Biology subjects

Nogueira, M.

Publications and source records attributed to Nogueira, M..

10 recordsLinked to original sources

bioRxiv2026

nf_xpatial: A Reproducible Framework for Standardized Preprocessing and Clustering of Xenium Data

Recent advances in spatial transcriptomics have enabled the profiling of increasingly larger numbers of genes while retaining single-cell and subcellular resolution in situ. However, standardized bioinformatics workflows for analyzing these datasets have lagged behind, with existing pipelines focusing primarily on image processing and cell segmentation. To address this gap, we present nf_xpatial, a best-practices Nextflow pipeline for the downstream analysis of 10x Genomics Xenium data. The pipeline performs quality control, filtering, log and cell area normalization, multi-sample integration, and both expression-driven and spatially informed clustering across systematic parameter sweeps, allowing users to evaluate and compare clustering resolutions and spatial modeling parameters within a single reproducible run. Overall, nf_xpatial streamlines the processing of Xenium data from platform outputs to integrated single-cell and spatial clustering datasets, providing a standardized starting point from which biologists can fine-tune parameters and proceed to hypothesis-driven spatial analyses.

bioinformatics↗

bioRxiv2026

The free amino acid-rich biostimulant, Leafamine, promotes cell division in tomato roots and alleviates heat stress effects

Several tomato (Solanum lycopersicum) varieties are sensitive to heat stress, which compromises plant growth, development, and ultimately yield. Biostimulants represent a promising approach to improve crop performance, yet their widespread adoption is hindered by the incomplete understanding of their mechanisms of action. This study aimed to elucidate the physiological and molecular effects of a protein hydrolysate-based biostimulant (Leafamine(R)), in tomato, under both optimal and heat stress conditions. Leafamine(R) increased primary root length by 15 to 20% compared to the controls, independent of the tested conditions, through promotion of cell division and potentially expansion. Transcriptomic analyses revealed the upregulation of genes involved in cell division and expansion under both optimal and heat stress conditions and the downregulation of heat stress markers under heat stress conditions. Hormone and metabolite profiling showed elevated levels of jasmonic and salicylic acid, putrescine, citrulline, and GABA, after Leafamine(R) treatment, consistent with the activation of stress tolerance pathways. Leafamine(R) pre-treated seedlings exhibited reduced growth inhibition during heat exposure, suggesting a priming effect. These findings highlight Leafamine(R) as a promising biostimulant for enhancing tomato growth in the context of climate change and the potential of biostimulants generically.

plant biology↗

bioRxiv2026

THE STRUCTURES OF MATURE AND IMMATURE ST. LOUIS ENCEPHALITIS VIRUS REVEAL CONSERVED HISTIDINE RESIDUES AFFECTING VIRUS FITNESS

Orthoflaviviruses undergo significant structural changes through maturation and infection, yet the molecular mechanisms remain incompletely understood. Using St. Louis encephalitis virus (SLEV) as a model, a reemerging mosquito-borne orthoflavivirus endemic in the Americas, we elucidated the structures of immature and mature SLEV particles at resolutions of 4.4 [A] and 3.3 [A], respectively, using cryo-EM. SLEV is characterized by glycosylated E and prM proteins, the presence of lipid pockets, and is stabilized by an intricate network of inter- and intra-protein interactions between E and (pr)M across maturation stages. Several interactions were mediated by histidines that play different roles depending on SLEV maturation and pH. Non-lethal single mutations of H285R and H443R in E protein affect SLEV replication in mammalian and mosquito cell lines, and delay death in mouse models of infection. These histidine residues are conserved across orthoflaviviruses, illustrating the complexity of orthoflavivirus particles and indicating a possible strategy for attenuation.

