Biology subjects

Oliver, M.

Publications and source records attributed to Oliver, M..

13 recordsLinked to original sources

bioRxiv2025

TET2 loss impairs MPLA-induced innate immune memory during infection and disrupts hematopoiesis via RIPK1 in mice

Ten-eleven translocation protein 2 (TET2) is commonly mutated in hematologic disorders of bone marrow failure such as myelodysplastic syndrome (MDS), and loss of TET2 is associated with poor prognosis. TET2 loss is also associated with augmented inflammation, as well as impaired innate immune responses. However, many individuals harboring mutations do not develop hematologic disorders, indicating that additional factors, such as inflammation, cooperate with TET2 loss to promote disease progression. Innate immune memory is a phenomenon in which pre-treatment with microbial ligands, including monophosphoryl lipid A (MPLA), improves innate immune function while minimizing inflammation during subsequent infection. Given the previously reported innate immune impairments attributed to TET2 loss, we tested whether MPLA could induce an innate immune response in TET2-deficient mice infected with P. aeruginosa. Moreover, due to the inflammatory role of TET2 loss, we investigated whether MPLA with infection would promote disease-related phenotypes. We found that TET2-deficient mice display impaired infection response to P. aeruginosa which is partially improved with MPLA pretreatment. Assessments of pathogenic clearance functions further showed decreased capacity in TET2-deficient innate immune cells. Moreover, TET2-defcient cells also exhibit impaired differentiation. MPLA pretreatment in infected mice promotes myeloid-biased hematopoiesis at the expense of erythroid- and megakaryocyte-biased hematopoiesis, resembling MDS-like disease progression. Intriguingly, inhibition of receptor-interacting serine/threonine-protein kinase 1 (RIPK1) dampens the effects of TET2 loss on hematopoietic perturbation. Collectively, we find that TET2 loss impairs innate immune memory and infection responses, and MPLA with infection promotes hematopoietic skewing through RIPK1. KEY POINTS- TET2 loss increases susceptibility to infection, but immune response can be improved by MPLA-induced innate immune memory. - MPLA pretreatment and infection promotes aberrant hematopoiesis and myeloid bias in TET2 deficiency that is improved by RIPK1 inhibition.

cancer biology↗

bioRxiv2024

A biologically-inspired hierarchical convolutional energy model predicts V4 responses to natural videos

V4 is a key area within the visual processing hierarchy, and it represents features of intermediate complexity. However, no current computational model explains V4 responses under natural conditions. To address this, we developed a new hierarchical convolutional energy (HCE) model reflecting computations thought to occur in areas V1, V2, and V4, but which consists entirely of simple- and complex-like units like those found in V1. In contrast to prior models, the HCE model is trained end-to-end on neurophysiology data, without relying on pre-trained network features. We recorded 313 V4 neurons during full-color nature video stimulation and fit the HCE model to each neuron. The models predicted optimal patterns (POPs) revealed complex spatiotemporal pattern selectivity in V4, supporting its role in representing space, time, and color. These findings indicate that area V4 is crucial for image segmentation and grouping operations that are essential for complex vision. Thus, responses of V4 neurons under naturalistic conditions can be explained by a hierarchical three-stage model where each stage consists entirely of units like those found in area V1.

neuroscience↗

bioRxiv2023

Frequency-coded patterns of sympathetic vasomotor activity are differentially evoked by the paraventricular nucleus of the hypothalamus in the Goldblatt hypertension model

