Biology subjects

Rocha, A.

Publications and source records attributed to Rocha, A..

6 recordsLinked to original sources

bioRxiv2025

Senescence-Associated Chromatin Rewiring Promotes Inflammation and Transposable Element Activation

Cellular senescence is a stable form of cell cycle arrest that contributes to aging and age-associated diseases through the secretion of inflammatory factors collectively known as the senescence-associated secretory phenotype (SASP). While senescence is driven by transcriptional and epigenetic changes, the contribution of higher-order genome organization remains poorly defined. Here, we present the highest-resolution Hi-C maps ([~]3 kb) to date of proliferating, quiescent, and replicative senescent (RS) human fibroblasts, enabling a comprehensive analysis of 3D genome architecture during senescence. Our analyses reveal widespread senescence-associated remodeling of chromatin architecture, including extensive compartment and subcompartment switching toward transcriptionally active states, and a dramatic increase in unique chromatin loops. These structural features correlate with local DNA hypomethylation and are largely independent of canonical CTCF binding. The altered 3D genome landscape supports expression of SASP genes, inflammation-related pathways, and neuronal gene signatures consistent with age-associated epigenetic drift. We further demonstrate that architectural changes at multiple levels, including compartments, subcompartments, and loops, facilitate the derepression of LINE-1 retrotransposons, linking 3D chromatin structure to activation of proinflammatory transposable elements. Interestingly, quiescent cells, commonly used as senescence controls, exhibited substantial overlap in inflammatory gene expression with senescent cells, raising important considerations for experimental design. Structural analysis of cell cycle genes showed distinct chromatin configurations in senescence versus quiescence, despite similar transcriptional repression. Together, our results establish a high-resolution framework for understanding how genome architecture contributes to the senescent state.

genomics↗

bioRxiv2023

Hypothalamic representation of the imminence of predator threat detected by the vomeronasal organ in mice

Animals have the innate ability to select optimal defensive behaviors with appropriate intensity in response to predator threats within specific contexts. Such innate behavioral decisions are thought to be computed in the medial hypothalamic nuclei, which contain neural populations that directly control defensive behavioral outputs. The vomeronasal organ (VNO) serves as a primary sensory channel for detecting predator cues by relaying signals to the medial hypothalamic nuclei, particularly the ventromedial hypothalamus (VMH), via the medial amygdala (MeA) and bed nucleus of the stria terminalis (BNST). Here, we demonstrate that cat saliva contains predator cues that signal the imminence of predator threat and modulate the intensity of freezing behavior through the VNO in mice. Cat saliva activates neurons expressing the V2R-A4 subfamily of sensory receptors, suggesting that specific receptor groups are responsible for inducing the freezing behavior. The number of VNO neurons activated in response to saliva correlates with both the freshness of saliva and the intensity of freezing behavior. In contrast, the downstream neurons in the accessory olfactory bulb (AOB) and the defensive behavioral circuit are activated to a similar extent by fresh and old saliva. Strikingly, however, the number of VMH neurons activated by fresh, but not old, saliva positively correlates with the intensity of freezing behavior. Detailed analysis of the spatial distribution of neurons responding to fresh and old saliva, as well as the overlap of those activated within the same individual mice, revealed that fresh and old saliva predominantly activate distinct neuronal populations within the VMH. Collectively, this study suggests that there is an accessory olfactory circuit in mice that is specifically tuned to time-sensitive components of cat saliva, which optimizes their defensive behavior to maximize their chance of survival according to the imminence of threat.

neuroscience↗

bioRxiv2023

Dispersal in Kentish plovers (Charadrius alexandrinus): Adult females perform furthest movements

