Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans

Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations.

A mutation in Themis contributes to anaphylaxis severity following oral peanut challenge in CC027 mice

BACKGROUND

The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, unlike C3H/HeJ (C3H) mice.

OBJECTIVE

To determine the genetic basis of orally-induced anaphylaxis to peanut in CC027 mice.

METHODS

A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 and five additional CC strains.

RESULTS

Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis, and 4% having severe anaphylaxis. A total of eight genetic loci were associated with variation in response to peanut challenge, six associated with anaphylaxis (temperature decrease) and two associated with peanut-specific IgE levels. There were two major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis (thymocyte-expressed molecule involved in selection) gene. Consistent with Themis' described functions, we found that CC027 have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells.

CONCLUSION

Our results demonstrate a key role for Themis in the orally-reactive CC027 mouse model of peanut allergy.

Mapping of susceptibility loci for Ebola virus pathogenesis in mice

Ebola virus (EBOV), a major global health concern, causes severe, often fatal EBOV disease (EVD) in humans. Host genetic variation plays a critical role, yet the identity of host susceptibility loci in mammals remains unknown. Using genetic reference populations, we generate an F2 mapping cohort to identify host susceptibility loci that regulate EVD. While disease-resistant mice display minimal pathogenesis, susceptible mice display severe liver pathology consistent with EVD-like disease and transcriptional signatures associated with inflammatory and liver metabolic processes. A significant quantitative trait locus (QTL) for virus RNA load in blood is identified in chromosome (chr)8, and a severe clinical disease and mortality QTL is mapped to chr7, which includes the Trim5 locus. Using knockout mice, we validate the Trim5 locus as one potential driver of liver failure and mortality after infection. The identification of susceptibility loci provides insight into molecular genetic mechanisms regulating EVD progression and severity, potentially informing therapeutics and vaccination strategies.

Identification of genomic loci regulating platelet plasminogen activator inhibitor-1 in mice

BACKGROUND

Plasminogen activator inhibitor-1 (PAI-1, Serpine1) is an important circulating fibrinolysis inhibitor. PAI-1 exists in 2 pools, packaged within platelet α-granules and freely circulating in plasma. Elevated plasma PAI-1 levels are associated with cardiovascular disease. However, little is known about the regulation of platelet PAI-1 (pPAI-1).

OBJECTIVES

We investigated the genetic control of pPAI-1 levels in mice and humans.

METHODS

We measured pPAI-1 antigen levels via enzyme-linked immunosorbent assay in platelets isolated from 10 inbred mouse strains, including LEWES/EiJ (LEWES) and C57BL/6J (B6). LEWES and B6 were crossed to produce the F1 generation, B6LEWESF1. B6LEWESF1 mice were intercrossed to produce B6LEWESF2 mice. These mice were subjected to genome-wide genetic marker genotyping followed by quantitative trait locus analysis to identify pPAI-1 regulatory loci.

RESULTS

We identified differences in pPAI-1 between several laboratory strains, with LEWES having pPAI-1 levels more than 10-fold higher than those in B6. Quantitative trait locus analysis of B6LEWESF2 offspring identified a major pPAI-1 regulatory locus on chromosome 5 from 136.1 to 137.6 Mb (logarithm of the odds score, 16.2). Significant pPAI-1 modifier loci on chromosomes 6 and 13 were also identified.

CONCLUSION

Identification of pPAI-1 genomic regulatory elements provides insights into platelet/megakaryocyte-specific and cell type-specific gene expression. This information can be used to design more precise therapeutic targets for diseases where PAI-1 plays a role.

A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice

Background

The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, unlike C3H/HeJ (C3H) mice.

Objective

To determine the genetic basis of orally-induced anaphylaxis to peanut in CC027 mice.

Methods

A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 and five additional CC strains.

Results

Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis, and 4% having severe anaphylaxis. A total of eight genetic loci were associated with variation in response to peanut challenge, six associated with anaphylaxis (temperature decrease) and two associated with peanut-specific IgE levels. There were two major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis (thymocyte-expressed molecule involved in selection) gene. Consistent with Themis' described functions, we found that CC027 have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells.

Conclusion

Our results demonstrate a key role for Themis in the orally-reactive CC027 mouse model of peanut allergy.

Cerambycid Pheromones Attract Predators Temnoscheila virescens (Coleoptera: Trogossitidae), Chariessa pilosa (Coleoptera: Cleridae), and Apiomerus crassipes (Hemiptera: Reduviidae)

In 2011-2013, we determined the interactive effects of the cerambycid pheromones racemic syn-2,3-hexanediol, racemic 3-hydroxyhexan-2-one, and racemic 3-hydroxyoctan-2-one on trap catches of predators associated with bark and woodboring beetles in north Georgia and South Carolina. Temnoscheila virescens (F.) (Coleoptera: Trogossitidae) was attracted to traps baited with 3-hydroxyhexan-2-one; ethanol enhanced attraction. Traps baited with syn-2,3-hexanediol attracted Chariessa pilosa (Forster) (Coleoptera: Cleridae); attraction was interrupted by 3-hydroxyhexan-2-one. An assassin bug Apiomerus crassipes (F.) (Hemiptera: Reduviidae) was attracted to traps baited with 3-hydroxyhexan-2-one and/or 3-hydroxyoctan-2-one. Ethanol had no effect on trap catches of C. pilosa and A. crassipes. We compared response profiles of these predators to those of longhorn beetles captured in these same studies to provide insights on possible ecological interactions between these species.

Cerambycid Pheromones 3,2-Hydroxyketones Affect Catches of Some Bark and Ambrosia Beetles (Coleoptera: Curculionidae) in Ethanol-Baited Multiple-Funnel Traps in Southeastern United States

In 2012-2013, we assessed the interactive effects of the cerambycid pheromones syn-2,3-hexanediol, 3-hydroxyhexan-2-one, and 3-hydroxyoctan-2-one on catches of bark and ambrosia beetles (Coleoptera: Curculionidae) in ethanol-baited multiple-funnel traps in north Georgia and South Carolina. We found that catches for nine of eleven species of ambrosia beetles in ethanol-baited traps were either unaffected or enhanced by the addition of 3,2-hydroxyketones. Similarly catches of five species of bark beetles were either unaffected or enhanced by the addition of 3,2-hydroxyketones. In particular, catches of Xylosandrus crassiusculus (Motschulsky), Cnestus mutilatus (Blandford), and Monarthrum fasciatum (Say) in ethanol-baited traps increased with the addition of 3-hydroxyhexan-2-one and/or 3-hydroxyoctan-2-one. Catches of the bark beetles Hylocurus rudis (LeConte) and Hypothenemus rotundicollis (Eichhoff) were enhanced by the addition of 3-hydroxyhexan-2-one and 3-hydroxyoctan-2-one, respectively. syn-2,3-Hexanediol had no effect on catches of bark and ambrosia beetles in ethanol-baited traps. Our data provide support for the use of ethanol + cerambycid pheromones for targeting non-native species of bark and ambrosia beetles as well as cerambycids in detection programs.

