Biology subjects

Angeles-Albores, D.

Publications and source records attributed to Angeles-Albores, D..

5 recordsLinked to original sources

bioRxiv2023

A C. elegans male pheromone feminizes germline gene expression in hermaphrodites and imposes life-history costs

AO_SCPLOWBSTRACTC_SCPLOWSex pheromones improve reproductive success, but also impose costs. Here we show that even brief exposure to physiological amounts of the dominant C. elegans male pheromone, ascr#10, alters the expression of thousands of genes in hermaphrodites. The most dramatic effect on the transcriptome was the upregulation of genes expressed during oogenesis and downregulation of genes associated with male gametogenesis. Among the detrimental effects of ascr#10 on hermaphrodites is the increased risk of persistent infections caused by pathological pharyngeal hypertrophy. Our results reveal a way in which social signals help to resolve the inherent conflict between spermatogenesis and oogenesis in a simultaneous hermaphrodite, presumably to optimally align reproductive function to the presence of potential mating partners. They also show that the beneficial effects of the pheromone are accompanied by harmful consequences that reduce lifespan.

evolutionary biology↗

bioRxiv2023

Genome wide-analysis of anterior-posterior mRNA localization in Stentor coeruleus reveals a role for the microtubule cytoskeleton

Cells have complex and beautiful structures that are important for their function. However, understanding the molecular mechanisms that produce these structures is a challenging problem due to the gap in size scales between molecular interactions and cellular structures. The giant ciliate Stentor coeruleus is a unicellular model organism whose large size, reproducible structure, and ability to heal wounds and regenerate have historically allowed the formation of structure in a single cell to be addressed using methods of experimental embryology. Such studies have shown that specific cellular structures, such as the oral apparatus, always form in particular regions of the cell, which raises the question: what is the source of positional information within this organism? By analogy with embryonic development, in which regionalized mRNA is often used to mark position, we asked whether specific regionalized mRNAs might mark position along the anterior-posterior axis of Stentor. By physically bisecting cells and conducting bulk RNA sequencing, we were able to identify sets of messages enriched in either the anterior or posterior half and show that RNAi-mediated knockdown of posterior-enriched transcripts corresponding to MYB genes results in a cells inability to regenerate the posterior portion of the cell body. We then conducted half-cell RNA-sequencing in paired anteriors and posteriors of cells in which the microtubule cytoskeleton was disrupted by RNAi of {beta}-tubulin or dynein intermediate chains. We found that many messages either lost their regionalized distribution or switched to an opposite distribution, such that anterior-enriched messages in control became posterior-enriched in the RNAi cells, or vice versa. This study indicates that mRNA can be regionalized within a single giant cell and that microtubules may play a role, possibly by serving as tracks for the movement of the messages.

cell biology↗

bioRxiv2017

A study of allelic series using transcriptomic phenotypes in a metazoan

Although transcriptomes have recently been used to perform epistasis analyses, they are not yet used to study intragenic function/structure relationships. We developed a theoretical framework to study allelic series using transcriptomic phenotypes. As a proof-of-concept, we apply our methods to an allelic series of dpy-22, a highly pleiotropic Caenorhabditis elegans gene orthologous to the human gene MED12, which is a subunit of the Mediator complex. Our methods identify functional regions within dpy-22 that modulate Mediator activity upon various genetic modules.

genetics↗

bioRxiv2017

Phenotype and gene ontology enrichment as guides for disease modeling in C. elegans

Genome-wide experiments have the capacity to generate massive amounts of unbiased data about an organism. In order to interpret this data, dimensionality reduction techniques are required. One approach is to annotate genes using controlled languages and to test experimental datasets for term enrichment using probabilistic methods. Although gene, phenotype and anatomy ontologies exist for C. elegans, no unified software offers enrichment analyses of all the ontologies using the same methodology. Here, we present the WormBase Enrichment Suite, which offers users the ability to test all nematode ontologies simultaneously. We show that the WormBase Enrichment Suite provides valuable insight into different biological problems. Briefly, we show that phenotype enrichment analysis (PEA) can help researchers identify disease phenologs, phenotypes that are homologous across species, which can inform disease modeling in C. elegans. The WormBase Enrichment Suite analysis can also shed light on RNA-seq datasets by showing what molecular functions are enriched, which phenotypes these functions are implicated in and what tissues are overrepresented in the dataset. Finally, we explore the phenotype-anatomy relationship, showing that a small subset of highly specific tissues are disproportionately likely to cause an Egl phenotype, but inferring tissue expression from an Egl phenotype is limited to the largest tissues.

bioinformatics↗

bioRxiv2016

Transcriptomic Description of an Endogenous Female State in C. elegans

Understanding genome and gene function in a whole organism requires us to fully understand the life cycle and the physiology of the organism in question. Although it is traditionally though of as a hermaphrodite, C. elegans XX animals become (endogenous) females after 3 days of egg-laying. The molecular physiology of this state has not been studied as intensely as other parts of the life cycle, in spite of documented changes in behavior and metabolism that occur at this stage. To study the female state of C. elegans, we designed an experiment to measure the transcriptome of 1st day adult females, endogenous, 6th day adult females, as well as mutant feminized worms that never go through a hermaphrodite stage at these time points. Using this experimental design, we were able to measure the effects of biological aging from the transition into the female state. We find that spermless young adult animals partially phenocopy 6 day old wild-type animals that have depleted their sperm after egg-laying, and that spermless animals also exhibit fewer transcriptomic changes associated with aging throughout these 6 days. Our results indicate that sperm loss is responsible for some of the naturally occuring transcriptomic changes that occur during the life cycle of these animals. These changes involve a variety of factors, and they are enriched in transcription factors canonically associated with neuronal development and differentiation. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm.

genetics↗