Dispersal is an important behavioural process that plays a significant role in, among others, speciation, population viability, and individual fitness. Despite progress in avian dispersal research, there are still many knowledge gaps. For example, it is of interest to study how movement propensity (i.e., nomadic vs. philopatric) relates to age- and/or sex-specific patterns of dispersal. Here, we investigated the role of sex and life-stage on natal (i.e., displacement between birth site and first breeding site) and breeding dispersal (i.e., displacement between sequential breeding sites) in the Kentish plover (Charadrius alexandrinus). This small and inconspicuous wader is characterised by flexible mating behaviour that includes monogamy, and serial polygyandry. Using a continent-wide dataset of ringing and re-encounter data throughout the species range in Europe, we found that adult females generally dispersed further than adult males between seasons, but we detected no sex-difference in natal dispersal distances and no general difference between natal and breeding dispersal distances. Furthermore, females were the main group exhibiting long-distance breeding dispersal, which we defined as breeding movements greater than [≥]108 km (i.e., upper 10% percentile of our dataset). Our work detected two females breeding in the Mediterranean before dispersing and breeding at the North Sea in the subsequent year, distances of 1,290 and 1,704 km, respectively - this represents the longest known breeding dispersal within the genus Charadrius. The long-distance dispersal records we identified are consistent with low genetic differentiation between mainland populations shown in previous work. The dispersive nature of the Kentish plover is likely attributed to its breeding behaviour: polyandrous females exhibit extensive mate searching and habitat prospecting. We recommend that the dispersal traits of Kentish plover be incorporated into the species conservation and management planning to more accurately inform models of population connectivity and metapopulation dynamics.

animal behavior and cognition↗

bioRxiv2021

immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires

Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. To date, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency, and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (i) reproducing a large-scale study on immune state prediction, (ii) developing, integrating, and applying a novel method for antigen specificity prediction, and (iii) showcasing streamlined interpretability-focused benchmarking of AIRR ML.

bioinformatics↗

bioRxiv2021

LINE-1 Retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5'-single cell RNA-Seq

LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method - 5 scL1seq - that makes use of a widely available library preparation method (10x Genomics 5 single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors - present in cancer cells, absent from immune cells - and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.

bioinformatics↗

bioRxiv2017

Construction of soil defined media using quantitative exometabolomic analysis of soil metabolites

Exometabolomics enables analysis of metabolite utilization of low molecular weight organic substances by soil isolates. Environmentally-based defined media are needed to examine ecologically relevant patterns of substrate utilization. Here, we describe an approach for the construction of defined media using untargeted characterization of water soluble soil metabolites. To broadly characterize soil metabolites, both liquid chromatography mass spectrometry (LC/MS) and gas chromatography mass spectrometry (GC/MS) were used. With this approach, 96 metabolites were identified, including amino acids, amino acid derivatives, sugars, sugar alcohols, mono- and di-carboxylic acids, osmolytes, nucleobases, and nucleosides. From this pool of metabolites, 25 were quantified. Water soluble organic carbon was fractionated by molecular weight and measured to determine the fraction of carbon accounted for by the quantified metabolites. This revealed that, community structures, these soil metabolites have an uneven quantitative distribution, with a single metabolite, trehalose accounting for 9.9 percent of much like soil microbial the (< 1 kDa) water extractable organic carbon. This quantitative information was used to formulate two soil defined media (SDM), one containing 23 metabolites (SDM1) and one containing 46 (SDM2). To evaluate SDM for supporting the growth of bacteria found at this field site, we examined the growth of 30 phylogenetically diverse soil isolates obtained using standard R2A medium. The simpler SDM1 supported the growth of up to 13 isolates while the more complex SDM2 supported up to 25 isolates. One isolate, Pseudomonas corrugata strain FW300-N2E2 was selected for a time-series exometabolomics analysis to investigate SDM1 substrate preferences. Interestingly, it was found that this organism preferred lower-abundance substrates such as guanine, glycine, proline and arginine and glucose and did not utilize the more abundant substrates maltose, mannitol, trehalose and uridine. These results demonstrate the viability and utility of using exometabolomics to construct a tractable environmentally relevant media. We anticipate that this approach can be expanded to other environments to enhance isolation and characterization of diverse microbial communities.\n\nHighlights O_LILC/MS and GC/MS analyses of soil extracts revealed a diversity of 96 metabolites.\nC_LIO_LISoil defined media were constructed based on water extractable soil metabolomics data.\nC_LIO_LIThe defined media supported the growth of 25 out of 30 bacterial isolates.\nC_LIO_LIExometabolomics demonstrated preferential consumption of amino acids for one isolate.\nC_LIO_LIThese media can be used to understand environmentally relevant microbial substrate preferences.\nC_LI\n\nAbbreviationsDOM dissolved organic matter; SOM soil organic matter; WEOC water extractable organic carbon; LMWOS low molecular weight organic substances; SDM(1/2) soil defined media (1 and 2); R2A Reasoners 2A agar medium; ORFRC Oak Ridge Field Research Center; LC/MS liquid chromatography mass spectrometry; GC/MS gas chromatography/ mass spectrometry; TOC total organic carbon; HILIC hydrophilic interaction liquid chromatography

microbiology↗