Biology subjects

Salinas, I.

Publications and source records attributed to Salinas, I..

14 recordsLinked to original sources

bioRxiv2026

Opioid withdrawal engages a habenular subpopulation responsive to aversive states

AO_SCPLOWBSTRACTC_SCPLOWOpioid withdrawal produces a protracted aversive state that is a driving factor towards relapse for patients with opioid use disorder. The habenula is known to mediate symptoms of withdrawal across several substance use disorders, including alcohol, nicotine, and opioid use disorder. However, it is unclear which habenular populations contribute to withdrawal symptoms. Here, we identify a cell type marker for habenular neurons active during opioid withdrawal. Using immediate early gene analysis, we find that glutamic acid decarboxylase 2-expressing (GAD2+) cells in the lateral habenula (LHbGAD2) increase activity in response to both spontaneous and naloxone-precipitated opioid withdrawal in mice. Recording neural activity in vivo revealed transient activity at the presentation of aversive stimuli, and a sustained increase in activity during aversive states such as opioid withdrawal and inescapable shock. These results highlight the cell type heterogeneity of the habenula, and the role of specific cell types in opioid withdrawal.

neuroscience↗

bioRxiv2026

Lungfish comparative genomics reveals ancient gene networks co-opted for life on land

The transition from water to land was a defining event in vertebrate evolution, requiring major changes in physiology and gene regulation. Lungfish, the closest extant relatives of tetrapods, offer a unique window into this process through their capacity for estivation, a physiological state that mirrors key demands of terrestrial life. Here, we constructed and compared gene co-expression networks across five vertebrate species using multi-tissue transcriptomic data. Focusing on estivating lungfish tissues, we identified conserved modules enriched in core functions, including metabolic regulation, RNA processing, and protein turnover. We further show that a subset of retained ohnologs from the vertebrate 2R-WGD act as network hubs under directional selection in key phylogenetic branches. These genes, involved in membrane trafficking, cytoskeletal regulation, water balance, and stress response, illustrate how duplicated, dosage-sensitive genes were co-opted to meet the physiological demands of terrestrial adaptation. Together, our findings support a model in which ancient whole-genome duplications supplied raw material later shaped by selection and network rewiring to enable extreme physiological adaptations such as estivation. TeaserAncient duplicated gene networks in lungfish estivation reveal how vertebrates repurposed genomic toolkits to adapt to land.

evolutionary biology↗

bioRxiv2024

The telencephalon is a neuronal substrate for systemic inflammatory responses in teleosts via polyamine metabolism

Systemic inflammation elicits sickness behaviors and fever by engaging a complex neuronal circuitry that begins in the preoptic area of the hypothalamus. Ectotherms such as teleost fish display sickness behaviors in response to infection or inflammation, seeking warmer temperatures to enhance survival via behavioral fever responses. To date, the hypothalamus is the only brain region implicated in sickness behaviors and behavioral fever in teleosts. Yet, the complexity of neurobehavioral manifestations underlying sickness responses in teleosts suggests engagement of higher processing areas of the brain. Using two in vivo models of systemic inflammation in rainbow trout, we find canonical pyrogenic cytokine responses in the hypothalamus whereas in the telencephalon il-1b and tnfa expression is decoupled from il-6 expression. Polyamine metabolism changes, characterized by accumulation of putrescine and decreases in spermine and spermidine, are recorded in the telencephalon but not hypothalamus upon systemic injection of bacteria. While systemic inflammation causes canonical behavioral fever in trout, blockade of bacterial polyamine metabolism prior to injection abrogates behavioral fever, polyamine responses and telencephalic but not hypothalamic cytokine responses. Combined, our work identifies the telencephalon as a neuronal substrate for brain responses to systemic inflammation in teleosts and uncovers the role of polyamines as critical chemical mediators in sickness behaviors. Significance StatementSystemic inflammation induces neuroimmune responses in the brain resulting in sickness behaviors and fever. In endotherms, sickness behaviors and fever are initiated in the hypothalamus but also engage a complex neuronal circuitry in higher areas of the brain. In ectotherms, only the hypothalamus has been linked to sickness behaviors and behavioral fever. Here we demonstrate that the telencephalon, a critical region of the teleost brain responsible for higher order processing, mounts pyrogenic cytokine responses to systemic inflammation in teleosts that are different from those of the hypothalamus. We identify polyamine metabolism as a core response of the teleost telencephalon to systemic inflammation and report that bacterial polyamines are triggers of behavioral fever in rainbow trout. Our work uncovers a previously unrecognized role for the telencephalon and polyamine metabolism in sickness behaviors and behavioral fever in teleosts with implications in fish health and fish conservation.