The activation of specific brain areas involved in regulating the vasomotor sympathetic activity can lead to distinct effects in the postganglionic nerves in both physiological and pathological conditions, suggesting that the sympathetic vasomotor activity is differentially coded depending on the nerve outflow and the target organs. Previous studies investigating such patterns have mostly focused on the global energy of the signal. However, recent evidence has suggested that relevant information is coded in the power distribution along the frequency range. Disturbing the sympathoexcitatory vasomotor tone in the paraventricular nucleus of the hypothalamus (PVN) allows to investigate the sympathetic nerve activity in overloaded conditions in both hypertensive and control animals. By disinhibiting the PVN through the microinjection of bicuculline, an antagonist of {gamma}-aminobutyric acid type A (GABAa) receptors, in the Goldblatt (2K1C) rat model of hypertension we addressed the territorially differential changes in the frequency parameters of the renal and splanchnic sympathetic nerve activity (rSNA and sSNA, respectively). We also tested the effect of the systemic administration of losartan, an antagonist of the angiotensin II type 1 receptors (AT1), in the attenuation of the increased rSNA and sSNA in 2K1C rats, once these changes are reported to be dependent on the AT1 activation in the Goldblatt model. Our results revealed that each nerve activity presents its own electrophysiological pattern of frequency-coded rhythm in each group, in basal condition and after bicuculline microinjection, but with no significant differences regarding total power comparison among groups. Additionally, the 2K1C animals treated with losartan showed no decrease in the hypertensive response triggered by the GABAa antagonism when compared to the non-treated 2K1C group. However, their spectral patterns of sympathetic nerve activity were different from the other two groups, suggesting that the systemic blockade of AT1 receptors does not totally recover the basal levels of neither the autonomic symptoms nor the electrophysiological patterns in the Goldblatt model, but act on their spectral frequency distribution. These results suggest that the differential responses evoked by the PVN were preferentially coded in frequency of vasomotor sympathetic responses, indicating that the PVN distinctly modulated each rhythmic activity. Financial Support - FAPESP (2019/25295-0)

neuroscience↗

bioRxiv2022

Ultraviolet radiation and dehydration stress induce overlapping transcriptional and metabolic responses in Syntrichia mosses

O_LIProtection from excess solar radiation and access to sufficient water are important problems for terrestrial plants to solve. Desiccation tolerance (DT), defined as the ability to equilibrate to dry air and resume normal metabolic activity after rehydration, allows organisms to survive dry periods by limiting metabolic activity to periods of moisture availability. We compared separate and combined effects of chronic ultraviolet radiation (UVR) treatments (UV-A and UV-A/B) and a dehydration treatment (as a surrogate for desiccation) in the mosses Syntrichia ruralis and S. caninervis to uncover the nature of correlation between DT and UVR tolerance (UVRT). C_LIO_LIUsing a fully factorial experiment with combined transcriptomics and metabolomics, we tested for cross-talk (overlap in signaling pathways in response to different stressors but separate mechanisms of protection) in the genetic underpinnings of DT and UVRT and cross-tolerance (overlap in the mechanism of protection) these two stressors. C_LIO_LIShared transcriptomic response to the two stressors with no significant interaction between them suggested cross-talk between UVRT and DT for S. caninervis. Phenolic metabolites and transcripts were involved in the response to UVR and dehydration in both species. C_LIO_LISome candidate UVRT genes and metabolites were induced by UVR in S. ruralis, but not S. caninervis, supporting the hypothesis that S. ruralis has a more plastic, acclimatable UVR response than S. caninervis, and that these differences are predictable by their unique interaction with these stressors as poikilohydric organisms. C_LI

plant biology↗

bioRxiv2022

ROS are evolutionary conserved cell-to-cell signals

Cell-to-cell communication is fundamental to multicellular organisms and unicellular organisms living in a microbiome. A unique cell-to-cell communication mechanism that uses reactive oxygen species (ROS) as a signal (termed the ROS wave) was recently identified in flowering plants. Here we report that a ROS-mediated cell-to-cell signaling process, like the ROS wave, can be found in ferns, mosses, unicellular algae, amoeba, mammalian cells, and isolated hearts. We further show that this process can be triggered by a localized stress treatment or H2O2 application and blocked by inhibition of NADPH oxidases, and that in unicellular algae, it communicates important stress-response signals between cells. Taken together, our findings suggest that cell-to-cell ROS signaling evolved before unicellular and multicellular organisms diverged. The finding of a ROS wave-like signaling process in mammalian cells further contributes to our understanding of different diseases and could impact the development of new drugs that target cancer or heart disease.

plant biology↗

bioRxiv2022

High-throughput widefield fluorescence imaging of 3D samples using deep learning for 2D projection image restoration