microbiology↗

bioRxiv2026

Ventral pallidal perineuronal nets regulate opioid relapse

Opioid use disorder remains a major health challenge worldwide. Neuronal activity in the ventral pallidum (VP) regulates opioid reward and relapse to opioid seeking but the underlying cellular mechanisms remain largely unknown. A sizable population of VP neurons previously linked to drug relapse expresses the calcium binding protein parvalbumin (VPPV). Across the brain parvalbumin neurons are often ensheathed by perineuronal nets (PNNs), specialized extracellular structures that regulate intrinsic activity and constrain synaptic plasticity onto these neurons. The VP contains high levels of PNNs but the role of these structures in the neurophysiology of VPPV neurons and in relapse to opioid seeking has not been studied. To investigate whether VP PNNs are altered by opioid exposure, male and female mice were trained to self-administer intravenous heroin. We found that heroin increased the density of PNNs in the VP, and that an intracranial microinfusion of the PNN-degrading enzyme, chondroitinase ABC, prevented cue-induced reinstatement of heroin seeking. VP PNN depletion also reduced the intrinsic excitability of VPPV neurons, potentiated inhibitory synaptic inputs onto these cells, and diminished Fos expression in VPPV neurons following reinstatement. The suppressive effect of VP PNN depletion on heroin seeking was rescued by chemogenetic activation of VPPV neurons and mimicked by chemogenetic VPPV neuron inhibition. Taken together, our results identify VPPV neurons and their associated PNNs as critical drivers of opioid seeking. Given the key role of PNNs in regulating neural plasticity and memory processes, targeting PNNs in the VP could provide a useful novel therapeutic avenue for treating persistent craving and relapse in opioid use disorder.

neuroscience↗

bioRxiv2025

Auditory regulation of hippocampal locomotion circuits by a non-canonical reticular-limbic pathway

The ability to rapidly detect and respond to unexpected auditory stimuli is critical for adaptive behavior, especially during locomotion. Since movement suppresses auditory cortical activity, it remains unclear how salient auditory information influences locomotor circuits. In this work, using in vivo calcium imaging, electrophysiology, chemo- and optogenetics, we investigate the path that relays loud broadband sounds to the dorsal hippocampus (dHPC) and modulates theta oscillations. We demonstrate that noise accelerates theta frequency and decreases its power, effects mediated by entorhinal cortex (EC) and medial septum (MS) inputs while independent of the primary auditory cortex. Activation of dorsal cochlear nucleus (DCN) neurons projecting to the pontine reticular nucleus (PRN) mimics noise-driven hippocampal responses, supporting a brainstem-limbic auditory processing route. Furthermore, noise selectively modulates CA1 pyramidal neuron and interneuron activity, reflecting diverse circuit dynamics. Finally, loud broadband noise stimulus increased theta coherence between the dHPC and the medial prefrontal cortex (mPFC), enhancing interregional synchronization. These results highlight the mechanisms in which the DCN filters behaviorally relevant sounds promoting acoustic motor integration in the hippocampus during locomotion, without direct influence of the auditory cortex.

neuroscience↗

bioRxiv2023

Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis?

Plants are sessile and therefore have developed an extraordinary capacity to adapt to external signals. Here, the focus is on the plasticity of the plant cell to respond to new intracellular cues. Ketocarotenoids are high-value natural red pigments with potent antioxidant activity. In the present study, system level analyses have revealed that the heterologous biosynthesis of ketocarotenoids in tomato initiated a series of cellular and metabolic mechanisms to cope with the formation of metabolites that are non-endogenous to the plant. The broad multilevel changes were linked to, among others, (i) the remodelling of the plastidial membrane, where the synthesis and storage of ketocarotenoids occurs, (ii) the recruiting of core metabolic pathways for the generation of metabolite precursors and energy, and (iii) redox control. The role of the metabolites as regulators of cellular processes shown here, reinforces their pivotal role suggested in the remodelled "central dogma" concept.

systems biology↗

bioRxiv2021

Zika Virus Infection of Murine and Human Neutrophils and their Function as Trojan Horses to the Placenta

