Biology subjects

Mota, B.

Publications and source records attributed to Mota, B..

4 recordsLinked to original sources

bioRxiv2025

Telomeric assemblies of Paracoccidioides genomes

Paracoccidioides is a genus of dimorphic fungal pathogens endemic to Latin America. We generated long-read de novo assemblies for 11 isolates representing four species of the brasiliensis complex (P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis) and P. lutzii. These include the first complete telomere-to-telomere assemblies for P. brasiliensis (Pb18) and P. americana (Pb03), each with five chromosomes. Comparative analyses revealed chromosomal fusion and fission events distinguishing P. brasiliensis and P. americana, and a 90 kb tandem duplication in P. americana containing siderophore biosynthesis genes (sid1, sid3, sid4), a cluster of putative virulence factors. Mitochondrial genomes showed conserved gene order but a phylogenetic topology inconsistent with the nuclear tree, suggesting mitochondrial introgression between P. lutzii and P. venezuelensis. RNA transposable elements were enriched near telomeres, correlated with genome size, and most abundant in P. lutzii. These assemblies provide key resources for understanding genome evolution and introgression in Paracoccidioides. SIGNIFICANCESpecies of Paracoccidioides cause paracoccidioidomycosis, a systemic mycosis that remains a major public health problem in Latin America. Despite their clinical importance, genome evolution across the genus is poorly understood owing to the lack of complete reference assemblies. Here, we present the first telomere-to-telomere reference genomes for P. brasiliensis and P. americana, enabling a comprehensive comparison of chromosomal structure across the genus. Our analyses reveal that the nuclear genome is highly dynamic and shaped by large-scale rearrangements and structural variants, including the duplication of a siderophore biosynthesis-related gene cluster linked to virulence. In contrast, the mitochondrial genome is structurally conserved but shows introgression between species, revealing hidden evolutionary exchange. Together, these genomic resources redefine our understanding of Paracoccidioides evolution and provide a foundation for advances in molecular diagnostics, epidemiological surveillance, and studies of fungal pathogenicity.

microbiology↗

bioRxiv2023

Folding of the cerebellar cortex is clade-specific in form, but universal in degree

Like the cerebral cortex, the surface of the cerebellum is repeatedly folded. Unlike the cerebral cortex, however, cerebellar folds in a given brain are much thinner and more numerous; repeat themselves largely along a single direction, forming long strips transverse to the mid-sagittal plane, like an accordion; and occur in the smallest of cerebella, including those of lissencephalic mammals and non-mammal vertebrates. We have shown previously that while the location of folds in mammalian cerebral cortex is clade-specific, the overall degree of folding strictly follows a universal power law relating cortical thickness, and the exposed and total surface areas. This law is derived from a statistical-physics model for gyrification that postulates that folding results from the interplay between axonal elongation dynamics and the self-avoiding nature of the expanding cortical surfaces. Since both aspects are present in the cerebellum, we hypothesize that a similar relation across species also exists therein. Furthermore, given the modular organization of cerebellar architecture and circuitry, as well as the transverse orientation of the folia, it is plausible that this relation is reflected in the degree of folding of the mid-sagittal section of the cerebellum, which greatly facilitates analysis. Here we show that a strict universal scaling law does apply to the folding of the mid-sagittal sections of the cerebellum of 53 species belonging to six mammalian clades, spanning a large range of sizes and degrees of gyrification. This folding is hierarchical and can be explicitly separated into branching orders, such that position of the 1st-order folds is largely stereotypical across all mammals examined. Subsequent nth-order folds become progressively less stereotypical, and folding within such cerebellar subsections scales with power laws whose exponents decrease monotonically with branching order, converging to the exponents predicted by a two-dimensional version of the same gyrification model that describes cortical folding. We propose that the changes in scaling exponent with branching order occurs as increasing amounts of white matter are included in the folding volume of the cerebellum, reflecting the difference between the outside-in development of the cerebellar cortex around a preexisting core of already connected white matter, compared to the inside-out development of the cerebral cortex with a white matter volume that develops as the cerebral cortex itself gains neurons. Our data strongly indicate that the mammalian cerebellum folds as a multi-fractal object, emerging from the interplay between clade-specificity and universality, and between phylogenetical contingency and the physics of self-organization. Thus, repeated folding, one of the most recognizable features of biology, can arise simply from the universal applicability of physical principles, without the need for invoking selective pressures in evolution; and diversity arises within the constraints imposed by physics.

neuroscience↗

bioRxiv2022

Predicting the principal components of cortical morphological variables

AO_SCPLOWBSTRACTC_SCPLOWThe generating mechanism for the gyrification of the mammalian cerebral cortex remains a central open question in neuroscience. Although many models have been proposed over the years, very few were able to provide empirically testable predictions. In this paper, we assume a model in which the cortex folds for all species of mammals according to a simple mechanism of effective free energy minimization of a growing self-avoiding surface subjected to inhomogeneous bulk stresses, to derive a new set of summary morphological variables that capture the most salient aspects of cortical shape and size. In terms of these new variables, we seek to understand the variance present in two morphometric datasets: a human MRI harmonized multi-site dataset comprised by 3324 healthy controls (CTL) from 4 to 96 years old and a collection of different mammalian cortices with morphological measurements extracted manually. This is done using a standard Principal Component Analysis (PCA) of the cortical morphometric space. We prove there is a remarkable coincidence (typically less than 8{whitebullet}) between the resulting principal components vectors in each datasets and the directions corresponding to the new variables. This shows that the new, theoretically-derived variables are a set of natural and independent morphometrics with which to express cortical shape and size.

neuroscience↗

bioRxiv2019

The reliability of the isotropic fractionator method for counting total cells and neurons

BackgroundThe Isotropic Fractionator (IF) is a method used to determine the cellular composition of nervous tissue. It has been mostly applied to assess variation across species, where differences are expected to be large enough not to be masked by methodological error. However, understanding the sources of variation in the method is important if the goal is to detect smaller differences, for example, in same-species comparisons. Comparisons between different mice strains suggest that the IF is consistent enough to detected these differences. Nevertheless, the internal validity of the method has not yet been examined directly.\n\nMethodIn this study, we evaluate the reliability of the IF method for the determination of cellular and neuronal numbers. We performed repeated cell counts of the same material by different experimenters to quantify different sources of variation.\n\nResultsIn total cell counts, we observed that for the cerebral cortex most of the variance was at the counter level. For the cerebellum, most of the variance is attributed to the sample itself. As for neurons, random error along with the immunological staining correspond to most of the variation, both in the cerebral cortex and in the cerebellum. Test-retest reliability coefficients were relatively high, especially for cell counts.\n\nConclusionsAlthough biases between counters and random variation in staining could be problematic when aggregating data from different sources, we offer practical suggestions to improve the reliability of the method. While small, this study is a most needed step towards more precise measurement of the brains cellular composition.\n\nHighlightsO_LIMost variance in cell counts was between counters ({eta} = 0.58) for cerebral cortices.\nC_LIO_LIFor cerebella, most of the variance was attributed to the samples ({eta} = 0.49).\nC_LIO_LIVariance in immunocytochemical counts was mostly residual/random ({eta} > 0.8).\nC_LIO_LITest-retest reliability was high (same counter, same sample).\nC_LIO_LIPractical suggestions are offered to improve the reliability of the method.\nC_LI

neuroscience↗