Biology subjects

Medina, J.

Publications and source records attributed to Medina, J..

14 recordsLinked to original sources

bioRxiv2026

MYB28 and MYB29 transcription factors regulate iron homeostasis and iron-mobilizing coumarin biosynthesis in Arabidopsis thaliana

Iron (Fe) deficiency is a major constraint for plant growth and triggers extensive physiological and transcriptional reprogramming to maintain Fe homeostasis. Here, we identify the glucosinolate-associated transcription factors MYB28 and MYB29 as previously unrecognized regulators of Arabidopsis thaliana adaptation to Fe deficiency. Across various growth systems, loss of MYB28 increased sensitivity to Fe deficiency, whereas the myb28myb29 double mutant displayed stronger chlorosis, reduced root growth and impaired biomass accumulation, indicating cooperative but unequal functions of these transcription factors. Despite their enhanced Fe-deficiency phenotype, double mutant plants accumulated higher Fe levels in roots and exhibited stronger induction of canonical Fe-deficiency responses, suggesting impaired Fe utilization or distribution rather than defective Fe uptake. RNA-seq revealed extensive transcriptional reprogramming under Fe deficiency, with pronounced deregulation of genes involved in Fe homeostasis, redox processes and growth, particularly in the double mutant. Among these, SCOPOLETIN 8-HYDROXYLASE (S8H) emerged as a major target gene of MYB28. The expression of S8H was almost abolished in myb28 and myb28myb29 mutants, whereas expression of other coumarin biosynthetic genes remained largely unaffected. Promoter activation assays demonstrated that MYB28 activates the S8H promoter, and metabolic analyses showed accumulation of scopolin together with reduced fraxin levels in the mutants, consistent with impaired S8H activity. Collectively, our results identify MYB28 as a key regulator linking specialized metabolism to Fe homeostasis through control of coumarin biosynthesis, thereby expanding the biological functions of MYB28 and MYB29 transcription factors.

plant biology↗

bioRxiv2025

New distribution records of Aedes aegypti, Aedes mediovittatus, and Toxorhynchites portoricensis (Diptera: Culicidae) in Puerto Rico and their relevance to Integrated Vector Management

As of October 2025, Puerto Rico has been experiencing an ongoing dengue outbreak that started in March 2024. The latest island-wide mosquito survey conducted in Puerto Rico during 2018- 2019 covered 41 of the 78 municipalities and detected the presence of Aedes aegypti in 27 of the municipalities. Given the prolonged elevated circulation of dengue virus on the island, we carried out an additional Ae. aegypti survey in June 2025 across 44 out of 78 municipalities, including areas with no prior records of the species. Here, we report the occurrence of Ae. aegypti in 43 out of 44 municipalities surveyed, including ten new municipalities where Ae. aegypti has not been reported. These findings provide insight into the dispersal of Ae. aegypti in Puerto Rico, indicating that the species is much more widespread than previously known. We also provide the expanded species occurrence of Aedes mediovittatus and Toxorhynchites portoricensis, which share the same larval habitat as Ae. aegypti. Notably, 96% of cemeteries surveyed across 24 municipalities served as oviposition sites for Ae. aegypti. However, a few cemeteries demonstrated effective preventative practices that minimize mosquito breeding. This effective management, which resulted in no mosquito breeding in some cemeteries and a tire shop, brings hope that communication and education of property/facility managers can reduce the mosquito populations.

ecology↗

bioRxiv2025

Reorganization of motor functions within visuomotor networks subsequent to somatosensory cortical damage

