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Gonzalez, C.

Publications and source records attributed to Gonzalez, C..

At least 37 records · Page 2Linked to original sources

Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism

By combining in-silico, biophysical and in-cellulo experiments, we decipher the topology, physical and potential biological properties of hybrid-parallel nucleic acids triplexes; an elusive structure at the basis of life. We found that hybrid triplex topology follows a stability order: r(Py)-d(Pu){middle dot}r(Py)> r(Py)-d(Pu){middle dot}d(Py)> d(Py)-d(Pu){middle dot}d(Py)> d(Py)-d(Pu){middle dot}r(Py). The r(Py)-d(Pu){middle dot}d(Py) triplex is expected to be the preferred in the cell as it avoids the need to open the duplex reducing the torsional stress required for triplex formation in the r(Py)-d(Pu){middle dot}r(Py) topology. Upon a massive collection of melting data, we have created the first predictor for hybrid triplex stability. Leveraging this predictor, we conducted a comprehensive scan to assess the likelihood of the human genome and transcriptome to engage in triplex formation. Our findings unveil a remarkable inclination - of both the human genome and transcriptome - to generate hybrid triplex formation, particularly within untranslated (UTRs) and regulatory regions, thereby corroborating the existence of a triplex-mediated regulatory mechanism. Furthermore, we found a correlation between nucleosome linkers and TFS which agree with a putative role of triplexes in arranging chromatin structure and local/global level.

molecular biology↗

The topography of DNA replication origins in Eukarya: GGN clusters, landmark nucleosomes, CDC6 and G4 structures

BackgroundWe recently identified tandem repeats of GGN triplets as a sequence motif strongly enriched in the DNA replication origins (ORIs) of the Arabidopsis thaliana genome, where it correlates with the ORI strength quantified through short nascent strands sequencing. ResultsHere we show that clusters of four or more GGN repeats separated by short tracts (<7 nucleotides) are present in more than 65% ORIs of six model eukaryotic organisms: Leishmania major, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens. The measured percentages vary with the experimental technique adopted for ORI determination. For all studied techniques and organisms, ORIs are significantly prone to be located within or near strong GGN clusters, although these are neither necessary nor sufficient for ORI activation. Interestingly, for same experimental technique, the association between ORIs and GGN clusters was stronger al later developmental stages for all organisms for which we could perform this comparison. In accordance with a biophysical model of nucleosome positioning, the GGN clusters strongly favor nucleosome occupancy. At the same time, both GGN clusters and ORIs occur frequently within 1kb from nucleosome-depleted regions (NDR). We propose a structural model based on chromatin secondary structure in which the NDR and the well-positioned nucleosome at the GGN are close in space, which may favor functional interactions. We hypothesize that the presence of GGN at ORIs arose in part for promoting the above nucleosome organization Moreover, at least in Arabidopsis, the replication protein CDC6 is very strongly associated with GGN clusters. NMR experiments showed that clusters of at least four GGN can form G-quadruplex (G4) in vitro. Our data support the view that GGN clusters are formed through the interplay of mutational processes (GC skew at ORIs plus triplet expansion), and that similar mutational processes, i.e. AT skew at transcription start sites (TSS) and ORIs, might facilitate the formation of the NDR, thus favoring the evolvability of chromatin. ConclusionsGGN clusters are easily evolvable sequence motifs enriched at ORIs of eukaryotic genomes. They favor G4 secondary structure and a nucleosome organization that may unify the apparent discrepancy between ORIs of higher eukaryotes and yeast.

genomics↗

The Drosophila cancer-germline, head-to-head gene pair TrxT and dhd is dispensable for normal brain development but plays a major role in l(3)malignant brain tumour growth.