immunology↗

bioRxiv2023

A niche-adapted brain microbiome in salmonids at homeostasis

Ectotherms have long been known to have peculiar relationships with microorganisms. For instance, bacteria can be recovered from blood and internal organs of healthy teleost fish. However, until now, the presence of a microbial community in the healthy teleost brain has not been proposed. Here we report a living bacterial community in the brain of healthy salmonids. Brain bacterial loads in salmonids are comparable to those found in the spleen and 1000-fold lower than in the gut. Brain bacterial communities share >50% of their diversity with gut and blood bacterial communities. Using culturomics, we obtained 54 bacterial isolates from the brain of healthy rainbow trout. Comparative genomics uncovered unique niche adaptations associated with brain colonization and polyamine biosynthesis. In a natural system, salmonid brain microbiomes shift with the host life cycle, becoming dysbiotic in reproductively mature Chinook salmon, a species that undergoes reproductive death. Our study redefines the relationship between the teleost brain and bacterial microbiomes under physiological conditions. We posit that this symbiosis may endow salmonids with a direct mechanism to sense and respond to environmental microbes. One-Sentence SummarySalmonids have a brain-adapted, resident bacterial community

microbiology↗

bioRxiv2023

Ontogeny of the organized nasopharynx-associated lymphoid tissue in rainbow trout

Understanding the ontogeny of teleost mucosa-associated lymphoid tissues (MALT) is critical for determining the earliest timepoint for effective mucosal vaccination of young fish. Here, we describe the developmental sequence that leads to the formation of an organized MALT structure in rainbow trout, the organized nasopharynx-associated lymphoid tissue (O-NALT). Control rainbow trout were sampled between 340 and 1860 degree days (DD) and routine histology and immunofluorescence staining were used to determine cellular changes in immune cells in the nasal cavity as well as O-NALT formation. We identified that O-NALT is first seeded by CD8+ T cells at 700DD followed by IgM+ B cells and CD4-2b+ T cells at 1000DD. Histomorphologically, trout O-NALT is fully formed at 1400DD when it is composed of 67% CD4-2b+ cells, 20% IgM+ cells, 13% CD8+ T cells, and no IgT+ B cells. Whole body gene expression analyses uncovered waves of igmh, cd4-2b, and cd8a expression that recapitulate the cellular seeding sequence of O-NALT by specific lymphocyte subsets. Our results indicate that 1) O-NALT formation results from a specific sequence of lymphocyte subset colonization pioneered by CD8+ T cells and 2) the presence of the full O-NALT structure at 1400DD may mark this timepoint as the earliest developmental stage at which mucosal vaccines can induce long lasting, specific immune responses.

immunology↗

bioRxiv2023

Signal Improved ultra-Fast Light-sheet Microscope (SIFT) for large tissue imaging

Light-sheet fluorescence microscopy (LSFM) in conjunction with tissue clearing techniques enables morphological investigation of large tissues faster and with excellent optical sectioning. Recently, cleared tissue axially swept light-sheet microscope (ctASLM) demonstrated three-dimensional isotropic resolution in millimeter-scaled tissues. But ASLM based microscopes suffer from low detection signal and slow imaging speed. Here we report a simple and efficient imaging platform that employs precise control of two fixed distant light-sheet foci to carry out ASLM. This allowed us to carry out full field of view (FOV) imaging at 40 frames per second (fps) which is a four-fold improvement compared to the current state-of-the-art. In addition, in a particular frame rate, our method doubles the signal compared to the current ASLM technique. To augment the overall imaging performance, we also developed a deep learning based tissue information classifier that enables faster determination of tissue boundary. We demonstrated the performance of our imaging platform on various cleared tissue samples and demonstrated its robustness over a wide range of clearing protocols.

