Biology subjects

Baker, R. P.

Publications and source records attributed to Baker, R. P..

6 recordsLinked to original sources

bioRxiv2025

Fungal proliferation before and after the Cretaceous-Paleogene mass extinction in North America

Palynological evidence of post-catastrophe fungal proliferation after global calamities has been found for the Permian-Triassic and Cretaceous-Paleogene (K/Pg) extinction events. However, unlike the globally documented post-Permian fungal bloom, evidence of a post-Cretaceous event has previously been limited to a single site in New Zealand. Our analysis of a K/Pg boundary section from the Denver Basin in Colorado revealed a fungal proliferative spike occurring immediately after the Chicxulub impact. The discovery of a post-impact fungal bloom in North America corroborates the New Zealand finding and supports the interpretation that this was a global phenomenon. We also identified a prolonged interval of elevated fungal abundance in the Late Cretaceous, dating to approximately 30,000-10,000 years before the impact, temporally correlated to a period of climatic cooling at the site and intriguingly coincident with the Poladpur phase of the Deccan Traps. Taken together with reports of fungal expansion following prior global calamities, these findings indicate that fungi can often flourish in the aftermath of ecosystem-level collapse. Given the capacity of fungi to cause disease in both plants and animals, the occurrence of fungal proliferative events has major potential implications for the recovery of surviving species after global cataclysms. Significance StatementFungal proliferation evidenced by spikes in fungal abundance in geologic samples can signify major ecosystem disruptions. Such spikes are well documented globally for the Permian-Triassic extinction but for the Cretaceous-Paleogene extinction have been reported previously only in New Zealand. Here, we describe a North American fungal bloom that occurred immediately after the Chicxulub impact, as well as an earlier fungal spike in the Late Cretaceous that coincided with a cooling event hypothesized to have been driven by Deccan volcanism. Identification of this pre-impact fungal proliferative episode provides additional support for the uranium-lead-based model of Deccan eruptive rates, which places the high-volume Poladpur pulse tens of thousands of years before the bolide impact.

microbiology↗

bioRxiv2024

Cell wall melanin impedes growth of the Cryptococcus neoformans polysaccharide capsule by sequestering calcium

Cryptococcus neoformans has emerged as a frontrunner among deadly fungal pathogens and is particularly life-threatening for many HIV-infected individuals with compromised immunity. Multiple virulence factors contribute to the growth and survival of C. neoformans within the human host, the two most prominent of which are the polysaccharide capsule and melanin. As both of these features are associated with the cell wall, we were interested to explore possible cooperative or competitive interactions between these two virulence factors. Whereas capsule thickness had no effect on the rate at which cells became melanized, build-up of the melanin pigment layer resulted in a concomitant loss of polysaccharide material, leaving melanized cells with significantly thinner capsules than their non-melanized counterparts. When melanin was provided exogenously to cells in a transwell culture system we observed a similar inhibition of capsule growth and maintenance. Our results show that melanin sequesters calcium thereby limiting its availability to form divalent bridges between polysaccharide subunits required for outer capsule assembly. The decreased ability of melanized cells to incorporate exported polysaccharide into the growing capsule correlated with the amount of shed polysaccharide, which could have profound negative impacts on the host immune response. Significance StatementCryptococcus neoformans is an opportunistic fungal pathogen that presents a significant health risk for immunocompromised individuals. We report an interaction between the two major cryptococcal virulence factors, the polysaccharide capsule and melanin. Melanin impacted the growth and maintenance of the polysaccharide capsule, resulting in loss of capsular material during melanization. Our results suggest that melanin can act as a sink for calcium, thereby limiting its availability to form ionic bridges between polysaccharide chains on the growing surface of the outer capsule. As polysaccharide is continuously exported to support capsule growth, failure of melanized cells to incorporate this material results in a higher concentration of shed polysaccharide in the extracellular milieu, which is expected to interfere with host immunity.

microbiology↗

bioRxiv2021

Cryptococcus neoformans melanization incorporates multiple catecholamines to produce polytypic melanin