A Multitrait Locus Regulates Sarbecovirus Pathogenesis

Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to SARS-CoV disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse Chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6 that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2 and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species.

Cocaine-Induced Locomotor Activation Differs Across Inbred Mouse Substrains

Cocaine use disorders (CUD) are devastating for affected individuals and impose a significant societal burden, but there are currently no FDA-approved therapies. The development of novel and effective treatments has been hindered by substantial gaps in our knowledge about the etiology of these disorders. The risk for developing a CUD is influenced by genetics, the environment and complex interactions between the two. Identifying specific genes and environmental risk factors that increase CUD risk would provide an avenue for the development of novel treatments. Rodent models of addiction-relevant behaviors have been a valuable tool for studying the genetics of behavioral responses to drugs of abuse. Traditional genetic mapping using genetically and phenotypically divergent inbred mice has been successful in identifying numerous chromosomal regions that influence addiction-relevant behaviors, but these strategies rarely result in identification of the causal gene or genetic variant. To overcome this challenge, reduced complexity crosses (RCC) between closely related inbred mouse strains have been proposed as a method for rapidly identifying and validating functional variants. The RCC approach is dependent on identifying phenotypic differences between substrains. To date, however, the study of addiction-relevant behaviors has been limited to very few sets of substrains, mostly comprising the C57BL/6 lineage. The present study expands upon the current literature to assess cocaine-induced locomotor activation in 20 inbred mouse substrains representing six inbred strain lineages (A/J, BALB/c, FVB/N, C3H/He, DBA/2 and NOD) that were either bred in-house or supplied directly by a commercial vendor. To our knowledge, we are the first to identify significant differences in cocaine-induced locomotor response in several of these inbred substrains. The identification of substrain differences allows for the initiation of RCC populations to more rapidly identify specific genetic variants associated with acute cocaine response. The observation of behavioral profiles that differ between mice generated in-house and those that are vendor-supplied also presents an opportunity to investigate the influence of environmental factors on cocaine-induced locomotor activity.

Interactions Between syn- and anti-2,3-Hexanediol Lures on Trap Catches of Woodboring Beetles and Associates in Southeastern United States

In 2016, we conducted three experiments to clarify the effects of 2,3-hexanediols isomers on trap catches of Neoclytus acuminatus (F.) (Coleoptera: Cerambycidae). We also noted the effects of the isomers on trap catches of other cerambycids and associated species of predators and competitors. Catches of N. acuminatus in traps baited with ethanol + syn-2,3-hexanediol + racemic 3-hydroxyoctan-2-one were reduced with the addition of anti-2,3-hexanediol, an attractant for Curius dentatus Newman (Coleoptera: Cerambycidae). A fourth experiment conducted in 2017 verified that racemic 3-hydroxyoctan-2-one increases catches of N. acuminatus in traps baited with ethanol + syn-2,3-hexanediol. The addition of anti-2,3-hexanediol increased catches of Knulliana cincta (Drury) (Coleoptera: Cerambycidae) in traps baited with ethanol + racemic 3-hydroxyoctan-2-one, whereas attraction of Neoclytus scutellaris (Olivier) to traps baited with ethanol + racemic 3-hydroxyhexan-2-one was reduced by syn-2,3-hexanediol. Trap catches of the beetle predators Chariessa pilosa (Forster), Enoclerus ichneumonus (F.), and Madoniella dislocata (Say) (Coleoptera: Cleridae) were affected by 2,3-hexanediol isomers, whereas other common predators were unaffected by the isomers. Attraction of the bostrichid Xylobiops basilaris (Say) (Coleoptera: Bostrichidae) was increased by the 2,3-hexanediols; the relative effect of the two isomeric blends was dependent on trap co-baits of 3-hydroxy-2-ketones. The two enantiomeric blends of 2,3-hexanediol had minimal effects on catches of most species of ambrosia beetles, whereas the 3-hydroxy-2-ketones affected trap catches of some species.

34th International mammalian genome conference: meeting overview

The 34th International Mammalian Genome Conference (IMGC) was held in conjunction with The Allied Genetics Conference (TAGC2020). Scientists from more than 30 countries participated in TAGC2020 to share advances in genetics and genomics research across species. The mammalian section, represented mostly by International Mammalian Genome Society (IMGS) members, had 239 in-person registrants and the number of registrants grew to 3520 virtual attendees when the meeting was converted from an in-person format to a virtual format. A diverse attendance of pre-doctoral and post-doctoral trainees, young investigators, established researchers, clinicians, bioinformaticians, and computational biologists enjoyed a rich scientific program selected from 184 submitted (Mammalian) abstracts in the fields of epigenetics, system genetics, developmental biology, cancer, human disease modeling, technical advances, and bioinformatics.

Common Mechanism of SARS-CoV and SARS-CoV-2 Pathogenesis across Species

Sarbecovirus (CoV) infections, including Severe Acute Respiratory CoV (SARS-CoV) and SARS-CoV-2, are considerable human threats. Human GWAS studies have recently identified loci associated with variation in SARS-CoV-2 susceptibility. However, genetically tractable models that reproduce human CoV disease outcomes are needed to mechanistically evaluate genetic determinants of CoV susceptibility. We used the Collaborative Cross (CC) and human GWAS datasets to elucidate host susceptibility loci that regulate CoV infections and to identify host quantitative trait loci that modulate severe CoV and pan-CoV disease outcomes including a major disease regulating loci including CCR9. CCR9 ablation resulted in enhanced titer, weight loss, respiratory dysfunction, mortality, and inflammation, providing mechanistic support in mitigating protection from severe SARS-CoV-2 pathogenesis across species. This study represents a comprehensive analysis of susceptibility loci for an entire genus of human pathogens conducted, identifies a large collection of susceptibility loci and candidate genes that regulate multiple aspects type-specific and cross-CoV pathogenesis, and also validates the paradigm of using the CC platform to identify common cross-species susceptibility loci and genes for newly emerging and pre-epidemic viruses.

Correlation of Regulatory T Cell Numbers with Disease Tolerance upon Virus Infection

The goal of a successful immune response is to clear the pathogen while sparing host tissues from damage associated with pathogen replication and active immunity. Regulatory T cells (Treg) have been implicated in maintaining this balance as they contribute both to the organization of immune responses as well as restriction of inflammation and immune activation to limit immunopathology. To determine if Treg abundance prior to pathogen encounter can be used to predict the success of an antiviral immune response, we used genetically diverse mice from the collaborative cross infected with West Nile virus (WNV). We identified collaborative cross lines with extreme Treg abundance at steady state, either high or low, and used mice with these extreme phenotypes to demonstrate that baseline Treg quantity predicted the magnitude of the CD8 T cell response to WNV infection, although higher numbers of baseline Tregs were associated with reduced CD8 T cell functionality in terms of TNF and granzyme B expression. Finally, we found that abundance of CD44⁺ Tregs in the spleen at steady state was correlated with an increased early viral load within the spleen without an association with clinical disease. Thus, we propose that Tregs participate in disease tolerance in the context of WNV infection by tuning an appropriately focused and balanced immune response to control the virus while at the same time minimizing immunopathology and clinical disease. We hypothesize that Tregs limit the antiviral CD8 T cell function to curb immunopathology at the expense of early viral control as an overall host survival strategy.

