Biology subjects

Pena, R.

Publications and source records attributed to Pena, R..

8 recordsLinked to original sources

bioRxiv2025

Spatial transcriptomic profiling of the human aortic valve reveals cellular sex differences near sites of calcification

Sex differences in aortic valve stenosis (AVS) progression have been documented clinically, but the underlying cellular mechanisms that drive sex-dependent calcification in aortic valve tissue remain poorly understood. Here, we harnessed single cell and spatial transcriptomics to investigate mechanisms that drive sex dependent spatial organization of valvular interstitial cell (VIC) and macrophage gene expression near calcification sites in human male and female aortic valve tissue. Histological analyses of aortic valve tissues stratified into healthy and diseased cohorts based on degree of calcification reveal increased valve calcification area in diseased male aortic valves relative to female, and increased valve thickening in diseased female aortic valves. Single cell sequencing analysis of heterogeneous valvular interstitial cell (VIC) populations reveals male-dependent gene expression of the Activator Protein 1 (AP-1) transcription factor complex. Spatial transcriptomics and RNA-FISH analyses of VIC populations near sites of calcification revealed male-dependent gene expression localization of Cartilage Oligomeric Matrix Protein (COMP), as opposed to diffuse COMP expression in female VICs. Cell-cell communication analyses were used to determine female-specific macrophage-VIC interactions. Secreted phosphoprotein 1 (also known as osteopontin) expressed from macrophages interacts with the cell surface receptor CD44 expressed by VICs to drive a pro-fibrotic phenotype in female aortic valves. Together, our results reveal sex differences in VIC and macrophage heterogeneity and functions near sites of calcification in aortic valve tissue. Our results highlight the importance of sex-based transcriptomics analyses to understand the cellular phenotypes responsible for causing sex differences in aortic valve fibrosis calcification.

genomics↗

bioRxiv2025

Epistasis between Na+/K+-ATPase Substitutions May Influence Salinity Tolerance in Steinernema Entomopathogenic Nematodes

Soil salinity varies widely across geographies both due to natural factors and human activities, including agriculture, road salt application, sea level rise, and desertification. Increases in soil salinity may affect organisms widely and particularly impact soil foodwebs. As parasites, entomopathogenic nematodes (EPNs) occupy crucial links in soil foodwebs and are important for agriculture as biological control agents of insect pests. Previous research found that the EPN Steinernema carpocapsae may exhibit higher salt tolerance than several of its congeners. We recently identified that S. carpocapsae uniquely evolved two amino acid substitutions in the first extracellular loop of the sodium pump (Na{square}/K{square}-ATPase). Here, we tested if these substitutions explain S. carpocapsaes reported lower sensitivity to salt. Our results confirm that S. carpocapsae exhibits higher salt tolerance and show it can more effectively locate and infect insect hosts than its congeners S. feltiae and S. hermaphroditum in highly saline environments. We then retraced the evolution of the two amino acid substitutions in S. carpocapsae by introducing them alone and in combination in Caenorhabditis elegans using CRISPR genome engineering. We found that C. elegans mutants with single substitutions showed improved salt tolerance. However, this improvement disappeared in the double mutant, whose sodium pump mimicked that of S. carpocapsae. This pattern of negative epistasis between the amino acid substitutions suggests they are not responsible for variation in salt tolerance between Steinernema species. Sodium pump evolution in S. carpocapsae might instead be driven by encounters with cardiac glycosides, which are released into soil by several clades of plants including milkweeds, sequestered by some of this EPNs herbivorous insect hosts, and known to target the first extracellular loop of the sodium pump. Our findings provide valuable insights into EPN adaptation to changes in environmental sodium levels and may have implications for their use in biological control.

ecology↗

bioRxiv2025

A secreted fatty acid- and retinol- binding protein from Heligmosomoides polygyrus suppresses host macrophage polarization

Parasitic nematodes are major pathogens of humans, animals, and plants, contributing to global health challenges and substantial agricultural losses. Fatty acid- and retinol-binding proteins (FARs), secreted by parasitic nematodes, are believed to play key roles in host-pathogen interactions, including immune modulation and nutrient acquisition. In this study, we characterize a FAR protein from the gastrointestinal nematode Heligmosomoides polygyrus, Hp-FAR-2. Unlike FARs from Caenorhabditis elegans, Steinernema carpocapsae, and Ancylostoma ceylanicum, Hp-FAR-2 did not influence immunity or survival in a Drosophila melanogaster infection model, suggesting functional divergence within the FAR family. Competitive lipid-binding assays revealed a preference for omega-3 and omega-6 polyunsaturated fatty acids, indicating selective binding to bioactive lipids that may modulate immunity. Using RAW 264.7 macrophages, we found that Hp-FAR-2 suppresses the expression of both M1-associated (TNF-, IL-6) and M2-associated (Chil3) markers during polarization, implicating it as a broad immunomodulator that may inhibit inflammatory responses and tissue repair mechanisms to promote chronic infection. Our findings support a model in which Hp-FAR-2 disrupts host lipid signaling and immune function to favor parasite persistence, suggesting its potential role in the excretory/secretory products of H. polygyrus. Together, these data enhance our understanding of FAR-mediated host manipulation and may inform the development of novel anthelmintic or immunoregulatory therapies.