Drosophila thioredoxins Deadhead (Dhd) and Thioredoxin-T (TrxT) are encoded by a head-to-head gene pair in the X chromosome. Akin to human cancer-germline (CG) genes, dhd and TrxT expression is normally sex and germline specific, but becomes upregulated in brain tumours of either sex caused by mutation in l(3)malignant brain tumour (l(3)mbt). Using CRISPR/Cas9-mediated knock-out alleles and RNA-seq, we show that while both TrxT and dhd are dispensable for normal brain development, each of them has a significant but partial effect on l(3)mbt brain tumour development as well as on tumour-linked transcriptomic signatures. Moreover, this effect is enhanced by the concomitant removal of both thioredoxins that strongly inhibits l(3)mbt larval brain tumour traits, reduces gene expression differences between tumour and wild-type tissue, and essentially erases all traces of gene expression differences between tumours from larvae of different sex. These results show that TrxT and dhd play a major synergistic role in the emergence of l(3)mbt tumour-linked transcriptomic signatures and tumour development, which is remarkable taking into account that these two genes are never expressed together under normal conditions. We have also found that TrxT is crucial but dhd has no effect on the growth of male-derived l(3)mbt allografts, hence suggesting that the initial stages of tumour development and sustained, long-term tumour growth may depend upon different molecular pathways. In humans, head-to-head inverted gene pairs are abundant among the CG genes that map to the X chromosome, some of which have been shown to work as a unit cancer. Our results identify the first instance of an X-linked, head-to-head CG gene pair in Drosophila and underpin the potential of such CG genes that are dispensable for normal development and homeostasis of somatic tissue, as targets to curtail malignant growth with minimal impact on overall health.

cancer biology↗

Metabolomic rearrangement controls the intrinsic microbial response to temperature changes

Temperature is one of the key determinants of microbial behavior and survival, whose impact is typically studied under heat- or cold-shock conditions that elicit specific regulation to combat lethal stress. At intermediate temperatures, cellular growth rate varies according to the Arrhenius law of thermodynamics without stress responses, a behavior whose origins have not yet been elucidated. Using single-cell microscopy during temperature perturbations, we show that bacteria exhibit a highly conserved, gradual response to temperature upshifts with a time scale of [~]1.5 doublings at the higher temperature, regardless of initial/final temperature or nutrient source. We find that this behavior is coupled to a temperature memory, which we rule out as being neither transcriptional, translational, nor membrane dependent. Instead, we demonstrate that an autocatalytic enzyme network incorporating temperature-sensitive Michaelis-Menten kinetics recapitulates all temperature-shift dynamics through metabolome rearrangement, which encodes a temperature memory and successfully predicts alterations in the upshift response observed under simple-sugar, low-nutrient conditions, and in fungi. This model also provides a mechanistic framework for both Arrhenius-dependent growth and the classical Monod Equation through temperature-dependent metabolite flux.

cell biology↗

Gene editing of putative cAMP and Ca2+-regulated proteins using an efficient cloning-free CRISPR/Cas9 system in Trypanosoma cruzi

Trypanosoma cruzi, the agent of Chagas disease, must adapt to a diversity of environmental conditions that it faces during its life cycle. The adaptation to these changes is mediated by signaling pathways that coordinate the cellular responses to the new environmental settings. Cyclic AMP (cAMP) and Calcium (Ca2+) signaling pathways regulate critical cellular processes in this parasite, such as differentiation, osmoregulation, host cell invasion and cell bioenergetics. Although the use of CRISPR/Cas9 technology prompted reverse genetics approaches for functional analysis in T. cruzi, it is still necessary to expand the toolbox for genome editing in this parasite, as for example to perform multigene analysis. Here we used an efficient T7RNAP/Cas9 strategy to tag and delete three genes predicted to be involved in cAMP and Ca2+ signaling pathways: a putative Ca2+/calmodulin-dependent protein kinase (CAMK), Flagellar Member 6 (FLAM6) and Cyclic nucleotide-binding domain/C2 domain-containing protein (CC2CP). We endogenously tagged these three genes and determined the subcellular localization of the tagged proteins. Furthermore, the strategy used to knockout these genes allow us to presume that TcCC2CP is an essential gene in T. cruzi epimastigotes. Our results will open new venues for future research on the role of these proteins in T. cruzi.

molecular biology↗

The infralimbic and prelimbic cortical areas bidirectionally regulate safety learning during normal and stress conditions.