Somatosensory inputs are critical to motor control. Animal studies have shown that primary somatosensory lesions cause sensorimotor deficits along with disrupted organization in primary motor cortex (M1). How does damage in primary somatosensory cortex (S1) influence motor networks in humans? Using fMRI, we examined two individuals with extensive damage to left somatosensory cortex, but primarily intact motor cortex and preserved motor abilities. Given left S1 damage, tactile detection and localization were impaired for the contralesional hand in both individuals. When moving the contralesional hand, LS, with near complete damage to the S1 hand area, showed increased activation in ipsilesional putamen and deactivation in contralesional cerebellum relative to age-matched controls. These findings demonstrate influences of S1 damage to subcortical sensorimotor areas that are distant from the lesion site, and a potential reweighting of the motor network with increased action selection in putamen and inhibition of sensory prediction in cerebellum in the face of sensory loss. In contrast, RF, who had a small island of spared S1 in the hand area, showed greater activation in contralesional S1 for movement versus rest. This same region was also activated by pure somatosensory stimulation in a second experiment, suggesting that the spared S1 area in RF still subserves sensorimotor processing. Finally, the right middle occipital gyrus was more strongly activated in both individuals compared with controls, suggesting a potential reliance on visual imagery in the face of degraded sensory feedback.

neuroscience↗

bioRxiv2025

NAc-DBS selectively enhances memory updating without effect on retrieval

Deep brain stimulation (DBS) has emerged as a widely used therapeutic option when pharmacological treatments prove ineffective or refractory for psychiatric patients. The nucleus accumbens (NAc) represents a frequently targeted site in DBS interventions due to its demonstrated safety profile and therapeutic efficacy in obsessive-compulsive disorder, major depression, and anorexia nervosa. However, limited mechanistic understanding hampers its broader clinical applicability. This study sought to delineate the distinct behavioural dimensions modulated by NAc-DBS, its impact on distinct facets of memory, and to elucidate the underlying brain-network mechanism of action. We developed a novel spatial navigation task for rats and employed a high-dimensional behavioural analysis complemented by fMRI to dissect the cognitive, behavioural and neurobiological effects of NAc-DBS. Active NAc-DBS produced a selective enhancement of long-term memory encoding without affecting memory recall or working memory. We found no effect of NAc-DBS on motor, appetitive or stress-related behaviours. Sustained neuronal activation in the NAc, septum, entorhinal and insular cortex demonstrated no desensitization to chronic NAc-DBS, which triggered a functional reorganization among dopaminergic-related structures. These findings suggest that NAc-DBS induces a functional reorganization in the mesocorticolimbic system, potentially mimicking a dopaminergic novelty signal to enhance memory updating. This provides a mechanistic basis for the therapeutic use of NAc-DBS, particularly in improving cognitive flexibility in psychiatric disorders.

neuroscience↗

bioRxiv2024

Alternatives to Friction Coefficient: Fine Touch Perception Relies on Frictional Instabilities

Fine touch perception is often correlated to material properties and friction coefficients, but the inherent variability of human motion has led to low correlations and contradictory findings. Instead, we hypothesized that humans use frictional instabilities to discriminate between objects. Here, we constructed a set of coated surfaces with minimal physical differences, but due to differences in surface chemistry, generated different types of instabilities depending on how quickly a finger is slid and pressed during sliding. In one experiment, we used a mechanical mock finger to quantify and classify differences in instability formation from different coated surfaces. In a second experiment, participants perform a discrimination task using the same coated surfaces. Using the data from these two experiments, we found that human discrimination response times were faster with surfaces where the mock finger produced more stiction spikes and discrimination accuracy was higher where the mock finger produced more steady sliding. Conversely, traditional metrics like surface roughness or average friction coefficient did not relate to tactile discriminability. In fact, the typical method of averaging friction coefficients led to a spurious correlation which erroneously suggests that distinct objects should feel identical and identical objects should feel distinct--similar to findings by others. Friction instabilities may offer a more predictive and tractable framework of fine touch perception than friction coefficients, which would accelerate the design of tactile interfaces.

