Biology subjects

Pereira, L.

Publications and source records attributed to Pereira, L..

4 recordsLinked to original sources

bioRxiv2018

Timing mechanism of sexually dimorphic nervous system differentiation

In all animals, sexual differentiation of somatic tissue is precisely timed, yet the molecular mechanisms that control the timing of sexual differentiation, particularly in the brain, are poorly understood. We have used sexually dimorphic molecular, anatomical and behavioral features of the C. elegans nervous system to decipher a regulatory pathway that controls the precise timing of sexual differentiation. We find that the sexually dimorphic differentiation of postmitotic neurons in the male nervous system is abrogated in animals that carry a mutation in the miRNA let-7 and prematurely executed in animals either lacking the let-7 inhibitor lin-28, or the direct let-7 target lin-41, an RNA-binding, posttranscriptional regulator. We show that an isoform of a phylogenetically conserved transcription factor, lin-29a, is a critical target of LIN-41 in controlling sexual maturation of sex-shared neurons. lin-29a is expressed in a male-specific manner in a subset of sex-shared neurons at the onset of sexual maturation. lin-29a acts cell-autonomously in these neurons to control the expression of sexually dimorphic neurotransmitter switches, sensory receptor expression, neurite anatomy and connectivity, and locomotor behavior. lin-29a is not only required but also sufficient to impose male-specific features at earlier stages of development and in the opposite sex. The temporal, sexual and spatial specificity of lin-29a expression is controlled intersectionally through the lin-28/let-7/lin-41 heterochronic pathway, sex chromosome configuration and neuron type-specific terminal selector transcription factors. Two Doublesex-like transcription factors represent additional neuron-type specific targets of LIN-41 and are regulated in a similar intersectional manner, indicating the existence of modular outputs downstream of the heterochronic pathway. In conclusion, we have provided insights into the molecular logic of the timing of sexual differentiation in the C. elegans nervous system. Remarkably, the lin28/let7 axis also controls the timing of sexual differentiation in mice and humans thereby hinting toward a striking universality of the control mechanisms of sexual differentiation.

neuroscience↗

bioRxiv2017

A methodology for unsupervised clustering using iterative pruning to capture fine-scale structure

SNP-based information is used in several existing clustering methods to detect shared genetic ancestry or to identify population substructure. Here, we present a methodology for unsupervised clustering using iterative pruning to capture fine-scale structure called IPCAPS. Our method supports ordinal data which can be applied directly to SNP data to identify fine-scale population structure. We compare our method to existing tools for detecting fine-scale structure via simulations. The simulated data do not take into account haplotype information, therefore all markers are independent. Although haplotypes may be more informative than SNPs, especially in fine-scale detection analyses, the haplotype inference process often remains too computationally intensive. Therefore, our strategy has been to restrict attention to SNPs and to investigate the scale of the structure we are able to detect with them. We show that the experimental results in simulated data can be highly accurate and an improvement to existing tools. We are convinced that our method has a potential to detect fine-scale structure.

bioinformatics↗

bioRxiv2017

IPCAPS: an R package for iterative pruning to capture population structure

BackgroundResolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target.\n\nResultsThis work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipPCA) framework that systematically assigns individuals to genetically similar subgroups. In each iteration, our tool is able to detect and eliminate outliers, hereby avoiding severe misclassification errors.\n\nConclusionsIPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated as well. The tool can also be applied in patient sub-phenotyping contexts. IPCAPS is developed in R and is freely available from bio3.giga.ulg.ac.be/ipcaps

bioinformatics↗

bioRxiv2017

Is it possible to keep the exoskeleton of the crab Callinectes ornatus soft for several days?

Soft-shell crab is considered a gastronomic delicacy, reaching high values in the international market. The process of hardening of the crabs exoskeleton after moulting takes approximately two days to complete; however, the duration for which the shell remains at the consistency of high commercial value is only 3 hours on average. After this period, the shell assumes a consistency classified as \"paper\", later becoming \"hard\" again. The goal of this work was to evaluate the use of the crabs themselves to alter the chemical characteristics of the water and thereby increase the amount of time during which they can be marketed as \"soft-shell crab\". In this work, 241 individuals of Callinectes ornatus were used in two experiments. In the first experiment, the animals were maintained in a collective system with filtration and partial daily water renewal. In the second experiment, the crabs were maintained in a collective system with filtration but no water renewal. In Experiment 1, the chemical characteristics of the water remained unchanged over time (p > 0.05), and the median time to hardening of the exoskeleton to the paper consistency after moulting was 3 hours. Over the course of Experiment 2, there was a significant reduction (p < 0.05) in pH and significant increases in the ammonia and nitrite concentrations. When moulting occurred in water with a pH below 7.3 and total ammonia concentrations above 6.0 mg/L, the crabs shells did not harden, and it was possible to keep them soft for up to 5 days.

physiology↗