Safety learning is a critical function for behavioral adaptation, environmental fitness, and mental health. Animal models have implicated the prelimbic (PL) and infralimbic (IL) subregions of the medial prefrontal cortex (mPFC) in safety learning. However, whether these regions differentially contribute to safety learning and how their contributions become affected by stress still remain poorly understood. In this study, we evaluated these issues using a novel semi-naturalistic mouse model for threat and safety learning. As mice navigated within a test arena, they learned that specific zones were associated with either noxious cold temperatures ("threat") or pleasant warm temperatures ("safety"). Optogenetic-mediated inhibition revealed critical roles for the IL and PL regions for selectively controlling safety learning during these naturalistic conditions. This form of safety learning was also highly susceptible to stress pre-exposure, and while IL inhibition mimicked the deficits produced by stress, PL inhibition fully rescued safety learning in stress-exposed mice. Collectively, these findings indicate that IL and PL bidirectionally regulate safety learning during naturalistic situations, with the IL region promoting this function and the PL region suppressing it, especially after stress. A model of balanced IL and PL activity is proposed as a fundamental mechanism for controlling safety learning. Visual Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=51 SRC="FIGDIR/small/539516v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@b7bd5aorg.highwire.dtl.DTLVardef@f06849org.highwire.dtl.DTLVardef@14e9848org.highwire.dtl.DTLVardef@efc491_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

A minimally-invasive method for ancient DNA sampling of Prehistoric bone and antler tools and hunting weapons

Internal and external bony tissues from diverse mammalian taxa are one of the primary animal raw materials exploited for technical and symbolic purposes by Eurasian Upper Palaeolithic hunter-gatherers. Identifying the source species used for osseous raw material is critical to gain insights into these populations behaviour, technology, and subsistence. The study of osseous tools has advanced in the last few years by combining archaeological and biomolecular methods. Ancient genomics opens many new analytical opportunities. Ancient DNA (aDNA) can provide a wealth of information about the animal sources of these objects. Unfortunately, aDNA analyses often involve destructive sampling. Here, we develop and apply a minimally-invasive aDNA sampling method for an assemblage of 42 prehistoric hunting weapons and tools from various Eurasian archaeological sites. We evaluated the impact of our approach on the specimens visually, microscopically and through Micro-CT scans. The surface impacts are marginal, ranging from 0.3-0.4 mm. Using a custom-made DNA capture kit for 54 mammalian species, we obtained sufficient aDNA to identify the taxa of 33% of the objects. For one of the tools, we recovered enough endogenous aDNA to infer the genetic affinities of the individual. Our results also demonstrate that ancient antler, one of the primary raw materials used during a large part of prehistory, is a reliable source of aDNA. Our minimally-invasive aDNA sampling method is therefore effective while preserving osseous objects for potential further analyses: morphometric, technical, genetic, radiometric and more.

genomics↗

The lectin receptor Clec4F participates in the capture of circulating parasite mucins by Kupffer cells in cystic echinococcosis.

Cystic echinococcosis is caused by the larval stages (hydatids) of cestode parasites belonging to the species cluster Echinococcus granulosus sensu lato, with E. granulosus sensu stricto being the main infecting species. Hydatids are bladder-like structures that attain large sizes within various internal organs of livestock ungulates and humans. Hydatids are protected by the massive acellular laminated layer (LL), composed mainly by mucins. Parasite growth requires LL turnover, and abundant LL-derived particles are found at infection sites in infected humans, raising the question of how LL materials are dealt with by the hosts. In this article, we show that E. granulosus sensu stricto LL mucins injected into mice are taken up by Kupffer cells, the liver macrophages exposed to the vascular space. This uptake is largely dependent on the intact mucin glycans and on Clec4F, a C-type lectin receptor which in rodents is selectively expressed in Kupffer cells. This uptake mechanism operates on mucins injected both in soluble form i.v. and in particulate form i.p. In mice harbouring intraperitoneal infections by the same species, LL mucins were found essentially only at the infection site and in the liver, where they were taken up by Kupffer cells via Clec4F. Therefore, shed LL materials circulate in the host and Kupffer cells can act as a sink for these materials even when the parasite grows in sites other than the liver.

