Biology subjects

Salazar, J.

Publications and source records attributed to Salazar, J..

5 recordsLinked to original sources

bioRxiv2026

Plasma Proteomic Profiling Identifies a Subset of HIV Elite Controllers with Inflammatory Profiles Resembling People Without HIV

Background: Elite controllers (ECs) are people with HIV (PWH) who suppress viral replication without antiretroviral therapy (ART). A subset, often termed exceptional elite controllers (EECs), harbor very small viral reservoirs, with few intact proviruses integrated into inactive chromosomal regions. Defining inflammatory signatures in ECs may clarify whether some approach a functionally cured state. Methods: We measured 384 plasma proteins in ART-naive ECs (n=62), ART-suppressed non-controllers (n=37), and people without HIV (PwoH) (n=50) using Olink proteomics, and compared proteomic profiles, clinical parameters, and intact reservoir data using FLIP-Seq. Hierarchical clustering identified ECs whose proteomic profiles most closely resembled PWoH; this subset was further analyzed using machine-learning approaches. Results: ART-suppressed non-controllers had higher inflammatory protein levels than ART-naive ECs, yet ECs still showed elevated inflammation and lower CD4:CD8 ratios compared with PWoH. Clustering analysis revealed a distinct subset of ECs (n=9) whose profiles closely matched those without HIV (ECs with PWoH-like proteomic profiles), a pattern not observed in ART-suppressed non-controllers. Compared to typical ECs, ECs with PWoH-like proteomic profiles had consistently lower IL-1{beta}, SCRN1, and BID, numerically lower intact proviral frequencies, and a high frequency of protective HLA alleles. Machine-learning analyses highlighted features that most strongly differentiated ECs with PWoH-like proteomic profiles from typical ECs, including reduced gut mucosal/intestinal epithelial-associated proteins, higher absolute CD4 counts, and lower levels of pro-inflammatory cytokines and cellular immune activation. Conclusions: These findings identify a subset of ECs with a PWoH-like inflammatory proteomic profile, accompanied by numerically lower intact HIV reservoirs and a high frequency of protective HLA alleles. Defining the mechanisms associated with this low-inflammatory state may provide insights into exceptional HIV control and inform strategies for durable HIV remission.

immunology↗

bioRxiv2025

Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis

Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illuminas platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long read sequencing with whole-length 16S rRNA sequencing can improve taxonomic resolution, but often only to the species level. StrainID is an alternative approach that amplifies a large segment of the ribosomal operon, including the entire 16S rRNA gene, internal transcribed spacer, and a portion of the 23S rRNA gene. This longer amplicon is designed to allow ribotype-level classification. Although studies have demonstrated the utility of StrainID for several sample types, it has not yet been validated for saliva. Here, we compared the performance of StrainID to short read amplicons with saliva samples as well as a synthetic mock DNA community and human and mouse fecal samples. Short reads were amplified with primer pairs appropriate for the corresponding sample type, and were classified with two different taxonomic databases. For both saliva and fecal samples, we found that StrainID performed similarly to short reads overall and demonstrated a key benefit with phylogenetic-based beta diversity tests and taxonomic classification. Our results further build on establishing StrainID as a valid method and specifically validate its use with saliva samples. ImportanceThe interpretation of microbiome composition studies is highly dependent on the methodologies chosen during experimental design, which affects factors such as resolution, throughput, cost, and accuracy. StrainID is an approach that can improve resolution while maintaining high-throughput and similar costs to short-read sequencing. The salivary microbiome represents a diverse community of microbes with links to a variety of health conditions and disease states. Closely related strains of bacteria can have drastically different effects on their host. Establishing StrainID as a valid approach for studying the salivary microbiome opens avenues for research that improve upon alternative methods by increasing sensitivity and accuracy compared to traditional short read approaches.