ZIKV is a 11Kb positive stranded flavivirus transmitted by infected Aedes aegypti and by sexual intercourse. After a short period of viremia of 5-7 days, the virus is cleared, and infection resolved in 80% of individuals. However, around 27% of the fetuses from pregnant infected mothers may develop several fetal brain and ocular pathology. Here we show that murine and peripheral blood human neutrophils support ZIKV infection and replication both in vitro and in vivo, which may correlate to the facilitation of vertical transmission. ZIKV did not interfere with cell viability, neither induced ROS production nor the release of NETs by infected neutrophils. Also, ZIKV infection of neutrophils did not trigger a pro-inflammatory profile, as evidenced by qPCR and proteomic analysis. Interestingly, ZIKV-infected neutrophils were isolated from the placenta were highly infected. The transference of in vitro ZIKV-infected neutrophils to pregnant female mice favored the transference of viral particles to the fetus. Conversely, neutrophil depletion with monoclonal antibodies reduced fetal viral loads whereas the treatment with recombinant G-CSF has the opposite effect. In summary, although it has already been shown that circulating monocytes harbor ZIKV, to our knowledge, this is the first report demonstrating the role of neutrophils during ZIKV infection, and most important, that it may act as a trojan horse to placental tissue directly impacting the pathogenesis of congenital syndrome.

immunology↗

bioRxiv2021

Laser Capture Microdissection optimization for high-quality RNA in mouse brain tissue

Laser Capture Microdissection (LCM) is a method that allows to select and dissecting specific structures, cell populations, or even single cells from different types of tissue to extract DNA, RNA, or proteins. It is easy to perform and precise, avoiding unwanted signals from irrelevant cells, because gene expression may be affected by a bulk of heterogeneous material in a sample. However, despite its efficiency, several steps can affect the sample RNA integrity. In comparison to DNA, RNA is a much more unstable molecule and represents a challenge in the LCM method. Here we describe an optimized protocol to provide good concentration and high-quality RNA in specific structures, such as Dentate Gyrus and CA1 in the hippocampus, basolateral amygdala and anterior cingulate cortex of mouse brain tissue.

neuroscience↗

bioRxiv2021

Follow-up of a hospital cohort during the first 3,530 suspected cases of COVID-19 in Sao Jose do Rio Preto, Sao Paulo, Brazil

IntroductionIn a global context, COVID-19 is the most significant health threat in the present days, evidenced by the fact that, in just over four months, SARS-CoV-2 has spread to 171 countries, reaching a Pandemic status. Most patients with COVID-19 have a mild course of the disease. However, approximately 20% develop severe illness with a high mortality rate which is associated with age, comorbidities, and immunosuppression. Epidemiological studies are used to reveal the extent of viral spread in homes, communities, and hospitals. Thus, preventive and control measures can be established by the authorities. ObjectiveIn this study, patients with suspect COVID-19 symptoms who search for hospital care at the city of Sao Jose do Rio Preto (Sao Paulo, Brazil) were monitored, in order to identify the first case of this new disease in the region. In the first two months (March and April), more than 3000 individuals looked for the public and private health system with suspected respiratory symptoms, but only 164 (8.4%) were COVID-19 confirmed. ResultsFrom those, males (56.1%) and patients of the age distribution of 16-59 (91.2%), with diarrhea (22.2%), runny nose (25%), altered taste (15.9%), and anosmia (11.6%) presented statistical significance, although none comorbidities were related with COVID-19 occurrence. The odds ratio analysis supports this finding. Days of onset of symptoms are positively associated with whit viral load, and the same happens with the occurrence of symptoms (dyspnea and low saturation).

molecular biology↗

bioRxiv2019

Cell competition regulates the kinetics of thymopoiesis and thymus cellularity

Cell competition in the thymus is a homeostatic process that drives turnover. If the process is impaired, thymopoiesis can be autonomously maintained for several weeks, but this causes leukemia. We aimed to understand the impact of cell competition on thymopoiesis, identify the cells involved and determine how the process is regulated. Using thymus transplantation experiments we found that cell competition occurs within the double negative 2 (DN2) and 3 early (DN3e) thymocytes and inhibits thymus autonomy. Furthermore, the expansion of DN2b is regulated by a negative feedback loop imposed by double positive thymocytes and determines the kinetics of thymopoiesis. This feedback loop impacts on cell cycle duration of DN2b, in a response controlled by interleukin 7 availability. Altogether, we show that thymocytes do not merely follow a pre-determined path if provided with the correct signals. Instead, thymopoiesis dynamically integrates cell autonomous and non-cell autonomous aspects that fine-tune normal thymus function.

immunology↗