Revealing the genome of the microsporidian Vairimorpha bombi, a potential driver of bumble bee declines in North America.

Pollinators are vital for food security and the maintenance of terrestrial ecosystems. Bumblebees are important pollinators across northern temperate, arctic, and alpine ecosystems, yet are in decline across the globe. Vairimorpha bombi is a parasite belonging to the fungal class Microsporidia that has been implicated in the rapid decline of bumblebees in North America, where it may be an emerging infectious disease. To investigate the evolutionary basis of pathogenicity of V. bombi, we sequenced and assembled its genome using Oxford Nanopore and Illumina technologies and performed phylogenetic and genomic evolutionary analyses. The genome assembly for V. bombi is 4.73 Mb, from which we predicted 1,870 protein-coding genes and 179 tRNA genes. The genome assembly has low repetitive content and low GC content. V. bombi's genome assembly is the smallest of the Vairimorpha and closely related Nosema genera, but larger than those found in the Encephalitozoon and Ordospora sister clades. Orthology and phylogenetic analysis revealed 18 core conserved single-copy microsporidian genes including the histone acetyltransferase (HAT) GCN5. Surprisingly, V. bombi was unique to the microsporidia in not encoding the second predicted HAT ESA1. The V. bombi genome assembly annotation included 265 unique genes (i.e. not predicted in other microsporidia genome assemblies), 20% of which encode a secretion signal, which is a significant enrichment. Intriguingly, of the 36 microsporidian genomes we analyzed, 26 also had a significant enrichment of secreted signals encoded by unique genes, ranging from 6 to 71% of those predicted genes. These results suggest that microsporidia are under selection to generate and purge diverse and unique genes encoding secreted proteins, potentially contributing to or facilitating infection of their diverse hosts. Furthermore, V. bombi has 5/7 conserved spore wall proteins (SWPs) with its closest relative V. ceranae (that primarily infects honeybees), while also uniquely encoding four additional SWPs. This gene class is thought to be essential for infection, providing both environmental protection and recognition and uptake into the host cell. Together, our results show that SWPs and unique genes encoding a secretion signal are rapidly evolving in the microsporidia, suggesting that they underpin key pathobiological traits including host specificity and pathogenicity.

Simulating muscular thin films using thermal contraction capabilities in finite element analysis tools.

In this study, new techniques for approximating the contractile properties of cells in biohybrid devices using Finite Element Analysis (FEA) have been investigated. Many current techniques for modeling biohybrid devices use individual cell forces to simulate the cellular contraction. However, such techniques result in long simulation runtimes. In this study we investigated the effect of the use of thermal contraction on simulation runtime. The thermal contraction model was significantly faster than models using individual cell forces, making it beneficial for rapidly designing or optimizing devices. Three techniques, Stoney׳s Approximation, a Modified Stoney׳s Approximation, and a Thermostat Model, were explored for calibrating thermal expansion/contraction parameters (TECPs) needed to simulate cellular contraction using thermal contraction. The TECP values were calibrated by using published data on the deflections of muscular thin films (MTFs). Using these techniques, TECP values that suitably approximate experimental deflections can be determined by using experimental data obtained from cardiomyocyte MTFs. Furthermore, a sensitivity analysis was performed in order to investigate the contribution of individual variables, such as elastic modulus and layer thickness, to the final calibrated TECP for each calibration technique. Additionally, the TECP values are applicable to other types of biohybrid devices. Two non-MTF models were simulated based on devices reported in the existing literature.

Effect of actuating cell source on locomotion of organic living machines with electrocompacted collagen skeleton.

In robotics, there is a need for small scale, compliant actuators for use in medical applications or minimally invasive environmental monitoring. Biohybrid devices offer one solution to this need by using muscle cells to actuate compliant scaffolds. Such devices typically use biocompatible synthetic polymers as compliant scaffolds, which require additional processing steps to promote cellular alignment and attachment. Instead, electrocompacted and aligned collagen (ELAC) can be used as a completely organic scaffold, requiring no additional processing steps, with alignment being innately promoted by the topography. Locomotive living machines have been fabricated in this study using ELAC scaffolds. Devices have been produced using either primary cardiomyocytes or primary skeletal muscle cells isolated from chick embryos as actuators. When tested under the same conditions, skeletal muscle cell powered devices were approximately an order of magnitude faster, having a mean velocity of 77.6 ± 86.4 µm min(-1), compared to 9.34 ± 6.69 µm min(-1) for cardiomyocyte powered devices. In conclusion, completely organic living machines have been fabricated using electrocompacted collagen skeletons, and it was found that skeletal muscle powered devices were significantly faster than cardiomyocyte powered devices.