neuroscience↗

bioRxiv2024

PicoCam: High-resolution 3D imaging of live animals and preserved specimens

1. The PicoCam system is a multi-camera photogrammetry rig used for generating high-resolution 3D models of animals in the field, or preserved specimens in laboratory or museum settings. The digital measurement of 3D models is increasingly useful for studying body shape. However, methods that capture sub-millimetric detail often do so at the cost of portability and versatility; this system aims to bridge this gap. 2. The PicoCam system employs 3D digital photogrammetry, a process that generates accurate, full-color, 3D models from sequences of photographs. By using six cameras and a rotating base, the system is able to capture multiple angles in rapid succession - a key advantage for both 3D-imaging live specimens and efficiently scanning museum specimens. Through the use of macro lenses and high-resolution camera sensors, this system can capture sub-millimetric detail without sacrificing portability. 3. In this study, we 3D imaged the bills of 19 species of hummingbirds using the PicoCam system and measured length, height, width, surface area, and volume of their bills. We examined eight species in the field and 11 from the Burke Museum in Seattle. We chose Hummingbird bills as a model system, as their fine-scale interspecific differences in 3D shape can have significant functional and behavioral implications, and could tell us more about how these traits predict habitat and resource use. 4. The prospect of a common 3D-imaging method for both museum and field use is compelling when documenting structures shape within and among species. The PicoCam system is also valuable for quantifying the 3D shape of fine-scale phenotypes (like hummingbird bills) that benefit from digital measurement, preservation, and improved accessibility. Lastly, the PicoCam system allows "digital 3D collection", by which the shape of biological structures in the field can be recorded and stored in a public database without the need to collect a specimen. This opens the door to studies in which multiple 3D image captures of the same individual across different time scales permit 3D shape/color comparisons (e.g., seasonal, ontogenetic changes).

evolutionary biology↗

bioRxiv2024

Parallel Evolution of Salinity Tolerance in Arabidopsis thaliana Accessions from Cape Verde Islands

Soil salinization poses a significant threat to crop production impacting one fifth of all cultivated land. The Cape Verde Islands are located 600 km from the coast of Africa and are characterized by high salinity soils and inland water sources. In this study we find that Arabidopsis thaliana plants native to these islands accumulate a metabolite that protects them from salt stress. We partially characterized this metabolite as glucuronyl-mannose. We find that the ability to produce glucuronyl-mannose evolved independently in two different islands from the same archipelago through mutations in the same gene, an alpha glycosidase protein that we named GH38cv. These cases of parallel evolution suggest positive selection towards the increase of salt tolerance with low fitness costs. Indeed, plants carrying derived alleles of GH38cv do not present growth defects or low defenses under normal conditions, but show better germination rates, longer roots and better hydric status than non-mutated plants when exposed to salt stress. These findings provide a knowledge-based method to develop salt resilient crops using natural mechanisms, which could be attractive both to conventional and organic agriculture.

plant biology↗

bioRxiv2023

Sord deficient rats develop a motor-predominant peripheral neuropathy unveiling novel pathophysiological insights

Biallelic SORD mutations cause one of the most frequent forms of recessive hereditary neuropathy, estimated to affect approximately 10,000 patients in North America and Europe alone. Pathogenic SORD loss-of-function changes in the encoded enzyme sorbitol dehydrogenase result in abnormally high sorbitol levels in cells and serum. How sorbitol accumulation leads to peripheral neuropathy remains to be elucidated. A reproducible animal model for SORD neuropathy is essential to illuminate the pathogenesis of SORD deficiency and for preclinical studies of potential therapies. Therefore, we have generated a Sord knockout (KO), Sord-/-, Sprague Dawley rat, to model the human disease and to investigate the pathophysiology underlying SORD deficiency. We have characterized the phenotype in these rats with a battery of behavioral tests as well as biochemical, physiological, and comprehensive histological examinations. Sord-/- rats had remarkably increased levels of sorbitol in serum, cerebral spinal fluid (CSF), and peripheral nerve. Moreover, serum from Sord-/- rats contained significantly increased levels of neurofilament light chain, NfL, an established biomarker for axonal degeneration. Motor performance significantly declined in Sord-/- animals starting at [~]7 months of age. Gait analysis evaluated with video motion tracking confirmed abnormal gait patterns in the hindlimbs. Motor nerve conduction velocities of the tibial nerves were slowed. Light and electron microscopy of the peripheral nervous system revealed degenerating myelinated axons, de- and remyelinated axons, and a likely pathognomonic finding - enlarged "ballooned" myelin sheaths. These findings mainly affected myelinated motor axons; myelinated sensory axons were largely spared. In summary, Sord-/- rats develop a motor-predominant neuropathy that closely resembles the human phenotype. Our studies revealed novel significant aspects of SORD deficiency, and this model will lead to an improved understanding of the pathophysiology and the therapeutic options for SORD neuropathy.

neuroscience↗

bioRxiv2023

In the social amoeba D. discoideum, shortened stalks limit obligate cheater success even when exploitable partners are available.