Fluorescence microscopy has become a core tool for visualizing and quantifying the spatial and temporal dynamics of complex biological processes. Thanks to its low cost and ease-of-use, widefield fluorescent imaging remains one of the most widely used fluorescence microscopy imaging modalities. To accomplish imaging of 3D samples, conventional fluorescence imaging entails acquiring a sequence of 2D images spaced along the z-dimension, typically called a z-stack. Oftentimes, the next step is to project the 3D volume into a single 2D image, as 3D image data can be cumbersome to manage and challenging to analyze and interpret, effectively limiting the utlity of z-dimensional information. Furthermore, z-stack acquisition is often time-consuming and consequently may induce photodamage to the biological sample, which are both major hurdles for its application in experiments that require high-throughput, such as drug screening. As an alternative to z-stacks, axial sweep acquisition schemes have been proposed to circumvent these drawbacks and offers potential of 100-fold faster image acquisition for 3D-samples compared to z-stack acquisition but unfortunately results in blurry, low-quality raw 2D z-projected images. We propose a novel workflow to combine axial z-sweep acquisition with deep learning-based image restoration, ultimately enabling high-throughput and high-quality imaging of complex 3D-samples using 2D projection images. To demonstrate the capabilities of our proposed workflow, we apply it to live-cell imaging of 3D tumor spheroids and find we can produce high-fidelity images appropriate for quantitative analysis. Therefore, we conclude that combining axial z-sweep image acquisition with deep learning-based image restoration enables high-throughput and high-quality fluorescence imaging of complex 3D biological samples.

cell biology↗

bioRxiv2021

Viability markers for determination of desiccation tolerance and critical stages during dehydration in Selaginella species

Plants can tolerate some degree of dehydration but below a threshold of water content most plants die. However, some species display specific physiological, biochemical, and molecular responses that allow survival to desiccation. Some of these responses are activated at critical stages during water loss and could represent the difference between desiccation tolerance (DT) and death. Here, we report the development of a simple and reproducible system to determine DT in Selaginella species. This system is based on the use of excised tissue (explants), exposed to a dehydration agent inside small containers, rather than whole plants making it faster, better controlled, and potential use under field conditions. We also report that the triphenyltetrazolium chloride test is a simple and accurate assay to determine tissue viability. The explant system is particularly useful to identify critical points during the dehydration process and was applied to identify novel desiccation-tolerant Selaginella species. Our data suggest that desiccation-sensitive Selaginella species have a change in viability when dehydrated to 40% RWC, indicating the onset of a critical condition at this water content. Comparative studies at these critical stages could provide a better understanding of DT mechanisms and unravel insights into the key responses to survive desiccation. HighlightIn this article, we developed a simple and efficient system to determine desiccation tolerance and critical stages during the dehydration process in Selaginella that can be applied to other plant species.

plant biology↗

bioRxiv2020

Removing independent noise in systems neuroscience data using DeepInterpolation

Progress in nearly every scientific discipline is hindered by the presence of independent noise in spatiotemporally structured datasets. Three widespread technologies for measuring neural activity--calcium imaging, extracellular electrophysiology, and fMRI--all operate in domains in which shot noise and/or thermal noise deteriorate the quality of measured physiological signals. Current denoising approaches sacrifice spatial and/or temporal resolution to increase the Signal-to-Noise Ratio of weak neuronal events, leading to missed opportunities for scientific discovery. Here, we introduce DeepInterpolation, a general-purpose denoising algorithm that trains a spatio-temporal nonlinear interpolation model using only noisy samples from the original raw data. Applying DeepInterpolation to in vivo two-photon Ca2+ imaging yields up to 6 times more segmented neuronal segments with a 15 fold increase in single pixel SNR, uncovering network dynamics at the single-trial level. In extracellular electrophysiology recordings, DeepInterpolation recovered 25% more high-quality spiking units compared to a standard data analysis pipeline. On fMRI datasets, DeepInterpolation increased the SNR of individual voxels 1.6-fold. All these improvements were attained without sacrificing spatial or temporal resolution. DeepInterpolation could well have a similar impact in other domains for which independent noise is present in experimental data.

neuroscience↗

bioRxiv2019

On the correspondence of electrical and optical physiology in in vivo population-scale two-photon calcium imaging.

