UC Santa Cruz

Microplastic (particles <5 mm) is an emerging environmental concern that threatens aquatic ecosystems worldwide. While extensive research has documented the ubiquity of microplastic in marine and coastal environments and its assimilation by organisms at all trophic levels, comparatively little is known about microplastic occurrence in rural riverine ecosystems. Even less information exists for salmon-bearing streams, where microplastic pollution may hinder salmonid conservation and recovery efforts. We examined the presence and concentration of microplastic in Scott Creek, a small coastal California (USA) watershed with minimal urban development. Our study quantified suspended microplastic in surface waters and in the gastrointestinal (GI) tracts of juvenile Steelhead Trout (Oncorhynchus mykiss). Microplastic was detected in 93 % of water samples, indicating that Scott Creek routinely transports and cycles microplastic. Concentrations were higher in late summer than in spring, although monthly spatial patterns were largely consistent among sites. In juvenile steelhead, 60.6 % of GI tracts contained one or more types of microplastic. For both surface waters and juvenile steelhead, microplastic was predominantly small (<5 mm) dark blue, black, and transparent fiber-type particles, with fragments, shards and foams encountered less frequently. These findings suggest that fish ingest microplastic at low frequencies, or that ingested particles may pass rapidly through their digestive systems. This study provides one of the first assessments of microplastic in a minimally urbanized, salmon-bearing watershed. Our results serve as a baseline for evaluating the ecological implications of microplastic pollution in small coastal creeks and its potential to influence native salmonid populations. Data Availability The surface water and steelhead microplastic datasets generated and analyzed during the current study are publicly available via Zenodo (DOI: 10.5281/zenodo.18038857).

Comprehenders in many of the world's languages exhibit a preference or a greater ease in comprehending transitive relative clauses (RCs) when associating the dislocated head with a subject position. Some theories relate this preference to an early prediction that an animate head will serve as a subject. We present a picture selection experiment with eye-tracking investigating the role of such predictions in comprehending transitive RCs in Santiago Laxopa Zapotec, an Oto-Manguean language of southern Mexico where RCs are ambiguous unless they contain a resumptive pronoun. Patterns of offline choices and incremental looking suggest that Santiago Laxopa Zapotec comprehenders avoid forming predictive interpretations of the RC head, and do not take its animacy into account in early processing. Instead, comprehenders exhibit a later, animacy-sensitive bias to interpret the RC-internal co-argument as a subject. Overall, we take this pattern as evidence that a comprehender's structural predictions must be somehow dependent on experience-based tuning, while more universal pressures like similarity-based interference remain fixed. The lingering question for theories of cross-linguistic processing is how much of our predictive mechanism is tunable: do we tune just the distribution of expected structures which directs predictions, or also the practice of deploying predictions itself? We discuss how either of these approaches might explain the pattern we observe in Santiago Laxopa Zapotec, and highlight that an answer to this question will depend on continued investigations across a diverse sample of the world's languages.

This study analyzes how changes in forage species distribution affected Coastal Pelagic Species (CPS) vessel participation and target decisions in the U.S. West Coast fishery over the 2013–2017 period. We develop discrete choice models for the choice of species targeted: Pacific sardine (Sardinops sagax), market squid (Doryteuthis opalescens), Northern anchovy (Engraulis mordax), Chub (Scomber japonicus) and Jack (Trachurus symmetricus) mackerels or other Non-CPS species, and landing port during a specific day. We estimate separate nested logit models by fleet segments, which were defined previously using cluster analysis on vessel attributes such as fished area, average annual revenue, CPS diversification, and degree of reliance on CPS. An environmentally informed species distribution model (SDM) is used as a proxy for expected availability of forage species. We find that harvesters demonstrate flexibility in their fishing strategies in response to environmental and economic conditions. The study suggests that while some decisions are state-dependent, harvesters still have the capacity for adaptation. These insights are crucial for understanding the resilience of fisheries in the face of environmental variability and for informing management strategies to support sustainable fishing into the future.

Biofilm formation underlies the environmental persistence and transmission of Vibrio cholerae, the etiological agent of cholera. The Vibrio polysaccharide (VPS) is the principal structural component of the mature biofilm matrix, yet the enzymatic logic governing its assembly has remained incompletely defined. VPS is synthesized as two closely related polymers that share a tetrasaccharide repeat unit but differ at a single monosaccharide position. Here, we systematically define VPS assembly by integrating targeted gene deletions with liquid chromatography-mass spectrometry profiling of lipid-linked intermediates, and comparative structural modeling of biosynthetic enzymes. Our results establish that VPS is produced through an ordered Wzx/Wzy-dependent pathway. VpsL functions as the initiating phosphoglycosyltransferase, generating bactoprenyl diphosphate-linked glucose. A VpsA/VpsB/VpsK module analogous to the enterobacterial common antigen machinery synthesizes and transfers an N-acetyl-mannosaminuronic acid (ManNAcA)-derived residue, after which VpsJ, which we propose as a new class of epimerase, catalyzes C5 epimerization to generate the rare bacterial sugar L-N-acetyl-gulosaminuronic acid (L-GulNAcA). Additional tailoring reactions mediated by VpsH, a previously unidentified protein with few sequence or structural homologs, and VpsG introduce glycine and acetyl modifications that are dispensable for repeat-unit assembly but influence matrix properties. Subsequently, glycosyltransfer reactions by VpsI and VpsD complete the tetrasaccharide repeat unit, with VpsD exhibiting substrate flexibility that accounts for the formation of both major and minor VPS variants. Downstream, VpsE and VpsF act following repeat-unit assembly, consistent with flippase and polymerase functions, respectively. Together, our findings establish a molecular framework for VPS assembly and deepen our understanding of the mechanisms that drive biofilm formation in Vibrio cholerae.IMPORTANCEBiofilm formation is an integral part of Vibrio cholerae's infection cycle, requiring production of the exopolysaccharide Vibrio polysaccharide (VPS). Together, these findings define the sequential enzymatic steps of VPS biosynthesis. This molecular map of VPS production identifies multiple enzymatic nodes as potential anti-biofilm targets and provides a mechanistic foundation for understanding how V. cholerae modulates biofilm architecture to enhance environmental survival and transmission.

