Single Cell Sequencing Provides Clues about the Developmental Genetic Basis of Evolutionary Adaptations in Syngnathid Fishes.

Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genome assemblies revealed suggestive gene content differences and provide the opportunity for detailed genetic analyses.

Host genomic variation shapes gut microbiome diversity in threespine stickleback fish.

A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment.

Improvements to the Gulf pipefish genome.

The Gulf pipefish has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation.

Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression.

Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype.

Genome-wide analysis facilitates estimation of the amount of male contribution in meiotic gynogenetic three-spined stickleback (Gasterosteus aculeatus).

Gynogenetic embryos - those inheriting only maternal DNA - can be experimentally created by fertilizing eggs with radiation-treated sperm containing inactivated paternal chromosomes. Diploidy in the zygotes can be maintained through prevention of the second meiosis or restored by preventing the first mitosis after the maternal chromosome complement has been replicated. These gynogenetic organisms are useful in many fields including aquaculture, evolutionary biology and genomics.

Reaching Latinx Communities with Algorithmic Optimization for SARS-CoV-2 Testing Locations.

The COVID-19 pandemic has disproportionately affected communities of color, including Latinx communities. Oregon Saludable: Juntos Podemos (OSJP) is a randomized clinical trial aimed at reducing this disparity by both increasing access to testing for SARS-CoV-2, the virus that causes COVID-19, for Oregon Latinx community members and studying the effectiveness of health and behavioral health interventions on turnout and health outcomes. OSJP established SARS-CoV-2 testing events at sites across Oregon.

Effects of a Health Education Intervention for COVID-19 Prevention in Latinx Communities: A Cluster-Randomized Controlled Trial.

To promote COVID-19 preventive attitudes and behaviors among Latinx individuals, researchers and community partners implemented a culturally tailored health education intervention across 12 Oregon counties from February 2021 through April 2022. We did not identify any significant intervention effects on preventive attitudes and behaviors but did observe significant decreases in psychological distress. Although Latinx individuals' preventive attitudes and behaviors were not associated with the health education intervention, findings suggest the intervention has value in promoting their well-being (ClinicalTrials.

Development and design of a culturally tailored intervention to address COVID-19 disparities among Oregon's Latinx communities: A community case study.

Background: Latinx communities are disproportionately affected by COVID-19 compared with non-Latinx White communities in Oregon and much of the United States. The COVID-19 pandemic presents a critical and urgent need to reach Latinx communities with innovative, culturally tailored outreach and health promotion interventions to reduce viral transmission and address disparities. The aims of this case study are to (1) outline the collaborative development of a culturally and trauma-informed COVID-19 preventive intervention for Latinx communities; (2) describe essential intervention elements; and (3) summarize strengths and lessons learned for future applications.

Extreme intraspecific divergence in mitochondrial haplotypes makes the threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions.

Mitochondrial DNA is primarily maternally inherited in most animals and evolves about 10 times faster than biparentally inherited nuclear DNA. Mitochondrial dysfunction (mt-dys) arises when interactions between the co-evolving mitochondrial and nuclear genomes are perturbed in essential processes like oxidative phosphorylation (OXPHOS). Over time mt-dys can lead to mitochondrial diseases (mt-diseases), which are surprisingly prevalent and include common diseases such as Alzheimer's, Parkinson's, and diabetes.

Evolution and developmental expression of the sodium-iodide symporter (, ) gene family: Implications for perchlorate toxicology.

The vertebrate sodium-iodide symporter (NIS or SLC5A5) transports iodide into the thyroid follicular cells that synthesize thyroid hormone. The SLC5A protein family includes transporters of vitamins, minerals, and nutrients. Disruption of SLC5A5 function by perchlorate, a pervasive environmental contaminant, leads to human pathologies, especially hypothyroidism.

Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes.

Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons.

Effectiveness of a COVID-19 Testing Outreach Intervention for Latinx Communities: A Cluster Randomized Trial.