immunology↗

Deadly and venomous Lonomia caterpillars are more than the two usual suspects

Caterpillars of the Neotropical genus Lonomia (Lepidoptera: Saturniidae) are responsible for some fatal envenomation of humans in South America inducing hemostatic disturbances in patients upon skin contact with the caterpillars spines. Currently, only two species have been reported to cause hemorrhagic syndromes in humans: Lonomia achelous and Lonomia obliqua. However, species identifications have remained largely unchallenged despite improved knowledge of venom diversity and growing evidence that the taxonomy used over past decades misrepresents and underestimates species diversity. Here, we revisit the taxonomy and distribution of Lonomia using the most extensive dataset assembled to date, combining DNA barcodes, morphological comparisons, and geographical information. Our integrative approach leads to the recognition of 60 species, of which seven are known or strongly suspected to cause severe envenomation in humans. From a newly compiled synthesis of epidemiological data, we also examine the consequences of our results for understanding Lonomia envenomation risks and call for further investigations of other species venom activities. This is required and necessary to improve alertness in areas at risk, and to define adequate treatment strategies for envenomed patients, including performing species identification and assessing the efficacy of anti-Lonomia serums against a broader diversity of species.

ecology↗

Optimization and validation of a Protein Phosphatase inhibition assay for accessible microcystin detection.

The presence of cyanobacterial toxins in freshwater constitutes an increasing public health concern, especially affecting developing countries where the high cost of available methods makes monitoring programs difficult. The phosphatase inhibition assay (PPIAs) is a sensitive method with low instrument requirements that allows the quantification of the most frequent cyanotoxins, microcystins (MC). In this work, we implemented a PPIAs, starting from Protein Phosphatase 1 (PP1) expression up to the validation with samples of algal blooms from Argentina. To do this, we optimized the expression and lyophilization of PP1, and the assay conditions. Also, we included robustness and possible interfering analysis. We evaluated the most widely used cyanobacterial lysis methods and determined that heating for 15 minutes at 95{degrees}C is simple and adequate for this assay. Then, we performed MC spikes recovery assays on water samples from three dams from Argentina, resulting in a recovery ranging from 77 to 115%. The limit of detection (LOD) was 0.4 g/L and the linear range is 0.4 g/L - 5 g/L. Finally, we evaluated 64 environmental samples where MC was measured by ELISA test containing from 0 g/L to 625 g/L. The PPIA showed excellent correlation (Pearson correlation coefficient = 0.967), no false negative and no false positives above the 1 g/L WHO guideline (0.11 false positive rate). In conclusion, we optimized and validated a PPIAs to be an effective and accessible alternative to available commercial tests.

biochemistry↗

Cell-free synthesis and reconstitution of Bax in nanodiscs: comparison between wild-type Bax and a constitutively active mutant

Bax is a major player in the mitochondrial pathway of apoptosis, by permeabilizing the Outer Mitochondrial Membrane (OMM) to various apoptogenic factors, including cytochrome c. In order to get further insight into the structure and function of Bax when it is inserted in the OMM, we attempted to reconstitute Bax in nanodiscs. Cell-free protein synthesis in the presence of nanodiscs did not allow to obtain Bax-containing nanodiscs, but it provided a simple way to purify full-length Bax without any tag. Purified wild-type Bax (BaxWT) and a constitutively active mutant (BaxP168A) displayed biochemical properties that were in line with previous characterizations following their expression in yeast and human cells followed by their reconstitution into liposomes. Both Bax variants were then reconstituted in nanodiscs. Size exclusion chromatography, dynamic light scattering and transmission electron microscopy showed that nanodiscs formed with BaxP168A were larger than nanodiscs formed with BaxWT. This was consistent with the hypothesis that BaxP168A was reconstituted in nanodiscs as an active oligomer.

biochemistry↗

Systematic optimization of Cas12a base editors in wheat and maize using the ITER platform

