr) 7, chr13 and chr17, that control distinct classes of mitochondrial proteins as well as heart hypertrophy. Follow-up high resolution regional mapping identified NDUFS4, LRPPRC and COQ7 as the candidate genes for chr13, chr17 and chr7 loci, respectively. All three are associated with heart mass in two independent heart stress models, namely, isoproterenol (ISO)-induced heart failure and diet-induced obesity (DIO) models. Next, to identify the aspects of mitochondrial metabolism regulated by these loci, we constructed co-expression protein networks using weighted gene co-expression network analysis (WGCNA) and identified five modules. Eigengenes, representing the first principal component of two of these modules (Brown and Green), mapped to the same regions as the chr13 and chr17 loci, respectively. DAVID enrichment analyses revealed that the Brown module (72 proteins, 96% overlap with chr13) was highly enriched for complex-I proteins (35 proteins, P = 8.8E-74) and the Green module (44 proteins, 73% overlap with chr17) for mitochondrial ribosomal proteins (25 proteins, P = 1.3E-53). The proteins in the chr7 locus were found primarily in the Turquoise module (393 proteins, 81% overlap) but this module was not enriched for any single mitochondrial protein complex. In summary, we now report the identification of three genetic loci that control distinct classes of mitochondrial proteins as well as heart hypertrophy. Our results provide strong support for a role of the mitochondrial proteome in heart pathophysiology.

Patterns and Mechanisms of Sex Ratio Distortion in the Collaborative Cross Mouse Mapping Population

In species with single-locus, chromosome-based mechanisms of sex determination, the laws of segregation predict an equal ratio of females to males at birth. Here, we show that departures from this Mendelian expectation are commonplace in the 8-way recombinant inbred Collaborative Cross (CC) mouse population. More than one-third of CC strains exhibit significant sex ratio distortion (SRD) at wean, with twice as many male-biased than female-biased strains. We show that these pervasive sex biases persist across multiple breeding environments, are stable over time, and are not mediated by random maternal effects. SRD exhibits a heritable component, but QTL mapping analyses fail to nominate any large effect loci. These findings, combined with the reported absence of sex ratio biases in the CC founder strains, suggest that SRD manifests from multilocus combinations of alleles only uncovered in recombined CC genomes. We explore several potential complex genetic mechanisms for SRD, including allelic interactions leading to sex-biased lethality, genetic sex reversal, chromosome drive mediated by sex-linked selfish elements, and incompatibilities between specific maternal and paternal genotypes. We show that no one mechanism offers a singular explanation for this population-wide SRD. Instead, our data present preliminary evidence for the action of distinct mechanisms of SRD at play in different strains. Taken together, our work exposes the pervasiveness of SRD in the CC population and nominates the CC as a powerful resource for investigating diverse genetic causes of biased sex chromosome transmission.

CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice

More humans have died of tuberculosis (TB) than any other infectious disease and millions still die each year. Experts advocate for blood-based, serum protein biomarkers to help diagnose TB, which afflicts millions of people in high-burden countries. However, the protein biomarker pipeline is small. Here, we used the Diversity Outbred (DO) mouse population to address this gap, identifying five protein biomarker candidates. One protein biomarker, serum CXCL1, met the World Health Organization’s Targeted Product Profile for a triage test to diagnose active TB from latent M.tb infection (LTBI), non-TB lung disease, and normal sera in HIV-negative, adults from South Africa and Vietnam. To find the biomarker candidates, we quantified seven immune cytokines and four inflammatory proteins corresponding to highly expressed genes unique to progressor DO mice. Next, we applied statistical and machine learning methods to the data, i.e., 11 proteins in lungs from 453 infected and 29 non-infected mice. After searching all combinations of five algorithms and 239 protein subsets, validating, and testing the findings on independent data, two combinations accurately diagnosed progressor DO mice: Logistic Regression using MMP8; and Gradient Tree Boosting using a panel of 4: CXCL1, CXCL2, TNF, IL-10. Of those five protein biomarker candidates, two (MMP8 and CXCL1) were crucial for classifying DO mice; were above the limit of detection in most human serum samples; and had not been widely assessed for diagnostic performance in humans before. In patient sera, CXCL1 exceeded the triage diagnostic test criteria (>90% sensitivity; >70% specificity), while MMP8 did not. Using Area Under the Curve analyses, CXCL1 averaged 94.5% sensitivity and 88.8% specificity for active pulmonary TB (ATB) vs LTBI; 90.9% sensitivity and 71.4% specificity for ATB vs non-TB; and 100.0% sensitivity and 98.4% specificity for ATB vs normal sera. Our findings overall show that the DO mouse population can discover diagnostic-quality, serum protein biomarkers of human TB.