Biology subjects

Lima, J.

Publications and source records attributed to Lima, J..

12 recordsLinked to original sources

bioRxiv2026

Quantitative MRI-based assessment of the ultrastructural compactness of myelin lamellae

Efficient neuronal communication relying on rapid saltatory conduction depends not only on the amount of myelin wrapping axons but also on myelin compact organisation. Yet, current quantitative MRI myelin imaging methods, such as Myelin Water Imaging (MWI) and quantitative Magnetization Transfer (qMT), are designed to estimate myelin content and are often treated as interchangeable, overlooking myelin organisation. We introduce Structural Myelin Integrity (SMI), a quantitative MRI metric designed to distinguish myelin compact organisation from content. SMI combines the distinct biophysical sensitivities of MWI and qMT to separate the water confined between myelin layers from the total myelin membrane mass. We evaluated SMI in two rodent models of myelin decompaction and one remyelination model, validating our findings with synchrotron small-angle X-ray scattering and electron microscopy. SMI detected myelin layers decompaction despite largely preserved myelin membranes, revealing structural abnormalities that were not explained by myelin content alone. During remyelination, SMI returned closer to healthy values at early timepoints than myelin-content metrics, consistent with the formation of thin-but-compact sheaths. These findings indicate that myelin content and organisation can dissociate and establish SMI as a non-invasive marker of myelin organisation, compatible with existing clinical MRI approaches for studying white matter changes not detected today.

neuroscience↗

bioRxiv2026

Mapping 3D tissue orientation with tensor-augmented light-sheet microscopy

Mapping the three-dimensional directional organization of biological tissues is essential for understanding their structure and function. However, existing methods cannot resolve micrometer-scale orientation in volumetric samples. We introduce tensor light-sheet scattering microscopy (tLSSM), a label-free method that reconstructs 3D fiber orientations at micrometer resolution in optically cleared tissues, enabling whole-organ imaging. We discovered that even in transparent samples, organized structures such as neural fibers scatter light in directional patterns, consistent with models of light scattering by cylinders. We compared tLSSM against diffusion MRI in the mouse brain, demonstrating strong agreement and orders of magnitude superior spatial resolution. Furthermore, we showcase tLSSMs versatility across diverse contexts, including whole-brain label-free tracing, pathological demyelination lesions, heart tissue, peripheral nerves, and human white matter. By enabling whole-organ fiber orientation mapping compatible with standard light-sheet microscopes, tLSSM establishes a new standard for mesoscopic connectivity studies by mapping tissue architecture beyond the limits of traditional sectioning.

neuroscience↗

bioRxiv2026

Development and Refinement of Microbial DNA Extraction Protocol from Bovine Milk

Milk is a challenging matrix to extract sufficient microbial DNA from for downstream analysis. This study assessed fourteen DNA extraction protocols for their DNA outputs. An adaptation of the QIAGEN DNeasy PowerSoil kit, which increased initial sample volume and maintained all volume of lysate following bead beating proved most effective.

molecular biology↗

bioRxiv2023

Hif-2α programmes oxygen chemosensitivity in chromaffin cells

The study of transcription factors that determine specialised neuronal functions has provided invaluable insights into the physiology of the nervous system. Peripheral chemoreceptors are neurone-like electro-physiologically excitable cells that link the oxygen content of arterial blood to the neuronal control of breathing. In the adult, this oxygen chemosensitivity is exemplified by the Type I cells of the carotid body and recent work has revealed one isoform of the transcription factor HIF, HIF-2, to have a non-redundant role in the development and function of that organ. Here we show that the activation of HIF-2, including isolated overexpression alone, is sufficient to induce oxygen chemosensitivity in the otherwise unresponsive adult adrenal medulla. This phenotypic change in the adrenal medulla was associated with retention of extra-adrenal paraganglioma-like tissues that resemble the foetal organ of Zuckerkandl and also manifest oxygen chemosensitivity. Acquisition of chemosensitivity was associated with changes in the adrenal medullary expression of classes of genes that are ordinarily characteristic of the carotid body, including G-protein regulators and atypical subunits of mitochondrial cytochrome oxidase. Overall, the findings suggest that, at least in certain tissues, HIF-2 acts as a phenotypic driver for cells that display oxygen chemosensitivity, providing a route to mechanistic understanding.