Cooperation is widespread across life, but its existence can be threatened by exploitation. The rise of obligate social cheaters that are incapable of contributing to a necessary cooperative function can lead to the loss of that function and to the extinction of populations. In the social amoeba Dictyostelium discoideum, obligate social cheaters cannot form dead stalk cells and in chimeras instead form living spore cells. This gives them a competitive advantage within chimeras. However, obligate cheaters of this kind are not found in nature, probably because they are often enough in clonal populations that they need to retain the ability to produce stalks. In this study we discovered an additional cost to obligate cheaters. Even when there are wild-type cells to parasitize, the chimeric fruiting bodies that result have shorter stalks and these are disadvantaged in spore dispersal. The inability of obligate cheaters to form fruiting bodies when they are on their own combined with the lower functionality of fruiting bodies when they are not represent limits on obligate social cheating as a strategy.

evolutionary biology↗

bioRxiv2023

An single oscillating proto-hypothalamic neuron gates taxis behavior in the primitive chordate Ciona

Ciona larvae display a number of behaviors, including negative phototaxis. In negative phototaxis, the larvae first perform short spontaneous rhythmic casting swims. As larvae cast in a light field, their photoreceptors are directionally shaded by an associated pigment cell, providing a phototactic cue. This then evokes an extended negative taxis swim. We report here that the larval forebrain of Ciona has a previously uncharacterized single slow-oscillating inhibitory neuron (neuron cor-assBVIN78) that projects to the midbrain, where it targets key interneurons of the phototaxis circuit known as the photoreceptor relay neurons. The anatomical location, gene expression and oscillation of cor-assBVIN78 suggest homology to oscillating neurons of the vertebrate hypothalamus. Ablation of cor-assBVIN78 results in larvae showing extended phototaxis-like swims, but which occur in the absence of phototactic cues. These results indicate that cor-assBVIN78 has a gating activity on phototaxis by projecting temporally-oscillating inhibition to the photoreceptor relay neurons. However, in intact larvae the frequency of cor-assBVIN78 oscillation does not match that of the rhythmic spontaneous swims, indicating that the troughs in oscillations do not themselves initiate swims, but rather that cor-assBVIN78 may modulate the phototaxis circuit by filtering out low level inputs while restricting them temporally to the troughs in inhibition.

neuroscience↗

bioRxiv2020

Predicting microbiomes through a deep latent space

MotivationMicrobial communities influence their environment by modifying the availability of compounds such as nutrients or chemical elicitors. Knowing the microbial composition of a site is therefore relevant to improving productivity or health. However, sequencing facilities are not always available, or may be prohibitively expensive in some cases. Thus, it would be desirable to computationally predict the microbial composition from more accessible, easily-measured features. ResultsIntegrating Deep Learning techniques with microbiome data, we propose an artificial neural network architecture based on heterogeneous autoencoders to condense the long vector of microbial abundance values into a deep latent space representation. Then, we design a model to predict the deep latent space and, consequently, to predict the complete microbial composition using environmental features as input. The performance of our system is examined using the rhizosphere microbiome of Maize. We reconstruct the microbial composition (717 taxa) from the deep latent space (10 values) with high fidelity ({inverted question}0.9 Pearson correlation). We then successfully predict microbial composition from environmental variables such as plant age, temperature or precipitation (0.73 Pearson correlation, 0.42 Bray-Curtis). We extend this to predict microbiome composition under hypothetical scenarios, such as future climate change conditions. Finally, via transfer learning, we predict microbial composition in a distinct scenario with only a hundred sequences, and distinct environmental features. We propose that our deep latent space may assist microbiome-engineering strategies when technical or financial resources are limited, through predicting current or future microbiome compositions. AvailabilitySoftware, results, and data are available at https://github.com/jorgemf/DeepLatentMicrobiome

bioinformatics↗

bioRxiv2018

Modelling the distribution of Aedes aegypti and Aedes albopictus using climate, host density and interspecies competitive effects