Melanin is a major virulence factor in pathogenic fungi that enhances the ability of fungal cells to resist immune clearance. Cryptococcus neoformans is an important human pathogenic fungus that synthesizes melanin from exogenous tissue catecholamine precursors during infection, but the type of melanin made in cryptococcal meningoencephalitis is unknown. We analyzed the efficacy of various catecholamines found in brain tissue in supporting melanization using animal brain tissue and synthetic catecholamine mixtures reflecting brain tissue proportions. Solid-state NMR spectra of the melanin pigment produced from such mixtures yielded more melanin than expected if only the preferred constituent dopamine had been incorporated, suggesting uptake of additional catecholamines. Probing the biosynthesis of melanin using radiolabeled catecholamines revealed that C. neoformans melanization simultaneously incorporated more than one catecholamine, implying that the pigment was polytypic in nature. Nonetheless, melanin derived from individual or mixed catecholamines had comparable ability to protect C. neoformans against ultraviolet light and oxidants. Our results indicate that melanin produced during infection differs depending on the catecholamine composition of tissue and that melanin pigment synthesized in vivo is likely to accrue from the polymerization of a mixture of precursors. From a practical standpoint our results strongly suggest that using dopamine as a polymerization precursor is capable of producing melanin pigment comparable to that produced during infection. On a more fundamental level our findings uncover additional structural complexity for natural cryptococcal melanin by demonstrating that pigment produced during human infection is likely to be composed of polymerized moieties derived from chemically different precursors.

microbiology↗

bioRxiv2018

Automated High-Throughput Light-Sheet Fluorescence Microscopy of Larval Zebrafish

AO_SCPCAPBSTRACTC_SCPCAPLight sheet fluorescence microscopy enables fast, minimally phototoxic, three-dimensional imaging of live specimens, but is currently limited by low throughput and tedious sample preparation. Here, we describe an automated high-throughput light sheet fluorescence microscope in which specimens are positioned by and imaged within a fluidic system integrated with the sheet excitation and detection optics. We demonstrate the ability of the instrument to rapidly examine live specimens with minimal manual intervention by imaging fluorescent neutrophils over a nearly 0.3 mm3 volume in dozens of larval zebrafish. In addition to revealing considerable inter-individual variability in neutrophil number, known previously from labor-intensive methods, three-dimensional imaging allows assessment of the correlation between the bulk measure of total cellular fluorescence and the spatially resolved measure of actual neutrophil number per animal. We suggest that our simple experimental design should considerably expand the scope and impact of light sheet imaging in the life sciences.

bioengineering↗

bioRxiv2017

The Vibrio cholerae Type VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria

Host-associated microbiota help defend against bacterial pathogens; the mechanisms that pathogens possess to overcome this defense, however, remain largely unknown. We developed a zebrafish model and used live imaging to directly study how the human pathogen Vibrio cholerae invades the intestine. The gut microbiota of fish mono-colonized by commensal strain Aeromonas veronii was displaced by V. cholerae expressing its Type VI Secretion System (T6SS), a syringe-like apparatus that deploys effector proteins into target cells. Surprisingly, displacement was independent of T6SS-mediated killing of Aeromonas, driven instead by T6SS-induced enhancement of zebrafish intestinal movements that led to expulsion of the resident commensal by the host. Deleting an actin crosslinking domain from the T6SS apparatus returned intestinal motility to normal and thwarted expulsion, without weakening V. cholerae's ability to kill Aeromonas in vitro. Our finding that bacteria can manipulate host physiology to influence inter-microbial competition has implications for both pathogenesis and microbiome engineering.

microbiology↗

bioRxiv2017

Image velocimetry and spectral analysis enable quantitative characterization of larval zebrafish gut motility

Summary StatementWe present a new image analysis technique using image velocimetry and spectral analysis that returns quantitative measures of gut contraction strength, frequency, and wave speed that can be used to study gut motility and other cellular movements.\n\nAbstractNormal gut function requires rhythmic and coordinated movements that are affected by developmental processes, physical and chemical stimuli, and many debilitating diseases. The imaging and characterization of gut motility, especially regarding periodic, propagative contractions driving material transport, are therefore critical goals. Whereas previous image analysis approaches have successfully extracted properties related to temporal frequency of motility modes, robust measures of contraction magnitude remain elusive. We developed a new image analysis method based on image velocimetry and spectral analysis that reveals temporal characteristics such as frequency and wave propagation speed, while also providing quantitative measures of the amplitude of gut motions. We validate this approach using several challenges to larval zebrafish, imaged with differential interference contrast microscopy. Both acetylcholine exposure and feeding increase frequency and amplitude of motility. Larvae lacking enteric nervous system gut innervation show the same average motility frequency, but reduced and less variable amplitude compared to wild-types. Our image analysis approach enables insights into gut dynamics in a wide variety of developmental and physiological contexts and can also be extended to analyze other types of cell movements.

developmental biology↗