microbiology↗

bioRxiv2025

White and Clearing: New Optical Tissue Clearing Method

AbstractOptical tissue clearing techniques can render large-scale tissue samples and whole organs transparent to apply cell-resolution 3D imaging techniques, revolutionizing the fields of biological research and pathological diagnosis, and providing never-before seen structural information. There are several widely used protocols, but they have shortcomings, both in complexity of use and in suboptimal results in certain tissues and organs. Here, we describe a new method dubbed "White and Clear" (WaC) using 2,2-thiodiethanol (TDE) as a dynamic Refractive Index (RI)-matching reagent alongside a lipid-extraction and a pigment-bleaching step using dilute hydrogen peroxide (H2O2), to provide ease of use and enhanced clearing effect on all kinds of samples and allow for the clearing parameters to be finely adjusted in order to obtain the best results in each situation.

physiology↗

bioRxiv2021

Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in mediating targeted therapy dosage challenges

Cancer cells display two modes of focal amplifications (FAs), extrachromosomal DNA/double-minutes (ecDNA/DMs) and intrachromosomal homogenously staining regions (HSRs). Understanding the plasticity of these two modes is critical for preventing targeted therapy resistance. We developed a combined BRAF plus MEK inhibitor resistance melanoma model that bears high BRAF amplifications through both DM and HSR modes, and investigated FA dynamics in the context of drug resistance plasticity. Cells harboring FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of preexisting subpopulations. We found that copy number plasticity is not exclusive to DMs. Single cell-derived clones with HSRs also exhibit BRAF copy number and corresponding HSR length plasticity that allows them to respond to dose reduction and recover from drug addiction. Upon kinase inhibitor escalation, we observed reproducible selection for cells with BRAF kinase domain duplications residing on DMs. In sum, the plasticity of FAs allows cancer cells to respond to drug dose changes through a myriad of mechanisms. These mechanisms include increases or decreases in DMs, shortening of HSRs, acquisition of secondary resistance mechanisms, and expression of alternative slicing oncogene variants. These results highlight the challenges in targeting the cellular vulnerabilities tied to focal amplifications. Statement of SignificanceUnderstanding the dynamics of oncogene amplifications is critical for appreciating tumorigenesis and preventing anticancer drug resistance. We found melanoma cells harboring BRAF amplifications in either DM or HSR formats to have high plasticity under different kinase inhibitor dosage challenges with evidence supporting de novo alterations, clonal selection, and coupling to additional resistance mechanisms. In in the absence of DMs, HSRs can offer comparable levels of plasticity as DMs.

cancer biology↗

bioRxiv2019

The Relationship between Resilient Mangroves and Fish Populations in the Largest Marine Reserve in Belize: A Case for Conservation

Mangrove forests are one of the most bio-diverse and productive wetland environments on earth. However, these unique tropical forest environments that occupy coastal areas are among the most threatened habitats globally. Approximately one-third of the worlds mangrove forests in tropical and subtropical coastlines have been lost to logging, conversion of land for agriculture and mariculture, and degradation due to general pollution over the past 50 years. The large population of mangroves occupying the Turneffe Atoll area in Belize face growing anthropogenic threats such as permanent clearing of land for housing and infrastructural development as well as pollution and natural factors (climate change). Despite these threats, mangroves have high resilience due to their fast rates of microbial decomposition and nutrient flux, large storage of nutrients below-ground, numerous feedbacks, keystone species redundancy and self-design, and highly efficient biotic controls. Given the few formal studies done to evaluate mangrove resilience at Turneffe Atoll, the purpose of this study was to evaluate mangrove resilience and nursery functions in the Turneffe Atoll Marine Reserve. Mangrove fish abundance, forest structure, and prop root length was assessed by means of visual census and point centred quarter method (PCQM) for 11 sites that span across conservation and general use zones. This study found that resilient mangroves (lower vulnerability ranks, higher standing biomass, and higher fish biomass and abundance) exist in conservation and general use zones and warrant the need for improved mangrove conservation measures. Some conservation measures include: greater reduction of non-climate stressors, establishment of more mangrove conservation areas, and implementation of more outreach and educational programmes.

ecology↗