Biology subjects

Barnett, A. A.

Publications and source records attributed to Barnett, A. A..

7 recordsLinked to original sources

bioRxiv2025

Developmental system drift in the patterning of the arthropod tarsus

The current understanding of proximodistal axis patterning in arthropod legs is grounded in insect models. The paradigm for appendage evolution in this phylum is that the gene regulatory network responsible for leg subdivision and patterning is broadly conserved. Recent surveys of these genes have suggested that chelicerate exemplars exhibit divergent appendage patterning dynamics, though functional data remain limited. One salient mismatch in expression occurs in homologs of the homeobox gene clawless. In insects, clawless is expressed in the distalmost leg territory, specifying the claw-bearing pretarsus. In the harvestman, Phalangium opilio, clawless occupies a broad tarsal domain early in development, localizing later to the metatarsus-tarsus boundary, suggestive of a tarsal patterning function. Here, we tested the function of harvestman clawless using RNAi. Unlike insects, we show that clawless knockdown results in disrupted tarsal growth and patterning of its proximal segmental boundary, with no effect on the claw. Truncation of the tarsus is associated with defective tarsomere formation. We additionally surveyed clawless homologs in exemplars of chelicerate diversity, which suggests that the tarsal-patterning function for clawless was likely present in the chelicerate common ancestor. These results, alongside available expression data, suggest panarthropod appendage patterning exhibits numerous cases of developmental system drift.

evolutionary biology↗

bioRxiv2025

The Expression of Pax6 Genes in an Eyeless Arachnid Suggests Their Ancestral Role in Arachnid Head Development

BackgroundMany animal lineages utilize Pax6 transcription factors during eye development. Within Arthropoda, evidence suggests that Pax6 genes are necessary for the specification of eyes in myriapods, crustaceans, and insects. However, recent data have argued that Pax6 genes lack a role in the development of the eyes in Chelicerata (=arachnids, horseshoe crabs, and sea spiders). An alternative hypothesis argues that the absence of Pax6 expression in developing chelicerate eyes could be explained by an earlier role for these genes in patterning eye precursor cells. The arachnid mite Archegozetes longisetosus lacks eyes, however it retains two Pax6 paralogs in its genome. By leveraging these aspects of A. longisetosus, we tested the hypothesis that ancestrally chelicerates did not use Pax6 genes to pattern their eyes but rather used them to pattern the central nervous system. We reasoned that if we observed comparable expression patterns of Pax6 genes in A. longisetosus in comparison to those in arachnids that have retained eyes, then this would support the hypothesis that Pax6 genes were not ancestrally used for eye specification in chelicerates. ResultsWe followed the expression of canonical arthropod retinal determination genes to confirm that A. longisetosus does not develop vestigial eyes. We found that the expression of the Pax6 paralogs was consistent with their roles in the development of the ocular region and central nervous system. By co- staining for these genes simultaneously with the conserved head patterning gene orthodenticle, we also observed early expression patterns of these genes in the protocerebrum of early A. longisetosus embryos that are comparable to those arachnids with embryonic eyes. ConclusionsOur data provide support for the hypothesis that Pax6 genes were not ancestrally used to pattern chelicerate eyes. The expression patterns of Pax6 genes in A. longisetosus were comparable to those of other arachnids that have eyes. This suggests that the retention of Pax6 genes in A. longisetosus is due to their ancestral, non-eye patterning roles. Further supporting this hypothesis is our observation that A. longisetosus does not pattern vestigial eyes. Lastly, our data suggests that the Pax6 genes, with orthodenticle, acted to specify the ancestral arachnid protocerebrum.

developmental biology↗

bioRxiv2024

A novel expression domain of extradenticle underlies the evolutionary developmental origin of the chelicerate patella

Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2, suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2, disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio, which lacks dachshund-2. Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle. Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.

evolutionary biology↗

bioRxiv2021

Establishment of CRISPR/Cas9-based knock-in in a hemimetabolous insect: targeted gene tagging in the cricket Gryllus bimaculatus