Bayesian modeling of skewed X inactivation in genetically diverse mice identifies a novel Xce allele associated with copy number changes

Female mammals are functional mosaics of their parental X-linked gene expression due to X chromosome inactivation (XCI). This process inactivates one copy of the X chromosome in each cell during embryogenesis and that state is maintained clonally through mitosis. In mice, the choice of which parental X chromosome remains active is determined by the X chromosome controlling element (Xce), which has been mapped to a 176-kb candidate interval. A series of functional Xce alleles has been characterized or inferred for classical inbred strains based on biased, or skewed, inactivation of the parental X chromosomes in crosses between strains. To further explore the function structure basis and location of the Xce, we measured allele-specific expression of X-linked genes in a large population of F1 females generated from Collaborative Cross (CC) strains. Using published sequence data and applying a Bayesian "Pólya urn" model of XCI skew, we report two major findings. First, inter-individual variability in XCI suggests mouse epiblasts contain on average 20-30 cells contributing to brain. Second, CC founder strain NOD/ShiLtJ has a novel and unique functional allele, Xceg, that is the weakest in the Xce allelic series. Despite phylogenetic analysis confirming that NOD/ShiLtJ carries a haplotype almost identical to the well-characterized C57BL/6J (Xceb), we observed unexpected patterns of XCI skewing in females carrying the NOD/ShiLtJ haplotype within the Xce. Copy number variation is common at the Xce locus and we conclude that the observed allelic series is a product of independent and recurring duplications shared between weak Xce alleles.

Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection in Collaborative Cross mice

The COVID-19 pandemic has revealed that infection with SARS-CoV-2 can result in a wide range of clinical outcomes in humans. An incomplete understanding of immune correlates of protection represents a major barrier to the design of vaccines and therapeutic approaches to prevent infection or limit disease. This deficit is largely due to the lack of prospectively collected, pre-infection samples from individuals that go on to become infected with SARS-CoV-2. Here, we utilized data from genetically diverse Collaborative Cross (CC) mice infected with SARS-CoV to determine whether baseline T cell signatures are associated with a lack of viral control and severe disease upon infection. SARS-CoV infection of CC mice results in a variety of viral load trajectories and disease outcomes. Overall, a dysregulated, pro-inflammatory signature of circulating T cells at baseline was associated with severe disease upon infection. Our study serves as proof of concept that circulating T cell signatures at baseline can predict clinical and virologic outcomes upon SARS-CoV infection. Identification of basal immune predictors in humans could allow for identification of individuals at highest risk of severe clinical and virologic outcomes upon infection, who may thus most benefit from available clinical interventions to restrict infection and disease.

Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.

Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection

The COVID-19 pandemic has revealed that infection with SARS-CoV-2 can result in a wide range of clinical outcomes in humans, from asymptomatic or mild disease to severe disease that can require mechanical ventilation. An incomplete understanding of immune correlates of protection represents a major barrier to the design of vaccines and therapeutic approaches to prevent infection or limit disease. This deficit is largely due to the lack of prospectively collected, pre-infection samples from indiviuals that go on to become infected with SARS-CoV-2. Here, we utilized data from a screen of genetically diverse mice from the Collaborative Cross (CC) infected with SARS-CoV to determine whether circulating baseline T cell signatures are associated with a lack of viral control and severe disease upon infection. SARS-CoV infection of CC mice results in a variety of viral load trajectories and disease outcomes. Further, early control of virus in the lung correlates with an increased abundance of activated CD4 and CD8 T cells and regulatory T cells prior to infections across strains. A basal propensity of T cells to express IFNg and IL17 over TNFa also correlated with early viral control. Overall, a dysregulated, pro-inflammatory signature of circulating T cells at baseline was associated with severe disease upon infection. While future studies of human samples prior to infection with SARS-CoV-2 are required, our studies in mice with SARS-CoV serve as proof of concept that circulating T cell signatures at baseline can predict clinical and virologic outcomes upon SARS-CoV infection. Identification of basal immune predictors in humans could allow for identification of individuals at highest risk of severe clinical and virologic outcomes upon infection, who may thus most benefit from available clinical interventions to restrict infection and disease.

SUMMARY

We used a screen of genetically diverse mice from the Collaborative Cross infected with mouse-adapted SARS-CoV in combination with comprehensive pre-infection immunophenotyping to identify baseline circulating immune correlates of severe virologic and clinical outcomes upon SARS-CoV infection.

Quantification of endospores in ancient permafrost using time-resolved terbium luminescence

We describe herein a simple procedure for quantifying endospore abundances in ancient and organic-rich permafrost. We repeatedly (10x) extracted and fractionated permafrost using a tandem filter assembly composed of 3 and 0.2 μm filters. Then, the 0.2 μm filter was washed (7x), autoclaved, and the contents eluted, including dipicolinic acid (DPA). Time-resolved luminescence using Tb(EDTA) yielded a LOD of 1.46 nM DPA (6.55 × 10³ endospores/mL). In review, DPA/endospore abundances were ~2.2-fold greater in older 33 ky permafrost (258 ± 36 pmol DPA gdw^-1; 1.15 × 10⁶ ± 0.16 × 10⁶ spores gdw^-1) versus younger 19 ky permafrost (p = 0.007297). This suggests that dormancy increases with permafrost age.

Collaborative Cross mice reveal extreme epilepsy phenotypes and genetic loci for seizure susceptibility

OBJECTIVE

Animal studies remain essential for understanding mechanisms of epilepsy and identifying new therapeutic targets. However, existing animal models of epilepsy do not reflect the high level of genetic diversity found in the human population. The Collaborative Cross (CC) population is a genetically diverse recombinant inbred panel of mice. The CC offers large genotypic and phenotypic diversity, inbred strains with stable genomes that allow for repeated phenotypic measurements, and genomic tools including whole genome sequence to identify candidate genes and candidate variants.

METHODS

We evaluated multiple complex epileptic traits in a sampling of 35 CC inbred strains using the flurothyl-induced seizure and kindling paradigm. We created an F2 population of 297 mice with extreme seizure susceptibility and performed quantitative trait loci (QTL) mapping to identify genomic regions associated with seizure sensitivity. We used quantitative RNA sequencing from CC hippocampal tissue to identify candidate genes and whole genome sequence to identify genetic variants likely affecting gene expression.

RESULTS

We identified new mouse models with extreme seizure susceptibility, seizure propagation, epileptogenesis, and SUDEP (sudden unexpected death in epilepsy). We performed QTL mapping and identified one known and seven novel loci associated with seizure sensitivity. We combined whole genome sequencing and hippocampal gene expression to pinpoint biologically plausible candidate genes (eg, Gabra2) and variants associated with seizure sensitivity.

