Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, ...including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.
The complete assembly of each human chromosome is essential for understanding human biology and evolution
. Here we use complementary long-read sequencing technologies to complete the linear assembly ...of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the β-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.
Neuroglia interactions are essential for the nervous system and in the retina Müller cells interact with most of the neurons in a symbiotic manner. Glutathione (GSH) is a low-molecular weight ...compound that undertakes major antioxidant roles in neurons and glia, however, whether this compound could act as a signaling molecule in neurons and/or glia is currently unknown. Here we used embryonic avian retina to obtain mixed retinal cells or purified Müller glia cells in culture to evaluate calcium shifts induced by GSH. A dose response curve (0.1-10 mM) showed that 5-10 mM GSH, induced calcium shifts exclusively in glial cells (later labeled and identified as 2M6 positive cells), while neurons responded to 50 mM KCl (labeled as βIII tubulin positive cells). BBG 100 nM, a P2X7 blocker, inhibited the effects of GSH on Müller glia. However, addition of DNQX 70 μM and MK-801 20 μM, non-NMDA and NMDA blockers, had no effect on GSH calcium induced shift. Oxidized glutathione (GSSG) at 5 mM failed to induce calcium mobilization in glia cells, indicating that the antioxidant and/or structural features of GSH are essential to promote elevations in cytoplasmic calcium levels. Indeed, a short GSH pulse (60s) protects Müller glia from oxidative damage after 30 min of incubation with 0.1% H2O2. Finally, GSH induced GABA release from chick embryonic retina, mixed neuron-glia or from Müller cell cultures, which were inhibited by BBG or in the absence of sodium. GSH also induced propidium iodide uptake in Müller cells in culture in a P2X7 receptor dependent manner. Our data suggest that GSH, in addition to antioxidant effects, could act signaling calcium shifts at the millimolar range particularly in Müller glia, and could regulate the release of GABA, with additional protective effects on retinal neuron-glial circuit.
Abstract
Satellite DNAs (SatDNA) are ubiquitously present in eukaryotic genomes and have been recently associated with several biological roles. Understanding the evolution and significance of SatDNA ...requires an extensive comparison across multiple phylogenetic depths. We combined the RepeatExplorer pipeline and cytogenetic approaches to conduct a comprehensive identification and analysis of the satellitome in 37 species from the genus Drosophila. We identified 188 SatDNA-like families, 112 of them being characterized for the first time. Repeat analysis within a phylogenetic framework has revealed the deeply divergent nature of SatDNA sequences in the Drosophila genus. The SatDNA content varied from 0.54% of the D. arizonae genome to 38.8% of the D. albomicans genome, with the SatDNA content often following a phylogenetic signal. Monomer size and guanine–cytosine-content also showed extreme variation ranging 2–570 bp and 9.1–71.4%, respectively. SatDNA families are shared among closely related species, consistent with the SatDNA library hypothesis. However, we uncovered the emergence of species-specific SatDNA families through amplification of unique or low abundant sequences in a lineage. Finally, we found that genome sizes of the Sophophora subgenus are positively correlated with transposable element content, whereas genome size in the Drosophila subgenus is positively correlated with SatDNA. This finding indicates genome size could be driven by different categories of repetitive elements in each subgenus. Altogether, we conducted the most comprehensive satellitome analysis in Drosophila from a phylogenetic perspective and generated the largest catalog of SatDNA sequences to date, enabling future discoveries in SatDNA evolution and Drosophila genome architecture.
Abstract
This study was aimed at establishing the subcorticals substrates of the cognitive and visceromotor circuits of the A32 and A25 cortices of the medial prefrontal cortex and their projections ...and interactions with subcortical complexes in the common marmoset monkey (
Callithrix jacchus
). The study was primarily restricted to the nuclei of the diencephalon and amygdala. The common marmoset is a neotropical primate of the new world, and the absence of telencephalic gyrus favors the mapping of neuronal fibers. The biotinylated dextran amine was employed as an anterograde tracer. There was an evident pattern of rostrocaudal distribution of fibers within the subcortical nuclei, with medial orientation. Considering this distribution, fibers originating from the A25 cortex were found to be more clustered in the diencephalon and amygdala than those originating in the A32 cortex. Most areas of the amygdala received fibers from both cortices. In the diencephalon, all regions received projections from the A32, while the A25 fibers were restricted to the thalamus, hypothalamus, and epithalamus at different densities. Precise deposits of neuronal tracers provided here may significantly contribute to expand our understanding of specific connectivity among the medial prefrontal cortex with limbic regions and diencephalic areas, key elements to the viscerocognitive process.
Global climate change is expected to increasingly affect climate-sensitive sectors of society, such as the economy and environment, with significant impacts on water, energy, agriculture and ...fisheries. This is the case in South America, whose economy is highly dependent on the agricultural sector. Here, we analyzed the sensitivity of South American climate to positive extremes of Antarctic sea ice (ASI) extent and volume at continental and regional scales. Sensitivity ensemble experiments were conducted with the GFDL-CM2.1 model and compared with the ERA-Interim reanalysis dataset. The results have shown significant impacts on the seasonal regime of precipitation, air temperature and humidity in South America, such as a gradual establishment of the South Atlantic Convergence Zone, the formation of the Upper Tropospheric Cyclonic Vortex, the strengthening of Bolivian High and the presence of a low level cyclonic circulation anomaly over the South Atlantic Subtropical High region which contributed, for instance, to increased precipitation over the Southeastern Brazil. A northward shift of the Intertropical Convergence Zone was initially also a response pattern to the increased ASI. Moreover, the greatest variance of the climatic signal generated from the disturbances applied on the high southern latitudes has occurred in the interseasonal timescale (110-120 days), especially over the Brazilian Amazon and the Southeastern Brazil regions.