biophysics↗

bioRxiv2023

Peripheral detection of viruses shapes brain immunity and behavior in zebrafish

Olfactory sensory neurons (OSNs) are constantly exposed to pathogens, including viruses. However, serious brain infection via the olfactory route rarely occurs. When OSNs detect a virus, they coordinate local antiviral immune responses to stop virus progression to the brain. Despite effective immune control in the olfactory periphery, pathogen-triggered neuronal signals reach the CNS via the olfactory bulb (OB). We hypothesized that neuronal detection of a virus by OSNs initiates neuroimmune responses in the OB that prevent pathogen invasion. Using zebrafish (Danio rerio) as a model, we demonstrate viral-specific neuronal activation of OSNs projecting into the OB, indicating that OSNs are electrically activated by viruses. Further, behavioral changes are seen in both adult and larval zebrafish after viral exposure. By profiling the transcription of single cells in the OB after OSNs are exposed to virus, we found that both microglia and neurons enter a protective state. Microglia and macrophage populations in the OB respond within minutes of nasal viral delivery followed decreased expression of neuronal differentiation factors and enrichment of genes in the neuropeptide signaling pathway in neuronal clusters. Pituitary adenylate-cyclase-activating polypeptide (pacap), a known antimicrobial, was especially enriched in a neuronal cluster. We confirm that PACAP is antiviral in vitro and that PACAP expression increases in the OB 1 day post-viral treatment. Our work reveals how encounters with viruses in the olfactory periphery shape the vertebrate brain by inducing antimicrobial programs in neurons and by altering host behavior.

immunology↗

bioRxiv2023

Secretory IgM (sIgM) is an ancient master regulator of microbiota homeostasis and metabolism

The co-evolution between secretory immunoglobulins (sIgs) and microbiota began with the emergence of IgM over half a billion years ago. Yet, IgM function in vertebrates is mostly associated with systemic immunity against pathogens. sIgA and sIgT are the only sIgs known to be required in the control of microbiota homeostasis in warm- and cold-blooded vertebrates respectively. Recent studies have shown that sIgM coats a large proportion of the gut microbiota of humans and teleost fish, thus suggesting an ancient and conserved relationship between sIgM and microbiota early in vertebrate evolution. To test this hypothesis, we temporarily and selectively depleted IgM from rainbow trout, an old bony fish species. IgM depletion resulted in a drastic reduction in microbiota IgM coating levels and losses in gutassociated bacteria. These were accompanied by bacterial translocation, severe gut tissue damage, inflammation and dysbiosis predictive of metabolic shifts. Furthermore, depletion of IgM resulted in body weight loss and lethality in an experimental colitis model. Recovery of sIgM to physiological levels restores tissue barrier integrity, while microbiome homeostasis and their predictive metabolic capabilities are not fully restituted. Our findings uncover a previously unrecognized role of sIgM as an ancient master regulator of microbiota homeostasis and metabolism and challenge the current paradigm that sIgA and sIgT are the key vertebrate sIgs regulating microbiome homeostasis. One-Sentence SummaryIgM, the most ancient and conserved immunoglobulin in jawed vertebrates, is required for successful symbiosis with the gut microbiota.

immunology↗

bioRxiv2021

Exploring zebrafish larvae as a COVID-19 model: probable SARS-COV-2 replication in the swim bladder

Animal models are essential to understand COVID-19 pathophysiology and for pre-clinical assessment of drugs and other therapeutic or prophylactic interventions. We explored the small, cheap and transparent zebrafish larva as a potential host for SARS-CoV-2. Bath exposure, as well as microinjection in the coelom, pericardium, brain ventricle, bloodstream, or yolk, did not result in detectable SARS-CoV-2 replication in wild-type larvae. However, when the virus was inoculated in the swim bladder, a modest increase in viral RNA was observed after 24 hours, suggesting a successful infection in some animals. This was confirmed by immunohistochemistry, with cells positive for SARS-CoV-2 nucleoprotein observed in the swim bladder. Several variants of concern were also tested with no evidence of increased infectivity in our model. Low infectivity of SARS-CoV-2 in zebrafish larvae was not due to the host type I interferon response, as comparable viral loads were detected in type I interferon-deficient animals. Mosaic overexpression of human ACE2 was not sufficient to increase SARS-CoV-2 infectivity in zebrafish embryos or in fish cells in vitro. In conclusion, wild-type zebrafish larvae appear mostly non-permissive to SARS-CoV-2, except in the swim bladder, an aerial organ sharing similarities with the mammalian lung.

