Biology subjects

Curd, E. E.

Publications and source records attributed to Curd, E. E..

6 recordsLinked to original sources

bioRxiv2026

Giant spider neurons uncover a myelin-derived waste-internalizing canal system that fails in neurodegeneration

The underlying causes for Alzheimer disease are presumed to lie in failed waste removal from the brain. However, the mechanisms by which waste is cleared from neurons, and how this system fails in neurodegeneration are poorly understood. A novel glial-canal-hypothesis postulates that myelin-forming macroglia give rise to waste internalizing canals that project into neuronal somata and remove cellular debris in an aquaporin4-dependent manner. We postulate that abnormal swelling of the aquaporin4-expressing glial cells leads to spongiform abnormalities, gradual depletion, and death of associated neurons. Due to the novelty of this postulation little is known about the cellular architecture of this canal system that was first discovered in giant neurons of the wandering spider Cupiennius salei. Here we have utilized histological, ultrastructural and immunohistochemical methods to describe the structural foundation of this glial canal system in giant spider neurons in which waste-internalizing canals and associated structures are clearly visible. Sequencing the spider genome, we show compelling homologies of key proteins that are implicated in neurodegeneration between phylogenetically distant species. Based on this work, we provide a testable functional hypothesis regarding waste removal from neuronal somata and how this system fails in neurodegeneration. We highlight structural similarities of this system in rodent and human brain. Supported by the findings presented here we postulate that (i) neurodegeneration in C. salei may be caused by hypertrophic swelling of myelin-forming waste-internalizing macroglia, and (ii) that a similar canal system, although structurally modified, is likely highly conserved in the mammalian brain.

neuroscience↗

bioRxiv2023

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa to meet taxonomic classification goals then are currently curated by professional staff. Thus, there is a growing need for an easy to implement tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire seed sequences containing a user-defined primer set. Next these seeds are used to iteratively blast search seed sequences against a local NCBI formatted database using a taxonomic rank based stratified random sampling approach (blast_seeds()) that results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer specific reference barcode sequences from NCBI. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, and fungal ITS locus than CRABS, METACURATOR, RESCRIPt, and ECOPCR reference databases. We then further demonstrate the utility of rCRUX by generating 16 reference databases for metabarcoding loci that lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

bioinformatics↗

bioRxiv2020

A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation

Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. We offer a way to use environmental DNA, community science and remote sensing together as methods to reduce the discrepancy between the magnitude of change and historical approaches to measure it. Taking advantages of modern ecological models, we integrate environmental DNA and Earth observations to evaluate regional biodiversity patterns for a snapshot of time, and provide critical community-level characterization. We collected 278 samples in Spring 2017 from coastal, shrub and lowland forest sites in California, a large-scale biodiversity hotspot. We applied gradient forest to model 915 family occurrences and community composition together with environmental variables and multi-scalar habitat classifications to produce a statewide biodiversity-based map. 16,118 taxonomic entries recovered were associated with environmental variables to test their predictive strength on alpha, beta, and zeta diversity. Local habitat classification was diagnostic of community composition, illuminating a characteristic of biodiversity hotspots. Using gradient forest models, environmental variables predicted 35% of the variance in eDNA patterns at the family level, with elevation, sand percentage, and greenness (NDVI32) as the top predictors. This predictive power was higher than we found in published literature at global scale. In addition to this indication of substantial environmental filtering, we also found a positive relationship between environmentally predicted families and their numbers of biotic interactions. In aggregate, these analyses showed that strong eDNA community-environment correlation is a general characteristic of temperate ecosystems, and may explain why communities easily destabilize under disturbances. Our study provides the first example of integrating citizen science based eDNA with biodiversity mapping across the tree of life, with promises to produce large scale, high resolution assessments that promote a more comprehensive and predictive understanding of the factors that influence biodiversity and enhance its maintenance.

ecology↗

bioRxiv2019

Beach environmental DNA fills gaps in photographic biomonitoring to track spatiotemporal community turnover across 82 phyla

AbstractEnvironmental DNA (eDNA) metabarcoding is emerging as a biomonitoring tool available to the citizen science community that promises to augment or replace photographic observation. However, eDNA results and photographic observations have rarely been compared to document their individual or combined power. Here, we use eDNA multilocus metabarcoding, a method deployed by the CALeDNA Program, to inventory and evaluate biodiversity variation along the Pillar Point headland near Half Moon Bay, California. We describe variation in presence of 13,000 taxa spanning 82 phyla, analyze spatiotemporal patterns of beta diversity, and identify metacommunities. Inventory and measures of turnover across space and time from eDNA analysis are compared to the same measures from Global Biodiversity Information Facility (GBIF) data, which contain information largely contributed by iNaturalist photographic observations. We find eDNA depicts local signals with high seasonal turnover, especially in prokaryotes. We find a diverse community dense with pathogens and parasites in the embayment, and a State Marine Conservation Area (SMCA) with lower species richness than the rest of the beach peninsula, but with beta diversity signals showing resemblance to adjacent unprotected tidepools. The SMCA differs in observation density, with higher density of protozoans, and animals in Ascidiacea, Echinoidea, and Polycladida. Local contributions to beta diversity are elevated in a section of East-facing beach. GBIF observations are mostly from outside the SMCA, limiting some spatial comparisons. However, our findings suggest eDNA samples can link the SMCA sites to sites with better GBIF inventory, which may be useful for imputing species from one site given observations from another. Results additionally support >3800 largely novel biological interactions. This research, and accompanying interactive website support eDNA as a gap-filling tool to measure biodiversity that is available to community and citizen scientists.

ecology↗

bioRxiv2019

The California Environmental DNA \"CALeDNA\" Program

Global change is leading to habitat shifts that threaten species persistence throughout Californias unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program, a community science initiative monitoring Californias biodiversity through environmental DNA (eDNA)--DNA shed from organisms through fur, mucus, spores, pollen, etc. Community scientists collect soil and sediment samples, then researchers analyze the eDNA in the samples and share results with the public. The results are catalogues of thousands of organisms per sample, ranging from microbes to mammals. The CALeDNA website presents biodiversity inventories in a platform designed for the public and researchers alike, as well as user-friendly analysis tools and educational modules. Here, we present CALeDNA as a scalable community science framework that can harmonize with future biodiversity research and education initiatives.

scientific communication and education↗

bioRxiv2018

Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality.\n\n2. We present the modular metabarcode sequence toolkit Anacapa (https://github.com/limey-bean/Anacapa/), which addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data A novel aspect of Anacapa is our database building module, Creating Reference libraries Using eXisting tools (CRUX), which generates comprehensive reference databases for specific user-defined metabarcode loci. The Quality Control and Dereplication module sorts and processes multiple metabarcode loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. Followed by amplicon sequence variants (ASVs) detection using DADA2. The Anacapa Classifier module aligns these ASVs to CRUX-generated reference databases using Bowtie2. Taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an R package, ranacapa, for automated results exploration through standard biodiversity statistical analysis.\n\n3. We performed a series of benchmarking tests to verify that the Anacapa Toolkit generates comprehensive reference databases that capture wide taxonomic diversity and that it can assign high-quality taxonomy to both MiSeq-length and Hi-Seq length sequence data. We demonstrate the value of the Anacapa Toolkit to assigning taxonomy to eDNA sequences from seawater samples from southern California including capability of this tool kit to process multilocus metabarcoding data.\n\n4. The Anacapa Toolkit broadens the exploration of eDNA and assists in biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining all read types, and expanding non-traditional eDNA targets. Anacapa software and source code are open and available in a virtual container to ease installation.

bioinformatics↗