Biology subjects

Herrera, S.

Publications and source records attributed to Herrera, S..

25 records · Page 2Linked to original sources

bioRxiv2021

Seascape genomics reveals metapopulation connectivity network of Paramuricea biscaya in the northern Gulf of Mexico

The degree of connectivity among populations influences their ability to respond to natural and anthropogenic stressors. In marine systems, determining the scale, rate, and directionality of larval dispersal is therefore central to understanding how coral metapopulations are interconnected and the degree of resiliency in the event of a localized disturbance. Understanding these source-sink dynamics is essential to guide restoration efforts and for the study of ecology and evolution in the ocean. The patterns and mechanisms of connectivity in the deep-sea (> 200 meters deep) are largely understudied. In this study, we investigated the spatial diversity patterns and metapopulation connectivity of the octocoral Paramuricea biscaya throughout the northern Gulf of Mexico (GoM). Paramuricea biscaya is one of the most abundant corals on the lower continental slope (between 1200 and 2500 m) in the GoM. The 2010 Deepwater Horizon oil spill (DWH) directly impacted populations of this species and thus are considered primary targets for restoration. We used a combination of seascape genomic analyses, high-resolution ocean circulation modeling, and larval dispersal simulations to quantify the degree of population structuring and connectivity among P. biscaya populations. Evidence supports the hypotheses that the genetic diversity of P. biscaya is predominantly structured by depth, and that larval dispersal among connected populations is asymmetric due to dominant ocean circulation patterns. Our results suggest that there are intermediate unsampled populations in the central GoM that serve as stepping stones for dispersal. The data suggest that the DeSoto Canyon area, and possibly the West Florida Escarpment, critically act as sources of larvae for areas impacted by the DWH oil spill in the Mississippi Canyon. This work illustrates that the management of deep-sea marine protected areas should incorporate knowledge of connectivity networks and depth-dependent processes throughout the water column.

ecology↗

bioRxiv2021

Kilometer-scale larval dispersal processes predict metapopulation connectivity pathways for Paramuricea biscaya in the northern Gulf of Mexico

Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramuricea biscaya, found in the northern Gulf of Mexico by evaluating predictions of physical models with estimates of genetic connectivity. While genetic approaches provide estimates of realized connectivity, they do not provide information on the dispersal process. Physical circulation models can now achieve kilometer-scale resolution sufficient to provide detailed insight into the pathways and scales of larval dispersal. A high-resolution regional ocean circulation model is integrated for 2015 and its advective pathways are compared with the outcome of the genetic connectivity estimates of corals collected at six locations over the continental slope at depths comprised between 1000 and 3000 meters. Furthermore, the likely interannual variability is extrapolated using ocean hindcasts available for this basin. The general connectivity pattern exhibits a dispersal trend from east to west following 1000 to 2000-meter isobaths, corresponding to the overall westward near-bottom circulation. The connectivity networks predicted by our model were mostly congruent with the estimated genetic connectivity patterns. Our results show that although dispersal distances of 100 km or less are common, depth differences between tens to a few hundred meters can effectively limit larval dispersal. A probabilistic graphic model suggests that stepping-stone dispersal mediated by intermediate sites provides a likely mechanism for long-distance connectivity between the populations separated by distances of 300 km or greater, such as those found in the DeSoto and Keathley canyons.

ecology↗

bioRxiv2021

Metabolic snapshot of plasma samples reveals new pathways implicated in SARS-CoV-2 pathogenesis

Despite of the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of severe disease. Here, we used untargeted metabolomics to examine novel metabolic pathways related to SARS-CoV-2 susceptibility and COVID-19 clinical severity using capillary electrophoresis coupled to a time-of-flight mass spectrometer (CE-TOF-MS) in plasma samples. We included 27 patients with confirmed COVID-19 early after symptom onset who were prospectively followed and 29 healthcare workers heavily exposed to SARS-CoV-2 but with low susceptibility to infection ( nonsusceptible). We found that the metabolite profile was predictive of the study group. We identified a total of 55 metabolites as biomarkers of SARS-CoV-2 susceptibility or COVID-19 clinical severity. We report the discovery of new plasma biomarkers for COVID-19 that provide mechanistic explanations for the clinical consequences of SARS-CoV-2, including mitochondrial and liver dysfunction as a consequence of hypoxemia (citrulline, citrate, and BAIBA), energy production and amino acid catabolism (L-glycine, L-alanine, L-serine, L-proline, L-aspartic acid and L-histidine), endothelial dysfunction and thrombosis (citrulline, L-ADMA, 2-AB, and Neu5Ac), and we found interconnections between these pathways. In summary, in this first report of the metabolomic profile of individuals with severe COVID-19 and SARS-CoV-2 susceptibility by CE-MS, we define several metabolic pathways implicated in SARS-CoV-2 susceptibility and COVID-19 clinical progression that could be developed as biomarkers of COVID-19.

