Biology subjects

Miranda, M.

Publications and source records attributed to Miranda, M..

32 records · Page 2Linked to original sources

bioRxiv2022

Metabolic profiling of drought tolerance: revealing how citrus rootstocks modulate plant metabolism under varying water availability

Water stress is a major environmental factor affecting Citrus spp. and Rangpur lime is a drought-tolerant rootstock used to enhance orange yield in rainfed orchards. Here, we combined morpho-physiological analyses with metabolic profiling of roots and leaves of Valencia orange scions grafted onto Rangpur lime, Swingle citrumelo or Sunki mandarin rootstocks under water deficit. Our aim was to present a comprehensive spatio-temporal evaluation of citrus responses to drought and highlight the metabolic adjustments associated with drought tolerance induced by Rangpur lime. Plant responses were evaluated during the initial phase of reduction in water availability, when water deficit was maximum and also after rehydration. Fifty-eight primary metabolites were modulated by water deficit, mainly amino acids, organic acids and sugars. Metabolic changes indicated adjustments related to osmotic, energetic and redox processes under low water availability, which were dependent on rootstock and varied between roots and leaves and along the experimental period. Rangpur lime prioritized root growth in the initial phase of water deficit, which was linked to less sugar accumulation, changes in nucleotide metabolism, downregulation in Shikimic acid pathway and accumulation of arginine. After rehydration, the resume of shoot growth was associated with high accumulation of arginine and asparagine. The better performance of Rangpur lime seems to be associated with its high sensitivity of roots to changes in water availability and possible signaling compounds have been suggested.

plant biology↗

bioRxiv2021

Acute and chronic physical activity improve spatial pattern separation in humans

Physical activity benefits both fitness and cognition. However, its effect on long-term memory is unclear. Successful memory involves not only remembering information over time but also keeping memories distinct and less confusing. The ability to separate similar experiences into distinct memories is one of the main features of episodic memory. In this work, we evaluated the effect of acute and chronic physical activity on a new task to assess spatial pattern separation in a 3D virtual reality environment. We manipulated the load of memory similarity and found that 25 minutes of cycling after encoding - but not before retrieval - was sufficient to improve similar, but not dissimilar memories, 24 hours after encoding. Furthermore, we found that participants who engaged in regular physical activity, but not sedentary subjects, showed memory for the similar condition the next day. Thus, physical activity could be a simple way to improve discrimination of spatial memories in humans.

animal behavior and cognition↗

bioRxiv2021

Can intraspecific variation in a herbivorous mite alter responses to drought-stressed host plant? A common garden experiment in the context of climate change

Drought associated with climate change can stress plants, altering their interactions with phytophagous arthropods. Drought not only impacts cultivated plants but also their parasites, which in some cases are favored by drought. Herbivorous arthropods feeding on drought-stressed plants typically produce bigger offspring and develop faster. However, it is unclear how much responses to drought stress differ among populations of herbivore species. Here, we evaluate variability among populations of a major agricultural pest, the two spotted spider mite, Tetranychus urticae, in response to drought stress. We compare key life history parameters of twelve populations that originate from climates ranging from wet and cool Atlantic locations to medium to dry hot Mediterranean locations. We evaluated how plant drought stress affects four life history traits: development time, fecundity, sex-ratio and emigration rate in an experiment comparing well-watered and drought-stressed bean plants. Mites feeding on drought-stressed plants developed faster and attempted to leave leaves less often, and young females were more fecund. The mites from wet temperate climates exhibited greater plasticity between the two water regimes than mites originating from dryer and hot climates, suggesting that the climate in the area of origin influences mite response to drought.

zoology↗

bioRxiv2021

A complex CTCF binding code defines TAD boundary structure and function

Topologically Associating Domains (TADs) compartmentalize vertebrate genomes into sub-Megabase functional neighbourhoods for gene regulation, DNA replication, recombination and repair1-10. TADs are formed by Cohesin-mediated loop extrusion, which compacts the DNA within the domain, followed by blocking of loop extrusion by the CTCF insulator protein at their boundaries11-20. CTCF blocks loop extrusion in an orientation dependent manner, with both experimental and in-silico studies assuming that a single site of static CTCF binding is sufficient to create a stable TAD boundary21-24. Here, we report that most TAD boundaries in mouse cells are modular entities where CTCF binding clusters within extended genomic intervals. Optimized ChIP-seq analysis reveals that this clustering of CTCF binding does not only occur among peaks but also frequently within those peaks. Using a newly developed multi-contact Nano-C assay, we confirm that individual CTCF binding sites additively contribute to TAD separation. This clustering of CTCF binding may counter against the dynamic DNA-binding kinetics of CTCF25-27, which urges a re-evaluation of current models for the blocking of loop extrusion21-23. Our work thus reveals an unanticipatedly complex code of CTCF binding at TAD boundaries that expands the regulatory potential for TAD structure and function and can help to explain how distant non-coding structural variation influences gene regulation, DNA replication, recombination and repair5,28-34.

