Biology subjects

Salcedo, E.

Publications and source records attributed to Salcedo, E..

10 recordsLinked to original sources

bioRxiv2025

Characterization of Phytoplankton-Excreted Metabolites Mediating Carbon Flux through the Surface Ocean

The marine labile dissolved organic carbon (DOC) pool is a dynamic reservoir of thousands of molecules that cycles approximately one-quarter of Earths primary production within days to weeks. After excretion by phytoplankton and other microbes, metabolites are rapidly consumed, resulting in low standing concentrations (picomolar to low nanomolar). Despite the decades-long search for labile DOC sources and molecular identities, marine phytoplankton exometabolomes are not well characterized, largely due to difficulties in measuring small polar molecules in saline water. Here, we profiled the exometabolomes of six axenic phytoplankton species representing key functional groups including a diatom (Thalassiosira pseudonana CCMP1335), a picoeukaryote (Micromonas commoda RCC299), a coccolithophore (Gephyrocapsa huxleyi CCMP371), a diazotrophic cyanobacterium (Crocosphaera watsonii WH8501), and two picocyanobacteria (Prochlorococcus marinus MIT 9301 and Synechococcus WH8102). From these cultures, we quantified 56 amine- and alcohol-containing exometabolites representing 11 compound classes which in sum comprised up to 23.4% of phytoplankton-excreted DOC. We estimated that these phytoplankton-derived exometabolites could supply up to 5% of the daily carbon quota of the dominant heterotrophic bacterium SAR11 in the surface ocean. Substantial variations in exometabolite identity and concentration across phytoplankton taxa underscore taxonomic diversity as a key driver in the supply and composition of labile DOC. This taxonomic variation predicts geographic and seasonal differences in the distribution of marine dissolved metabolites that underpin the cycling of labile DOC back to CO2. Overall, our work suggests that phytoplankton exometabolites are key chemical currencies that mediate significant carbon fluxes within the oceans carbon cycle. Significance StatementPhytoplankton exometabolites are key components of the marine labile dissolved organic carbon (DOC) pool, which drives major a fraction of the oceanic carbon flux. Yet, their composition and flux are poorly constrained. Leveraging new methods, we quantified amine- and alcohol-containing exometabolites in diverse phytoplankton and found they varied taxonomically. These exometabolites accounted for up to 23.4% of excreted DOC, potentially supporting a sizable fraction of the global heterotrophic growth. Integrating our results with ecological models suggest that exometabolite composition varies geographically and seasonally in response to changing phytoplankton community structures. Our findings illuminate the long-standing "black box" of labile DOC and link taxonomic diversity to the chemical currencies underpinning the microbe-metabolite networks at the heart of the marine carbon cycle.

ecology↗

bioRxiv2025

The shared and distinct roles of Prochlorococcus and co-occurring heterotrophic bacteria in regulating community dynamics

Prochlorococcus is the worlds most abundant photosynthetic organism with over 1027 cells distributed across much of Earths oceans, and is collectively responsible for almost 10% of marine carbon fixation. Naturally co-occurring heterotrophic bacteria at roughly 105-106 cells mL-1 in the oceans have been shown to increase Prochlorococcus fitness and productivity. Despite this massive scale, our understanding of these globally important interactions remains limited, with past research largely focused on single Prochlorococcus-heterotroph pairings involving only a few species. In this study, we extend this perspective by using synthetic communities containing multiple diverse heterotrophic strains isolated from Prochlorococcus enrichment cultures. Specifically, we isolated the four most abundant co-occurring heterotroph species and examined both individual Prochlorococcus-heterotroph interactions and interactions within a synthetic community comprising Prochlorococcus and all four heterotrophs. Using absolute quantification of RNA, DNA, and cell counts over the course of Prochlorococcus growth curves, we find that Prochlorococcus has a modest, species-independent transcriptional response to heterotrophs, whereas each heterotroph displays a markedly different transcriptional response to the community and fulfills distinct metabolic roles. Transcriptional analyses reveal several potential crossfeeding interactions and indicate that community dynamics are influenced not only by metabolic activity but also antagonistic mechanisms, defense responses, and coordinated group behaviors. By pairing synthetic community approaches with absolute abundance measurements, we can gain deeper insight into the forces that shape microbial community assembly in the oceans and their role in driving the global carbon cycle.

microbiology↗

bioRxiv2025

Tyrosine kinase inhibitors affect sweet taste and dysregulate fate selection of specific taste cell subtypes via KIT inhibition.

