Biology subjects

Fajardo, A.

Publications and source records attributed to Fajardo, A..

7 recordsLinked to original sources

bioRxiv2026

Intra-host IRES heterogeneity shapes hepatitis C virus translation through epistatic and population-level effects

Hepatitis C virus (HCV) circulates within each patient as a diverse population of closely related genomes, yet RNA functional properties are commonly inferred from a single consensus or dominant genome. The contribution of non-coding intra-host variability, particularly within the internal ribosome entry site (IRES), to translational efficiency remains poorly defined. Here we investigated how naturally occurring HCV IRES variation influences viral RNA translation. Complete IRES sequences from chronically infected patients were analyzed using molecular cloning, bicistronic reporters, full-length replication-deficient viral RNAs and reconstructed intra-host populations. We found that natural IRES mutations displayed context-dependent effects, and combinations of mutations produced translational phenotypes that could not be predicted from the corresponding single mutations, consistent with intragenic epistasis. Moreover, several variants behaved differently in bicistronic reporters and full-length viral RNAs, demonstrating that both genomic and cellular context shape IRES function. Reconstructed genotype 1a populations largely reproduced the activity of their dominant haplotypes. In contrast, reconstructed genotype 3a populations translated substantially more efficiently than their corresponding dominant sequences, showing that low-frequency variants can collectively modulate translation at the population level. These findings demonstrate that the translational phenotype of HCV cannot always be inferred from the dominant sequence alone and identify epistasis, genomic context, and intra-host population composition as interacting determinants of viral RNA translation. ImportanceHepatitis C virus (HCV) exists within each infected person as a diverse population of closely related viruses rather than as a single genetic sequence. This study shows that natural variation in a key RNA region controlling viral protein production can alter how efficiently the virus functions, and that these effects depend on combinations of mutations rather than on individual changes alone. By analyzing complete viral RNAs in addition to widely used reporter systems, we demonstrate that the full viral genome can substantially influence the activity of this regulatory region, providing a more realistic view of how translation occurs during natural infection. Our findings also reveal that rare viral variants can collectively shape the behavior of the viral population, challenging the common practice of relying on a single dominant sequence to represent an infection. These results provide new insight into how genetic diversity drives HCV evolution and adaptation.

molecular biology↗

bioRxiv2026

Defensive lipid droplets are PUFA reservoirs driving bacterial clearance and inflammation

Lipid droplets (LDs) rapidly form in infected cells to participate in the defence against microbes. Here, we investigate the involvement of LD lipids in these immune responses. Comparative shotgun and targeted lipidomics demonstrate that in vivo host LDs accumulate polyunsaturated fatty acids (PUFAs). PUFAs arrive at cells from the bloodstream to be further metabolised into complex PUFAs accrued by LD-triglycerides and -phospholipids. Host lipid metabolism is transcriptionally controlled by rapid, transient, and intricate immune programs initiated by pathogen-associated molecular patterns and relayed by cytokines such as interferons (type I and II), interleukins (IL-1{beta}), and tumour necrosis factor. When this lipid and signalling environment is reproduced in cultured macrophages, newly formed LDs accumulate defensive proteins, coordinate the synthesis of complex PUFAs, and become PUFA reservoirs and suppliers. Among LD-PUFAs, the {omega}-6 arachidonic acid is the most actively metabolised during the initial phases of innate immunity. Released from LDs by adipose triglyceride lipase, arachidonic acid is used by macrophages for prostaglandin synthesis, bacterial phagocytosis, and elimination of microbes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=163 HEIGHT=200 SRC="FIGDIR/small/711356v2_ufig1.gif" ALT="Figure 1"> View larger version (107K): org.highwire.dtl.DTLVardef@14d65eorg.highwire.dtl.DTLVardef@5ecc1org.highwire.dtl.DTLVardef@fa99e5org.highwire.dtl.DTLVardef@8d9632_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Extended tissue tropism and vertical transmission in a murine model of Mayaro virus infection

Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus associated with acute febrile illness and persistent arthralgia, with increasing reports in Latin America and potential for geographic expansion. However, its dissemination dynamics, tissue tropism and transmission routes remain incompletely defined. Here, we developed a murine model to characterize systemic viral dissemination, tissue tropism and the impact of gestational stage on maternal-fetal outcomes. A nanoluciferase-expressing MAYV reporter enabled non-invasive in vivo imaging, revealing rapid and widespread systemic dissemination under controlled conditions. Complementary infection with wild-type (WT) virus confirmed broad tropism across lymphoid, musculoskeletal and reproductive tissues. At 24 hours post-infection (hpi), viral distribution was relatively homogeneous across tissues, whereas at 48 hpi, tissue-specific differences emerged, with increased viral loads in selected organs, including the spleen and male reproductive tissues. Transient sex-dependent differences were observed at 24 hpi but were not sustained at later time points. Hematological and biochemical analyses revealed early systemic alterations consistent with changes in leukocyte distribution during acute infection. Infectious viral particles were detected in reproductive tissues of both sexes, including in sperm, supporting the biological plausibility of non-vector transmission, although detection in exposed animals was limited. Gestational stage influenced infection outcomes: early gestation (infected at 7.5-8.5 dpc; analyzed at 9.5-10.5 dpc) was associated with detection of infectious virus in fetal tissues, whereas mid-gestation (infected at 13.5-14.5 dpc; analyzed at 15.5-16.5 dpc) showed no detectable infectious virus in fetuses despite evidence of viral antigen persistence and sustained infectious viral presence in maternal and placental compartments. Together, these findings provide a preclinical framework for investigating MAYV pathogenesis and underscore the role of tissue tropism and gestational context in shaping infection dynamics and maternal-fetal involvement. Author summaryMayaro virus (MAYV) is an emerging mosquito-borne virus that causes fever and long-lasting joint pain, with increasing reports in Latin America and potential for wider geographic spread. Despite its growing relevance, key aspects of MAYV pathogenesis remain to be fully defined, including the mechanisms underlying systemic dissemination and tissue tropism, as well as its potential to affect pregnancy or be transmitted through non-vector routes. Here, we used a mouse model with a luminescent reporter virus to track MAYV dissemination in vivo, revealing rapid and widespread distribution across multiple tissues. In studies using wild-type virus, infectious virus was detected not only in muscle and immune-related organs but also in reproductive tissues of both females and males. Importantly, gestational stage influenced viral distribution. When infection occurred early in gestation, infectious viral particles were detected in fetal tissues. In contrast, at later stages of pregnancy, infectious virus was no longer detectable in fetuses, despite evidence of viral antigen persistence and sustained infectious viral presence in maternal and placental tissues. Together, these findings advance our understanding of MAYV infection, highlight gestational timing as a factor associated with fetal exposure and suggest the possibility of transmission through routes other than mosquitoes, providing a framework for future studies on this emerging virus.

