Biology subjects

Azevedo, R.

Publications and source records attributed to Azevedo, R..

9 recordsLinked to original sources

bioRxiv2025

A novel approach to tagging tubulin reveals microtubule assembly dynamics of the axoneme in Trypanosoma brucei

The protozoan parasite Trypanosoma brucei is a mono-flagellated cell during the G1-phase of its cell cycle. In order to duplicate, it assembles a new flagellum alongside the mature one, in which further elongation is prevented. Our group proposed a model where the mature flagellum is locked after construction to full length (Bertiaux et al. 2018) and access of new building blocks for elongation is exclusive to the new flagellum. To test this hypothesis directly, we developed a tool for the inducible expression of tagged tubulin. Alpha-tubulin that was tagged with an intragenic Ty-1-epitope behaved indistinguishable from untagged tubulin. Its incorporation was monitored after inducible expression, to follow the assembly dynamics of microtubules in the cell body, the mitotic spindle and the flagellum. In this study we observed that integration of tubulin occurs at the distal flagellum tip at a linear rate and is indeed restricted to the new flagellum in bi-flagellated cells. This is direct evidence that trypanosomes avoid competition between the two flagella by allowing tubulin incorporation only in the new organelle. However, by tracing flagella over several cell cycles we could also show that mature flagella do not remain locked indefinitely. The restriction is lifted briefly after the bi-flagellated cell has divided and the daughter cell inheriting the old flagellum shows incorporation of newly synthesized building blocks again. It then has to lock again before the cell can assemble a new flagellum. Our findings suggest regular incorporation of tubulin at the tip of previously locked flagella. This evidence was supported with an orthogonal approach, with which we monitored the incorporation of HaloTag-tagged radial spoke protein 4/6. Since flagellum length in trypanosomes is stable, this indicates that the entire axoneme is subject to regular events of transient disassembly followed by assembly at its distal tip.

cell biology↗

bioRxiv2024

Enhancing Gene Set Overrepresentation Analysis with Large Language Models

Gene set overrepresentation analysis is widely used to interpret high-throughput transcriptomics and proteomics data, but traditional methods rely on static, human-curated gene set databases that lack flexibility. We introduce llm2geneset, a framework that leverages large language models (LLMs) to dynamically generate gene set databases tailored to input query genes, such as differentially expressed genes (DEGs) and a biological context specified in natural language. These databases integrate with methods, such as overrepresentation analysis (ORA), to assign biological functions to input genes. Benchmarking against human-curated gene sets demonstrates that LLMs generate gene sets comparable in quality to those curated by humans. llm2geneset also identifies biological processes represented by input gene sets, outperforming traditional ORA and direct LLM prompting. Applying the framework to RNA-seq data from iPSC-derived microglia treated with a TREM2 agonist highlights its potential for flexible, context-aware gene set generation and improved interpretation of high-throughput biological data. llm2geneset is available as open source at https://github.com/Alector-BIO/llm2geneset and via a web interface at https://llm2geneset.streamlit.app.

bioinformatics↗

bioRxiv2022

Reputation risk during dishonest social decision-making modulates anterior insular and cingulate cortex activity and connectivity

To explore the neural underpinnings of (dis)honest decision making under quasi-ecological conditions, we used an fMRI adapted version of a card game in which deceptive or truthful decisions are made to an opponent, with or without the risk of getting caught by them. Dishonest decisions were associated to increased activity in a cortico-subcortical circuit including the bilateral anterior cingulate cortex (ACC), anterior insula (AI), left dorsolateral prefrontal cortex, supplementary motor area, and right caudate. Crucially, deceptive immoral decisions under reputation risk enhanced activity of - and functional connectivity between - the bilateral ACC and left AI, suggesting the need for heightened emotional processing and cognitive control when making immoral decisions under reputation risk. Tellingly, more manipulative individuals required less involvement of the ACC during risky self-gain lies but more involvement during other-gain truths, pointing to the need of cognitive control only when going against ones own moral code.

neuroscience↗

bioRxiv2021

Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila

Understanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional processes that may also generate substantial genetic variation in some populations and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. Tetrahymena thermophila is a ciliate with an unusual mechanism of nuclear division, called amitosis, which can generate genetic variation among the asexual descendants of a newly produced sexual progeny. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.

evolutionary biology↗

bioRxiv2021

Glycoproteogenomics characterizes the CD44 splicing code driving bladder cancer invasion

Bladder cancer (BC) management demands the introduction of novel molecular targets for precision medicine. Cell surface glycoprotein CD44 has been widely studied as a potential biomarker of BC aggressiveness and cancer stem cells. However, significant alternative splicing and multiple glycosylation generate a myriad of glycoproteoforms with potentially distinct functional roles. The lack of tools for precise molecular characterization has led to conflicting results, delaying clinical applications. Addressing these limitations, we have interrogated the transcriptome of a large BC patient cohort for splicing signatures. Remarkable CD44 heterogeneity was observed, as well as associations between short CD44 standard splicing isoform (CD44s), invasion and poor prognosis. In parallel, immunoassays showed that targeting short O-glycoforms could hold the key to improve CD44 cancer specificity. This prompted the development of a glycoproteogenomics approach, building on the integration of transcriptomics-customized datasets and glycomics for protein annotation from nanoLC-ESI-MS/MS experiments. The concept was applied to invasive human BC cell lines, glycoengineered cells, and tumor tissues, enabling unequivocal CD44s identification. Finally, we confirmed the link between CD44s and invasion in vitro by siRNA knockdown, supporting findings from BC tissues. The key role played by short-chain O-glycans in CD44-mediated invasion was also demonstrated through glycoengineered cell models. Overall, CD44s emerged as biomarker of poor prognosis and CD44-Tn/STn as promising molecular signatures for targeted interventions. This study materializes the concept of glycoproteogenomics and provides a key vision to address the cancer splicing code at the protein level, which may now be expanded to better understand CD44 functional role in health and disease. Significance StatementThe biological role of CD44, a cell membrane glycoprotein involved in most cancer hallmarks and widely explored in BC, is intimately linked to its protein isoforms. mRNA alternative splicing generates several closely related polypeptide sequences, which have so far been inferred from transcripts analysis, in the absence of workflows for unequivocal protein annotation. Dense O-glycosylation is also key for protein function and may exponentiate the number of proteoforms, rendering CD44 molecular characterization a daunting enterprise. Here, we integrated multiple molecular information (RNA, proteins, glycans) for definitive CD44 characterization by mass spectrometry, materializing the concept of glycoproteogenomics. BC specific glycoproteoforms linked to invasion have been identified, holding potential for precise cancer targeting. The approach may be transferable to other tumors, paving the way for precision oncology.