Florida faces the challenge of repeated introduction and autochthonous transmission of arboviruses transmitted by Aedes aegypti and Aedes albopictus. Empirically-based predictive models of the spatial distribution of these species would aid surveillance and vector control efforts. To predict the occurrence and abundance of these species, we fit mixed-effects zero-inflated negative binomial regression to a mosquito surveillance dataset with records from more than 200,000 trap days, covering 73% of the land area and ranging from 2004 to 2018 in Florida. We found an asymmetrical competitive interaction between adult populations of Aedes aegypti and Aedes albopictus for the sampled sites. Wind speed was negatively associated with the occurrence and abundance of both vectors. Our model predictions show high accuracy (72.9% to 94.5%) in the validation tests leaving out a random 10% subset of sites and data from 2018, suggesting a potential for predicting the distribution of the two Aedes vectors.

ecology↗

bioRxiv2018

Phylogenomics, biogeography, and evolution in the American palm genus Brahea

Background and AimsSlow rates of molecular evolution at low taxonomic levels hamper studies of relationships among species, and subsequent biogeographic and evolutionary analyses. An example is the genus Brahea, which is among the most poorly understood lineages of American palms and is characterized by a wide variety of growth forms and intermediate morphological features.\n\nMethodsWe generated approximately 400 kb of genome-scale data from all three genomes for the 11 currently described species of Brahea to infer phylogenetic relationships, reconstruct ancestral growth form, estimate ancestral geographic ranges, and test for niche equivalency among closely related species with geographic overlap.\n\nKey ResultsRelationships receive strong support, and conform to previous subgeneric assignments, except for placement of the dwarf species B. moorei within subgenus Erythea. Our robust phylogenetic hypothesis reveals trends in growth form including an overall increase in height in the B. armata clade, and independent evolution of dwarf forms from taller ancestors in the B. pimo and B. dulcis clades. Ancestral range estimation reveals roles of dispersal (e.g. B. edulis on Guadalupe Island) and sympatric speciation in some cases (e.g. in the B. armata clade), but is equivocal in others (e.g. in the B. pimo clade). We find evidence of niche non-equivalency among species within the B. armata clade in northwestern Mexico, and some evidence of niche non-equivalency between B. berlandieri and B. dulcis, the former of which is synonymized under B. dulcis.\n\nConclusionsOur findings have implications for the complex biogeographic history in Central America and Mexico, suggesting that sympatric speciation and dispersal are the predominant processes of species diversification. Future studies should include population-level sampling across the genus, along with morphological and ecological information, to assess distinctness among species and, particularly, levels of gene flow, in an integrative fashion.

evolutionary biology↗

bioRxiv2017

Kombucha as a model system for multispecies microbial cooperation: theoretical promise, methodological challenges and new solutions ‘in solution’

Kombucha is a sweetened tea fermented by bacteria and yeast into a carbonated, acidic drink, producing a surface biofilm pellicle (colloquially called a SCOBY) during the process. Typically, liquid and a biofilm pellicle from a previously fermented culture is used as a starter for new cultures; however, there is no standard protocol for growing kombucha in the laboratory. In order to establish a standard protocol with low variability between replicates, we tested whether we could begin a kombucha culture with only well-mixed liquid stock. We found that viable kombucha cultures can be grown from low percentages of initial inoculum stock liquid, that new pellicles can form from liquid alone (with no starter pellicle), and that the variation in the pellicle characteristics is lower when only a liquid starter is used (p = 0.0004). We also found that blending the pellicle before including it significantly reduces the variation among replicates, though the final pellicle was abnormal. We conclude that growing kombucha from only liquid stock is viable and provides a greater degree of experimental control and reproducibility compared to alternatives. Standardizing methodologies for studying kombucha in the lab can facilitate the use of this system for exploring questions about the evolutionary, ecological and cooperative/competitive dynamics within this multi-species system including resource transfers, functional dependence, genetic divergence, collective defense, and ecological succession. A better understanding of kombucha and other fermented foods may eventually allow us to leverage their pathogen inhibitory properties to develop novel antibiotics and bacteriocins.

microbiology↗