Using surface elevation tables and marker horizons to evaluate resiliency and trajectories of tidal marshes and restoration projects in the Snohomish River estuary

The abundance of tidal wetlands has been increasingly impacted by environmental changes, human alterations and sea-level rise around the world. Elevation and sediment dynamics control tidal wetland vegetation colonization, assemblages, resiliency, and recovery trajectories. Seal level rise and hydromodifications may threaten the resiliency of existing tidal marshes, and impact the recovery trajectories of restoration projects. The Snohomish river delta currently supports the second largest extent of tidal wetlands in the Puget Sound, and has become the focus of what could be the largest cumulative estuary restoration effort in Puget Sound. However, we currently know very little about elevation and sediment dynamics in the Snohomish River estuary and the resiliency of existing vegetated marshes and restoration projects. To address this need, we installed surface elevation tables (SETs) and marker horizons (MHs) in 2013-2014 inside several tidal marsh complexes that represent a gradient of land use histories and recovery trajectories to determine sediment accretion rates and shallow soil processes (e.g., subsidence, compaction, uplift) in the Snohomish River estuary. SETs and MHs were installed in two emergent marshes in the lower estuary that have not been previously diked, inside Ebey Island where dikes failed naturally about 75 years ago, and inside a restoration site that was breached in 1994. Preliminary data from these SETs and MHs indicate that accretion rates range from 4-15 mm per year, and that shallow subsidence is occurring at all sites at a rate of 2-10 mm per year. Although continued long-term monitoring will provide better estimates of elevation and sediment dynamics at these sites and within the Snohomish River estuary, we use these preliminary data to evaluate tidal marsh resiliency and recovery trajectories within the context of sea level rise and restoration in the Snohomish River estuary

Alternative roles for Pseudomonas aeruginosa bacteriocins

Bacteriocins are multi-protein assemblies that bear striking resemblance to bacteriophage (virus) tails. Bacteriocins are an extracellular contractile injection system that kill closely related bacteria by puncturing their cell membrane. Mounting evidence suggests that besides interbacterial competition, bacteriocins also mediate interactions between bacteria and diverse eukaryotic hosts by assembling extracellular hexagonal-bacteriocin arrays composed of numerous bacteriocin particles. Pseudomonas aeruginosa is an opportunistic bacterial pathogen that produces bacteriocins called R2 pyocins which lyse susceptible bacteria. Based on homology to other contractile injection systems, we hypothesize that P. aeruginosa produces bacteriocin arrays that modulate host responses during infection. We have developed a method to quantify R2 pyocins utilizing the lysis of susceptible strains of P. aeruginosa. We are currently applying this quantification method to optimize the production and purification of pyocins to test in host-pathogen models. We have also generated a fluorescently labelled R2 pyocin for the detection of bacteriocin arrays using fluorescence microscopy. These experiments are essential to enable future evaluation of the effect of R2 pyocins on host pathogen interactions

Synthesis and characterization of bio-compatible shape memory polymers with potential applications to endovascular embolization of intracranial aneurysms

This is the post print for the version of record: Kunkel, Robert, Devin Laurence, Jingyu Wang, Donnie Robinson, Joshua Scherrer, Yi Wu, Bradley N. Bohnstedt, Aichi Chien, Yingtao Liu, and Chung-Hao Lee. "Synthesis and characterization of bio-compatible shape memory polymers with potential applications to endovascular embolization of intracranial aneurysms." Journal of the mechanical behavior of biomedical materials (2018). This post print is licensed CC BY-NC-ND and was retrieved from http://www.ou.edu/coe/ame/bbdl/publications.Intracranial aneurysms (ICAs) are focal dilations in the brain's arteries. When left untreated, ICAs can grow to the point of rupture, accounting for 50–80% of subarachnoid hemorrhage cases. Current treatments include surgical clipping and endovascular coil embolization to block circulation into the aneurysmal space for preventing aneurysm rupture. As for endovascular embolization, patients could experience aneurysm recurrence due to an incomplete coil filling or compaction over time. The use of shape memory polymers (SMPs) in place of conventional platinum coils could provide more control and predictability for mitigating these complications. This study was focused on characterization of an aliphatic urethane-based SMP to evaluate its potential as a novel biomaterial for endovascular embolization. Twelve compositions of the SMP were synthesized and their thermomechanical properties together with the shape recovery behavior were comprehensively investigated. Our results showed that the SMPs experienced a significant decrease in storage and loss moduli as heated above their glass transition temperatures (32.3–83.2 °C), and that all SMPs were thermally stable up to 265 °C. Moreover, the SMPs exhibited both composition-dependent stress relaxation and a decrease in elastic modulus during cyclic loading. The shape recovery time was less than 11 s for all SMP compositions, which is sufficiently short for shape changing during embolization procedures. Several candidate compositions were identified, which possess a glass transition temperature above body temperature (37 °C) and below the threshold of causing tissue damage (45 °C). They also exhibit high material strength and low stress relaxation behavior, suggesting their potential applicability to endovascular embolization of ICAs. This is the post print for the version of record: Kunkel, Robert, Devin Laurence, Jingyu Wang, Donnie Robinson, Joshua Scherrer, Yi Wu, Bradley N. Bohnstedt, Aichi Chien, Yingtao Liu, and Chung-Hao Lee. "Synthesis and characterization of bio-compatible shape memory polymers with potential applications to endovascular embolization of intracranial aneurysms." Journal of the mechanical behavior of biomedical materials (2018). This post print is licensed CC BY-NC-ND and was retrieved from http://www.ou.edu/coe/ame/bbdl/publications.Ye

The human secretome

The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immuno-assays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood

Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci

Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators

After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males are ZZ, but in mammals females are XX and males are XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W chromosome did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction-related genes on sex chromosomes may be specific to the male germ line

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

[Background] Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva.[Results] We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously.[Conclusions] Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.The work (proposal: 10.46936/10.25585/60000940) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. RS, MB, JL, and TW are supported by NIH grant R01AI168993. The John Templeton Foundation (grant nos. 51250 and 60973) supported TT and SVD, and the Gordon and Betty Moore Foundation grants (GBMF7617 and GBMF9340) supported SVD. MD is supported by the Generalitat Valenciana program GenT grant number CDEIGENT/2021/008. SPE is supported by a FPU grant from the Spanish Ministry of Universities (Reference: FPU20/05756).Peer reviewe