Biology subjects

Wagner, J. M.

Publications and source records attributed to Wagner, J. M..

11 recordsLinked to original sources

bioRxiv2025

Symbiotic entrenchment through ecological Catch-22

Symbiotic organisms frequently evolve obligate dependencies on hosts, but the evolutionary changes that entrench such lifestyles are poorly understood. Ant societies are vulnerable to parasitic "myrmecophiles": impostor species that infiltrate colonies and are often unable to survive outside of them. Here we show that obligate dependence of a myrmecophile on its host arises from irreversibility of the fundamental steps that achieve social acceptance inside the nest. We report a convergent system in which parallel rove beetle lineages (Staphylinidae) evolved from free-living ancestors to parasitize the same host ant. Exploiting this system, we uncover cellular mechanisms by which these beetles mimic host ant cuticular hydrocarbons (CHCs): nestmate recognition pheromones, which function pleiotropically to prevent desiccation. We present evidence of a biological stealth mechanism in a rove beetle in which the CHC biosynthetic machinery becomes transcriptionally silenced on entering the nest. Silencing transforms the beetle into a chemical blank slate onto which ant CHCs are horizontally transferred via interspecies grooming behavior. This strategy leads to identical chemical resemblance and seamless social integration within the colony. CHC pathway silencing is irreversible, however, forcing the beetle into a chronic, physically close dependence on ants to both maintain nestmate status and prevent desiccation. Loss of CHC silencing renders the beetle detectable to ants; conversely, loss of behavioral attraction to ants renders the beetle desiccation prone. Our findings show how symbiotic entrenchment can arise from a Catch-22-like ratchet operating at the organismal level.

evolutionary biology↗

bioRxiv2024

Enforced specificity of an animal symbiosis

Insect diversification has been catalyzed by widespread specialization on novel hosts--a process underlying exceptional radiations of phytophagous beetles, lepidopterans, parasitoid wasps, and inordinate lineages of symbionts, predators and other trophic specialists. The strict fidelity of many such interspecies associations is posited to hinge on sensory tuning to host-derived cues, a model supported by studies of neural function in host-specific model species. Here, we investigated the sensory basis of symbiotic interactions between a myrmecophile rove beetle and its single, natural host ant species. We show that host cues trigger analogous behaviors in both ant and symbiont. Cuticular hydrocarbons--the ants nestmate recognition pheromones--elicit partner recognition by the beetle and execution of ant grooming behavior, integrating the beetle into the colony via chemical mimicry. The beetle also follows host trail pheromones, permitting inter-colony dispersal. Remarkably, the rove beetle also performs its symbiotic behaviors with non-host ants separated by [~]95 million years, and shows minimal preference for its natural host over non-host ants. Experimentally validated agent-based modeling supports a scenario in which specificity is enforced by physiological constraints on symbiont dispersal, and negative fitness interactions with alternative hosts, rather than via sensory tuning. Enforced specificity may be a pervasive mechanism of host range restriction of specialists embedded within host niches. Chance realization of latent compatibilities with alternative hosts may facilitate host switching, enabling deep-time persistence of obligately symbiotic lineages.

evolutionary biology↗

bioRxiv2023

The genomic and cellular basis of biosynthetic innovation in rove beetles

How evolution at the cellular level potentiates change at the macroevolutionary level is a major question in evolutionary biology. With >66,000 described species, rove beetles (Staphylinidae) comprise the largest metazoan family. Their exceptional radiation has been coupled to pervasive biosynthetic innovation whereby numerous lineages bear defensive glands with diverse chemistries. Here, we combine comparative genomic and single-cell transcriptomic data from across the largest rove beetle clade, Aleocharinae. We retrace the functional evolution of two novel secretory cell types that together comprise the tergal gland--a putative catalyst behind Aleocharinaes megadiversity. We identify key genomic contingencies that were critical to the assembly of each cell type and their organ-level partnership in manufacturing the beetles defensive secretion. This process hinged on evolving a mechanism for regulated production of noxious benzoquinones that appears convergent with plant toxin release systems, and synthesis of an effective benzoquinone solvent that weaponized the total secretion. We show that this cooperative biosynthetic system arose at the Jurassic-Cretaceous boundary, and that following its establishment, both cell types underwent [~]150 million years of stasis, their chemistry and core molecular architecture maintained almost clade-wide as Aleocharinae radiated globally into tens of thousands of lineages. Despite this deep conservation, we show that the two cell types have acted as substrates for the emergence of adaptive, biochemical novelties--most dramatically in symbiotic lineages that have infiltrated social insect colonies and produce host behavior-manipulating secretions. Our findings uncover genomic and cell type evolutionary processes underlying the origin, functional conservation and evolvability of a chemical innovation in beetles.