The ever-increasing number of CRISPR components creates a significant burden when developing new genome engineering tools. Plant biotechnology in particular has few high-throughput options to perform iterative design-build-test-learn cycles when creating new gene-editing reagents. We have established ITER (Iterative Testing of Editing Reagents) based on arrayed protoplast transfections and high-content imaging, allowing one optimization cycle - from design to results- within three weeks. We validated ITER in wheat and maize protoplasts using Cas9 cytosine and adenine base editors. Given that previous LbCas12a-ABEs have low or no activity in plants, we used ITER to develop an optimized LbCas12a-ABE. We show that the sequential improvement of five components -NLS, crRNA, LbCas12a, adenine deaminase and linker- led to a remarkable increase in ABE activity from almost undetectable levels to 40% on an extrachromosomal GFP reporter. We confirmed the activity of LbCas12a-ABE at endogenous targets and in stable wheat transformants and leveraged these improvements to develop a highly mutagenic LbCas12a nuclease and LbCas12a-CBE. Our data show that ITER is a sensitive, versatile, and high-throughput platform that can be harnessed to accelerate the development of genome editing technologies in plants.

synthetic biology↗

Autophagy modulates apical growth and development in the moss Physcomitrium patens

Different to root hairs and pollen tubes, Physcomitrium patens apical growing protonemal cells have the singularity that they continue to undergo cell divisions as the plant develops, allowing to study autophagy in the context of a multicellular apical growing tissue coupled to development. Herein, we showed that the core autophagy machinery is present in the moss P. patens, and deeply characterized the growth and development of wild-type, atg5 and atg7 loss-of-function mutants under optimal and nutrient-deprived conditions. Our results showed that the growth of the different morphological and functional protonemata apical growing cells, chloronema and caulonema, is differentially modulated by this process. These differences depend on the protonema cell type and position along the protonemal filament, and growth condition. As a global plant response, the absence of autophagy triggers the spread of the colony through protonemata growth at the expense of a reduction in buds and gametophore development, and thus the adult gametophytic and reproductive phases. Altogether this study provides valuable information indicating that autophagy has roles during apical growth with differential responses within the cell types of the same tissue and contributes to life cycle progression and thus the development of the 2D and 3D tissues of P. patens. HIGHLIGHTAutophagy is differentially induced in protonemal cells, and contributes to apical growth, life cycle progression, and thus the development of the 2D and 3D tissues of P. patens.

plant biology↗

High genetic diversity in the pelagic deep-sea fauna of the Atacama Trench revealed by environmental DNA

A current paradigm in marine biodiversity states that faunal richness decreases with depth. However, the deep-ocean ecosystem has been significantly under-sampled, hindering a complete view of its biodiversity. This situation is accentuated in ultra-deep waters, where the remote and extreme conditions unfit the traditional sampling methods. Using environmental DNA, we assessed the pelagic metazoan diversity of the Atacama Trench from the high-productive near-surface level down to ~8000 m depth. Our results show that waters deeper than 4000 m contributed up to 50% of the overall genetic diversity. These findings contrast with similar observations in the less-productive Kermadec Trench, where the diversity in deep waters was lower than in shallower waters. Moreover, both deep pelagic ecosystems exhibited some unknown phylogenetic clades within the dominant taxonomic groups: hydrozoans and copepods. The deep-ocean biota may thus contribute to global biodiversity far more than hitherto suggested, especially in zones influenced by high primary production. Our results underline the need for increased effort to study these remote ecosystems and improve our understanding of their contribution to the ecology and biogeochemistry of the deep-sea pelagic and benthic realms.

ecology↗

Electroencephalographic Signatures of Canine Cognitive Dysfunction

Canine cognitive dysfunction (CCD) is a highly prevalent neurodegenerative disease considered the canine analog of Alzheimers disease (AD). Unfortunately, CCD cannot be cured. However, early therapeutic interventions can slow the progression of cognitive decline and improve quality of life of the patients; therefore, early diagnosis is ideal. In humans, electroencephalogram (EEG) findings specific to AD have been described, and some of them have successfully detect early stages of the disease. In this study we characterized the EEG correlates of CCD, and we compared them with the EEGs of healthy aging dogs and dogs at risk of developing CCD. EEG recordings were performed in 25 senior dogs during wakefulness. Dogs were categorized in normal, at risk of CCD or with CCD according to their score in the Rofina questionnaire. We demonstrated that, quantitative EEG can detect differences between normal dogs and dogs with CCD. Dogs with CCD experience a reduction in beta and gamma interhemispheric coherence, and higher Joint Lempel Ziv complexity. Dogs at risk of developing CCD, had higher alpha power and interhemispheric coherence, making these features potential markers of early stages of the disease. These results demonstrate that EEG could be an additional biomarker that can contribute to the diagnosis of CCD, and reinforce the CCD as a translational model of AD.

animal behavior and cognition↗

Freshwater dissolved oxygen dynamics: changes due to glyphosate, 2,4-D and their mixture, both under clear and turbid-organic conditions.