microbiology↗

bioRxiv2020

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)

The microbial communities that live in symbiosis with the mucosal surfaces of animals provide the host with defense strategies against pathogens. These microbial communities are largely shaped by the environment and the host genetics. Triploid Atlantic salmon (Salmo salar) are being considered for aquaculture as they are reproductively sterile and thus cannot contaminate the natural gene pool. It has not been previously investigated how the microbiome of triploid salmon compares to that of their diploid counterparts. In this study, we compare the steady-state skin and gill microbiome of both diploid and triploid salmon, and determine the effects of salmonid alphavirus 3 experimental infection on their microbial composition. Our results show limited differences in the skin-associated microbiome between triploid and diploid salmon, irrespective of infection. In the gills, we observed a high incidence of the bacterial pathogen Candidatus Branchiomonas, with higher abundance in diploid compared to triploid control fish. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to controls, a phenomenon not observed in triploid fish. Our results indicate that ploidy can affect the alpha diversity of the gills but not the skin-associated microbial community. Importantly, during a natural outbreak of Branchiomonas sp. the gill microbiome of diploid Atlantic salmon became significantly more dominated by this pathogen than in triploid animals. Thus, our results suggest that ploidy may play a role on Atlantic salmon gill health and provide insights into co-infection with SAV3 and C. Branchiomonas in Atlantic salmon.

microbiology↗

bioRxiv2020

A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2

The COVID-19 pandemic has prompted the search for animal models that recapitulate the pathophysiology observed in humans infected with SARS-CoV-2 and allow rapid and high throughput testing of drugs and vaccines. Exposure of larvae to SARS-CoV-2 Spike (S) receptor binding domain (RBD) recombinant protein was sufficient to elevate larval heart rate and treatment with captopril, an ACE inhibitor, reverted this effect. Intranasal administration of SARS-CoV-2 S RBD in adult zebrafish recombinant protein caused severe olfactory and mild renal histopathology. Zebrafish intranasally treated with SARS-CoV-2 S RBD became hyposmic within minutes and completely anosmic by 1 day to a broad-spectrum of odorants including bile acids and food. Single cell RNA-Seq of the adult zebrafish olfactory organ indicated widespread loss of expression of olfactory receptors as well as inflammatory responses in sustentacular, endothelial, and myeloid cell clusters. Exposure of wildtype zebrafish larvae to SARS-CoV-2 in water did not support active viral replication but caused a sustained inhibition of ace2 expression, triggered type 1 cytokine responses and inhibited type 2 cytokine responses. Combined, our results establish adult and larval zebrafish as useful models to investigate pathophysiological effects of SARS-CoV-2 and perform pre-clinical drug testing and validation in an inexpensive, high throughput vertebrate model.

immunology↗

bioRxiv2018

Olfactory sensory neurons mediate ultra-rapid antiviral immune responses in teleosts in a TrkA-dependent manner

The nervous system is known to regulate host immune responses. However, the ability of neurons to detect danger and initiate immune responses at barrier tissues is unclear. Vertebrate olfactory sensory neurons (OSNs) are located in direct contact with the external environment and therefore directly exposed to pathogens. Here, we report that nasal delivery of rhadboviruses induced apoptosis in crypt OSNs in rainbow trout olfactory organ (OO) via the interaction of the OSN TrkA receptor with viral glycoprotein. This signal resulted in pro-inflammatory responses in the OO and dampened inflammation in the olfactory bulb (OB). CD8+ cells infiltrated the OO within minutes of nasal viral delivery and this response was abrogated when TrkA was blocked. Infiltrating CD8+ cells originated from the microvasculature surrounding the OB and not the periphery. Ablation of crypt neurons in zebrafish resulted in increased susceptibility to rhabdoviral challenge. Our results, therefore, indicate a novel function for OSNs as a first layer of pathogen detection in vertebrates.

immunology↗

bioRxiv2018

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)