evolutionary biology↗

bioRxiv2022

Isometric Spiracular Scaling in Scarab Beetles: Implications for Diffusive and Advective Oxygen Transport

The scaling of respiratory structures has been hypothesized to be a major driving factor in the evolution of many aspects of animal physiology. Here we provide the first assessment of the scaling of the spiracles in insects using ten scarab beetle species differing 180x in mass, including some of the most massive extant insect species. Using X-ray microtomography, we measured the cross-sectional area and depth of all eight spiracles, enabling the calculation of their diffusive and advective capacities. Each of these metrics scaled with geometric isometry.Because diffusive capacities scale with lower slopes than metabolic rates, the largest beetles measured require 10-fold higher PO2 gradients across the spiracles to sustain metabolism by diffusion compared to the smallest species. Large beetles can exchange sufficient oxygen for resting metabolism by diffusion across the spiracles, but not during flight. In contrast, spiracular advective capacities scale similarly or more steeply than metabolic rates, so spiracular advective capacities should match or exceed respiratory demands in the largest beetles. These data illustrate a general principle of gas exchange: scaling of respiratory transport structures with geometric isometry diminishes the potential for diffusive gas exchange but enhances advective capacities; combining such structural scaling with muscle-driven ventilation allows larger animals to achieve high metabolic rates when active.

physiology↗

bioRxiv2020

Characterization of a RAD51C-Silenced High Grade Serous Ovarian Cancer Model During PARP Inhibitor Resistance Development

Acquired PARP inhibitor (PARPi) resistance in BRCA1- or BRCA2-mutant ovarian cancer often results from secondary mutations that restore expression of functional protein. RAD51C is a less commonly studied ovarian cancer susceptibility gene whose promoter is sometimes methylated in the tumor, leading to homologous recombination deficiency and PARPi sensitivity. For this study, the PARPi-sensitive patient-derived xenograft PH039, which lacks demonstrable repair gene mutations but harbors RAD51C promoter methylation, was selected for PARPi resistance by repeated 21-day niraparib treatments in vivo. PH039 acquired PARPi resistance by the third cycle of treatment and demonstrated unimpeded growth during subsequent exposure to either niraparib or rucaparib. Transcriptional profiling throughout the time course of resistance development showed widespread pathway level changes along with a marked increase in RAD51C mRNA, which reflected loss of RAD51C promoter methylation. Analysis of RAD51C methylation in patient tumor samples from the ARIEL2 Part 1 clinical trial of rucaparib monotherapy likewise indicated that loss of RAD51C methylation prior to on-study biopsy was associated with limited response. Interestingly, the PARPi resistant PH039 model remained platinum sensitive. Collectively, these results not only indicate that PARPi treatment pressure can reverse RAD51C methylation and restore RAD51C expression, but also provide an important model for studying the clinical observation that PARPi and platinum sensitivity are sometimes dissociated.

cancer biology↗

bioRxiv2020

Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera

Benzoquinones are a phylogenetically widespread compound class within arthropods, appearing in harvestman, millipedes and insects. Whereas the function of benzoquinones as defensive compounds against potential predators and microbes has been well established, the full extent of benzoquinone usage across arthropods, and especially within Insecta, has yet to be established. Adding to the growing list of unique evolutionary origins of benzoquinone employment, we describe in this paper the metathoracic scent gland secretion of the mirid bug Pamillia behrensii, which is composed of heptan-2-one, 2-heptyl acetate, 2,3-dimethyl-1-4-benzoquinone, 2,3-dimethyl-1-4-hydroquinone as well as one unknown compound. Similarly, to many other arthropods that use benzoquinones, Pamillia releases the contents of its gland as a defensive mechanism in response to harassment by other arthropod predators. Morphological investigation of the gland showed that the benzoquinone-producing gland complex of P. behrensii follows a similar blueprint to metathoracic scent glands described in other Heteropterans. Overall, our data further underpins the widespread convergent evolution and use of benzoquinones for defense across the Arthropoda, now including the order Hemiptera.

evolutionary biology↗

bioRxiv2020

Gait asymmetry, and bilateral coordination of gait during a six-minute walk test in persons with multiple sclerosis