biochemistry↗

bioRxiv2025

FRAZZLED/DCC REGULATES GAP JUNCTION FORMATION AT A DROSOPHILA GIANT SYNAPSE THROUGH TRANSCRIPTION

Loss of function Frazzled/DCC mutants demonstrate that the gene regulates synaptogenesis in the Giant Fiber System of Drosophila. In frazzled loss of function (LOF) mutants, we observe weaker physiology, characterized by longer latencies and reduced response frequencies between the GFs and the motor neurons. These physiological phenotypes are linked to a loss of gap junctions in the GFs, specifically the loss of the shaking-B(neural+16) isoform of innexin in the presynaptic terminal. A GF biophysical computational model is provided to test the role of gap junctions and the function of the Giant Fiber System. We present evidence of Frazzleds role in gap junction regulation by utilizing the UAS-GAL4 system in Drosophila to rescue mutant phenotypes. Expression of various UAS-Frazzled constructs in a Frazzled LOF background was used to dissect the role of different parts of the Frazzled receptor in the assembly of electrical synapses. Driving Frazzleds intracellular domain in Frazzled LOF mutants rescued axon pathfinding and synaptogenesis. This is supported by the fact that Frazzled fails to rescue the synaptic function when its transcriptional activation domain is disrupted, as shown by the deletion of the highly conserved intracellular P3 domain or by a construct with a point-mutation in the highly conserved P3 domain known to be required for transcriptional activation. The present work is the first to show how a guidance molecule regulates synaptogenesis through transcriptional regulation of synaptic components.

neuroscience↗

bioRxiv2025

Amino Acid Substitutions in the Na+/K+-ATPase May Contribute to Salinity Tolerance in Insects

O_LIEnvironmental salinity levels vary naturally across terrestrial ecosystems but can be heightened locally by coastal proximity and desertification as well as human activities such as road salt application and agriculture. Since salt is essential for many physiological processes in insects, rising environmental sodium concentrations may drive behavioral changes, where insects select environments and food sources with suitable sodium levels, or evolutionary changes in constitutive or plastic physiological mechanisms to process salt, potentially altering ecological dynamics and species interactions. C_LIO_LINumerous hematophagous (blood feeding) insects such as the yellow-fever mosquito Aedes aeqypti are known to be able to breed in relatively saline environments. Among phytophagous (plant feeding) insects, grasshoppers can be important herbivores in arid and coastal salt-affected regions, whereas the monarch butterfly (Danaus plexippus) appears to perform relatively well on milkweed host plants growing in roadsides influenced by salt runoff. Several of these insects share a common trait: amino acid substitutions in the first extracellular loop of the Na+/K+-ATPase (NKA), a sodium pump crucial for maintaining ion balance. For the monarch these substitutions confer resistance to toxic cardenolides from milkweeds, but it is unclear whether NKA substitutions may influence salt tolerance. C_LIO_LIHere, we investigate whether the NKA substitutions found in these insects may contribute to salt tolerance using gene-edited Drosophila melanogaster mutant strains as models. We show that flies with substitution Q111L (found in Aedes mosquitoes) or a combination of Q111L and A119S (found in grasshoppers) exhibited greater salt tolerance, whereas flies carrying the combination of substitutions found in the monarch (Q111V, A119S, and N122H) did not. C_LIO_LIOur results suggest that the monarch may rely on alternate mechanisms for salt tolerance and that its NKA substitutions are important primarily for cardenolide resistance. However, substitution Q111L and the combination of Q111L and A119S may be relevant for salt tolerance in a variety of insects. Uncovering mechanisms of salt tolerance enhances our understanding of species distributions, ecological interactions, and evolutionary physiology in response to changing environmental salinity levels. C_LI

genetics↗

bioRxiv2022

Polyploidy and plant-fungus symbiosis: evidence of cytotype-specific microbiomes in the halophyte Salicornia (Amaranthaceae)