developmental biology↗

bioRxiv2021

Epithelial-mesenchymal plasticity induced by discontinuous exposure to TGFβ1 promotes tumour growth

Transitions between epithelial and mesenchymal cellular states (EMT/MET) contribute to cancer progression. We hypothesize that EMT followed by MET promotes cell population heterogeneity favouring tumour growth. We developed an EMT model by on/off exposure of epithelial EpH4 cells (E-cells) to TGF{beta}1 that mimics phenotypic EMT (M-cells) and MET. We aimed at understanding whether phenotypic MET is accompanied by molecular and functional reversion back to epithelia, by using RNA sequencing, Immunofluorescence (IF), proliferation, wound healing, focus formation and mamosphere formation assays, as well as cell-xenografts in nude mice. Phenotypic reverted-epithelial cells (RE-cells), obtained after MET induction, presented pure epithelial morphology and proliferation rate resembling E-cells. However, RE transcriptomic profile and IF staining of epithelial and mesenchymal markers revealed a unique and heterogeneous mixture of cell-subpopulations, with high self-renewal ability fed by oxidative phosporylation. RE-cells heterogeneity is stably maintained for long periods after TGF{beta}1 removal, both in vitro and in large derived tumours in nude mice. Overall, we show that phenotypic reverted-epithelial cells (RE-cells) do not return to the molecular and functional epithelial state, present mesenchymal features related with aggressiveness and cellular heterogeneity that favour tumour growth in vivo. This work strengthens epithelial cells reprogramming and cellular heterogeneity fostered by inflammatory cues as a tumour-growth promoting factor in vivo.

cell biology↗

bioRxiv2020

Growth hormone receptor (GHR)-expressing neurons in the hypothalamic arcuate nucleus regulate glucose metabolism and energy homeostasis

Growth hormone (GH) receptor (GHR), expressed in different brain regions, is known to participate in the regulation of whole-body energy homeostasis and glucose metabolism. However, GH activation of these GHR-expressing neurons is less studied. We have generated a novel GHR-driven Cre recombinase transgenic mouse line (GHRcre) in combination with the floxed tdTomato reporter mouse line we tracked and activated GHR-expressing neurons in different regions of the brain. We focused on neurons of the hypothalamic arcuate nucleus (ARC) where GHR was shown to elicit a negative feedback loop that regulates GH production. We found that ARCGHR+ neurons are co-localized with AgRP, GHRH, and somatostatin neurons, which were activated by GH stimulation. Using designer receptors exclusively activated by designer drugs (DREADDs) to control GHRARC neuronal activity, we revealed that activation of GHRARC neurons was sufficient in regulating distinct aspects of energy balance and glucose metabolism. Overall, our study provides a novel mouse model to study in vivo regulation and physiological function of GHR-expressing neurons in various brain regions. Furthermore, we identified for the first time specific neuronal population that responds to GH and directly linked it to metabolic responses in vivo.