We performed two independent outdoor mesocosm experiments where we measured the variation of DO saturation (DO%) in freshwater after a single input of Roundup Max(R) (G) (glyphosate-based formulation), AsiMax 50(R) (2,4-D) (2,4-D-based formulation) and their mixture (M). Two concentration levels were tested; 0.3 mg/L G and 0.135 mg/L 2,4-D (Low; L) and 3 mg/L G and 1.35 mg/L 2,4-D (High; H). We assayed consolidated microbial communities coming from a system in organic turbid eutrophic status and a system in clear mesotrophic status during 21 and 23 days, respectively. A sample of phytoplankton (micro+nano, pico-eukaryotes, pico-cyanobacteria), mixotrophic algae and heterotrophic bacteria was collected to determine abundances at each of four sampling dates. The clear and turbid systems showed similar, but not synchronized, patterns of daily DO% changes in relation to the controls (DO%v), after exposure to both single and combined formulations. Under glyphosate scenarios (GL, GH, ML and MH), the two types of systems showed similar DO%v but different microbial abundances, being associated to an increase in the micro+nano and pico-eukaryotic phytoplankton fractions for the clear system. In contrast, in the turbid system changes were associated with increased pico-cyanobacteria and decreased mixotrophic algae. Effects of 2,4-D were only observed in the turbid system, leading to decreased micro+nano phytoplankton abundances. Under the turbid scenario, the herbicide mixture at high concentration had a synergistic effect on DO%v and recovery was not detected by the end of the experiment. Our results revealed that herbicides inputs induced changes in phytoplankton abundances that leads to measurable DO variations.

ecology↗

Comparative and systems analyses of Leishmania spp. non-coding RNAs through developmental stages

Leishmania spp. is the etiological agent of leishmaniases, neglected diseases that seek to be eradicated in the coming years. The life cycle of these parasites involve different host and stress environments. In recent years, many studies have shown that several protein coding genes are directly involved with the development and host interactions, however, little is still known about the role of ncRNAs in life cycle progression. In this study, we aimed to identify the genomic structure and function of ncRNAs from Leishmania spp. and to get insights into the RNAome of this protozoan genus. We studied 26 strains corresponding to 16 different species of Leishmania. Our RNAome analysis revealed the presence of several ncRNAs that are shared through different species, allowing us to differentiate between subgenus as well as species that are canonically related to visceral leishmaniasis. We also studied co-expression relationships between coding genes and ncRNAs which in the amastigote developmental stage for Leishmania braziliensis and L. donovani revealed the presence of miRNA-like co-expressed with several coding genes involved in starvation, survival and histone modification. This work constitutes the first effort to characterize the Leishmania RNAome, supporting further approaches to better understand the role of ncRNAs in the gene regulation, infective process and host-parasite interaction.

genomics↗

Illuminati, a novel form of gene expression plasticity in Drosophila neural stem cells

With the aim of developing a genetic instability (GI) sensor in vivo we used the well-established Gal80/Gal4-UAS system combined with a visual GFP marker in Drosophila. We generated a collection of 25 Drosophila lines carrying GAL80 transgenes in different locations in all major chromosomes (X, Y, II, and III). We found low rates of GFP cells in epithelial tissues such as wing discs. In contrast, in larval brains, GFP positive clusters containing neural stem cells- also called neuroblasts (NBs)- and their offspring, were highly frequent. Using genetic and imaging-based approaches, we show that GFP NBs do not result from aneuploidy or mutations in the GAL80 gene, but rather by stochastic repression of GAL80 expression. We named this novel type of gene expression instability Illuminati. Importantly, Illuminati frequency is influenced by environmental and stress conditions. Further, we found that once established, Illuminati can be propagated over many cell cycles.

developmental biology↗