Biology subjects

Ryan, J. P.

Publications and source records attributed to Ryan, J. P..

4 recordsLinked to original sources

bioRxiv2023

Long-distance communication can enable collective migration in a dynamic seascape

Social information is predicted to enhance migratory performance, but the relative benefits of social information in the long-range movements of marine megafauna are unknown. In particular, whether and how migrants use nonlocal information gained through social communication at the extreme spatial scale of oceanic ecosystems remains unclear. Here we combine long-term acoustic recordings of foraging and migratory blue whales, oceanographic and prey data, and individual-based modeling to discern the cues underlying timing of blue whales breeding migration in the Northeast Pacific. We find that individual whales rely on both personal and social sources of information about forage availability in deciding when to depart from their vast and dynamic foraging habitat and initiate breeding migration. Empirical patterns of migratory phenology can only be reproduced by models in which individuals use long-distance social information about conspecifics behavioral state, which is known to be encoded in the patterning of their widely-propagating songs. Further, social communication improves pre-migration seasonal foraging performance by over 60% relative to asocial movement mechanisms. Our results suggest that long-range communication enhances the perceptual ranges of migrating whales beyond that of any individual, resulting in increased foraging performance. These findings indicate the value of nonlocal social information in an oceanic migrant and highlight the importance of long-distance acoustic communication in the collective migration of wide-ranging marine megafauna.

ecology↗

bioRxiv2023

Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom

In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis, this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcriptional characterization of 52 near-weekly phytoplankton net-tow samples collected at a bloom hotspot in Monterey Bay, California, we identified active transcription of known DA biosynthesis (dab) genes from the three identified toxigenic species, including P. australis as the primary origin of toxicity. Elevated expression of silicon transporters (sit1) during the bloom supports the previously hypothesized role of dissolved silica (Si) exhaustion in contributing to bloom physiology and toxicity. We find that co-expression of the dabA and sit1 genes serves as a robust predictor of DA one week in advance, potentially enabling the forecasting of DA-producing HABs. We additionally present evidence that low levels of iron could have co-limited the diatom population along with low Si. Iron limitation represents a previously unrecognized driver of both toxin production and ecological success of the low iron adapted Pseudo-nitzschia genus during the 2015 bloom, and increasing pervasiveness of iron limitation may fuel the escalating magnitude and frequency of toxic Pseudo-nitzschia blooms globally. Our results advance understanding of bloom physiology underlying toxin production, bloom prediction, and the impact of global change on toxic blooms. SignificancePseudo-nitzschia diatoms form oceanic harmful algal blooms that threaten human health through production of the neurotoxin domoic acid (DA). DA biosynthetic gene expression is hypothesized to control DA production in the environment, yet what regulates expression of these genes is yet to be discovered. In this study, we uncovered expression of DA biosynthesis genes by multiple toxigenic Pseudo-nitzschia species during an economically impactful bloom along the North American West Coast, and identified genes that predict DA in advance of its production. We discovered that iron and silica co-limitation restrained the bloom and likely promoted toxin production. This work suggests that increasing iron limitation due to global change may play a previously unrecognized role in driving bloom frequency and toxicity.

ecology↗

bioRxiv2023

High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones

Ocean microbes are the foundation of marine food webs, regulating carbon cycling and ecosystem dynamics. How they proliferate, die, move, and interact is regulated by physical, chemical, and biological factors that are dynamic and challenging to quantify in the natural environment. A significant limitation in many marine field studies is the inability to continuously sample the ever-changing ocean environment over space and time. In this study, we integrated spatiotemporal and multi-omic sample collection in an intensive sampling effort of phytoplankton ecology in Monterey Bay, California during the spring of 2021. Sampling methods coupled: (1) manual shipboard CTD sampling, (2) autonomous sampling using a Long-Range Autonomous Underwater Vehicle (LRAUV) equipped with an Environmental Sampling Processor (ESP), and (3) high-resolution physical measurements by an autonomous vertical profiler (Wirewalker). Sampling occurred as upwelling waned alongside declining domoic acid (DA) and low abundances of toxigenic Pseudo-nitzschia. Conditions needed to spark a widespread and toxic Pseudo-nitzschia bloom were absent, yet low-level DA was driven by similar mechanisms to those causing elevated DA. Three DA biosynthetic intermediate molecules were reported in the environment for the first time. Both shipboard and ESP sampling approaches identified DA biosynthetic gene expression at frontal zones. DA and expression of dabA, the gene encoding the first committed step of DA biosynthesis, were higher in association with recently upwelled water that supplied nutrients for growth and DA biosynthesis. Detection of subtle variations in dab gene expression in response to environmental variation provide a window into the ecological dynamics underpinning major toxic events. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/562961v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1c1f554org.highwire.dtl.DTLVardef@d16b02org.highwire.dtl.DTLVardef@c856e1org.highwire.dtl.DTLVardef@bfd248_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Characterizing Adeno-Associated Virus Capsids with both Denaturing and Intact Analysis Methods

Adeno-associated virus (AAV) capsids are among the leading gene delivery platforms used to treat a vast array of human diseases and conditions. AAVs exist in a variety of serotypes due to differences in viral protein (VP) sequences, with distinct serotypes targeting specific cells and tissues. As the utility of AAVs in gene therapy increases, ensuring their specific composition is imperative for correct targeting and gene delivery. From a quality control perspective, current analytical tools are limited in their selectivity for viral protein (VP) subunits due to their sequence similiaries, instrumental difficulties in assessing the large molecular weights of intact capsids, and the uncertainity in distinguishing empty and filled capsids. To address these challenges, we combine two distinct analytical workflows that assess the intact capsids and VP subunits separately. First, charge detection-mass spectrometry (CD-MS) was applied for characterization of the intact capsids and then liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations were used for capsid denaturing measurements. This multi-method combination was applied to 3 AAV serotypes (AAV2, AAV6, and AAV8) to evaluate their intact empty and filled capsid ratios and then examine the distinct VP sequences and modifications present.

biochemistry↗