neuroscience↗

bioRxiv2020

Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane

During the initial stages of mitosis, multiple mechanisms drive centrosome separation and positioning. How they are functionally coordinated to promote centrosome migration to opposite sides of the nucleus remains unclear. Imaging analysis software has been used to quantitatively study centrosome dynamics at this stage. However, available tracking tools are generic and not fine-tuned for the constrains and motion dynamics of centrosome pairs. Such generality limits the tracking performance and may require exhaustive optimization of parameters. Here, we present Trackosome, a freely available open-source computational tool to track the centrosomes and reconstruct the nuclear and cellular membranes, based on volumetric live-imaging data. The toolbox runs in MATLAB and provides a graphical user interface for easy and efficient access to the tracking and analysis algorithms. It outputs key metrics describing the spatiotemporal relations between centrosomes, nucleus and cellular membrane. Trackosome can also be used to measure the dynamic fluctuations of the nuclear envelope. A fine description of these fluctuations is important because they are correlated with the mechanical forces exerted on the nucleus by its adjacent cytoskeletal structures. Unlike previous algorithms based on circular/elliptical approximations of the nucleus, Trackosome measures membrane movement in a model-free condition, making it viable for irregularly shaped nuclei. Using Trackosome, we demonstrate significant correlations between the movements of the two centrosomes, and identify specific modes of oscillation of the nuclear envelope. Overall, Trackosome is a powerful tool to help unravel new elements in the spatiotemporal dynamics of subcellular structures.

cell biology↗

bioRxiv2019

Population structure determined by comparative amplicon gene sequencing in biofilm and planktonic bacterial communities from pesticide-contaminated water

Molecular and bioinformatics tools for research are very important for biodiversity characterization in contaminated environments due the presence of a high percentage of nonculturable microorganisms. The wide use of pesticides in agriculture exposes microbiomes to stressful and selective conditions that demand survival strategies such as biofilm formation. The purpose of this work was to evaluate the bacterial population structure in planktonic and biofilm communities of water that was used for washing the packaging of herbicides and stored for six months in tanks. This substance is highly contaminated waste. Samples of water and biofilms from tanks and biofilms developed for short times in flasks were used for DNA isolation and 16S rRNA gene sequencing. The physicochemical conditions imposed by water used for washing the containers were inadequate for killing the bacterial genera identified according to water and wastewater standards. The variation in population structure and diversity was lower in the planktonic samples than in the biofilm samples, indicating a possible combination of genetic drift and subsequent selection of individuals surviving under stressful water conditions, such as heating and contact with agrochemicals, over a six-month period. The biofilm formation in water tanks contaminated with pesticides enabled the survival of bacterial genera harboring the essential processes for adaptation to these environments; the presence of these processes was determined according to descriptions obtained from the genomic databases. This study suggests the potential of bacterial genera identified in biofilms obtained from tanks to adapt to contaminated environments through their metabolic complexity. Thus, herbicide biodegradation kinetics can be accessed through a culturable collection obtained from these communities.

microbiology↗

bioRxiv2018

APOBEC-mediated DNA alterations: a possible new mechanism of carcinogenesis in EBV-positive gastric cancer

Mechanisms of viral oncogenesis are diverse and include the off-target activity of enzymes expressed by the infected cells, which evolved to target viral genomes for controlling their infection. Among these enzymes, the single-strand DNA editing capability of APOBECs represent a well-conserved viral infection response that can also cause untoward mutations in host DNA. Here we show, after evaluating somatic single-nucleotide variations and transcriptome data in 240 gastric cancer samples, a positive correlation between APOBEC3s mRNA-expression and the APOBEC-mutation signature, both increased in EBV+ tumors. The correlation was reinforced by the observation of APOBEC-mutations preferentially occuring in transcriptionally-active loci. The EBV-infection and APOBEC3 mutation-signature axis was confirmed in a validation cohort of 112 gastric cancer patients. Our findings suggest that APOBEC3 upregulation in EBV+ cancer may boost the mutation load, providing further clues to the mechanisms of EBV-induced gastric carcinogenesis. After further validation, this EBV-APOBEC axis may prove to be a secondary driving force in the mutational evolution of EBV+ gastric tumors, whose consequences in terms of prognosis and treatment implications should be vetted.