cancer biology↗

bioRxiv2021

Divergent sex differences in functional brain connectivity networks in excessively drinking C57BL/6J mice

Individuals with alcohol use disorder continue to drink in excess despite the health and societal consequences, and the rate of problematic drinking and alcohol-related harms is increased in women. Clinical imaging studies report widespread adaptations in brain structure after chronic, heavy drinking, and alcohol-related cues enhance brain reactivity in reward-related regions. In rodents, alcohol drinking induces expression of the immediate early gene c-Fos, which can be a marker of cellular activity, across multiple brain regions. Recent evidence also suggests that abstinence from chronic intermittent alcohol exposure can produce mesoscale changes in c-Fos expression. However, there is a substantial gap in our understanding of how excessive drinking affects functional connectivity networks to influence alcohol-seeking behaviors. For this study, male and female C57BL/6J mice were given access to either water or a choice between water and ethanol in the intermittent access drinking model for 4 weeks. After a short-access drinking session, whole brains from high alcohol drinking male and female mice and water drinking controls were then subjected to c-Fos immunolabeling, iDISCO+ clearing, light sheet imaging, and whole-brain c-Fos mapping. Correlation matrices were then generated and graph theoretical statistical approaches were used to determine changes in functional connectivity across sex and drinking condition. We observed robust sex differences in the network of c-Fos+ cells in water drinking mice, and excessive alcohol drinking produce divergent and robust changes in functional network connectivity in male and female mice. In addition, these analyses identified novel hub regions in excessively drinking mice that were unique for each sex. In conclusion, the whole-brain c-Fos mapping analysis identified sex difference in functional network connectivity and unique and understudied regions that may play a critical role in controlling excessive ethanol drinking in male and female mice.

neuroscience↗

bioRxiv2020

Neural divergence and convergence for interoceptive and somatosensory attention and detection

Body awareness is constructed by signals originating from within and outside the body. How do these apparently divergent signals converge? We developed a signal detection task to study the neural convergence and divergence of interoceptive and somatosensory signals. Participants focused on either cardiac or tactile events and reported their presence or absence. Beyond some evidence of divergence, we observed a robust overlap in the pattern of activation evoked across both conditions in frontal areas including the insular cortex, as well as parietal and occipital areas, and for both attention and detection of these signals. Psycho-physiological interaction analysis revealed that right insular cortex connectivity was modulated by the conscious detection of cardiac compared to somatosensory sensations, with greater connectivity to occipito-parietal regions when attending to cardiac signals. Our findings speak in favour of the inherent convergence of bodily-related signals and move beyond the apparent antagonism between exteroception and interoception.

neuroscience↗

bioRxiv2020

TraIT, Translational research IT bridging the valley of death in translational medicine

Translating new technology and biological findings into clinical applications is hampered by insufficient translational research IT. The Dutch Translational research IT (TraIT) initiative organizes, deploys, and manages data and workflows in an on-line "office suite", supplemented with efficient training and user support. TraIT has been adopted by a wide user community providing an excellent large-scale demonstrator for the nation-wide Health-RI initiative.

bioinformatics↗

bioRxiv2017

accuMUlate: A mutation caller designed for mutation accumulation experiments

MotivationMutation accumulation (MA) is the most widely used method for directly studying the effects of mutation. Modern sequencing technologies have led to an increased interest in MA experiments. By sequencing whole genomes from MA lines, researchers can directly study the rate and molecular spectra of spontaneous mutations and use these results to understand how mutation contributes to biological processes. At present there is no software designed specifically for identifying mutations from MA lines. Studies that combine MA with whole genome sequencing use custom bioinformatic pipelines that implement heuristic rules to identify putative mutations.\n\nResultsHere we describe O_SCPLOWACCUC_SCPLOWMUO_SCPLOWLATEC_SCPLOW, a program that is designed to detect mutations from MA experiments. O_SCPLOWACCUC_SCPLOWMUO_SCPLOWLATEC_SCPLOW implements a probabilistic model that reflects the design of a typical MA experiments while being flexible enough to accommodate properties unique to any particular experiment. For each putative mutation identified from this model O_SCPLOWACCUC_SCPLOWMUO_SCPLOWLATEC_SCPLOW calculates a set of summary statistics that can be used to filter sites that may be false positives. A companion tool, O_SCPLOWDENOMINATEC_SCPLOW, can be used to apply filtering rules based on these statistics to simulated mutations and thus identify the number of callable sites per sample.\n\nAvailabilitySource code and releases available from https://github.com/dwinter/accuMUlate.

bioinformatics↗