Biology subjects

Ramirez, G. A.

Publications and source records attributed to Ramirez, G. A..

7 recordsLinked to original sources

bioRxiv2025

Neutrophil Reprogramming Underlie Vasculopathy and Lung Disease in Systemic Sclerosis

The role of neutrophils in systemic sclerosis (SSc) remains incompletely understood. To address this, blood samples from 39 SSc patients, 39 healthy controls, and 22 systemic lupus erythematosus (SLE) patients were analyzed. In SSc, neutrophils exhibited substantial activation, evidenced by granule mobilization, elevated plasma levels of Neutrophil Extracellular Trap (NET) byproducts, and upregulated TIE2 expression. In parallel, they underwent metabolic reprogramming, characterized by increased autophagy, likely to support the heightened energy demands of activation. By contrast, neutrophils from SLE patients displayed minimal autophagy, lacked TIE2 expression, and shifted toward low-density granulocytes. Neutrophil reprogramming in SSc correlated with plasma levels of HMGB1+ EVs. Mechanistically, EVs purified from the plasma of patients with SSc adhered to neutrophils when injected in immunodeficient NSG mice, inducing autophagy, TIE2 expression, and promoting lung inflammation and fibrosis. These effects were abrogated by HMGB1 inhibitors and required the HMGB1 receptor, RAGE. Recombinant HMGB1 recapitulated EV-induced effects, while neutrophil targeting by liposome-encapsulated clodronate prevented them. In summary, neutrophils in SSc exhibit a dual phenotype of autophagy and activation driven by HMGB1+ EVs, representing a pathogenic mechanism and a potential therapeutic target in SSc. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=139 HEIGHT=200 SRC="FIGDIR/small/637866v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@dbf3dcorg.highwire.dtl.DTLVardef@67243forg.highwire.dtl.DTLVardef@17cb6c4org.highwire.dtl.DTLVardef@c3370a_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

The DNA event horizon in the Guaymas Basin subsurface biosphere: technical advances and re-defined limits in bulk extractions of nucleic acids from deep marine sediments

We compiled DNA and RNA isolation protocols for sediment bulk extraction and their yields from Guaymas Basin subsurface sediments, and evaluated their sensitivity for metagenomic and amplicon analyses of subsurface microbial communities. Guaymas Basin sediments present a challenge for DNA and RNA recovery due to high concentrations of hydrocarbons, steep thermal gradients and rapidly declining cell numbers downcore. Metagenomic library construction and sequencing was possible from as little as 0.2 to 0.5 ng DNA/cm3 sediment; PCR amplification of 16S rRNA genes required in most cases approx. 1-2 ng DNA/cm3 sediment. At in-situ temperatures of 50 to 60{degrees}C, decreasing DNA recovery leads to increasingly uncertain "hit or miss" outcomes and to failures for metagenomic and amplicon analyses. DNA concentration profiles show that, even before these hot temperatures are reached, relatively moderate temperatures have a major effect on microbial abundance and DNA yield. Comparison with cell count profiles shows that hydrothermal influence is reducing downcore cell densities by multiple orders of magnitude faster compared to non-hydrothermal sediments; this effect is also visible at relatively moderate temperatures. To an even greater degree than DNA, RNA recovery is highly sensitive to downcore increasing temperatures and decreasing cell numbers, and worked best for microbial communities in cool, relatively shallow subsurface sediments.

microbiology↗

bioRxiv2024

Distribution-driven disturbance of a molecular community: a theoretical framework

An important and understudied area in microbial ecology concerns the very large number of very rare species within an environment. Study of such species based on non-specific sequencing of environmental samples is practically difficult simply due to their rarity. A previous report demonstrated that pretreating samples with the photoactive dye PMA before subsequent PCR and sequencing can increase sensitivity to rare species. Here we propose a mathematical model based on equilibrium chemical thermodynamics that explains this effect and suggests a simple quantitative experiment.

microbiology↗

bioRxiv2022

Bacterial aerobic methane cycling by the marine sponge-associated microbiome

BackgroundMethanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed. ResultsHere, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methanogenesis occurring in fully oxygenated shallow water habitats. Specifically, we suggest methanogenesis occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C1-metabolic loop that involves both the sponge host and specific members of the associated microbial community. ConclusionGiven the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methanogenesis and methanotrophy, sponges may serve as marine sources or sinks of this potent greenhouse gas.

microbiology↗

bioRxiv2020

Broiler Chickens and Early Life Programming: Microbiome transplant-induced cecal bacteriome dynamics and phenotypic effects