ENU-induced phenovariance in mice: inferences from 587 mutations.

BACKGROUND: We present a compendium of N-ethyl-N-nitrosourea (ENU)-induced mouse mutations, identified in our laboratory over a period of 10 years either on the basis of phenotype or whole genome and/or whole exome sequencing, and archived in the Mutagenetix database. Our purpose is threefold: 1) to formally describe many point mutations, including those that were not previously disclosed in peer-reviewed publications; 2) to assess the characteristics of these mutations; and 3) to estimate the likelihood that a missense mutation induced by ENU will create a detectable phenotype. FINDINGS: In the context of an ENU mutagenesis program for C57BL/6J mice, a total of 185 phenotypes were tracked to mutations in 129 genes. In addition, 402 incidental mutations were identified and predicted to affect 390 genes. As previously reported, ENU shows strand asymmetry in its induction of mutations, particularly favoring T to A rather than A to T in the sense strand of coding regions and splice junctions. Some amino acid substitutions are far more likely to be damaging than others, and some are far more likely to be observed. Indeed, from among a total of 494 non-synonymous coding mutations, ENU was observed to create only 114 of the 182 possible amino acid substitutions that single base changes can achieve. Based on differences in overt null allele frequencies observed in phenotypic vs. non-phenotypic mutation sets, we infer that ENU-induced missense mutations create detectable phenotype only about 1 in 4.7 times. While the remaining mutations may not be functionally neutral, they are, on average, beneath the limits of detection of the phenotypic assays we applied. CONCLUSIONS: Collectively, these mutations add to our understanding of the chemical specificity of ENU, the types of amino acid substitutions it creates, and its efficiency in causing phenovariance. Our data support the validity of computational algorithms for the prediction of damage caused by amino acid substitutions, and may lead to refined predictions as to whether specific amino acid changes are responsible for observed phenotypes. These data form the basis for closer in silico estimations of the number of genes mutated to a state of phenovariance by ENU within a population of G3 mice.

A diffusion tensor imaging and neurocognitive study of HIV-positive children who are HAART-naïve "slow progressors".

There are few neuropsychological or neuroimaging studies of HIV-positive children with "slow progression". "Slow progressors" are typically defined as children or adolescents who were vertically infected with HIV, but who received no or minimal antiretroviral therapy. We compared 12 asymptomatic HIV-positive children (8 to 12 years) with matched controls on a neuropsychological battery as well as diffusion tensor imaging in a masked region of interest analysis focusing on the corpus callosum, internal capsule and superior longitudinal fasciculus. The "slow progressor" group performed significantly worse than controls on the Wechsler Abbreviated Scale of Intelligence Verbal and Performance IQ scales, and on standardised tests of visuospatial processing, visual memory and executive functioning. "Slow progressors" had lower fractional anisotropy (FA), higher mean diffusivity (MD) and radial diffusivity (RD) in the corpus callosum (p= <0.05), and increased MD in the superior longitudinal fasciculus, compared to controls. A correlation was found between poor performance on a test of executive function and a test of attention with corpus callosum FA, and a test of executive function with lowered FA in the superior longitudinal fasiculus. These data suggest that demyelination as reflected by the increase in RD may be a prominent disease process in paediatric HIV infection.

The importance of context: evidence that contextual representations increase intrusive memories.

BACKGROUND AND OBJECTIVES: Intrusive memories appear to enter consciousness via involuntary rather than deliberate recollection. Some clinical accounts of PTSD seek to explain this phenomenon by making a clear distinction between the encoding of sensory-based and contextual representations. Contextual representations have been claimed to actively reduce intrusions by anchoring encoded perceptual data for an event in memory. The current analogue trauma study examined this hypothesis by manipulating contextual information independently from encoded sensory-perceptual information. METHOD: Participants' viewed images selected from the International Affective Picture System that depicted scenes of violence and bodily injury. Images were viewed either under neutral conditions or paired with contextual information. RESULTS: Two experiments revealed a significant increase in memory intrusions for images paired with contextual information in comparison to the same images viewed under neutral conditions. In contrast to the observed increase in intrusion frequency there was no effect of contextual representations on voluntary memory for the images. The vividness and emotionality of memory intrusions were also unaffected. LIMITATIONS: The analogue trauma paradigm may fail to replicate the effect of extreme stress on encoding postulated to occur during PTSD. CONCLUSIONS: These findings question the assertion that intrusive memories develop from a lack of integration between sensory-based and contextual representations in memory. Instead it is argued contextual representations play a causal role in increasing the frequency of intrusions by increasing the sensitivity of memory to involuntary retrieval by associated internal and external cues.