Importance: Latinx individuals have been disproportionately affected during the COVID-19 pandemic caused by the spread of SARS-CoV-2. It is imperative to evaluate newly developed preventive interventions to assess their effect on COVID-19 health disparities.

Objective: To examine the effectiveness of a culturally tailored outreach intervention designed to increase SARS-CoV-2 testing rates among Latinx populations.

Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis.

Single-cell RNA sequencing is a powerful technique that continues to expand across various biological applications. However, incomplete 3'-UTR annotations can impede single-cell analysis resulting in genes that are partially or completely uncounted. Performing single-cell RNA sequencing with incomplete 3'-UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences.

A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae).

The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons-the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red).

Advancing human disease research with fish evolutionary mutant models.

Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease.

Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays.

Hoxa2 genes provide critical patterning signals during development, and their regulation and function have been extensively studied. We report a previously uncharacterized significant sequence divergence of a highly conserved hindbrain hoxa2b enhancer element in the family syngnathidae (pipefishes, seahorses, pipehorses, seadragons). We compared the hox cis-regulatory element variation in the Gulf pipefish and two species of seahorse against eight other species of fish, as well as human and mouse.

Shared Environment and Genetics Shape the Gut Microbiome after Infant Adoption.

The composition of the human gut microbiome is highly variable, and this variation has been repeatedly tied to variation in human health. However, the sources of microbial variation remain unclear, especially early in life. It is particularly important to understand sources of early life variation in the microbiome because the state of the microbiome in childhood can influence lifelong health.

Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei.

The adaptation of complex organisms to changing environments has been a central question in evolutionary quantitative genetics since its inception. The structure of the genotype-phenotype maps is critical because pleiotropic effects can generate widespread correlated responses to selection and potentially restrict the extent of evolutionary change. In this study, we use experimental evolution to dissect the genetic architecture of natural variation for acute heat stress and oxidative stress response in the nematode Caenorhabiditis remanei.

Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.

Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment.

QTL Mapping of Intestinal Neutrophil Variation in Threespine Stickleback Reveals Possible Gene Targets Connecting Intestinal Inflammation and Systemic Health.

Selection, via host immunity, is often required to foster beneficial microbial symbionts and suppress deleterious pathogens. In animals, the host immune system is at the center of this relationship. Failed host immune system-microbial interactions can result in a persistent inflammatory response in which the immune system indiscriminately attacks resident microbes, and at times the host cells themselves, leading to diseases such as Ulcerative Colitis, Crohn's Disease, and Psoriasis.

A Few Stickleback Suffice for the Transport of Alleles to New Lakes.

Threespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established "de novo" from marine colonists. Independently evolved freshwater populations exhibit similar phenotypes that have been shown to derive largely from the same standing genetic variants.

Genetic divergence outpaces phenotypic evolution among threespine stickleback populations in old freshwater habitats.

Species such as threespine stickleback () that inhabit divergent selective environments and that have diversified on different time scales can be of value for understanding evolutionary processes. Here we synthesize high-resolution genotypic and phenotypic data to explore a largely unstudied distribution of threespine stickleback populations living in oceanic and freshwater habitats along coastal and inland regions of Oregon. Many inland aquatic habitats of Oregon remained unglaciated during the last ice age, meaning that some extant Oregon lake and river stickleback may have descended from freshwater populations established long before more well-studied, post-glacial freshwater populations.

Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.

Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment.

Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback.

Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information.

Selection, Linkage, and Population Structure Interact To Shape Genetic Variation Among Threespine Stickleback Genomes.

The outcome of selection on genetic variation depends on the geographic organization of individuals and populations as well as the organization of loci within the genome. Spatially variable selection between marine and freshwater habitats has had a significant and heterogeneous impact on patterns of genetic variation across the genome of threespine stickleback fish. When marine stickleback invade freshwater habitats, more than a quarter of the genome can respond to divergent selection, even in as little as 50 years.