SIGNIFICANCE

New mouse models of epilepsy are needed to better understand the complex genetic architecture of seizures and to identify therapeutics. We performed a phenotypic screen utilizing a novel genetic reference population of CC mice. The data we provide enable the identification of protective/risk genes and novel molecular mechanisms linked to complex seizure traits that are currently challenging to study and treat.

Immune Predictors of Mortality After Ribonucleic Acid Virus Infection

BACKGROUND

Virus infections result in a range of clinical outcomes for the host, from asymptomatic to severe or even lethal disease. Despite global efforts to prevent and treat virus infections to limit morbidity and mortality, the continued emergence and re-emergence of new outbreaks as well as common infections such as influenza persist as a health threat. Challenges to the prevention of severe disease after virus infection include both a paucity of protective vaccines as well as the early identification of individuals with the highest risk that may require supportive treatment.

METHODS

We completed a screen of mice from the Collaborative Cross (CC) that we infected with influenza, severe acute respiratory syndrome-coronavirus, and West Nile virus.

RESULTS

The CC mice exhibited a range of disease manifestations upon infections, and we used this natural variation to identify strains with mortality after infection and strains exhibiting no mortality. We then used comprehensive preinfection immunophenotyping to identify global baseline immune correlates of protection from mortality to virus infection.

CONCLUSIONS

These data suggest that immune phenotypes might be leveraged to identify humans at highest risk of adverse clinical outcomes upon infection, who may most benefit from intensive clinical interventions, in addition to providing insight for rational vaccine design.

Sulcatol: Enantiospecific Attractant for Monarthrum mali (Coleoptera: Curculionidae: Scolytinae), Leptostylus asperatus (Coleoptera: Cerambycidae) and Associated Predators

In 2014-2019, we conducted six experiments in north-central Georgia in an attempt to verify the aggregation pheromone response of the ambrosia beetle Gnathotrichus materiarius (Fitch) (Coleoptera: Curculionidae: Scolytinae: Scolytini: Corthylina) to sulcatol known to be produced by male G. materiarius; we failed to catch any G. materiarius. However, we did find that another corthyline ambrosia beetle species Monarthrum mali (Fitch) was attracted to (R)-(-)-sulcatol, whereas the longhorn beetle Leptostylus asperatus (Haldeman) (Coleoptera: Cerambycidae: Lamiinae) was attracted to (S)-(+)-sulcatol. Attraction of both species was unaffected by the respective antipodes. Ethanol enhanced attraction of both species to traps baited with sulcatol. In at least one experiment, attraction to ethanol-baited traps was enhanced by sulcatol for Xylosandrus crassiusculus (Motschulsky), Xyleborus spp., and Hypothenemus spp. but reduced for Cnestus mutilatus (Blandford) (Coleoptera: Curculionidae: Scolytinae). Additionally, traps baited with ethanol and racemic sulcatol [50% (S)-(+): 50% (R)-(-)] caught the greatest numbers of four species of beetle predators: Coptodera aerata Dejean (Coleoptera: Carabidae), Colydium lineola Say (Coleoptera: Zopheridae), Madoniella dislocata (Say), and Pyticeroides laticornis (Say) (Coleoptera: Cleridae). Ethanol but not sulcatol attracted Temnoscheila virescens (F.) (Coleoptera: Trogossitidae). Information on interspecific relationships within forested communities may help us to better determine the roles of these species in maintaining stable and resilient forested ecosystems.

Trap Height Affects Catches of Bark and Woodboring Beetles (Coleoptera: Curculionidae, Cerambycidae) in Baited Multiple-Funnel Traps in Southeastern United States

In north-central Georgia, trap height affected catches of some species of bark and woodboring beetles (Coleoptera) in traps baited with lures used in surveillance programs to detect non-native forest insects. Traps were placed within the canopy and understory of mature oak trees (Quercus spp.) with collection cups placed 18-23 m above ground level (AGL), and 0.3-0.5 m AGL, respectively. Traps were baited with ethanol to target ambrosia beetles (Curculionidae: Scolytinae) in one experiment, ethanol + syn-2,3-hexanediol + racemic 3-hydroxyhexan-2-one + racemic 3-hydroxyoctan-2-one to target hardwood woodborers (Cerambycidae) in a second experiment, and α-pinene + racemic ipsenol + racemic ipsdienol to target pine bark beetles (Curculionidae) and woodborers (Cerambycidae) in a third experiment. Canopy traps were more effective than understory traps for detecting Cnestus mutilatus (Blandford) (Curculionidae), Neoclytus scutellaris (Olivier), and Monochamus titillator (F.) (Cerambycidae). The reverse was true for Xylosandrus crassiusculus (Motschulsky), Dendroctonus terebrans (Olivier) (Curculionidae), and Neoclytus acuminatus (F.) (Cerambycidae). Catches of a third group which included Hylobius pales (Herbst), Ips grandicollis (Eichhoff) (Curculionidae), Neoclytus mucronatus (F.), and Anelaphus pumilus (Newman) (Cerambycidae) were largely unaffected by trap height. Similar patterns were noted for species of Cleridae, Scarabaeidae, Trogossitidae, and Zopheridae but not Histeridae or Tenebrionidae (Coleoptera). Catches of the bee assassin Apiomerus crassipes (F.) (Hemiptera: Reduviidae) in traps baited with the hardwood borer blend were greater in canopy traps than in understory traps.

Long-term comparative safety analysis of the risks associated with adding or switching to a sulfonylurea as second-line Type 2 diabetes mellitus treatment in a US veteran population

AIM

To examine the risks of all-cause mortality and cardiovascular events associated with adding vs switching to second-line therapies in a comparative safety study of people with Type 2 diabetes mellitus.

METHODS

We conducted a retrospective cohort study using an as-treated analysis of people served by the Veterans Health Administration who were on metformin and subsequently augmented this treatment or switched to other oral glucose-lowering treatments between 1998 and 2012. This study included 145 250 people with long follow-up. Confounding was addressed through several strategies, involving weighted propensity score models with rich confounder adjustment and strict inclusion criteria, coupled with an incident-user design.

RESULTS

Second-line use of sulfonylureas was related to higher mortality (hazard ratio 1.39, 95% CI 1.14, 1.70) and cardiovascular risks (hazard ratio 1.19, 95% CI 1.09, 1.30) compared with thiazolidinedione therapy. Differential hazards were associated with discontinuing or not discontinuing metformin; switching to sulfonylurea therapy was associated with a higher risk of all-cause mortality and cardiovascular events compared with all other therapies. Furthermore, add-on sulfonylurea therapy was associated with an elevated risk for both outcomes when compared with thiazolidinedione add-on therapy.

CONCLUSIONS

The results of the present study may inform decisions on whether to augment or discontinue metformin; when considering the long-term risks, switching to a sulfonylurea appears unfavourable compared with other therapies. Instead, adding a thiazolidinedione to existing metformin therapy appears to be superior to adding or switching to a sulfonylurea.

Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population

Two key features of recombinant inbred panels are well-characterized genomes and reproducibility. Here we report on the sequenced genomes of six additional Collaborative Cross (CC) strains and on inbreeding progress of 72 CC strains. We have previously reported on the sequences of 69 CC strains that were publicly available, bringing the total of CC strains with whole genome sequence up to 75. The sequencing of these six CC strains updates the efforts toward inbreeding undertaken by the UNC Systems Genetics Core. The timing reflects our competing mandates to release to the public as many CC strains as possible while achieving an acceptable level of inbreeding. The new six strains have a higher than average founder contribution from non-domesticus strains than the previously released CC strains. Five of the six strains also have high residual heterozygosity (>14%), which may be related to non-domesticus founder contributions. Finally, we report on updated estimates on residual heterozygosity across the entire CC population using a novel, simple and cost effective genotyping platform on three mice from each strain. We observe a reduction in residual heterozygosity across all previously released CC strains. We discuss the optimal use of different genetic resources available for the CC population.

Genetic diversity between mouse strains allows identification of the CC027/GeniUnc strain as an orally reactive model of peanut allergy

BACKGROUND

Improved animal models are needed to understand the genetic and environmental factors that contribute to food allergy.

OBJECTIVE

We sought to assess food allergy phenotypes in a genetically diverse collection of mice.

METHODS

We selected 16 Collaborative Cross (CC) mouse strains, as well as the classic inbred C57BL/6J, C3H/HeJ, and BALB/cJ strains, for screening. Female mice were sensitized to peanut intragastrically with or without cholera toxin and then challenged with peanut by means of oral gavage or intraperitoneal injection and assessed for anaphylaxis. Peanut-specific immunoglobulins, T-cell cytokines, regulatory T cells, mast cells, and basophils were quantified.

RESULTS

Eleven of the 16 CC strains had allergic reactions to intraperitoneal peanut challenge, whereas only CC027/GeniUnc mice reproducibly experienced severe symptoms after oral food challenge (OFC). CC027/GeniUnc, C3H/HeJ, and C57BL/6J mice all mounted a T_H2 response against peanut, leading to production of IL-4 and IgE, but only the CC027/GeniUnc mice reacted to OFC. Orally induced anaphylaxis in CC027/GeniUnc mice was correlated with serum levels of Ara h 2 in circulation but not with allergen-specific IgE or mucosal mast cell protease 1 levels, indicating systemic allergen absorption is important for anaphylaxis through the gastrointestinal tract. Furthermore, CC027/GeniUnc, but not C3H/HeJ or BALB/cJ, mice can be sensitized in the absence of cholera toxin and react on OFC to peanut.

CONCLUSIONS

We have identified and characterized CC027/GeniUnc mice as a strain that is genetically susceptible to peanut allergy and prone to severe reactions after OFC. More broadly, these findings demonstrate the untapped potential of the CC population in developing novel models for allergy research.

Extensive Homeostatic T Cell Phenotypic Variation within the Collaborative Cross

The Collaborative Cross (CC) is a panel of reproducible recombinant inbred mouse strains with high levels of standing genetic variation, affording an unprecedented opportunity to perform experiments in a small animal model containing controlled genetic diversity while allowing for genetic replicates. Here, we advance the utility of this unique mouse resource for immunology research because it allows for both examination and genetic dissection of mechanisms behind adaptive immune states in mice with distinct and defined genetic makeups. This approach is based on quantitative trait locus mapping: identifying genetically variant genome regions associated with phenotypic variance in traits of interest. Furthermore, the CC can be utilized for mouse model development; distinct strains have unique immunophenotypes and immune properties, making them suitable for research on particular diseases and infections. Here, we describe variations in cellular immune phenotypes across F1 crosses of CC strains and reveal quantitative trait loci responsible for several immune phenotypes.

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The Collaborative Cross models the phenotypic diversity observed in human immunity

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QTL mapping in the CC reveals candidate genes linked to T cell phenotypes

Perinatal nutrition interacts with genetic background to alter behavior in a parent-of-origin-dependent manner in adult Collaborative Cross mice

Previous studies in animal models and humans have shown that exposure to nutritional deficiencies in the perinatal period increases the risk of psychiatric disease. Less well understood is how such effects are modulated by the combination of genetic background and parent-of-origin (PO). To explore this, we exposed female mice from 20 Collaborative Cross (CC) strains to protein deficient, vitamin D deficient, methyl donor enriched or standard diet during the perinatal period. These CC females were then crossed to a male from a different CC strain to produce reciprocal F1 hybrid females comprising 10 distinct genetic backgrounds. The adult F1 females were then tested in the open field, light/dark, stress-induced hyperthermia, forced swim and restraint stress assays. Our experimental design allowed us to estimate effects of genetic background, perinatal diet, PO and their interactions on behavior. Genetic background significantly affected all assessed phenotypes. Perinatal diet exposure interacted with genetic background to affect body weight, basal body temperature, anxiety-like behavior and stress response. In 8 of 9 genetic backgrounds, PO effects were observed on multiple phenotypes. Additionally, we identified a small number of diet-by-PO effects on body weight, stress response, anxiety- and depressive-like behavior. Our data show that rodent behaviors that model psychiatric disorders are affected by genetic background, PO and perinatal diet, as well as interactions among these factors.

Interactions between Ethanol, syn-2,3-Hexanediol, 3-Hydroxyhexan-2-one, and 3-Hydroxyoctan-2-one Lures on Trap Catches of Hardwood Longhorn Beetles in Southeastern United States

The effectiveness of a four-component "super lure" consisting of ethanol (E) and the cerambycid pheromones syn-2,3-hexanediol (D6), racemic 3-hydroxyhexan-2-one (K6), and racemic 3-hydroxyoctan-2-one (K8) on trap catches of Cerambycidae (Coleoptera) was determined in southeast United States with seven trapping experiments in 2011-2013. We captured 74 species of longhorn beetles in our three-year study. Ethanol significantly increased the mean catches of seven species and increased the number of cerambycid species detected. Traps with the "super lure" were effective for 8 of 13 species of Cerambycidae previously shown to be attracted to binary combinations of ethanol plus one of the three pheromones. However, the "super lure" was less effective for the remaining five species with catch reductions of 40-90% compared with combinations of ethanol and one or two of the pheromones. For example, K6 + K8 lures reduced catches of Anelaphus villosus (F.) in traps with E + D6 by 90%. Similarly, catches of Anelaphus pumilus (Newman) in traps with E + K6 + D6 were reduced by 50% with the addition of K8. Catches of Knulliana cincta (Drury) in traps with K6 + K8 lures were interrupted by D6, an effect negated by the addition of ethanol. Given the interruptive effects on trap catches of some species when lures are combined in a single trap, developing optimal lure blends to maximize detection efficacy will be a challenge for managers of detection programs for non-native invasive species of longhorn beetles.