Studies of traditional model organisms like the fruit fly Drosophila melanogaster have contributed immensely to our understanding of the genetic basis of developmental processes. However, the generalizability of these findings cannot be confirmed without functional genetic analyses in additional organisms. Direct genome editing using targeted nucleases has the potential to transform hitherto poorly-understood organisms into viable laboratory organisms for functional genetic study. To this end, here we present a method to induce targeted genome knock-out and knock-in of desired sequences in an insect that serves as an informative contrast to Drosophila, the cricket Gryllus bimaculatus. The efficiency of germ line transmission of induced mutations is comparable to that reported for other well-studied laboratory organisms, and knock-ins targeting introns yield viable, fertile animals in which knock-in events are directly detectable by visualization of a fluorescent marker in the expression pattern of the targeted gene. Combined with the recently assembled and annotated genome of this cricket, this knock-in/knock-out method increases the viability of G. bimaculatus as a tractable system for functional genetics in a basally branching insect.

developmental biology↗

bioRxiv2020

Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus

Oribatid mites are a specious order of microarthropods within the subphylum Chelicerata, compromising about 11,000 described species. They are ubiquitously distributed across different microhabitats in all terrestrial ecosystems around the world and were among the first animals colonizing terrestrial habitats as decomposers and scavengers. Despite their species richness and ecological importance genomic resources are lacking for oribatids. Here, we present a 190-Mb genome assembly of the clonal, all-female oribatid mite species Archegozetes longisetosus Aoki, a model species used by numerous laboratories for the past 30 years. Comparative genomic and transcriptional analyses revealed patterns of reduced body segmentation and loss of segmental identity gene abd-A within Acariformes, and unexpected expression of key eye development genes in these eyeless mites across developmental stages. Consistent with their soil dwelling lifestyle, investigation of the sensory genes revealed a species-specific expansion of gustatory receptors, the largest chemoreceptor family in the genome used in olfaction, and evidence of horizontally transferred enzymes used in cell wall degradation of plant and fungal matter, both components of the A. longisetosus diet. Oribatid mites are also noted for their biosynthesis capacities and biochemical diversity. Using biochemical and genomic data, we were able to delineate the backbone biosynthesis of monoterpenes, an important class of compounds found in the major exocrine gland system of Oribatida - the oil glands. Given the mites strength as an experimental model, the new high-quality resources provided here will serve as the foundation for molecular research in Oribatida and will enable a broader understanding of chelicerate evolution.

zoology↗

bioRxiv2020

Evaluations of CRC2631 toxicity, tumor colonization, and genetic stability in the TRAMP prostate cancer model

Conventional cancer chemotherapies are not fully efficacious and do not target tumors, leading to significant treatment-related morbidities. A number of genetically attenuated cancer-targeting bacteria are being developed to safely target tumors in vivo. Here we report the toxicological, tumor-targeting, and efficacy profiles of Salmonella enterica serovar Typhimurium CRC2631 in a syngeneic and autochthonous TRAMP model of aggressive prostate cancer. CRC2631 preferentially colonize primary and metastatic tumors in the TRAMP animals. In addition, longitudinal whole genome sequencing studies of CRC2631 recovered from prostate tumor tissues demonstrate that CRC2631 is genetically stable. Moreover, tumor-targeted CRC2631 generates an anti-tumor immune response. Combination of CRC2631 with checkpoint blockade reduces metastasis burden. Collectively, these findings demonstrate a potential for CRC2631 in cancer immunotherapy strategies.

cancer biology↗

bioRxiv2018

Hox genes limit germ cell formation in the short germ insect Gryllus bimaculatus.

Hox genes are conserved transcription factor-encoding genes that specify the identity of body regions in bilaterally symmetrical animals. In the cricket Gryllus bimaculatus, a member of the hemimetabolous insect group Orthoptera, the induction of a subset of mesodermal cells to form the primordial germ cells (PGCs) is restricted to the second through the fourth abdominal segments (A2-A4). In numerous insect species, the Hox genes Sex-combs reduced (Scr), Antennapedia (Antp), Ultrabithorax (Ubx) and abdominal-A (abd-A) jointly regulate the identities of middle and posterior body segments, suggesting that these genes may restrict PGC formation to specific abdominal segments in G. bimaculatus. Here we show that all of these Hox genes, either individually or in segment-specific combinations, restrict PGC formation. Our data provides evidence for a segmental Hox code used to regulate the placement of PGC formation, reminiscent of the segmental Hox codes used in other arthropod groups to establish other aspects of segmental identity. These data also provide, to our knowledge, the first evidence for this ancient group of genes in determining PGC placement within the context of axial patterning in any animal studied thus far.

developmental biology↗