Biology subjects

Reed, F. A.

Publications and source records attributed to Reed, F. A..

5 recordsLinked to original sources

bioRxiv2021

Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered tropical birds

The gut microbiome of an animal has a strong influence on the health, fitness, and behavior of its host, and is thus a critical component of the animal itself. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawai i, several threats have caused widespread population declines of Hawaiian honeycreepers (subfamily Carduelinae). These threats, and the environmental changes that result, can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, no previous study has explored the natural patterns of the gut microbiome of a honeycreeper species in the wild. This project used amplicon-based sequencing of the 16S rRNA gene to characterize the gut microbiome of two critically endangered species of Hawaiian honeycreepers. The two species differed significantly in both alpha and beta diversity. Intraspecific variation of the gut microbiome among individual birds was a major factor. However, small but significant differences also exist between sampling location and sexes. This baseline knowledge will help inform management decisions for these honeycreeper species both in their native habitats and in captivity.

zoology↗

bioRxiv2021

Oncofly: A CURE for Cancer

Course-based Undergraduate Research Experiences (CUREs) are emerging as a means to engage large numbers of undergraduate students in meaningful inquiry-based research activities. We describe here a simple laboratory exercise as part of an undergraduate genetics course that illustrates the contributions of oncogenes and tumor suppressors to the formation of neoplasms in an invertebrate model system. In addition, students were challenged to investigate whether flies reared on a diet containing a variety of additives display a higher number of invasive tumors in the larval abdomen. The goal of the exercise was to (i) familiarize students with the multigenic origin of the cancer phenotype, to (ii) introduce some of the fundamental molecular cancer hallmarks, and to (iii) highlight the significance of invertebrate model systems in biomedical research. Furthermore, (iv) students learn to execute a molecular test for transgenic produce and (v) apply statistical tools to test a simple hypothesis. We evaluated student learning and changes in opinions and attitudes relating to environmental versus genetic causes of cancer and several common misconceptions using a questionnaire before and after completing the exercise. Overall, significant improvements in the rate of factually correct responses and reductions in uncertainty were demonstrated. Although resistance to change was apparent in regard to identifying some risk factors, there was clear learning and understanding of the core concepts of carcinogenesis and the utility of basic research with model organisms.

scientific communication and education↗

bioRxiv2020

Perturbations of Ribosomal Protein Expression Reveal Overlapping Gene Networks between Drosophila Minutes and Human Cancer

Ribosomal proteins (RPs) are critical to all cellular operations through their key roles in ribosome biogenesis and translation, as well as their extra-ribosomal functions. Leveraging previously identified RP mutants we characterised the RP macro transcriptome and sought to compare it with transcriptomes of pathologies associated with failures of ribosomal function, cancer and Zika virus (ZIKV). Single gene-based analysis revealed highly variable transcriptomes of RP mutations with little overlap in genes that were differentially expressed. In contrast, weighted gene co-expression network analysis revealed a highly conserved transcriptomic network pattern across all RP mutants studied. In addition, when we compared network changes in RP mutants, we observed similarities to transcriptome alterations in human cancer, and thus confirming the oncogenic role of RPs. Finally, it is known that ZIKV infection influences translational machinery, but this study shows infection network changes dissimilar to those of either the RP mutation or cancer.

genetics↗

bioRxiv2020

Evaluation of pigmentation gene knock-outs by CRISPR as potential targets for the genetic engineering of Culex quinquefasciatus

Culex quinquefasciatus mosquitoes are a globally widespread vector of several human and animal pathogens. Their biology and behavior allow them to thrive in proximity to urban areas, rendering them a constant public health threat. Their mixed bird/mammal feeding behavior further offers a vehicle for zoonotic pathogens transmission to people, and separately, poses a threat to the conservation of insular birds. The advent of CRISPR has led to the development of novel technologies for the genetic engineering of wild mosquito populations, yet research in Culex quinquefasciatus has been lagging compared to other disease vectors. Here we use this tool to disrupt a set of five pigmentation genes in Culex quinquefasciatus that, when altered, lead to visible, homozygous-viable phenotypes. We further validate this approach in separate laboratories and in two distinct strains of Culex quinquefasciatus that are relevant to potential future public health and bird conservation applications. We generate a double-mutant line, demonstrating the possibility of sequentially combining multiple such mutations in a single individual. Lastly, we target two loci, doublesex in the sex-determination pathway and proboscipedia a hox gene, demonstrating the flexibility of these methods applied to novel targets. Our work provides a platform of seven validated loci that could be used for targeted mutagenesis in Culex quinquefasciatus and the future development of genetic suppression strategies for this species. Furthermore, the mutant lines generated here could have widespread utility to the research community using this model organism, as they could be used as targets for transgene delivery, where a copy of the disrupted gene could be included as an easily-scored transgenesis marker.

genetics↗

bioRxiv2018

Gene expression across tissues, sex, and life stages in the sea urchin Tripneustes gratilla

The pan-tropical sea urchin Tripneustes gratilla is an ecologically and economically important shallow water algal grazer. The aquaculture of T. gratilla has spurred growing interest in the population biology of the species, and by extension the generation of more molecular resources. To this purpose, de novo transcriptomes of T. gratilla were generated for two adults, a male and a female, as well as for a cohort of approximately 1,000 plutei larvae. Gene expression profiles of three adult tissue samples were quantified and compared. These samples were of gonadal tissue, the neural ring, and pooled tube feet and pedicellariae. Levels of shared and different gene expression between sexes, as well as across functional categories of interest, including the immune system, toxins, genes involved in fertilization, and sensory genes are highlighted. Differences in expression of Sex determining Region Y-related High Mobility Group box groups and general isoform expression between the sexes is observed. Additionally an expansion of the tumor suppressor DMBT1 was observed in T. gratilla when compared to the annotated genome of the sea urchin Strongylocentrotus purpuratus. The draft transcriptome of T. gratilla is presented here in order to facilitate more genomic level analysis of de-novo sea urchin systems.

molecular biology↗