Biology subjects

Kirk, D.

Publications and source records attributed to Kirk, D..

7 recordsLinked to original sources

bioRxiv2026

DNA Sequence-Programmed Protein Coronas Determine Intracellular Fate and Proteostatic Stress of Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) show promise for optical biosensing, imaging, and drug delivery, but turning them into safe, precision nanomedicine tools requires understanding how nanotube surface chemistry dictates recognition and processing by cells. Like other nanomaterials, carbon nanotubes acquire a biomolecular corona on contact with biological fluids, and corona identity is increasingly recognized as central to sensor performance and drug delivery efficacy. However, whether corona identity also governs the intracellular fate of carbon nanotubes remains largely unknown. Here, we show that the single-stranded DNA wrapping of (6,5)-enriched single-walled carbon nanotubes reprograms their protein corona, intracellular trafficking, and macrophage response. By profiling (AT)15, (GT)15, and (CT)15 wrapped SWCNTs, we show that the wrapping sequence programs both the protein corona and the resulting proteostatic stress on macrophages. Photoluminescence imaging and confocal Raman measurements reported that (AT)15 is internalized the most yet leaves the proteome and nanotube structure largely undisturbed, whereas (CT)15, taken up the least, undergoes the most aggressive intracellular degradation and drives the highest oxidative and proteostatic stress. Corona proteomics indicated that all three tested nanotubes form coronas with distinct functional identities that are responsible for divergent intracellular routes. Time-resolved intracellular proteomics combined with functional assays resolved how the host cell reorganizes its biomolecular complexity over time, including oxidative outputs, aside from a sequence-independent core response involving particle engagement, phagosomal sorting, and lysosomal processing. These findings provide mechanistic insight into nanomaterial-cell interactions and the wrapping sequence as a tunable, nucleotide-level design handle for controlling the intracellular fate of carbon nanomaterials, with potential implications for safe and effective nanomedicine platforms.

bioengineering↗

bioRxiv2025

Early warning signals do not predict a warming-induced experimental epidemic

Climate change can impact the rates at which parasites are transmitted between hosts, ultimately determining if and when an epidemic will emerge. As such, our ability to predict climate-mediated epidemic emergence will become increasingly important in our efforts to prepare for and mitigate the effects of disease outbreaks on ecological systems and human health. Theory suggests that statistical signatures termed "early warning signals" (EWS), can function as predictors of disease emergence. Here, we analyze experimental and simulated time series of disease spread within populations of the model disease system Daphnia magna-Ordospora colligata for EWS of epidemic emergence. In this system, low temperatures prevent disease emergence, while sufficiently high temperatures force the system through a critical transition to an epidemic state. We found that EWS of epidemic emergence were nearly as likely to be detected in populations maintained at a sub-epidemic temperature as they were to be detected in populations subjected to a warming treatment that induced epidemic spread. Our findings suggest that the detection of false positives may limit the reliability of EWS as predictors of climate-mediated epidemic emergence.

ecology↗

bioRxiv2024

Addition of Soil Protists Enhances Performance of Agrochemical Seed Treatments

Chemicals are an integral part of modern agriculture, and are applied through a variety of methods. Some agrochemicals applied for crop protection function by absorption through the root before translocation to the rest of the plant. To be absorbed by the root, the agrochemical must first be transported through the soil, often by water. Some agrochemicals suffer from poor water-based soil transmission due to their chemical properties, limiting their application as a traditional seed treatment. Two such agrochemicals are chlorantraniliprole and spinosad. Soil protists are an important component of the soil microbial community. Certain soil protists have been previously shown to facilitate transport and targeted delivery of suspended particles and cells through soil and microfluidic devices. We provide practical evidence that a soil protist, Colpoda sp., when co-inoculated with an agrochemical seed treatment, can substantially and robustly reduce subsequent pest feeding damage compared with the agrochemical alone. Using maize (Zea mays L.) and fall armyworm, Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera: Noctuidae), in a plant damage assay, we directly compare pest feeding damage and mortality in plants that received no additional treatment, only protists, only agrochemical, and co-inoculation of agrochemical with protists. We discover for both agrochemicals tested, the co-inoculation of protists with the agrochemical increases protection in leaves when the efficacy of the agrochemical alone declines. Protist amendment is a simple, natural, inexpensive, chemical-free, soil-based transport enhancer that thus may be widely useful in a variety of contexts including more sustainable and cost-effective integrated pest management. ImportancePest resistance, regulatory pressure, and environmental concerns are limiting many classes of pesticides which can be effectively used to protect valuable crops from pests. Other classes of pesticides, however, are limited by physical characteristics - water solubility or octane-water partition coefficient (KOW) fall outside the limit for an effective seed coating, or the per-unit cost is high enough to discourage broad application. Here, we provide data which supports the co-inoculation of a high value, low solubility, high KOW pesticides with a naturally-occurring soil protist as a seed treatment can enhance crop protection relative to the pesticide alone. This co-formulation reduced feeding damage by up to 30% compared with the pesticide alone. Co-inoculation of crop-protecting agrochemicals with natural soil protists may be employed as a more sustainable agriculture biotechnology, enabling the use of classes of agrochemicals which may not otherwise show sufficient performance for use as a seed treatment.