BDNF genotype is associated with hippocampal volume in mild traumatic brain injury

The negative long-term effects of mild traumatic brain injury (mTBI) have been a growing concern in recent years, with accumulating evidence suggesting that mTBI combined with additional vulnerability factors may induce neurodegenerative-type changes in the brain. However, the factors instantiating risk for neurodegenerative disease following mTBI are unknown. This study examined the link between mTBI and brain-derived neurotrophic factor (BDNF) genotype, which has previously been shown to regulate processes involved in neurodegeneration including synaptic plasticity and facilitation of neural survival through its expression. Specifically, we examined nine BDNF single-nucleotide polymorphisms (SNPs; rs908867, rs11030094, rs6265, rs10501087, rs1157659, rs1491850, rs11030107, rs7127507 and rs12273363) previously associated with brain atrophy or memory deficits in mTBI. Participants were 165 white, non-Hispanic Iraq and Afghanistan war veterans between the ages of 19 and 58, 110 of whom had at least one mTBI in their lifetime. Results showed that the BDNF SNP rs1157659 interacted with mTBI to predict hippocampal volume. Furthermore, exploratory analysis of functional resting state data showed that rs1157659 minor allele homozygotes with a history of mTBI had reduced functional connectivity in the default mode network compared to major allele homozygotes and heterozygotes. Apolipoprotein E (APOE) was not a significant predictor of hippocampal volume or functional connectivity. These results suggest that rs1157659 minor allele homozygotes may be at greater risk for neurodegeneration after exposure to mTBI and provide further evidence for a potential role for BDNF in regulating neural processes following mTBI.

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome

Although the gut microbiome plays important roles in host physiology, health and disease¹, we lack understanding of the complex interplay between host genetics and early life environment on the microbial and metabolic composition of the gut. We used the genetically diverse Collaborative Cross mouse system² to discover that early life history impacts the microbiome composition, whereas dietary changes have only a moderate effect. By contrast, the gut metabolome was shaped mostly by diet, with specific non-dietary metabolites explained by microbial metabolism. Quantitative trait analysis identified mouse genetic trait loci (QTL) that impact the abundances of specific microbes. Human orthologues of genes in the mouse QTL are implicated in gastrointestinal cancer. Additionally, genes located in mouse QTL for Lactobacillales abundance are implicated in arthritis, rheumatic disease and diabetes. Furthermore, Lactobacillales abundance was predictive of higher host T-helper cell counts, suggesting an important link between Lactobacillales and host adaptive immunity.

Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population

With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while expression remained unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population was observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.

Value of wound biopsy in chronic venous ulceration

Objectives: Malignant transformation in chronic venous ulcers (CVU) is a limb threatening complication, which has an insidious onset. Clinical experience in our practice suggests a lack of suspicious macroscopic features making diagnosis difficult. The aim of this study is to evaluate the role of routine wound biopsy in the outpatient clinic for CVU without suspicious appearances but with no signs of healing despite appropriate treatment.

Methods: A three-year (2000-2003) retrospective review of records for all patients who underwent biopsy of a CVU in the outpatient clinic in a specialist wound healing clinic set in a university hospital.

Results: In our series ( n =76), three indications for biopsy were identified: CVU that had developed features suspicious of carcinoma ( n =17), CVU that had no suspicious features but were non-healing ( n =24) and CVU that had developed features of inflammatory ulceration ( n =35). A positive finding of carcinoma (squamous or basal cell carcinoma) or intraepidermal carcinoma (Bowen's disease) was made in four (24%), nine (37.5%) and 0 cases respectively.

Conclusions: Malignancy may arise in CVU without showing suspicious features and wound biopsy should be advocated for any ulcer that fails to respond to appropriate treatment.

Pine Sawyers (Coleoptera: Cerambycidae) Attracted to α-Pinene, Monochamol, and Ipsenol in North America

Detection tools are needed for Monochamus species (Coleoptera: Cerambycidae) because they are known to introduce pine wilt disease by vectoring nematodes in Asia, Europe, and North America. In 2012-2014, we examined the effects of the semiochemicals monochamol and ipsenol on the flight responses of the sawyer beetles Monochamus carolinensis (Olivier), Monochamus clamator (LeConte), Monochamus mutator LeConte, Monochamus notatus (Drury), Monochamus obtusus Casey, Monochamus scutellatus (Say), and Monochamus titillator (F.) complex (Coleoptera: Cerambycidae) to traps baited with α-pinene. Experiments were set in pine forests in New Brunswick and Ontario (Canada), and Arizona, Georgia, Michigan, Montana, Oregon, South Carolina, Utah, and Washington (United States). In brief, 40 traps were placed in 10 blocks of 4 traps per block per location. Traps were baited with: 1) α-pinene; 2) α-pinene + monochamol; 3) α-pinene + ipsenol; and 4) α-pinene + monochamol + ipsenol. Monochamol increased catches of six species and one species complex of Monochamus with an additive effect of ipsenol for five species and one species complex. There was no evidence of synergy between monochamol and ipsenol on beetle catches. Monochamol had no effect on catches of other Cerambycidae or on any associated species of bark beetles, weevils, or bark beetle predators. We present a robust data set suggesting that the combination of α-pinene, ipsenol, and monochamol may be a useful lure for detecting Monochamus species.

Maternal vitamin D and E intakes during early pregnancy are associated with airway epithelial cell responses in neonates

BACKGROUND

Antenatal factors including maternal diet may predispose to airway disease, possibly by impacting on fetal airway development.

OBJECTIVE

This cohort study tested the hypothesis that maternal vitamin D and E status in early pregnancy is associated with airway epithelial cell (AEC) responses in new born infants and examined constitutive and TNFα/IL-1β, house dust mite (HDM) extract or lipopolysaccharide (LPS)-stimulated neonatal AEC responses in vitro.

METHODS

Maternal dietary vitamin D and E intakes (plasma 25[OH]D3 or α-tocopherol) were characterized at 10-12 weeks gestation. Neonatal nasal AECs were collected soon after birth and cultured to tertiary passage. Constitutive and stimulated - TNFα/IL-1β, HDM extract or LPS - secretory responses (VEGF, RANTES, MCP-1, IL-17A, IFN-γ, GM-CSF, eotaxin, MIP1-α, MIP1-β, ICAM, IL-6, IL-8, IL-10, TNF) in 139 AEC cultures were quantified.

RESULTS

AEC mediator release was greater following TNF-α/IL-1β, HDM or LPS stimulation compared to constitutive release. Increased maternal dietary vitamin D was associated with significant increases in IL-10 release by AEC after stimulation with TNF-α/IL-1β (P = 0.024) or HDM (P = 0.049). Maternal plasma α-tocopherol at 10-12 weeks gestation was positively associated with MIP1α (Spearman's rho 0.242, P = 0.009) and IL-3 (ρ 0.189, P = 0.043) responses after TNF-α/IL-1β stimulation and negatively associated with TNF (ρ -0.404, P = 0.011) and MIP1β (ρ -0.322, P = 0.046) responses after LPS stimulation.

DISCUSSION

Neonatal AECs respond to pro-inflammatory and allergenic stimuli in vitro demonstrating their potential to function as components of the innate immune response. Our findings suggest that associations exist between maternal micronutrient intake during early pregnancy and aspects of stimulated neonatal airway epithelial cell secretory function that may in turn impact on the development of asthma and/or allergic rhinitis in later life.

IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity

We have developed a statistical method named IsoDOT to assess differential isoform expression (DIE) and differential isoform usage (DIU) using RNA-seq data. Here isoform usage refers to relative isoform expression given the total expression of the corresponding gene. IsoDOT performs two tasks that cannot be accomplished by existing methods: to test DIE/DIU with respect to a continuous covariate, and to test DIE/DIU for one case versus one control. The latter task is not an uncommon situation in practice, e.g., comparing the paternal and maternal alleles of one individual or comparing tumor and normal samples of one cancer patient. Simulation studies demonstrate the high sensitivity and specificity of IsoDOT. We apply IsoDOT to study the effects of haloperidol treatment on the mouse transcriptome and identify a group of genes whose isoform usages respond to haloperidol treatment.

Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross

New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes. Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel, we demonstrate a greatly expanded range of phenotypes relative to classical mouse models of SARS-CoV infection including lung pathology, weight loss and viral titer. Genetic mapping revealed several loci contributing to differential disease responses, including an 8.5Mb locus associated with vascular cuffing on chromosome 3 that contained 23 genes and 13 noncoding RNAs. Integrating phenotypic and genetic data narrowed this region to a single gene, Trim55, an E3 ubiquitin ligase with a role in muscle fiber maintenance. Lung pathology and transcriptomic data from mice genetically deficient in Trim55 were used to validate its role in SARS-CoV-induced vascular cuffing and inflammation. These data establish the Collaborative Cross platform as a powerful genetic resource for uncovering genetic contributions of complex traits in microbial disease severity, inflammation and virus replication in models of outbred populations.

Responses of Cerambycidae and Other Insects to Traps Baited With Ethanol, 2,3-Hexanediol, and 3,2-Hydroxyketone Lures in North-Central Georgia

In north-central Georgia, 13 species of woodboring beetles (Coleoptera: Cerambycidae: Cerambycinae) were attracted to multiple-funnel traps baited with ethanol and one of the following pheromones: (1) racemic 3-hydroxyhexan-2-one; (2) racemic 3-hydroxyoctan-2-one; and (3) syn-2,3-hexanediol. The following species were attracted to traps baited with ethanol and 3-hydroxyhexan-2-one: Anelaphus pumilus (Newman), Eburia quadrigeminata (Say), Euderces pini (Olivier), Knulliana cincta (Drury), Neoclytus mucronatus (F.), Neoclytus scutellaris (Olivier), and Xylotrechus colonus (F.). Clytus marginicollis Castelnau & Gory, and Anelaphus parallelus (Newman) were attracted to traps baited with ethanol and 3-hydroxyoctan-2-one, whereas traps baited with ethanol and syn-2,3-hexanediol were attractive to Anelaphus villosus (F.), A. parallelus, Neoclytus acuminatus (F.), Neoclytus jouteli jouteli Davis, and Megacyllene caryae (Gahan). Ethanol enhanced catches of seven cerambycid species in traps baited with syn-2,3-hexanediol and 3,2-hydroxyketones. Catches of bark and ambrosia beetles (Curculionidae: Scolytinae) in ethanol-baited traps were largely unaffected by the addition of syn-2,3-hexanediol and 3,2-hydroxyketone lures, except for two species. The mean catches of Hypothenemus rotundicollis Wood & Bright and Dryoxylon onoharaensum (Murayama) in ethanol-baited traps increased and decreased, respectively, with the addition of racemic 3-hydroxyoctan-2-one. Traps baited with ethanol and syn-2,3-hexanediol were attractive to Xylobiops basilaris (Say) (Bostrichidae) and Chariessa pilosa (Forster) (Cleridae), whereas Temnoscheila virescens (F.) (Trogossitidae) were attracted to traps baited with ethanol and 3-hydroxyhexan-2-one. The assassin bug, Apiomerus crassipes (F.) (Hemiptera: Reduviidae), was attracted to traps baited with ethanol and 3,2-hydroxyketones.

Ipsenol, Ipsdienol, Ethanol, and α-Pinene: Trap Lure Blend for Cerambycidae and Buprestidae (Coleoptera) in Pine Forests of Eastern North America

In 2007-2008, we examined the flight responses of wood-boring beetles (Coleoptera: Cerambycidae and Buprestidae) to multiple-funnel traps baited with the pine volatiles, ethanol, and α-pinene [85% (-)], and the bark beetle pheromones, racemic ipsenol and racemic ipsdienol. Experiments were conducted in mature pine stands in Canada (Ontario and New Brunswick) and the United States (Arkansas, Florida, Michigan, New Hampshire, North Carolina, Ohio, Tennessee, and Wisconsin). At each location, traps were deployed in 10 replicate blocks of four traps per block. The trap treatments were: 1) blank control; 2) ipsenol and ipsdienol; 3) ethanol and α-pinene; and 4) a quaternary blend of ipsenol, ipsdienol, ethanol, and α-pinene. Traps baited with the quaternary blend caught the greatest numbers of Acanthocinus nodosus (F.), Acanthocinus obsoletus (Olivier), Acmaeops proteus (Kirby), Astylopsis sexguttata (Say), Rhagium inquisitor (L.) (Cerambycidae), and Buprestis lineata (F.) (Buprestidae). Traps baited with ethanol and α-pinene caught the greatest numbers of Arhopalus rusticus (LeConte), Asemum striatum (L.), Tetropium spp., Xylotrechus sagittatus (Germar) (Cerambycidae), and Buprestis maculipennis Gory (Buprestidae) with minimal interruption by ipsenol and ipsdienol. Our results suggest that multiple-funnel traps baited with the quaternary lure blend of ipsenol, ipsdienol, ethanol, and α-pinene are effective for trapping various species of wood-boring beetles in pine forests of eastern North America, and may have utility in detection programs for adventive species in North America and overseas.

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Since regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in this process. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. These effects influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a novel, global allelic imbalance in favor of the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.

Variation in Effects of Conophthorin on Catches of Ambrosia Beetles (Coleoptera: Curculionidae: Scolytinae) in Ethanol-Baited Traps in the United States

In 2013, we examined the effects of conophthorin on flight responses of ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) to multiple-funnel traps baited with ethanol in Georgia, Michigan, New Hampshire, and Oregon. Adventive species (=exotic, nonnative, immigrant, introduced) accounted for 91.4% of total catches of ambrosia beetles. Conophthorin increased catches of Xyleborinus saxesenii (Ratzeburg) in Georgia, New Hampshire, and Oregon. Catches of Cyclorhipidion pelliculosum (Eichhoff) were increased by conophthorin in New Hampshire but not in Michigan. In Oregon, conophthorin decreased catches of Xylosandrus germanus (Blandford) to ethanol-baited traps but not in Michigan and New Hampshire. In Georgia, conophthorin increased catches of Gnathotrichus materiarius (Fitch), Xyleborus spp., and Xylosandrus crassiusculus (Motschulsky) but decreased catches of Cnestus mutilatus (Blandford), Dryoxylon onoharaensum (Murayama), and Cyclorhipidion bodoanum (Reitter). Conophthorin had no effect on catches of Ambrosiophilus atratus (Eichhoff), Anisandrus dispar (F.), Anisandrus sayi (Hopkins), Gnathotrichus sulcatus (Leconte), Monarthrum fasciatum (Say), Monarthrum mali (Fitch), and Xylosandrus compactus (Eichhoff). Attraction of the bark beetle, Hypothenemus rotundicollis (Eichhoff), was interrupted by conophthorin in Georgia. Our results suggest that adding conophthorin lures to traps baited with ethanol may have utility in detection programs in North America and overseas. However, traps baited with ethanol alone should also be used due to interruption in attraction for some species of ambrosia beetles.

