Biology subjects

Perkins, A. C.

Publications and source records attributed to Perkins, A. C..

4 recordsLinked to original sources

bioRxiv2025

Spatiotemporal dynamics of questing activity by four tick species in the central Great Plains

In this study, we explore a suite of new ecological niche modeling approaches to illuminate the distributional potential and distributional dynamics of questing individuals of four tick species in the central Great Plains region. Specifically, we improve on typical approaches in distributional ecology by (1) assigning time-specific environmental values to sampling events so that repeated sampling at the same points yields additional information, (2) using both positive and negative records of the species as inputs in model development, and (3) constraining model response shapes in models to resemble the shapes of fundamental ecological niches. Model outcomes demonstrate both seasonal dynamics and differences between species in terms of the geographic potential of questing behavior by Great Plains tick species. These improved approaches in distributional ecology have considerable potential to enrich distributional understanding of vector species distributions.

ecology↗

bioRxiv2021

Fragmentation of macrophages during isolation confounds analysis of single cell preparations from mouse hematopoietic tissues

Mouse hematopoietic tissues contain abundant and heterogeneous populations of tissue-resident macrophages attributed trophic functions in control of immunity, hematopoiesis and bone homeostasis. A systematic strategy to characterise macrophage subsets in mouse bone marrow (BM), spleen and lymph node, unexpectedly revealed macrophage surface marker staining typically emanated from membrane-bound subcellular remnants associated with unrelated cell types. Remnant-restricted macrophage-specific membrane markers, cytoplasmic fluorescent reporters and mRNA were all detected in non-macrophage cell populations including isolated stem and progenitor cells. The profile of macrophage remnant association reflects adhesive interactions between macrophages and other cell types in vivo. Applying this knowledge, reduced macrophage remnant attachment to BM granulocytes in Siglec1 deficient mice was associated with compromised emergency granulocytosis, revealing a function for Siglec1-dependent granulocyte-macrophage interactions. Analysis of published RNA-seq data for purified macrophage and non-macrophage populations indicates that macrophage fragmentation is a general phenomenon that confounds bulk and single cell analysis of disaggregated tissues.

immunology↗

bioRxiv2020

Increased seed carbohydrate reserves associated with domestication influence the optimal seminal root number of Zea mays

Background and AimsDomesticated maize (Zea mays ssp. mays) generally forms between two and six seminal roots, while its wild ancestor, Mexican annual teosinte (Zea mays ssp. parviglumis), typically lacks seminal roots. Maize also produces larger seeds than teosinte, and it generally has higher growth rates as a seedling. Maize was originally domesticated in the tropical soils of southern Mexico, but it was later brought to the Mexican highlands before spreading to other parts of the continent, where it experienced different soil resource constraints. The aims of this study were to understand the impact of increased seminal root number on seedling nitrogen acquisition and to model how differences in maize and teosinte phenotypes might have contributed to increased seminal root number in domesticated maize. MethodsSeedling root architectural models of a teosinte accession and a maize landrace were constructed by parameterizing the functional-structural plant model OpenSimRoot using plants grown in mesocosms. Seedling growth was simulated in a low-phosphorus environment, multiple low-nitrogen environments, and at variable planting densities. Models were also constructed to combine individual components of the maize and teosinte phenotypes. Key ResultsSeminal roots contributed about 35% of the nitrogen and phosphorus acquired by maize landrace seedlings in the first 25 days after planting. Increased seminal root number improved plant N acquisition under low-N environments with varying precipitation patterns, fertilization rates, soil textures, and planting densities. Models suggested that the optimal number of seminal roots for nutrient acquisition in teosinte is constrained by its limited seed carbohydrate reserves. ConclusionsSeminal roots can improve the acquisition of both nitrogen and phosphorus in maize seedlings, and the increase in seed size associated with maize domestication may have facilitated increased seminal root number.

plant biology↗

bioRxiv2016

High temporal resolution of gene expression dynamics in developing mouse embryonic stem cells

Investigations of transcriptional responses during developmental transitions typically use time courses with intervals that are not commensurate with the timescales of known biological processes. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We evaluated coding and noncoding expression dynamics at high temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report the effects of increased temporal resolution on the characterization of the underlying molecular processes. We present a refined resolution of global transcriptional alterations, including regulatory network interactions, coding and noncoding gene expression changes as well as alternative splicing events, many of which cannot be resolved by existing coarse developmental time-{-}-courses. We describe novel short lived and cycling patterns of gene expression and temporally dissect ordered gene expression at bidirectional promoters and responses to transcription factors. These findings demonstrate the importance of temporal resolution for understanding gene interactions in mammalian systems.\n\nLinks to dataData has been deposited into GEO: The Reviewer access link is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=cnglummejbkltyj@acc=GSE75028

systems biology↗