Biology subjects

Kelley, D.

Publications and source records attributed to Kelley, D..

4 recordsLinked to original sources

bioRxiv2025

THE HARD AND SOFT OF IT: THE ROLE OF SUBSTRATE IN PATTERNS OF PHASE DOMINANCE AND PHENOLOGY IN GRACILARIA VERMICULOPHYLLA

Despite the importance of the seasonal timing of life cycle events for understanding population dynamics, we lack information on the phenology of most macroalgal species. The red macroalga Gracilaria vermiculophylla is now common in both hard and soft bottom habitats following its invasion throughout the Northern Hemisphere. In sites with sufficient hard substratum, thalli are fixed by holdfasts to hard substrate. By contrast, in sites with soft substratum, thalli are free-living and either drift free-floating or anchored by the tube building polychaete Diopatra cuprea. The difference in substrate type has profound implications on the evolutionary ecology of G. vermiculophylla populations whereby the life cycle is disrupted in soft bottom habitats leading to tetrasporophytic dominance. To investigate these patterns across seasons, we determined the reproductive state via microscopy and phase via a sex-linked PCR assay for >4,800 thalli over the course of three years at hard and soft bottom sites with fixed and free-living G. vermiculophylla thalli, respectively, along the Eastern Shore of Virginia and Maryland. At hard bottom sites, most thalli were reproductive in the summer and sites were composed of gametophytes and tetrasporophytes, though there was a tetrasporophytic bias. By contrast, soft bottom sites were overwhelming tetrasporophyte dominated and fewer thalli were reproductive at any point in the year. Moreover, each soft bottom site displayed different patterns in the proportion of reproductive thalli, with G. vermiculophylla abundance fluctuating through time. Phenology surveys critical for understanding the spread of introduced macroalgae, including the on-going spread of G. vermiculophylla.

evolutionary biology↗

bioRxiv2024

Exposure to novel females increases fecundity in adult male prairie voles

Social circuitry of the mammalian brain can influence male reproductive physiology. This often manifests as plasticity in sperm production or allocation, particularly in response to male-male competition. However, socially mediated testicular plasticity has not been investigated with respect to mating and parental strategy. Testis mass and sperm production of sexually naive and female-exposed adult male individuals of three rodent species were compared: the socially monogamous and paternal prairie vole (Microtus ochrogaster), the promiscuous and non-paternal meadow vole (Microtus pennsylvanicus), and the promiscuous and non-paternal house mouse (Mus musculus). Monogamously paired prairie vole males exhibited significantly larger testes and greater sperm production than naive prairie vole males. Comparatively, there were no significant differences between naive and monogamously paired male meadow voles or mice. To investigate the role of olfactory cues for regulating this phenomenon in prairie voles, a group of naive males exposed to soiled bedding from novel females was used. These males were more similar to paired males than to naive males not exposed to novel female odors, demonstrating a strong role of the social olfactory system. Further, while the predictions of sperm competition theory (species with greater female promiscuity have larger testes than closely related species with less female promiscuity) are consistent between naive meadow voles and prairie voles, the prediction does not hold for monogamously paired prairie voles and meadow voles. This demonstrates the complexity of internal social dynamics and reproductive pressures which socially monogamous paternal males face and the evolutionary adaptions that may develop in response.

physiology↗

bioRxiv2017

Quantitative proteomic analysis of auxin signaling during seedling development

Auxin induces rapid gene expression changes throughout plant development. How these transcriptional responses relate to changes in protein abundance is not well characterized. We have identified auxin regulated proteins in whole seedlings, roots and hypocotyls and at three different time points (30 min, 120 min and 3 hours) using an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics approach. These profiling experiments detected 4,701 proteins from seedling tissue, 6,740 proteins from root tissue and 3,925 proteins from hypocotyl tissue. Comparisons between the differentially expressed proteins data sets showed little overlap, suggesting that auxin proteomes exhibit both temporal and spatial specificity. Numerous proteins showed significant changes in abundance following auxin treatment independent of changes in cognate transcript abundance. This includes several well characterized proteins with various roles in auxin pathways, suggesting that complex gene regulation mechanisms follow auxin signaling events. Specifically, regulation of translation may play a role as inferred from MapMan categorization analyses and protein interaction networks comprised of auxin regulated proteins. Additionally, functional categorization of auxin regulated proteins indicates rapid and complex metabolic changes occur in both roots and hypocotyls in response to auxin which are not apparent from transcriptome analyses. Altogether these data describe novel auxin-regulated proteomes and are an excellent resource for identifying new downstream signaling components related to auxin-mediated plant growth and development.

plant biology↗

bioRxiv2017

Epigenetic Regulation of Gene Expression in Cancer: Techniques, Resources, and Analysis

Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, non-coding RNAs, post-translational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations, once thought to be crucial only for the malignant phenotype maintenance, are now recognized as critical also for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. While associated with cancer, the precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems, and bioinformatics algorithms for their analysis. Advances in bioinformatics data integration techniques that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer, and are therefore also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations to cause tumorigenesis initiation and progression. This deeper understanding is essential to future studies that will precisely infer patients prognosis and select patients who will be responsive to emerging epigenetic therapies.

cancer biology↗