genetics↗

bioRxiv2021

Dopamine modulates adaptive forgetting in medial prefrontal cortex

Active forgetting occurs in many species, but how the mechanisms that control behavior contribute to determining which memories are forgotten is still unknown. We previously found that when rats need to retrieve particular memories to guide exploration, it reduces later retention of other memories encoded in that environment. As with humans, this retrieval-induced forgetting relies on prefrontal control processes. The dopaminergic input to the prefrontal cortex is important for executive functions and cognitive flexibility. We found that, in a similar way, prefrontal dopamine signaling through D1 receptors is required for retrieval-induced forgetting in rats. Blockade of medial prefrontal cortex D1 receptors as animals encountered a familiar object impaired forgetting of the memory of a competing object in a subsequent long-term memory test. Inactivation of the ventral tegmental area produced the same pattern of behavior, a pattern that could be reversed by concomitant activation of prefrontal D1 receptors. We observed a bidirectional modulation of retrieval-induced forgetting by agonists and antagonists of D1 receptors in the medial prefrontal cortex. These findings establish the essential role of prefrontal dopamine in the active forgetting of competing memories, contributing to the shaping of retention in response to an organisms behavioral goals.

animal behavior and cognition↗

bioRxiv2021

Epigenome erosion drives neural crest-like phenotypic mimicry in triple-negative breast cancer and other SOX10+ malignancies

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSIntratumoural heterogeneity is a poor prognostic feature in triple-negative breast cancer (TNBC) and other high-grade malignancies. It is caused by genomic instability and phenotypic plasticity, but how these features co-evolve during tumour development remains unclear. SOX10 is a transcription factor, neural crest stem cell (NCSC) specifier and candidate mediator of cancer-associated phenotypic plasticity. MethodsUsing immunophenotyping, we investigated the expression of SOX10 in normal human breast tissue and breast cancer (n=21 cosmetic breast reduction and 1,860 tumour samples with clinical annotation). We then defined the context and evolution of its expression in TNBC compared to 21 other malignancies using systems-level transcriptomics. ResultsSOX10 was detected in nuclei of normal mammary luminal progenitor cells, the histogenic origin of most TNBCs. In breast cancer, nuclear SOX10 predicted poor outcome amongst cross-sectional (log-rank p=0.0015, hazard ratio 2.02, n=224) and metaplastic (log-rank p=0.04, n=66) TNBCs. Systems-level transcriptional network analysis identified a core module in SOX10s normal mammary epithelial transcription program that is rewired to NCSC genes in TNBC. Reprogramming was proportional to DNA damage and genome-wide promoter hypomethylation, particularly at CpG island shores. Using a novel network analysis pipeline, we found that NCSC-like transcriptional reprogramming is also strongly associated with promoter hypomethylation in other SOX10+ malignancies: glioma and melanoma. ConclusionsWe propose that cancer-associated genome hypomethylation simulates the open chromatin landscape of more primitive cell states, and that on this relatively unrestricted background, SOX10 recreates its ancestral gene regulatory circuits by default. These findings provide new insights about the basis of intratumoural heterogeneity and resurrection of developmental phenotypes in cancer; and highlight the potential for therapeutics that limit chromatin remodelling.

cancer biology↗

bioRxiv2021

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus

Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ. It demonstrated its capability to discover the key regulatory elements that determine cell fate during developmental programs such as brain or heart development. Single-cell analysis requires the isolation and labeling of the messenger RNA (mRNA) derived from each cell. These challenges were primarily addressed in mammals by developing microfluidic-based approaches. For plant species whose cells contain cell walls, these approaches have generally required the generation of isolated protoplasts. Many plant tissues secondary cell wall hinders enzymatic digestion required for individual protoplast isolation, resulting in an unequal representation of cell types in a protoplast population. This limitation is especially critical for cell types located in the inner layers of a tissue or the inner tissues of an organ. Consequently, single-cell RNA sequencing (scRNA-seq) studies using microfluidic approaches in plants have mainly been restricted to Arabidopsis roots, for which well-established procedures of protoplast isolation are available. Here we present a simple alternative approach to generating high-quality protoplasts from plant tissue by characterizing the mRNA extracted from individual nuclei instead of whole cells. We developed the protocol using two different plant materials with varying cellular complexity levels and cell-wall structure, Populus shoot apices, and more lignified stems. Using the 10x Genomics Chromium technology, we show that this procedure results in intact mRNA isolation and limited leakage, with a broad representation of individual cell transcriptomes.