cancer biology↗

bioRxiv2018

Skin microbiome modulation induced by probiotic solutions

BackgroundThe skin is colonized by a large number of microorganisms, of which most are beneficial or harmless. However, disease states of skin have specific microbiome compositions that are different from those of healthy skin. Gut microbiome modulation through fecal transplant has proven as a valid therapeutic strategy in diseases such as Clostridium difficile infections. Therefore, techniques to modulate the skin microbiome composition may become an interesting therapeutic option in diseases affecting the skin such as psoriasis or acnes vulgaris.\n\nHere we have used mixtures of different skin microbiome components to alter the composition of a recipient skin microbiome.\n\nResultsWe show that after sequential applications of a donor microbiome, the recipient microbiome becomes similar to that of the donor. After intervention, an initial, week-long phase is characterized by dominance of donor strains. The level of engraftment depends on the composition of the recipient and donor microbiomes, and the applied bacterial load. We observed higher engraftment using a multi-strain donor solution with recipient skin rich in Cutibacterium acnes subtype H1 and Leifsonia.\n\nConclusionsWe have demonstrated the use of living bacteria to modulate skin microbiome composition.

microbiology↗

bioRxiv2018

HaploVectors: an integrative analytical tool for phylogeography

Sets of local populations show different degrees of gene flow due to dispersal barriers and environmental constraints, which renders genetic composition gradients among populations (genetic turnover). Unveiling biogeographic correlates of genetic turnover is paramount for phylogeography. While some processes (genetic drift, secondary contact) may erase the historical track of genetic turnover, vicariance or ancient dispersal likely leads to genetic divergence among populations. Yet available analyses do not permit direct inference about mechanisms driving genetic turnover. We propose a novel analytical approach called genvector analysis, which fulfills this gap by decomposing genetic compositional dissimilarities between populations based on either haplotypes or other genetic data into genetic eigenvectors. Such procedure allows exploring genetic turnover among sets of local populations, and analyzing their biogeographic correlates based on null model tests. We evaluate the statistical performance of the method on simulated datasets. We also analyzed biogeographic correlates of genetic turnover of Akodon cursor in the Brazilian Atlantic Forest. Results revealed that genvector analysis is robust to discriminate biogeographic drivers of genetic turnover. For Akodon cursor analysis, we observed that while for the entire species, all predictors considered (except for elevation) explained genetic turnover, within phylogroups some factors varied their importance. Genvector analysis was demonstrated to be useful for several different purposes in phylogeography, and complementary to classic analytical tools widely used by phylogeographers, such as AMOVA or DAPC. The role of ancient versus recent biogeographic events, the relationship between morphological divergence or abiotic variables and genetic turnover can easily be investigated using genvector analysis.

ecology↗

bioRxiv2017

Discriminative aversive learning and amygdala responsivity is enhanced in mice with reduced serotonin transporter activity

The serotonin (5-HT) transporter (5-HTT) regulates 5-HT availability at the synapse. Low or null 5-HTT expression results in increased 5-HT availability and has been reported to produce anxious and depressive phenotypes, although this remains highly controversial despite two decades of investigation. Paradoxically, SSRIs, which also increase 5-HT availability, reduce the symptoms of anxiety and depression. An emerging network plasticity theory of 5-HT function argues that, rather than influencing mood directly, increasing 5-HT availability enhances learning about emotionally-significant events but evidence supporting this theory is inconclusive. Here, we tested one key prediction of this theory: that increased 5-HT availability enhances aversive learning. In experiment 1, we trained 5-HTT knock-out mice (5-HTTKO), which have increased 5-HT availability, and wild-type mice (WT) on an aversive discrimination learning task in which one auditory cue was paired with an aversive outcome whereas a second auditory cue was not. Simultaneously we recorded neuronal and hemodynamic responses from the amygdala, a brain region necessary for aversive learning. 5-HTTKO mice exhibited superior discrimination learning than WTs, and had stronger theta-frequency neuronal oscillations and larger amygdala hemodynamic responses to the aversive cues, which predicted the extent of learning. In experiment 2, we found that acute SSRI treatment (in naive non-transgenic mice), given specifically before fear learning sessions, enhanced subsequent fear memory recall. Collectively, our data demonstrate that reducing 5-HTT activity (and thereby increasing 5-HT availability) enhances amygdala responsivity to aversive events and facilitates learning for emotionally-relevant cues. Our findings support the network plasticity theory of 5-HT function.

neuroscience↗