Abstract
Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp ...satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ∼27 Mya. We found that the 1.688 satDNA family has two major subfamilies spread throughout Drosophila phylogeny (∼360 bp and ∼190 bp). Phylogenetic analysis of ∼10,000 repeats extracted from 14 of the species revealed that the 1.688 satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the 1.688 satDNA as the most perduring satDNA family described in Drosophila phylogeny to date. Our study provides a strong foundation for future work on the functional roles of 1.688 satDNA across many Drosophila species.
The formation of dense water masses at polar regions has been largely influenced by climate changes arising from global warming. In this context, based on ensemble simulations with a coupled model we ...evaluate the meridional shift of a climate signal (i.e., a cold and fresh water input pulse generated from melting of positive Antarctic sea ice (ASI) extremes) towards the Tropical Atlantic Ocean (TAO). This oceanic signal propagated from Southern Ocean towards the equator through the upper layers due to an increase in its buoyance. Its northward shift has given by the Subantarctic Mode Water (SAMW) and Antarctic Intermediate Water (AAIW) flows, that inject cold and fresh mode/intermediate waters from into subtropical basin. The signal has reached low latitudes through the equatorial upwelling and spreads out southwards, through the upper branch of southern subtropical gyre. We concluded that 10 years of coupled simulations was enough time to propagate the climate signal generated by ASI positive extremes melting, which reached TOA around 2 year later. The oceanic connection between Southern Ocean and TAO is indeed established within the timescale analyzed in the study (10 years). Nonetheless, the period needed to completely dissipate the disturbance generated from ASI seems to be longer.
Successful highly active antiretroviral therapy (HAART) has changed the outcome of AIDS patients worldwide because the complete suppression of viremia improves health and prolongs life expectancy of ...HIV-1+ patients. However, little attention has been given to the immunological profile of patients under distinct HAART regimens. This work aimed to investigate the differences in the immunological pattern of HIV-1+ patients under the first- or second-line HAART in Brazil.
CD4+ T cell counts, Viral load, and plasma concentration of sCD14, sCD163, MCP-1, RANTES, IP-10, IL-1β, IL-6, TNF-α, IL-12, IFN-α, IFN-γ, IL-4, IL-5, and IL-10 were assessed for immunological characterization of the following clinical groups: Non-infected individuals (NI; n = 66), HIV-1+ untreated (HIV; n = 46), HIV-1+ treated with first-line HAART (HAART 1; n = 15); and HIV-1+ treated with second-line HAART (HAART 2; n = 15).
We found that the immunological biosignature pattern of HAART 1 is similar to that of NI individuals, especially in patients presenting slow progression of the disease, while patients under HAART 2 remain in a moderate inflammatory state, which is similar to that of untreated HIV patients pattern. Network correlations revealed that differences in IP-10, TNF-α, IL-6, IFN-α, and IL-10 interactions were primordial in HIV disease and treatment. Heat map and decision tree analysis identified that IP-10>TNF-α>IFN-α were the best respective HAART segregation biomarkers.
HIV patients in different HAART regimens develop distinct immunological biosignature, introducing a novel perspective into disease outcome and potential new therapies that consider HAART patients as a heterogeneous group.
Mucoadhesive drug formulations have been studied and used as alternatives to conventional formulations in order to achieve prolonged retention at the intended site. In addition to providing a ...controlled drug release, several drugs and disease conditions might benefit from mucoadhesive formulations, contributing to better therapeutic outcomes. Here, we describe the development and the in vitro/in vivo characterization of a mucoadhesive in situ gellifying formulation using PF127, a thermo reversible polymer, entrapping budesonide (BUD), a potent corticosteroid used for the treatment of a wide range of inflammatory diseases, including those affecting mucosas, such as in the GI tract. PF127 formulations (15-17%) were successfully prepared by a cold method as a thermo reversible in situ gelling dispersion for mucosal drug delivery, as confirmed by DSC. Sol-gel temperatures of PF127 formulations (25-39 °C) were observed by dynamic gelation and determined by microrheology and oscillatory rheometry. X-ray diffractograms and TEM images showed that BUD was completely solubilized within the polymeric micelles. In vitro, the gels showed 5-14 g force of mucoadhesion, and the ex vivo studies confirmed that the formulation efficiently adhered to the mucosa. Histopathological analysis combined with fluorescence images and ex vivo intestinal permeation confirmed that the formulation remained on the TGI mucosa for at least 4 h after administration. In vivo studies conducted in a murine model of intestinal mucositis demonstrated that the 16% PF127 BUD formulation was able to resolve the inflammatory injury in the intestinal mucosa. Results demonstrate that fine-tuning of PF127 formulations along with adequate selection of the drug agent, thorough characterization of the dispersions and their interactions with biological interfaces leads to the development of effective controlled drug delivery systems targeted to GI inflammatory diseases.
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