Motivation: Existing pangenome file formats are designed for batch processing. Graphs must be loaded into memory, and alignment files must be read sequentially. Indexed file formats that can be used directly from disk would be more appropriate for interactive applications. Results: We propose GBZ-base and GAF-base - SQLite-backed file formats comparable to GBZ and GAF. GBZ-base supports efficient extraction of local subgraphs, and GAF-base lets us extract all alignments to the subgraph. Additionally, GAF-base is smaller than any other file format for sequence-to-graph alignments. Availability and implementation: From https://github.com/jltsiren/gbz-base and https://crates.io/crates/gbz-base under the MIT license.

A combination of measurements of the properties of Higgs boson interactions with electroweak gauge bosons is presented, using of proton-proton collisions at recorded by the ATLAS detector. Results from vector boson fusion , inclusive , and channels are combined. No evidence of violation is observed, and constrains on the -violating operators in the Standard Model effective field theory framework (SMEFT) are set in the Warsaw basis. The results from the combination improve by over 40% on previous individual limits on and, for the first time, simultaneous constraints on three coefficients , , and are set. These limits are the most stringent constraints to date on the relevant Wilson coefficients in the SMEFT framework with minimum model dependence.

At the base of the Sun’s convective zone, a narrow shear layer called the tachocline separates strong latitudinal differential rotation above from nearly rigid rotation in the radiative zone below. The observed thinness of the tachocline is a long-standing dynamical puzzle because the tachocline should have spread significantly due to inward-burrowing meridional circulation, also called “radiative spreading.” We recently presented the first pair of global simulations to reveal a statistically stationary tachocline confined against radiative spreading by the Maxwell stresses from the large-scale nonaxisymmetric modes of a dynamo, which penetrated into and below the tachocline through a novel magnetic skin effect. In the work presented here, we systematically examine how this “dynamo confinement scenario” works against radiative spreading in a suite of simulations as the governing parameters trend in the direction of the true solar regime. We find that as the stable stratification of the radiative zone is made progressively stronger, the dynamo cycles get longer, the magnetic field consequently penetrates deeper due to the skin effect, and the tachocline becomes more confined. Furthermore, these results have interesting consequences for solar spin-down. In all of our radiatively spreading simulations, the tachocline region spins down due to the burrowing circulation. Below the tachocline, the Maxwell stresses transmit this spin-down further to rigidify the deeper radiative zone. We thus speculate that, in addition to confining the tachocline, the dynamo may provide a pathway to communicate spin-down from the near-surface layers to the deep interior.

We present genome assemblies for two cyprinoid fishes, the tui chub (Siphateles bicolor) and the arroyo chub (Gila orcuttii). These fishes are ecologically important representatives of native fish assemblages in the western United States and are both species of conservation concern. The two species hybridize where introductions bring them into contact, with potentially important ecological and evolutionary implications that have not yet been thoroughly examined from a genomic perspective. We present de novo assemblies for both species, representing the first scaffold-level genomes within their respective genera, which were developed as part of the California Conservation Genomics Project using Pacific Biosciences HiFi and Omni-C data. Our tui chub assembly consists of 258 scaffolds spanning 1,148,084,093 base pairs, has a scaffold N50 of 45.9 mb, a contig N50 of 23.7 mb, and a BUSCO completeness score of 98.1%. Our arroyo chub assembly consists of 179 scaffolds spanning 1,263,410,250 base pairs, has a scaffold N50 of 50.5 mb, a contig N50 of 13.1 mb, and a BUSCO completeness score of 97.8%. A comparative analysis of the two species revealed relatively conserved genomes, with the exception of two inversions at chromosome 20. We annotated a total of 34,090 genes with a BUSCO completeness score of 98.1% for the tui chub, and 28,193 genes with a score of 97.4% for the arroyo chub. These assemblies will be valuable resources for characterizing the species' phylogeographic histories and delineating the role of hybridization in their evolution.

Acmispon is a legume genus that has diversified within the California Floristic Province. Acmispon species live in a variety of habitats, including coastal sage scrub, deserts, grasslands, and woodlands, and form symbiotic associations with nitrogen-fixing bacteria. Here, we report the first chromosome-level assembly of Acmispon strigosus (strigose bird's-foot trefoil or strigose lotus) as part of the California Conservation Genomics Project. Consistent with the reference genome pipelines of the California Conservation Genomics Project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly is 519 Mb in length, with a contig N50 of 22.97 Mb, scaffolded into seven pseudochromosomes. Using the NCBI EGAPx pipeline, we annotated a total of 21,347 genes resulting in a protein Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 91.5%. This is the first genome assembled for Acmispon and among the first genomic resources available for a native California legume. The assembly BUSCO completeness score of 94.8% makes it one of the most complete genomes for the tribe Loteae (Fabaceae). Generating whole-genome sequences will contribute to our general understanding of nitrogen-fixing legume's adaptations to diverse soil and environmental conditions, interactions with nitrogen fixing Bradyrhizobium and Mesorhizobium symbionts, and the degrading effects of pollution-induced nitrogen deposition on the legume-rhizobium symbiosis in California. These data will also help to reconstruct phylogenetic relationships among Acmispon spp., which remain unresolved.