A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2

Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 - 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation (R2d2WSBdel1) that eliminates the majority of the R2d2WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2WSBdel1, the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2WSBdel1, thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system.

Host genetic diversity enables Ebola hemorrhagic fever pathogenesis and resistance

Existing mouse models of lethal Ebola virus infection do not reproduce hallmark symptoms of Ebola hemorrhagic fever, neither delayed blood coagulation and disseminated intravascular coagulation nor death from shock, thus restricting pathogenesis studies to nonhuman primates. Here we show that mice from the Collaborative Cross panel of recombinant inbred mice exhibit distinct disease phenotypes after mouse-adapted Ebola virus infection. Phenotypes range from complete resistance to lethal disease to severe hemorrhagic fever characterized by prolonged coagulation times and 100% mortality. Inflammatory signaling was associated with vascular permeability and endothelial activation, and resistance to lethal infection arose by induction of lymphocyte differentiation and cellular adhesion, probably mediated by the susceptibility allele Tek. These data indicate that genetic background determines susceptibility to Ebola hemorrhagic fever.

The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis

Inflammatory bowel disease (IBD) is an immune-mediated condition driven by improper responses to intestinal microflora in the context of environmental and genetic background. GWAS in humans have identified many loci associated with IBD, but animal models are valuable for dissecting the underlying molecular mechanisms, characterizing environmental and genetic contributions and developing treatments. Mouse models rely on interventions such as chemical treatment or introduction of an infectious agent to induce disease. Here, we describe a new model for IBD in which the disease develops spontaneously in 20-week-old mice in the absence of known murine pathogens. The model is part of the Collaborative Cross and came to our attention due to a high incidence of rectal prolapse in an incompletely inbred line. Necropsies revealed a profound proliferative colitis with variable degrees of ulceration and vasculitis, splenomegaly and enlarged mesenteric lymph nodes with no discernible anomalies of other organ systems. Phenotypic characterization of the CC011/Unc mice with homozygosity ranging from 94.1 to 99.8% suggested that the trait was fixed and acted recessively in crosses to the colitis-resistant C57BL/6J inbred strain. Using a QTL approach, we identified four loci, Ccc1, Ccc2, Ccc3 and Ccc4 on chromosomes 12, 14, 1 and 8 that collectively explain 27.7% of the phenotypic variation. Surprisingly, we also found that minute levels of residual heterozygosity in CC011/Unc have significant impact on the phenotype. This work demonstrates the utility of the CC as a source of models of human disease that arises through new combinations of alleles at susceptibility loci.

Genetics of adverse reactions to haloperidol in a mouse diallel: a drug-placebo experiment and Bayesian causal analysis

Haloperidol is an efficacious antipsychotic drug that has serious, unpredictable motor side effects that limit its utility and cause noncompliance in many patients. Using a drug-placebo diallel of the eight founder strains of the Collaborative Cross and their F1 hybrids, we characterized aggregate effects of genetics, sex, parent of origin, and their combinations on haloperidol response. Treating matched pairs of both sexes with drug or placebo, we measured changes in the following: open field activity, inclined screen rigidity, orofacial movements, prepulse inhibition of the acoustic startle response, plasma and brain drug level measurements, and body weight. To understand the genetic architecture of haloperidol response we introduce new statistical methodology linking heritable variation with causal effect of drug treatment. Our new estimators, "difference of models" and "multiple-impute matched pairs", are motivated by the Neyman-Rubin potential outcomes framework and extend our existing Bayesian hierarchical model for the diallel (Lenarcic et al. 2012). Drug-induced rigidity after chronic treatment was affected by mainly additive genetics and parent-of-origin effects (accounting for 28% and 14.8% of the variance), with NZO/HILtJ and 129S1/SvlmJ contributions tending to increase this side effect. Locomotor activity after acute treatment, by contrast, was more affected by strain-specific inbreeding (12.8%). In addition to drug response phenotypes, we examined diallel effects on behavior before treatment and found not only effects of additive genetics (10.2-53.2%) but also strong effects of epistasis (10.64-25.2%). In particular: prepulse inhibition showed additivity and epistasis in about equal proportions (26.1% and 23.7%); there was evidence of nonreciprocal epistasis in pretreatment activity and rigidity; and we estimated a range of effects on body weight that replicate those found in our previous work. Our results provide the first quantitative description of the genetic architecture of haloperidol response in mice and indicate that additive, dominance-like inbreeding and parent-of-origin effects contribute strongly to treatment effect heterogeneity for this drug.

Determination of chirality of alcohol or latent alcohol semiochemicals in individual insects

A method is described for determining the enantiomeric composition of chiral alcohols, lactones, and hydroxy acids in quantities ranging from 25 ng to 10 μg. Derivatization of the substance with chirally pure acetyl lactate, followed by splitless capillary gas chromatography, enables enantiomeric determinations to be made within 1-3% of the actual value. This technique was applied in the determination of semiochemical inIps pini (Say),Apis mellifera (L.), andCryptolestes ferrugineus (Stephens). The results indicate that considerable variability exists within populations of some insects in the composition of their chiral semiochemicals, whereas others produce substances of constant composition.

Inter- and intrapopulation variation of the pheromone, ipsdienol produced by male pine engravers,Ips pini (Say) (Coleoptera: Scolytidae)

We determined the chirality of ipsdienol in individual male pine engravers,Ips pini (Say), from New York, California, and two localities in British Columbia (BC). Both quantity and chirality of ipsdienol varied significantly between and within populations ofI. pini. Beetles from California and southeastern BC produced primarily (R)-(-)-ipsdienol with mean ratios of (S)-(+) : (R)-(-) of 9 : 91 and 11 : 89, respectively, while beetles from New York produced primarily (S)-(+)-ipsdienol with a mean (S)-(+) : (R)-(-) ratio of 57 : 43. A population from southwestern BC was unlike any other known western population, producing primarily (S)-(+)-ipsdienol with a mean (S)-(+) : (R)-(-) ratio of 66 : 34. In contrast to the unimodal chirality profiles for ipsdienol production in populations from California and southeastern BC, the profiles of the populations from southwestern BC and New York were bimodal, with a common mode at approximately 44 : 56 (S)-(+) : (R)-(-). Bimodality in the profiles of ipsdienol chirality in two populations ofI. pini and remarkably high levels of intrapopulation variation in pheromone chirality in all four populations suggest that evolutionary change in pheromone channels of communication could occur, possibly in response to artificial selection pressures such as mass trapping.