Taste dysfunction, or dysgeusia, is a common side effect of many cancer drugs. Dysgeusia is often reported by patients treated with anti-angiogenic tyrosine kinase inhibitors (TKIs), which inhibit receptor tyrosine kinases (RTKs). However, the mechanisms by which TKIs cause dysgeusia are not understood, as the role of RTKs in adult taste homeostasis is unknown. Here, we find that treating adult mice with the TKI cabozantinib shifts the fate of differentiating functional taste cell subtypes within taste buds. Through behavioral assays, we find this cell fate shift leads to blunted responses to sweet in cabozantinib-treated mice. Finally, we show that inducible knockout of the RTK KIT, which is inhibited by cabozantinib, phenocopies taste cell fate shifts induced by TKI treatment. Our results establish KIT as a regulator of taste cell homeostasis and suggest that KIT inhibition may underlie TKI-induced dysgeusia in patients. SummaryKIT signaling blockade by tyrosine kinase inhibitors alters the fate of functional taste bud cell subtypes.

neuroscience↗

bioRxiv2025

ProSynTaxDB: A curated protein database and workflow for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes

Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.

bioinformatics↗

bioRxiv2025

Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models

A protective vaccine against HIV will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. Nearly all vaccine strategies to induce bnAbs require the use of relatively complex immunization regimens involving a series of different immunogens, most of which are Env trimers. Producing protein-based clinical material to evaluate such relatively complex regimens in humans presents major challenges in cost and time. Furthermore, immunization with HIV trimers as soluble proteins induces strong non-neutralizing responses to the trimer base, which is normally occluded on the virion. These base responses could potentially detract from the induction of nAbs and the eventual induction of bnAbs. mRNA vaccine platforms offer potential advantages over protein delivery for HIV vaccine development, including increased production speed, reduced cost, and the ability to deliver membrane-bound trimers that might facilitate improved immuno-focusing to non-base epitopes. We report the design of mRNA-delivered soluble and membrane-bound forms of a stabilized native-like Env trimer (BG505 MD39.3), initial immunogenicity evaluation in rabbits that triggered clinical evaluation, and more comprehensive evaluation of B cell, T cell, and antibody responses in non-human primates. mRNA-encoded membrane-bound Env immunization elicited reduced off-target base-directed Env responses and stronger neutralizing antibody responses, compared with mRNA-encoded soluble Env. Overall, mRNA delivery of membrane-bound Env appears promising for enhancing B cell responses to subdominant epitopes and facilitating rapid translation to clinical testing, which should assist HIV vaccine development. One Sentence SummaryHIV envelope trimer mRNA enables membrane-bound expression and represents a functional immunogen in pre-clinical mammalian models.

immunology↗

bioRxiv2024

Death in the taste bud: Morphological features of dying taste cells and engulfment by Type I cells

Taste buds comprise 50-100 epithelial derived cells, including glial-like cells (Type I) and two types of receptor cells (Types II and III). All of these taste cells are renewed throughout the life of an organism from a pool of uncommitted basal cells. Immature cells enter the bud at its base, maturing into one of the three mature cell types. How taste cells die and/or exit the bud, as well as the role of the glial-like cells in this process, remains unclear. Here we present morphological data obtained through Serial Blockface Scanning Electron Microscopy of murine circumvallate taste buds, revealing taste cells at the end of their life. Cells we identify as dying share morpholowgical features typical of apoptosis: swollen endoplasmic reticulum, large lysosomes, degrading organelles, distended outer nuclear membranes, heterochromatin reorganization, cell shrinkage, and cell and/or nuclear fragmentation. Most early stage dying cells have Type II cell morphologies, while a few display Type III cell features. Many dying cells maintain contacts with nerve fibers, but those postsynaptic fibers often appear to be detached from the main trunk of an afferent nerve. Dying cells, like mature Type II and III taste cells, are surrounded by glial-like Type I cells. In many instances Type I cells appear to be engulfing their dying neighbors, suggesting for them a novel, phagocytic role. Surprisingly, virtually no Type I cells display features of apoptosis, although they reportedly have the shortest residence time in taste buds. The ultimate fate of Type I cells therefore remains unknown. Table of Contents EntryO_ST_ABSMain PointsC_ST_ABSO_LIDying taste cells display morphologies consistent with apoptosis. C_LIO_LIGlial-like Type I cells engulf dying neighbors, perhaps acting as "undertakers." C_LIO_LIWe find no dying Type I cells--all early dying cells are taste transducing Type II or III cells. C_LI

neuroscience↗

bioRxiv2022

Efficient isolation of rare B cells using next-generation antigen barcoding

The ability to efficiently isolate antigen-specific B cells in high throughput will greatly accelerate the discovery of therapeutic monoclonal antibodies (mAbs) and catalyze rational vaccine development. Traditional mAb discovery is a costly and labor-intensive process, although recent advances in single-cell genomics using emulsion microfluidics allow simultaneous processing of thousands of individual cells. Here we present a streamlined method for isolation and analysis of large numbers of antigen-specific B cells, including next generation antigen barcoding and an integrated computational framework for B cell multi-omics. We demonstrate the power of this approach by recovering thousands of antigen-specific mAbs, including the efficient isolation of extremely rare precursors of VRC01-class and IOMA-class broadly neutralizing HIV mAbs.

immunology↗

bioRxiv2021

Traumatic Brain Injury Exacerbates Alzheimer's Disease Pathology in the Retinas of TgF344-AD Rats

