Biology subjects

Correa, C.

Publications and source records attributed to Correa, C..

7 recordsLinked to original sources

bioRxiv2023

Nucleosome reorganisation in breast cancer tissues

Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. Here we have generated high resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with [~]20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. In addition, tumour tissues were characterised by a 5-10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. These effects were correlated with gene activity, DNA sequence repeats abundance, differential DNA methylation and binding of linker histone variants H1.4 and H1X. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient stratification and monitoring using liquid biopsies.

genomics↗

bioRxiv2021

The pace of modern life, revisited

Wild populations must continuously adapt to environmental changes or they risk extinction. Such adaptations can be measured as phenotypic rates of change and can allow us to predict patterns of contemporary evolutionary change. About two decades ago, a dataset of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this dataset to look at microevolutionary processes in relation to specific types of human disturbances. Here, we have updated the dataset adding 5675 estimates of phenotypic changes and used it to revisit established patterns of contemporary evolutionary change. Using this newer version, containing 7338 estimates of phenotypic changes, we revisit the conclusions of four published articles. We then synthesize the expanded dataset to compare rates of change across different types of human disturbance. Analyses of this expanded dataset suggests that: I. a small absolute difference in rates of change exists between human disturbed and natural populations, II. harvesting by humans results in larger rates of change than other types of disturbances, III. introduced populations have increased rates of change, and IV. body size does not increase through time. Overall, findings from earlier analyses have largely held-up in analyses of our new dataset that encompass a much larger breadth of species, traits, and human disturbances. Lastly, we found that types of human disturbances affect rates of phenotypic change, and we call for this database to serve as a steppingstone for further analyses to understand patterns of contemporary evolution.

evolutionary biology↗

bioRxiv2021

The heart rate discrimination task: a psychophysical method to estimate the accuracy and precision of interoceptive beliefs

Interoception - the physiological sense of our inner bodies - has risen to the forefront of psychological and psychiatric research. Much of this research utilizes tasks that attempt to measure the ability to accurately detect cardiac signals. Unfortunately, these approaches are confounded by well-known issues limiting their validity and interpretation. At the core of this controversy is the role of subjective beliefs about the heart rate in confounding measures of interoceptive accuracy. Here, we recast these beliefs as an important part of the causal machinery of interoception, and offer a novel psychophysical "heart rate discrimination" method to estimate their accuracy and precision. By applying this task in 223 healthy participants, we demonstrate that cardiac interoceptive beliefs are more biased, less precise, and are associated with poorer metacognitive insight relative to an exteroceptive control condition. Our task, provided as an open-source python package, offers a robust approach to quantifying cardiac beliefs. HighlightsO_LICurrent interoception tasks conflate cardiac beliefs with accuracy. C_LIO_LIWe introduce a Bayesian method for estimating cardiac belief accuracy and precision. C_LIO_LIIndividuals underestimate their heart rate by -7 BPM (95% CI [-8.6 -5.3]) on average. C_LIO_LICardiac beliefs are associated with reduced precision and metacognitive insight. C_LIO_LIThe task and modelling tools are provided in the Python Cardioception Package. C_LI

neuroscience↗

bioRxiv2020

Pupil dilation and P3 reflect subjective surprise about decision outcome

Central to human and animal cognition is the ability to learn from feedback in order to optimize future rewards. Such a learning signal might be encoded and broadcasted by the brains arousal systems, including the noradrenergic locus coeruleus. Pupil responses and the positive slow wave component of event-related potentials reflect rapid changes in the arousal level of the brain. Here we ask whether and how these variables may reflect surprise: the mismatch between ones expectation about being correct and the outcome of a decision, when expectations fluctuate due to internal factors (e.g., engagement). We show that during an elementary decision-task in the face of uncertainty both physiological markers of phasic arousal reflect surprise. We further show that pupil responses and slow wave ERP are unrelated to each other, and that prediction error computations depend on feedback awareness. These results further advance our understanding of the role of central arousal systems in decision-making under uncertainty.