biochemistry↗

bioRxiv2018

Profiling gene expression of the host response to a Plasmodium vivax irradiated sporozoite immunization and infectious challenge

The development of vaccines that provide sterile protection against human malaria is a major global public health priority requiring a better understanding of the mechanisms involved in natural and vaccine-induced sterile immunity. RNAseq was used to profile gene expression of peripheral blood samples from 12 Duffy positive (Fy+) (Plasmodium vivax susceptible) volunteers enrolled in a phase 2 trial who were vaccinated with radiation attenuated P. vivax sporozoites (RAS; 5 were protected, 7 not) and from 5 Fy- (P. vivax resistant) volunteers exposed to mosquitoes harboring live non-attenuated sporozoites. Blood samples were obtained before and after immunization as well as after controlled infection with live P vivax sporozoites. The most profound changes in gene expression were observed between baseline and post-challenge, with 97 distinct signatures differentiating protected and not protected Fy+ individuals. Differentiation was also observed between Fy- and Fy+ protected individuals, notably with downregulation of multiple inflammatory responses as well as extracellular matrix-related gene activity. Analysis of transcriptional modules shows that both B-cell and T-cell signaling are reduced while cell cycle regulation, interferon response, and other informative signatures are elevated in individuals who are not protected against malaria. An asymptomatic individual had an intermediate profile indicative of differential transcription associated with pathology and symptomology. Systems biology thus provides insight into how whole malaria-attenuated sporozoites prime the immune system to protect against malaria, as well as the transcription responses that are associated with sterile protection.\n\nAUTHOR SUMMARYTranscriptomic analysis has shed considerable light on the molecular mechanisms of vaccine efficacy against a variety of viral pathogens, but has not yet been used in relation to parasite vaccinology. Here we describe whole peripheral blood gene expression profiling to contrast the contributions of myeloid and lymphoid immune responses to vaccine-induced and natural protection against Plasmodium vivax- mediated malaria. Two modes of modular bioinformatic analyses are applied to RNAseq data from pre- and post-vaccination samples from 19 volunteer participants in a clinical trial investigating the efficacy of an irradiated sporozoite vaccine. During active infection, both B- and T-cell activity are reduced in individuals who are not protected by vaccination relative to those who are protected. Lack of the Fy antigen prevents entry of parasite into red blood cells, thereby providing natural clinical immunity, but we also document differences in T-cell and neutrophil activity in these individuals relative to those protected by irradiation of the parasite. One individual who was asymptomatic for malaria but had blood parasite despite vaccination showed an intermediate response indicating how systems biology approaches can distinguish gene expression associated with pathology and infection.

genomics↗

bioRxiv2018

Population Genomics of Rapidly Invading Lionfish in the Caribbean Reveals Signals of Range Expansion in the Absence of Spatial Population Structure

Range expansions driven by global change and species invasions are likely to have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo-Pacific lionfish, Pterois volitans, into waters off the U.S. East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 loci sequenced by restriction enzyme associated DNA sequencing for nine P. volitans populations in the invaded range, including Florida and other Caribbean sites, as well as mitochondrial control region D-loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure in the study area, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from reports of between-basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant throughout sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an FST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.

evolutionary biology↗

bioRxiv2017

Genome-Epigenome Interactions Associated with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is an example of a complex disease of unknown etiology. Multiple studies point to disruptions in immune functioning in ME/CFS patients as well as with specific genetic polymorphisms and alterations of the DNA methylome in lymphocytes. However, the association between DNA methylation and genetic background in relation to the ME/CFS is currently unknown. In this study we explored this association by characterizing the genomic (~4.3 million SNPs) and epigenomic (~480 thousand CpG loci) variability between populations of ME/CFS patients and healthy controls. We found significant associations of methylation states in T-lymphocytes at several CpG loci and regions with ME/CFS phenotype. These methylation anomalies are in close proximity to genes involved with immune function and cellular metabolism. Finally, we found significant correlations of genotypes with methylation phenotypes associated with ME/CFS. The findings from this study highlight the role of epigenetic and genetic interactions in complex diseases, and suggest several genetic and epigenetic elements potentially involved in the mechanisms of disease in ME/CFS.

genomics↗

bioRxiv2017

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the [~]7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 {+/-} 222, with more loci recovered from octocorals (783 {+/-} 138 loci) than hexacorals (475 {+/-}187 loci). Phylogenetically informative sites ranged from 26-49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Re-designing the baits with improved affinities to capture loci within each sub-class will provide a valuable toolset to address systematic questions and further our understanding of the timing of diversifications in the class Anthozoa.

genomics↗