Alzheimers disease (AD) is a neurodegenerative condition that affects 6.2 million people age 65 and older in the U.S. alone, and is the leading cause of dementia. Moreover, AD can lead to visual impairment, and AD histopathology also manifests in the retina. However, the factors that modulate AD pathophysiology and lead to varied susceptibility and presentation in the population are not well understood. In this context, traumatic brain injury (TBI), which can arise from sport concussions, military combat, and other causes, is associated with a 2.3-fold higher risk of developing AD and AD-related dementias (ADRD). Thus, we set out to evaluate the effects of TBI, AD, and their combination, on retinal histopathology. Several animal models have been developed to investigate the mechanisms underlying AD, but many have been limited by imperfect recapitulation of human pathology, and no model of TBI-associated AD (AD-TBI) has been characterized. To address this gap, we generated an innovative model of AD-TBI by taking advantage of a transgenic rat model (Tg-F344-AD) shown to recapitulate the main features of human AD pathology, and combining it with a twotime unilateral controlled cortical impact paradigm to mimic repetitive mild TBI (rmTBI). Histopathological analyses at four months post-impact confirm the presence of AD markers in transgenic retinas, and an increased severity of AD pathology due to TBI. Together, these results contribute to our understanding of the effects of TBI on AD retinopathy, with implications for patient care and therapeutic development.

neuroscience↗

bioRxiv2019

Differential Expression of Mucins in Murine Olfactory Versus Respiratory Epithelium

Mucins are a key component of the airway surface liquid and serve many functions. Given the numerous differences in olfactory versus respiratory nasal epithelia, we hypothesized that mucins would be differentially expressed between these two areas. Secondarily, we evaluated for changes in mucin expression with radiation exposure, given the clinical observations of nasal dryness, altered mucus rheology, and smell loss in radiated patients. Immunofluorescence staining was performed in a mouse model to determine the expression of mucins 1, 2, 5AC and 5B in nasal respiratory and olfactory epithelia of control mice and one week after exposure to 8 gy of radiation. Mucins 1, 5AC and 5B exhibited differential expression between olfactory and respiratory epithelium while mucin 2 showed no difference. Within the olfactory epithelium, mucin 1 was located in a lattice-like pattern around gaps corresponding to dendritic knobs of olfactory sensory neurons, whereas in respiratory epithelium it was only intermittently expressed. Mucin 5AC was expressed by subepithelial glands in both epithelial types but to a higher degree in the olfactory epithelium. Mucin 5B was expressed by submucosal glands in the olfactory epithelium but by surface epithelial cells in respiratory epithelium. At one-week after exposure to single-dose 8 gy of radiation, no qualitative effects were seen on mucin expression. Our findings demonstrate that murine olfactory and respiratory epithelia express mucins differently, and characteristic patterns of mucins 1, 5AC, and 5B can be used to define the underlying epithelium. Radiation (8 gy) does not appear to affect mucin expression at one week.\n\nAuthor RolesChristopher Kennel conceived, organized and executed the study, performed the analysis, and contributed to the manuscript.\n\nElizabeth Gould conceived and executed the study, and contributed to the manuscript.\n\nDiego Restrepo conceived and executed the study, supervised the experiments, reviewed the analysis, and contributed to the manuscript.\n\nErnesto Salcedo performed experiments and reviewed the manuscript.\n\nThad Vickery performed experiments and reviewed the manuscript.\n\nEric Larson performed experiments and reviewed the manuscript.\n\nVijay Ramakrishnan conceived and executed the study, reviewed the analysis, and contributed to the manuscript.\n\nAll authors discussed the results and implications and contributed to the final manuscript.

neuroscience↗

bioRxiv2019

Three-Dimensional Reconstructions of Mouse Circumvallate Taste Buds Using Serial Blockface Scanning Electron Microscopy: I. Cell Types and the Apical Region of the Taste Bud

Taste buds comprise four types of taste cells: 3 mature, elongate types: Type I, Type II, Type III; and basally-situated, immature post-mitotic Type IV cells. We employed serial blockface scanning electron microscopy to delineate the characteristics and interrelationships of the taste cells in the circumvallate papillae of adult mice. Type I cells have an indented, elongate nucleus with invaginations, folded plasma membrane, and multiple apical microvilli in the taste pore. Type I microvilli may be either restricted to the bottom of the pore or extend outward reaching midway up into the taste pore. Type II cells (aka receptor cells) are characterized by a large round or oval nucleus, a single apical microvillus extending through the taste pore, and specialized \"atypical\" mitochondria at functional points of contact with nerve fibers. Type III cells (aka \"synaptic cells\") are elongate with an indented nucleus, possess a single, apical microvillus extending through the taste pore and are characterized by a small accumulation of synaptic vesicles at points of contact with nerve fibers. About one-quarter of Type III cells also exhibit an atypical mitochondrion amidst the presynaptic vesicle clusters at the synapse. Type IV cells (non-proliferative \"basal cells\") have a nucleus in the lower quarter of the taste bud but have a foot process extending to the basement membrane often contacting nerve processes along the way. Type I cells represent just over 50% of the population, whereas Type II, Type III, and Type IV (basal cells) represent 19%, 15%, and 14% respectively.

neuroscience↗