plant biology↗

bioRxiv2020

A semi-automated method for measuring xylem vessel length distribution

Knowledge about the length of xylem vessels is essential to understand water transport in plants because these multicellular units show a 100-fold variation, from less than a centimeter to many meters. However, the available methods to estimate vessel length distribution (VLD) are excessively time consuming and do not allow large and in-depth surveys. Here, we describe a semi-automated method to measure VLD using an automated Pneumatron device. Gas conductivity of a xylem tissue with a certain length is estimated in a straightforward and precise way with the Pneumatron in a way theoretically similar to the air-injection method. The method presented enables fast and easy measurements using multiple devices simultaneously (>50 samples day-1), which is a significant advantage. Here, the apparatus is described in detail as well as how measurements are taken. We also present the software and an R-script for data analysis. The method described represents an important contribution to studies on plant hydraulic architecture and can improve our understanding about the role of VLD in plant performance under varying water availability.

plant biology↗

bioRxiv2020

Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is already responsible for far more deaths than previous pathogenic coronaviruses (CoVs) from 2002 and 2012. The identification of clinically approved drugs to be repurposed to combat 2019 CoV disease (COVID-19) would allow the rapid implementation of potentially life-saving procedures. The major protease (Mpro) of SARS-CoV-2 is considered a promising target, based on previous results from related CoVs with lopinavir (LPV), an HIV protease inhibitor. However, limited evidence exists for other clinically approved antiretroviral protease inhibitors, such as atazanavir (ATV). ATV is of high interest because of its bioavailability within the respiratory tract. Our results show that ATV could dock in the active site of SARS-CoV-2 Mpro, with greater strength than LPV. ATV blocked Mpro activity. We confirmed that ATV inhibits SARS-CoV-2 replication, alone or in combination with ritonavir (RTV) in Vero cells, human pulmonary epithelial cell line and primary monocytes, impairing virus-induced enhancement of IL-6 and TNF- levels. Together, our data strongly suggest that ATV and ATV/RTV should be considered among the candidate repurposed drugs undergoing clinical trials in the fight against COVID-19.

microbiology↗

bioRxiv2020

SMN1 copy-number and sequence variant analysis from next generation sequencing data

Spinal Muscular Atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next generation sequencing (NGS) very difficult Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available on Github at: www.github.com/babelomics/SMAca

bioinformatics↗

bioRxiv2019

Oral feeding with probiotic Lactobacillus rhamnosus attenuates cigarette smoke-induced COPD in C57Bl/6 mice: Relevance to inflammatory markers in human bronchial epithelial cells

COPD is a prevalent lung disease with significant impacts on public health. Affected airways exhibit pulmonary neutrophilia and consequent secretion of pro-inflammatory cytokines and proteases, which result in lung emphysema. Probiotics act as nonspecific modulators of the innate immune system that improve several inflammatory responses. To investigate the effect of Lactobacillus rhamnosus (Lr) on cigarette smoke (CS)-induced COPD C57Bl/6 mice were treated with Lr during the week before COPD induction and three times/week until euthanasia. For in vitro assays, murine bronchial epithelial cells as well as human bronchial epithelial cells exposed to cigarette smoke extract during 24 hours were treated with Lr 1 hour before CSE addition. Lr treatment attenuated the inflammatory response both in the airways and lung parenchyma, reducing neutrophilic infiltration and the production of pro-inflammatory cytokines and chemokines. Also, Lr-treated mice presented with lower metalloproteases in lung tissue and lung remodeling. In parallel to the reduction in the expression of TLR2, TLR4, TLR9, STAT3, and NF-{kappa}B in lung tissue, Lr increased the levels of IL-10 as well as SOCS3 and TIMP1/2, indicating the induction of an anti-inflammatory environment. Similarly, murine bronchial epithelial cells as well as human bronchial epithelial cells (BEAS) exposed to CSE produced pro-inflammatory cytokines and chemokines, which were inhibited by Lr treatment in association with the production of anti-inflammatory molecules. Moreover, the presence of Lr also modulated the expression of COPD-associated transcription found into BALF of COPD mice group, i.e., Lr downregulated expression of NF-{kappa}B and STAT3, and inversely upregulated increased expression of SOCS3. Thus, our findings indicate that Lr modulates the balance between pro- and anti-inflammatory cytokines in human bronchial epithelial cells upon CS exposure and it can be a useful tool to improve the lung inflammatory response associated with COPD.

