Biology subjects

Saenz, V.

Publications and source records attributed to Saenz, V..

3 recordsLinked to original sources

bioRxiv2026

Comparing morphological and molecular methods for stream macroinvertebrate biodiversity assessment across seven watersheds in the southern United States

Freshwater biodiversity is declining at alarming rates globally, yet our capacity to monitor it depends heavily on the methods used for biodiversity assessment. Stream benthic macroinvertebrates are widely used as bioindicators, but traditional morphological identification is labor-intensive and limited by taxonomic expertise, while DNA metabarcoding offers a promising but incompletely evaluated alternative. Here, we compared biodiversity patterns detected by four macroinvertebrate sampling and identification methods (morphological identification of benthic samples, morphological identification of combined benthic and stream-edge samples, eDNA metabarcoding of bulk benthic samples, and eDNA metabarcoding of streamwater) across 62 sites in seven watersheds spanning the southern continental United States. We compared methods across three facets of biodiversity (gamma diversity, alpha diversity, and taxonomic composition) and three taxonomic levels (family, genus, and species). We found that which method detected more taxa shifted with taxonomic resolution: morphological methods detected more families and genera, while metabarcoding methods detected more species. Bulk benthic metabarcoding detected more families and genera than water eDNA metabarcoding, consistent with the "watered-down biodiversity" effect of DNA dilution in water samples, but the two metabarcoding methods did not differ significantly in species richness. All four methods detected largely distinct suites of taxa, with metabarcoding methods yielding more unique taxa than morphological methods. Notably, taxa uniquely detected by water eDNA were dominated by soft-bodied organisms (oligochaetes, leeches, earthworms) and water-column-associated taxa, while benthic eDNA uniquely detected hard-bodied EPT insects. We attribute this pattern to fundamental differences in eDNA shedding, transport, and deposition dynamics across organism types. These results demonstrate that no single method captures a complete picture of stream macroinvertebrate biodiversity, and that method choice should be guided by the taxonomic resolution and community components most relevant to the goals of the bioassessment program.

ecology↗

bioRxiv2025

Erasable Synthetic Serum Markers

Gene expression in the brain is typically evaluated using invasive biopsy or postmortem histology. Serum markers provide an alternative way to monitor the brain, but relatively few such markers exist. Additionally, the origin of serum markers often cannot be localized to a specific cell population, and monitoring dynamic changes in their gene expression is compromised by the same factor that makes the markers detectable - long serum half-life. Here we propose a paradigm to improve the sensitivity of serum marker measurement by modifying the markers in vivo, called erasable serum markers, or ESM. As a proof of concept, we use a well-controlled system with known half-life and tunable serum levels. This system, released markers of activity, or RMAs enable measurement of transgene expression in the brain through a simple blood test. RMAs are stable in blood, with a half-life of >100 h and can detect expression from as few as 12 neurons in mice. However, their long serum half-life also generates long-lasting background signals when RMA are used to track temporal changes in gene expression. By engineering on-demand erasable RMAs and injecting an intravenous targeted protease, we reduced RMA background signal by more than an order of magnitude without compromising the detection sensitivity. Similarly to previous RMA iteration, our approach showed a 65,000-fold increase in their signal over the baseline when expressed in a single brain region. Furthermore, we demonstrated that this erasable RMA system improves the dynamic range of detection for low-level promoter activity that is driven by physiological levels of c-Fos.

bioengineering↗

bioRxiv2021

Host Species is Linked to Pathogen Genotype for the Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis)

Host-pathogen specificity can arise from certain selective environments mediated by both the host and pathogen. Therefore, understanding the degree to which host species identity is correlated with pathogen genotype can help reveal historical host-pathogen dynamics. One animal disease of particular concern is chytridiomycosis, typically caused by the global panzootic lineage of the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd), termed the Bd-GPL. This pathogen lineage has caused devastating declines in amphibian communities around the world. However, the origin of Bd-GPL and the fine-scale transmission dynamics of this lineage have remained a mystery. This is especially the case in North America where Bd-GPL is widespread, but disease outbreaks occur sporadically. Herein, we use Bd genetic data collected throughout the United States from amphibian skin swab and cultured isolate samples to investigate Bd genetic patterns. We highlight two case studies in Pennsylvania and Nevada where Bd-GPL genotypes are strongly correlated with host species identity. Specifically, in some localities bullfrogs (Rana catesbeiana) are infected with Bd-GPL lineages that are distinct from those infecting other sympatric amphibian species. Overall, we reveal a previously unknown association of Bd genotype with host species and identify the eastern United States as a Bd diversity hotspot and potential ancestral population for Bd-GPL.

molecular biology↗