neuroscience↗

bioRxiv2020

Emotional Metacognition: Stimulus Valence Modulates Cardiac Arousal and Metamemory

Emotion alters how we feel, see, and experience the world. In the domain of memory, the emotional valence and arousal of memorised stimuli can modulate both the acuity and content of episodic recall. However, no experiment has investigated whether arousal and valence also influence metacognition for memory (i.e., the process of self-monitoring memories). In a pre-registered study, we applied a novel psychophysiological design together with computational models of metacognition to assess the influence of stimulus valence and arousal on the sensitivity, bias, and efficiency of metamemory. To estimate the role of physiological arousal in mediating these effects, we recorded cardiac measures through pulse oximetry. We found that negative valence substantially decreased both memory performance and subjective confidence, in particular for low arousal words. Simultaneously, we found that emotional valence modulated both heart rate and heart-rate variability (HRV) during recognition memory. Exploratory trial-level analyses further revealed that subjective confidence was encoded in instantaneous heart-rate fluctuations and that this relationship was also modulated by emotional valence. Our results demonstrate that recognition memory and metacognition are influenced by the emotional valence of encoded items and that this correlation is in part related to cardiac activity.

neuroscience↗

bioRxiv2018

How the level of reward awareness changes the computational and electrophysiological signatures of reinforcement learning

The extent to which subjective awareness influences reward processing, and thereby affects future decisions is currently largely unknown. In the present report, we investigated this question in a reinforcement-learning framework, combining perceptual masking, computational modeling and electroencephalographic recordings (human male and female participants). Our results indicate that degrading the visibility of the reward decreased -without completely obliterating- the ability of participants to learn from outcomes, but concurrently increased their tendency to repeat previous choices. We dissociated electrophysiological signatures evoked by the reward-based learning processes from those elicited by the reward-independent repetition of previous choices and showed that these neural activities were significantly modulated by reward visibility. Overall, this report sheds new light on the neural computations underlying reward-based learning and decision-making and highlights that awareness is beneficial for the trial-by-trial adjustment of decision-making strategies.\n\nSignificance statementThe notion of reward is strongly associated with subjective evaluation, related to conscious processes such as \"pleasure\", \"liking\" and \"wanting\". Here we show that degrading reward visibility in a reinforcement learning task decreases -without completely obliterating- the ability of participants to learn from outcomes, but concurrently increases subjects tendency to repeat previous choices. Electrophysiological recordings, in combination with computational modelling, show that neural activities were significantly modulated by reward visibility. Overall, we dissociate different neural computations underlying reward-based learning and decision-making, which highlights a beneficial role of reward awareness in adjusting decision-making strategies.

neuroscience↗

bioRxiv2017

Otolith microchemistry identifies diadromous populations of Patagonian river fishes

Compliance with Ethical StandardsOtolith analysis was funded by a RAC grant from the University of New Mexico, USA. The Government of Chile supported the drafting of this document with a CONICYT Doctoral Fellowship to D. Alo in 2015 and to C. Correa through grants CONICYT-PAI N{degrees}82130009, and FONDECYT-Iniciacion en la Investigacion N{degrees}11150990.\n\nAll applicable international, national, and/or institutional guidelines for the care and use of animals were followed. Specimens were collected under permits No. 3587, 29 December 2006, and No. 2886, 4 November 2008 (amendment No. 602, 12 February 2009) granted by the Chilean Subsecretary of Fishing to C. Correa. The McGill University Animal Care Committee (UACC), Animal Use Protocol No. 5291, approved use and handling of animals.\n\nAbstractCoastal habitats in Chile are hypothesized to support a number of diadromous fishes. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39-48{degrees}S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was detected for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited anadromous migratory patterns, whereas the population of O. mykiss screened appeared restricted to freshwater. Salmo trutta exhibited variable habitat use consistent with establishment of an ocean-type life history in some populations. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.

ecology↗