immunology↗

bioRxiv2019

Crystal violet structural analogues identified by in silico drug repositioning present anti-Trypanosoma cruzi activity through inhibition of proline transporter TcAAAP069

BackgroundCrystal violet (CV) was used for several years in blood banks to eliminate the parasite Trypanosoma cruzi in endemic areas in order to prevent transfusion-transmitted Chagas disease. One mechanism of action described for CV involves inhibition of proline uptake. In T. cruzi, proline is essential for host cell infection and intracellular differentiation among other processes, and can be obtained through the proline permease TcAAAP069.\n\nMethodology/Principal FindingsCV inhibited proline transporter TcAAAP069 and parasites overexpressing this permease were 47-fold more sensitive to this compound than control parasites. Using CV as reference molecule, loratadine, cyproheptadine, olanzapine and clofazimine were identified as structurally related compounds to CV (structural analogues) by in silico drug repurposing through a similarity-based virtual screening protocol. All these already-approved drugs for clinical use inhibited TcAAAP069 activity with different efficacies and also presented trypanocidal action in epimastigotes, trypomastigotes and amastigotes of the Y strain. Additionally, loratadine, cyproheptadine and clofazimine showed trypanocidal effect on epimastigotes of the CL Brener and DM28c strains. Finally, a synergistic effect between benznidazole and the CV chemical analogues was evidenced by combination and dose-reduction indexes values in epimastigotes of the Y strain.\n\nConclusions/SignificanceLoratadine, cyproheptadine and clofazimine inhibit TcAAAP069 proline transporter and also present trypanocidal effect against all T. cruzi life stages. These CV structural analogues could be a starting point to design therapeutic alternatives to treat Chagas disease by finding new indications for old drugs. This approach, called drug repurposing is a recommended strategy by the World Health Organization to treat neglected diseases, like Chagas disease, and combination therapy may improve the possibility of success of repositioned drugs.\n\nAuthor summaryChagas disease, caused by the parasite Trypanosoma cruzi, affects 7 million people worldwide. Despite there are two drugs available since 50 years ago, the therapy present severe side effects and is not effective in the chronic phase of the disease were most of the patients are diagnosed. Crystal violet (CV) was utilized as additive in blood banks to prevent transfusion-transmitted Chagas disease. Proline is involved in many pathways, like infection establishment and life cycle progression. In this work we first demonstrate that CV has the proline permease TcAAAP069 as one of its molecular targets. Then we search in a database of already-approved drugs for compounds that were structurally related to CV under the premise \"similar structure, similar activity\". We identified three drugs that inhibit proline transport and present at least the same trypanocidal effect than benznidazole, the current treatment for Chagas disease. Finally we observed a synergistic effect with the multidrug combination therapy. Drug discovery is an expensive and time-consuming process and Chagas disease is associated with poverty. The discovery of new indications to old drugs, called drug repurposing, can facilitate a rapid and more profitable therapy application since preclinical trials and pharmacokinetic studies are already available.

microbiology↗

bioRxiv2018

High impact journals in ecology cover proportionally more statistically significant findings

Unbiased scientific reporting is crucial for data and research synthesis. Previous studies suggest that statistically significant results are more likely to be published and more likely to be submitted to high impact journals. However, the most recent research on statistical significance in relation to journal impact factors in ecological research was published more than two decades ago or addressed a small subset of the literature. Here, we extract p-values from all articles published in 11 journals in 2012 and 2014 across a wide range of impact factors with six journals sampled in both years. Our results indicate that the proportion of statistically significant results increases with rising impact factor. Such a trend can have important consequences for syntheses of ecological data and it highlights the importance of covering a wide range of impact factors when identifying published studies for data syntheses. This trend can also lead to a biased understanding of the probability of true effects in ecology and conservation. We caution against the possible downplaying of non-significant results by either journals or authors.

scientific communication and education↗

bioRxiv2018

HEx: a heterologous expression platform for the discovery of fungal natural products

For decades, fungi have been a source of FDA-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.\n\nSummaryHere we present the largest scale effort reported to date toward the complete refactoring and heterologous expression of fungal biosynthetic gene clusters utilizing HEx, a novel synthetic biology platform.

synthetic biology↗