Multiphoton calcium imaging is commonly used to monitor the spiking of large populations of neurons. Recovering action potentials from fluorescence necessitates calibration experiments, often with simultaneous imaging and cell-attached recording. Here we performed calibration for imaging conditions matching those of the Allen Brain Observatory. We developed a novel crowd-sourced, algorithmic approach to quality control. Our final data set was 50 recordings from 35 neurons in 3 mouse lines. Our calibration indicated that 3 or more spikes were required to produce consistent changes in fluorescence. Moreover, neither a simple linear model nor a more complex biophysical model accurately predicted fluorescence for small numbers of spikes (1-3). We observed increases in fluorescence corresponding to prolonged depolarizations, particularly in Emx1-IRES-Cre mouse line crosses. Our results indicate that deriving spike times from fluorescence measurements may be an intractable problem in some mouse lines.

neuroscience↗

bioRxiv2019

Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses

O_LIMosses (Bryophyta) are a key group occupying important phylogenetic position for understanding land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage and contains more than 95% of the modern mosses, whereas the other classes are by nature species-poor. The phylogeny of mosses remains elusive at present.\nC_LIO_LIRecurrent whole genome duplications have shaped the evolution trajectory of angiosperms, but little is known about the genome evolutionary history in mosses. It remains to be answered if there existed a historical genome duplication event associated with the species radiation of class Bryopsida.\nC_LIO_LIHere, the high-confidence moss phylogeny was generated covering major moss lineages. Two episodes of ancient genomic duplication events were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida and Tetraphidopsida, with estimated ages of the gene duplications clustered around 329 and 182 million year ago, respectively.\nC_LIO_LIThe third episode of polyploidy event (termed {psi}) was tightly associated with the early diversification of Bryopsida with an estimated age of ~87 million years. By scrutinizing the phylogenetic timing of duplicated syntelogs in Physcomitrella patens, the WGD1 and WGD2 events were confidently re-recognized as the {psi} event and the Funarioideae duplication event (~65 mya), respectively. Together, our findings unveiled four episodes of polyploidy events in the evolutionary past of Physcomitrella patens.\nC_LI

evolutionary biology↗

bioRxiv2019

Evolution of Auxin Response Factors in plants characterized by phylogenomic synteny network analyses

Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Previous studies focusing genes from limited number of species were unable to uncover the evolutionary trajectory of this family. Here, more than 3,500 ARFs collected from plant genomes and transcriptomes covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting distinct groups. Recurrent duplication events, such as those that occurred in seed plant, angiosperms, core eudicots and grasses contributed the expansion of ARF genes which facilitated functional diversification. Ancestral transposition activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may have accelerated the functional diversification process of paralogues. Our study provides insights into the evolution of ARFs which will enhance our current understandings for this important transcription factor family.

genomics↗

bioRxiv2018

The DeepTune framework for modeling and characterizing neurons in visual cortex area V4

Deep neural network models have recently been shown to be effective in predicting single neuron responses in primate visual cortex areas V4. Despite their high predictive accuracy, these models are generally difficult to interpret. This limits their applicability in characterizing V4 neuron function. Here, we propose the DeepTune framework as a way to elicit interpretations of deep neural network-based models of single neurons in area V4. V4 is a midtier visual cortical area in the ventral visual pathway. Its functional role is not yet well understood. Using a dataset of recordings of 71 V4 neurons stimulated with thousands of static natural images, we build an ensemble of 18 neural network-based models per neuron that accurately predict its response given a stimulus image. To interpret and visualize these models, we use a stability criterion to form optimal stimuli (DeepTune images) by pooling the 18 models together. These DeepTune images not only confirm previous findings on the presence of diverse shape and texture tuning in area V4, but also provide rich, concrete and naturalistic characterization of receptive fields of individual V4 neurons. The population analysis of DeepTune images for 71 neurons reveals how different types of curvature tuning are distributed in V4. In addition, it also suggests strong suppressive tuning for nearly half of the V4 neurons. Though we focus exclusively on the area V4, the DeepTune framework could be applied more generally to enhance the understanding of other visual cortex areas.

neuroscience↗

bioRxiv2018

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.

neuroscience↗