microbiology↗

bioRxiv2025

Beyond species means - the intraspecific contribution to global wood density variation

Wood density is central for estimating vegetation carbon storage and a plant functional trait of great ecological and evolutionary importance. However, the global extent of wood density variation is unclear, especially at the intraspecific level. We assembled the most comprehensive wood density collection to date (GWDD v.2), including 109,626 records from 16,829 plant species across woody life forms and biomes. Using the GWDD v.2, we explored the sources of variation in wood density within individuals, within species, and across environmental gradients. Intraspecific variation accounted for up to 15% of overall wood density variation (sd = 0.068 g cm-3). Sapwood densities varied 50% less than heartwood densities, and branchwood densities varied 30% less than trunkwood densities. Individuals in extreme environments (dry, hot, acidic soils) had higher wood density than conspecifics elsewhere (+0.02 g cm-3, [~]4% of the mean). Intraspecific environmental effects strongly tracked interspecific patterns (r = 0.83) but were only 20-30% as large and varied considerably among taxa. Individual plant wood density was difficult to predict (RMSE > 0.08 g cm-3; single-measurement R2 = 0.59). We recommend (i) systematic within-species sampling for local applications, and (ii) expanded taxonomic coverage combined with integrative models for robust estimates across ecological scales.

plant biology↗

bioRxiv2025

A global map of wood density

Wood density influences how quickly woody plants grow, how long they live and how much carbon they store, yet its global variation remains poorly mapped. Here we combined 109,626 wood density measurements from 16,829 species with 300,949 vegetation plots to produce a km-scale map of community-weighted wood density for every woody biome. Our model led to a prediction accuracy 32-51 % higher than previous global products, and a 1.8-3.7-fold wider wood density range (0.28-1.00 g cm-3; global mean: 0.57 g cm-3) than previously assumed. Spatial cross-validation showed low bias ({+/-}2.5 % of the mean), and uncertainties decreased from 20% in poorly sampled drylands and boreal regions to 5% in data-rich temperate forests. Mean annual temperature was the best predictor of community-weighted mean wood density, increasing by 0.01 g cm-3 for every 1{degrees}C change. We deliver a low-bias, high-resolution wood density layer for Earth system models, together with spatially explicit error maps. This study represents a major step forward for carbon accounting and trait-based forecasts of vegetation change.

plant biology↗

bioRxiv2022

Proteostatic regulation of caveolins avoids premature oligomerisation and preserves ER homeostasis

Caveolin-1 (CAV1) and CAV3 are membrane sculpting proteins driving formation of plasma membrane caveolae. Caveola formation is unique as it requires oligomerisation of newly synthesised caveolins through the biosynthetic-secretory pathway. Here, we combine structural, biochemical, and microscopy analyses to examine the early proteostasis of caveolin family members and mutants. We describe striking trafficking differences between newly synthesised caveolins, with CAV1 rapidly exported to the Golgi but CAV3 showing ER retention and targeting to lipid droplets. Only monomeric/low oligomeric caveolins are efficiently exported from the ER, with oligomers assembling beyond the cis-Golgi and disease-causing mutations leading to detrimental non-functional complexes. Caveolins in the ER are maintained at low levels by active proteasomal degradation, avoiding premature oligomerisation and ER stress. Increasing lipid availability, cholesterol for CAV1 and fatty acids for CAV3, enhances trafficking and reduces proteasomal degradation. In conclusion, we identify proteostatic mechanisms that modulate stability and trafficking of newly synthesised caveolins, protecting cells against ER stress but perturbed in caveolin-related disease. SummaryUnderstanding the unique proteostasis of caveolins has important implications for cell biology and physiopathology. Combining structural, microscopy, and biochemical analyses, we uncover new insights into the mechanisms that differentiate the early biosynthetic steps of caveolin family members, isoforms, and pathogenic mutants.

cell biology↗

bioRxiv2020

Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples

The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low and middle income countries. In the interest of economy, time and availability of chemicals and consumables, the SYBR Green-based detection was implemented to establish a convenient assay. Therefore, we adapted one of WHO recommended Taqman-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results suggest that SYBR-Green detection represents a reliable cost-effective alternative to increase the testing capacity.

molecular biology↗