microbiology↗

bioRxiv2023

Abnormal weather drives disease outbreaks in wild and agricultural plants

Predicting effects of climate change on plant disease is critical for protecting ecosystems and food production. Climate change could exacerbate plant disease because parasites may be quicker to acclimate and adapt to novel climatic conditions than their hosts due to their smaller body sizes and faster generation times. Here we show how disease pressure responds to the anomalous weather that will increasingly occur with climate change by compiling a global database (5380 plant populations; 437 unique plant-disease combinations; 2,858,795 individual plant-disease samples) of disease incidence in both agricultural and wild plant systems. Because wild plant populations are assumed to be adapted to local climates, we hypothesized that large deviations from historical conditions would increase disease incidence. By contrast, since agricultural plants have been transported globally, we did not expect the historical climate where they are currently grown to be as predictive of disease incidence. Supporting these hypotheses, we found that disease outbreaks tended to occur during periods of warm temperatures in agricultural and cool-climate wild plant systems, but also occurred in warm-adapted wild (but not agricultural) plant systems experiencing anomalously cool weather. Outbreaks were additionally associated with higher rainfall in wild systems, especially those with historically wet climates. Our results suggest that historical climate affects susceptibility to disease for wild plant-disease systems, while warming drives risks for agricultural plant disease outbreaks regardless of historical climate.

ecology↗

bioRxiv2022

Temperature impacts on dengue incidence are nonlinear and mediated by climatic and socioeconomic factors

Temperature can influence mosquito-borne diseases like dengue. These effects are expected to vary geographically and over time in both magnitude and direction and may interact with other environmental variables, making it difficult to anticipate changes in response to climate change. Here, we investigate global variation in temperature-dengue relationship by analyzing published correlations between temperature and dengue and matching them with remotely sensed climatic and socioeconomic data. We found that the correlation between temperature and dengue was most positive at intermediate (near 24{degrees}C) temperatures, as predicted from the thermal biology of the mosquito and virus. Positive temperature-dengue associations were strongest when temperature variation and population density were high and decreased with infection burden and rainfall mean and variation, suggesting alternative limiting factors on transmission. Our results show that while climate effects on diseases are context-dependent they are also predictable from the thermal biology of transmission and its environmental and social mediators.

ecology↗

bioRxiv2020

Temperature effects on individual-level parasitism translate into predictable effects on parasitism in populations

Parasitism is expected to change in a warmer future, but whether warming leads to substantial increases in parasitism remains unclear. Understanding how warming effects on parasitism in individual hosts (e.g., parasite load) translate to effects on population-level parasitism (e.g., prevalence, R0) remains a major knowledge gap. We analyzed the temperature dependence of parasitism at both host and population levels in thirteen empirical vector-borne host-parasite systems and found a strong, significant positive correlation between the thermal optima of individual- and population-level parasitism. We also found a significant, positive correlation in eleven environmentally-transmitted parasite systems, though several of these systems exhibited thermal optima >5{o}C apart between individual and population levels. Similarly, parasitism thermal optima were close to host performance thermal optima in vector-borne systems but not in environmentally-transmitted systems. We then adapted and simulated simple models for both transmission modes and found a similar pattern to the empirical systems: thermal optima in vector-borne systems were more strongly correlated across scales compared to environmentally-transmitted systems. Generally, our results suggest that information on the temperature-dependence, and specifically the thermal optimum, at either the individual- or population-level should provide a useful--though not quantitatively exact--baseline for predicting temperature dependence at the other level, especially in vector-borne parasite systems. Environmentally-transmitted parasitism may operate by a different set of rules, in which temperature-dependence is decoupled in some systems, requiring the need for trait-based studies of temperature-dependence at individual and population levels.

ecology↗

bioRxiv2019

Four QTL underlie resistance to a microsporidian parasite that may drive genome evolution in its Daphnia host

Despite its pivotal role in evolutionary and ecological processes the genetic architecture underlying host-parasite interactions remains understudied. Here we use a quantitative trait loci approach to identify regions in the Daphnia magna genome that provide resistance against its microsporidium parasite Ordospora colligata. The probability that Daphnia became infected was affected by a single locus and an interaction between two additional loci. A fourth locus influenced the number of spores that grew within the host. Comparing our findings to previously published genetic work on Daphnia magna revealed that two of these loci may be the same as detected for another microsporidium parasite, suggesting a general immune response to this group of pathogens. More importantly, this comparison revealed that two regions previously identified to be under selection coincided with parasite resistance loci, highlighting the pivotal role parasites may play in shaping the host genome.

genetics↗