Polyploidy is recognized as a mechanism of speciation in plants with cascading effects on biotic interactions. However, a limited number of studies have investigated the effects of polyploidy on the association of plants and microorganisms. Herein, we investigated whether two Salicornia cytotypes (S. europaea - 2x and S. procumbens - 4x) show different root-associated fungal communities. Additionally, we explored the existence of cytotype-specific root anatomical traits, which could influence fungal recruitment and establishment. Salicornia spp. were identified based on their ploidy level. The root-associated fungal microbiome of Salicornia was analyzed using high throughput amplicon sequencing (ITS1 of rDNA) in spring and summer. The following root anatomical traits were investigated: maximum root diameter, periderma thickness, parenchyma thickness, diameter of the vascular cylinder and maximum diameter of parenchyma cells. Our results showed that Shannon diversity and evenness indices were higher in samples of Salicornia procumbens (4x) compared to those of S. europaea (2x), and in summer the root-associated fungal community of S. procumbens (4x) was significantly different from that of S. europaea (2x). The orders Xylariales, Malasseziales and Pleosporales were the most frequent root colonizers in both cytotypes and most of the taxa associated with Salicornia were functionally classified as saprophytes or plant pathogens. Finally, we observed larger periderma and parenchyma layers in S. procumbens (4x) than S. europaea (2x) that may contribute to the observed differences in community composition between the two cytotypes. Our results suggest that differences in ploidy may modulate plant interaction with fungi by affecting species recruitment and microbiome structure. In addition, cytotype-specific root traits may also have the potential to affect differently community assembly in the two cytotypes.

ecology↗

bioRxiv2019

Using variation in arbuscular mycorrhizal fungi to drive the productivity of the food security crop cassava

The unprecedented challenge to feed the rapidly growing human population can only be achieved with major changes in how we combine technology with agronomy1. Despite their potential few beneficial microbes have truly been demonstrated to significantly increase productivity of globally important crops in real farming conditions2,3. The way microbes are employed has largely ignored the successes of crop breeding where naturally occurring intraspecific variation of plants has been used to increase yields. Doing this with microbes requires establishing a link between variation in the microbes and quantitative traits of crop growth along with a clear demonstration that intraspecific microbial variation can potentially lead to large differences in crop productivity in real farming conditions. Arbuscular mycorrhizal fungi (AMF), form symbioses with globally important crops and show great potential to improve crop yields2. Here we demonstrate the first link between patterns of genome-wide intraspecific AMF variation and productivity of the globally important food crop cassava. Cassava, one of the most important food security crops, feeds approximately 800 million people daily4. In subsequent field trials, inoculation with genetically different isolates of the AMF Rhizophagus irregularis altered cassava root productivity by up to 1.46-fold in conventional cultivation in Colombia. In independent field trials in Colombia, Kenya and Tanzania, clonal sibling progeny of homokaryon and dikaryon parental AMF enormously altered cassava root productivity by up to 3 kg per plant and up to a 3.69-fold productivity difference. Siblings were clonal and, thus, qualitatively genetically identical. Heterokaryon siblings can vary quantitatively but monokaryon siblings are identical. Very large among-AMF sibling effects were observed at each location although which sibling AMF was most effective depended strongly on location and cassava variety. We demonstrate the enormous potential of genetic, and possibly epigenetic variation, in AMF to greatly alter productivity of a globally important crop that should not be ignored. A microbial improvement program to accelerate crop yield increases over that possible by plant breeding or GMO technology alone is feasible. However, such a paradigm shift can only be realised if researchers address how plant genetics and local environments affect mycorrhizal responsiveness of crops to predict which fungal variant will be effective in a given location.

microbiology↗

bioRxiv2019

Assessing the multiple dimensions of poverty. Data mining approaches to the 2004-14 Health and Demographic Surveillance System in Cuatro Santos, Nicaragua

We aimed to describe multiple dimensions of poverty according to the capability approach theory by applying data mining approaches to the Cuatro Santos Health and Demographic Surveillance databases, Nicaragua. Four municipalities in northern Nicaragua constitute the Cuatro Santos area, with 25,893 inhabitants in 5,966 households (2014). A local process analyzing poverty-related problems and prioritizing suggested actions, was initiated 1997 based on a community action plan 2002-2015. Priority interventions were school breakfasts, environmental protection, water and sanitation, preventive healthcare, home gardening, micro credits, technical training, stipends for university education, and the use of Internet. In 2004, a survey of basic health and demographic information was performed in the whole population followed by surveillance updates in 2007, 2009, and 2014 linking households and individuals by unique identifiers. Information included the house (floor, walls) and services (water, sanitation, electricity) as well as demographic data (birth, deaths, migration). Data on participation in interventions, on food security, household assets, and womens self-rated health were collected in 2014. A K-means algorithm were used to cluster the household data (54 variables). The poverty ranking of household clusters using the unsatisfied basic needs index (UBN) variables changed when including variables describing basic capabilities. The households in the fairly rich cluster, having assets as motorbikes and computers were described as modern. Those in the fairly poor cluster, having different degrees of food insecurity were labeled vulnerable. Poor and poorest clusters of households were traditional e.g. in using horses for transport. Results displayed a society transforming from traditional to a modern, where the forerunners were not the richest but educated, had more working members of household, fewer children and were food secure. Those lagging were the poor, traditional and food insecure. The approach and results may be useful for an improved understanding of poverty and to direct local interventions.

epidemiology↗