The concept of successional trajectories describes how small differences in initial community composition can magnify through time and lead to significant differences in mature communities. For many animals, the types and sources of early-life exposures to microbes have been shown to have significant and long-lasting effects on the community structure and/or function of the microbiome. In modern commercial poultry production, chicks are reared as a single age cohort and do not directly encounter adult birds. This scenario is likely to initiate a trajectory of microbial community development that is significantly different than non-industrial settings where chicks are exposed to a much broader range of environmental and fecal inocula; however, the comparative effects of these two scenarios on microbiome development and function remain largely unknown. In this work, we performed serial transfers of cecal material through multiple generations of birds to first derive a stable source of inoculum. Subsequently, we compared microbiome development between chicks receiving this passaged cecal material, versus an environmental inoculum, to test the hypothesis that the first exposure of newly hatched chicks to microbes determines early GI microbiome structure and may have longer-lasting effects on bird health and development. Cecal microbiome dynamics and bird weights were tracked for a two-week period, with half of the birds in each treatment group exposed to a pathogen challenge at 7 days of age. We report that: i) a relatively stable community was derived after a single passage of transplanted cecal material, ii) this cecal inoculum significantly but ephemerally altered community structure relative to the environmental inoculum and PBS controls, and iii) either microbiome transplant administered at day-of-hatch appeared to have some protective effects against pathogen challenge relative to uninoculated controls. Differentially abundant taxa were identified across treatment types that may inform future studies aimed at identifying strains associated with beneficial phenotypes.

microbiology↗

bioRxiv2020

The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories

We explore archaeal distribution and environmental niche differentiation in sedimentary subseafloor habitats of Guaymas Basin and the adjacent Sonora Margin, located in the Gulf of California, Mexico. Specifically, we survey diverse subseafloor habitats on the Guaymas Basin flanking regions that are extending from the spreading center, termed here "off-axis" sites. Sampling locations include (i) control sediments without hydrothermal or seep influence, (ii) Sonora Margin sediments underlying oxygen minimum zone water, (iii) compacted, highly reduced sediments from a pressure ridge with numerous seeps at the base of the Sonora Margin, and (iv) sediments impacted by hydrothermal circulation at the off-axis Ringvent site. Generally, archaeal 16S rRNA gene datasets are largely comprised of Bathyarchaeal lineages, members of the Hadesarchaea, MBG-D, TMEG, and ANME-1 groups. The most frequently observed 25 OTUs belong to members of these lineages, and correspond to approx. 40 to 80% of the sequence dataset in each sediment sample. Differential distribution patterns of these archaeal groups in downcore sediments uniquely characterize each major sedimentary environment. Variations in archaeal community composition reflect locally specific environmental challenges throughout the greater Guaymas Basin area. Background sediments are divided into surface and subsurface niches, reflecting increased selection of the archaeal community downcore. In sum, the environmental setting and history of a particular site, not isolated biogeochemical properties out of context, control the subseafloor archaeal communities in Guaymas Basin and Sonora Margin sediments.

ecology↗

bioRxiv2018

Genetically distinct clinical subsets, and associations with asthma and eosinophil abundance, within Eosinophilic Granulomatosis with Polyangiitis

Eosinophilic granulomatosis with polyangiitis (EGPA: formerly Churg-Strauss syndrome) is a rare inflammatory disease of unknown cause. 30% of patients have anti-neutrophil cytoplasm antibodies (ANCA) specific for myeloperoxidase (MPO). We performed a genome-wide association study (GWAS) of EGPA, testing 7.5 million genetic variants in 684 cases and 6,838 controls. Case-control analyses were performed for EGPA as a whole, and stratified by ANCA. To increase power, we used a conditional false discovery rate method to leverage findings from GWASs of related phenotypes. In total, 11 variants were associated with EGPA, two specifically with ANCA-negative EGPA, and one (HLA-DQ) with MPO+ANCA EGPA. Many variants were associated with asthma, eosinophilic and immune-mediated diseases and, strikingly, nine were associated with eosinophil count in the general population. Through Mendelian randomisation, we show that a primary tendency to eosinophilia underlies EGPA susceptibility. We demonstrate that EGPA comprises two genetically and clinically distinct syndromes, with ANCA-negative EGPA genetically more similar to asthma. MPO+ ANCA EGPA is an eosinophilic autoimmune disease sharing certain clinical features and an MHC association with MPO+ ANCA-associated vasculitis, while ANCA-negative EGPA may instead have a mucosal/barrier dysfunction origin. Five identified candidate genes are targets of therapies in development, supporting their exploration in EGPA.

genetics↗