Commensal microorganisms present at mucosal surfaces play a vital role in protecting the host organism from bacterial infection. There are multiple factors that contribute to selecting for the microbiome, key of which are host genetics. Flavobacterium psychrophillum, the causative agent of Bacterial Cold Water Disease in salmonids, accounts for acute losses in wild and farmed Rainbow Trout (Oncorhynchus mykiss). The U.S. National Center for Cool and Cold Water Aquaculture has used family-based selective breeding to generate a line of rainbow trout with enhanced resistance to F. psychrophilum. The goal of this study is to determine whether selective breeding impacts the gut and gill microbiome of the F. psychrophilum-resistant as compared to a background matched susceptible trout line. Mid-gut and gill samples were collected from juvenile fish (mean bwt 118g) and microbial diversity assessed by 16S rDNA amplicon sequencing. Results indicate that alpha diversity was significantly higher in the mid-gut of the susceptible line compared to the resistant line, while no significant differences in alpha diversity were observed in the gills. Mycoplasma sp. was the dominant taxon in the mid-gut of both groups, although it was present at a decreased abundance in the susceptible line. We also observed an increased abundance of taxa that could potentially be pathogenic in the susceptible line, including Brevinema sp. and Enterobacteriaceae members. Within the gills, both lines exhibited similar microbial profiles, with Candidatus Branchiomonas being the dominant taxon. Together, these results suggest that selectively bred Flavobacterium psychrophillum-resistant trout may harness a more resilient gut microbiome, attributing to the disease resistant phenotype, providing a framework for future experiments.

microbiology↗

bioRxiv2018

Mucosal immunoglobulins protect the olfactory organ of teleost fish against parasitic infection

The olfactory organ of vertebrates receives chemical cues present in the air or water and, at the same time, they are exposed to invading pathogens. Nasal-associated lymphoid tissue (NALT), which serves as a mucosal inductive site for humoral immune responses against antigen stimulation, is present in teleosts and mammals. IgT in teleosts is responsible for similar functions to those carried by IgA in mammals. Moreover, teleost NALT is known to contain B-cells and teleost nasal mucus contains immunoglobulins (Igs). Yet, whether nasal B cells and Igs respond to infection remains unknown. We hypothesized that water-borne parasites can invade the nasal cavity of fish and elicit local specific immune responses. To address this hypothesis, we developed a model of bath infection with the Ichthyophthirius multifiliis (Ich) parasite in rainbow trout, Oncorhynchus mykiss, an ancient bony fish, and investigated the nasal adaptive immune response against this parasite. Critically, we found that Ich parasites in water could be reach the nasal cavity and successfully invade the nasal mucosa. Moreover, strong parasite-specific IgT responses were exclusively detected in the nasal mucus, and the accumulation of IgT+ B-cells was noted in the nasal epidermis after Ich infection. Strikingly, local IgT+ B-cell proliferation and parasite-specific IgT generation were found in the trout olfactory organ, providing new evidence that nasal-specific immune responses were induced locally by a parasitic challenge. Overall, our findings suggest that nasal mucosal adaptive immune responses are similar to those reported in other fish mucosal sites and that an antibody system with a dedicated mucosal Ig performs evolutionary conserved functions across vertebrate mucosal surfaces.\n\nAuthor SummaryThe olfactory organ is a vitally important chemosensory organ in vertebrates but it is also continuously stimulated by pathogenic microorganisms in the external environment. In mammals and birds, nasopharynx-associated lymphoid tissue (NALT) is considered the first line of immune defense against inhaled antigens and in bony fish, protecting against water-borne infections. However, although B-cells and immunoglobulins (Igs) have been found in teleost NALT, the defensive mechanisms of parasite-specific immune responses after pathogen challenge in the olfactory organ of teleost fish remain poorly understood. Considering that the NALT of all vertebrates has been subjected to similar evolutionary forces, we hypothesize that mucosal Igs play a critical role in the defense of olfactory systems against parasites. To confirm this hypothesis, we show the local proliferation of IgT+ B-cells and production of pathogen-specific IgT within the nasal mucosa upon parasite infection, indicating that parasite-specific IgT is the main Ig isotype specialized for nasal-adaptive immune responses. From an evolutionary perspective, our findings contribute to expanding our view of nasal immune systems and determining the fate of the host-pathogen interaction.

immunology↗