Gait impairments in persons with multiple sclerosis (pwMS) underlying reduced walking endurance are still poorly understood. Thus, our objective was to assessed gait asymmetry (GA) and bilateral coordination of gait (BCG), among pwMS during the six-minute walk test (6MWT) and their association with disease severity. For this aim, we recruited ninety-two pwMS (age: 46.6 {+/-} 7.9; 83% females) with a broad range of clinical disability who completed the 6MWT wearing gait analysis system. GA was assessed by comparing left and right swing times, and BCG by using the phase coordination index (PCI). Several functional and subjective gait assessments were performed. Results show that gait is more asymmetric and less coordinated as the disease progresses (p<.0001). Participants with mild MS showed significant better BCG as reflected by lower PCI values in comparison to the other two MS severity groups (severe: p =.001, moderate: p=.02). GA and PCI also deteriorated significantly with time during the 6MWT (p<.0001). GA and PCI (i.e., BCG) show somewhat weaker associations with clinical MS status than associations observed between functional and subjective gait assessments and MS status. Similar to other neurological cohorts, GA and PCI are important parameters to assess and to target in interventions among pwMS.

physiology↗

bioRxiv2020

Assembly and Annotation of an Ashkenazi Human Reference Genome

Here we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are >99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. 40 of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. 11 genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes.

genomics↗

bioRxiv2020

New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

Integrative genetic elements (IGEs) are mobile multigene DNA units that integrate into and excise from host bacterial chromosomes. Each IGE usually targets a specific site within a conserved host gene, integrating in a manner that preserves target gene function. However, a small number of bacterial genes are known to be inactivated upon IGE integration and reactivated upon excision, regulating phenotypes of virulence, mutation rate, and terminal differentiation in multicellular bacteria. The list of regulated gene integrity (RGI) cases has been slow-growing because IGEs have been challenging to precisely and comprehensively locate in genomes. We present software (TIGER) that maps IGEs with unprecedented precision and without attB site bias. TIGER uses a comparative genomic, ping-pong BLAST approach, based on the principle that the IGE integration module (i.e., its int-attP region) is cohesive. The resultant IGEs, along with integrase phylogenetic analysis and gene inactivation tests, revealed 19 new cases of genes whose integrity is regulated by IGEs (including dut, eccCa1, gntT, hrpB, merA, ompN, prkA, tqsA, traG, yifB, yfaT and ynfE), as well as recovering previously known cases (in sigK, spsM, comK, mlrA, and hlb genes). It also recovered known clades of site-promiscuous integrases and identified possible new ones.

bioinformatics↗

bioRxiv2019

Increased synaptic facilitation and exploratory behavior in mice lacking the presynaptic protein Mover

In vertebrates and invertebrates, neurotransmitter release relies on a highly conserved molecular machinery. A surprisingly small number of presynaptic proteins evolved specifically in vertebrates. How they expand the power or versatility of the conserved core machinery is unclear. One of these vertebrate-specific proteins, called Mover / TPRGL / SVAP30, is heterogeneously expressed throughout the brain, suggesting that it adds special functions to subtypes of presynaptic terminals. In this study we generated Mover knockout mice to investigate the role of Mover from synaptic transmission to behavior. Deletion of Mover did not affect synaptic transmission at CA3 to CA1 synapses. In contrast, Mover deficient mice had strongly increased short-term facilitation at mossy fiber to CA3 synapses. This increase included frequency facilitation, a hallmark of mossy fiber terminal function. The effect was age- and Ca2+-dependent, and relied on the Kainate receptor/cAMP pathway in the mossy fiber terminals. Despite this change in presynaptic plasticity, the absence of Mover did not affect long-term spatial reference memory or working memory, but led to reduced anxiety. These discoveries suggest that Mover has distinct roles at different synapses. At mossy-fiber terminals, it acts to constrain the extent of presynaptic facilitation. Its role in activity-dependent neurotransmission could be necessary for normal anxiety responses. Significance StatementThe enormous increase in the complexity of brains during evolution is accompanied by a remarkably small number of new, vertebrate-specific presynaptic proteins. These proteins are unlikely to be essential for transmitter release, because invertebrate synapses do not need them. But what functions do they fulfill? We show that the vertebrate-specific protein Mover is involved in constraining the release of neurotransmitters in some synapses in the hippocampus, while not affecting others. We further demonstrate that the absence of this protein leads to decreased anxiety levels. Understanding the function of such a protein can help us further understand synaptic transmission, the specializations that are brought about in vertebrate synapses, and how this can help or hinder neurological or psychiatric disorders.

neuroscience↗

bioRxiv2018

Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica

Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. To address this limitation, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which functional determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified mutations that led to high lipid accumulation and eliminated pseudohyphal morphology.

synthetic biology↗