Biology subjects

Peixoto, R.

Publications and source records attributed to Peixoto, R..

10 recordsLinked to original sources

bioRxiv2025

The Two Frontiers Project Field Handbook and OpenTools: Standardizing microbial fieldwork for biobank-scale sequencing and culturomics

From medicines to materials, our planets microbial diversity comprises an enormous wellspring of biotechnological potential. For centuries, microbiologists have developed tools for interrogating microbial function, ranging from microscopy and culturing to, more recently, metagenomics. However, deploying these tools during fieldwork requires substantial forward planning, interdisciplinary technical expertise, and plans for navigating permitting and the ethical implications of bioprospecting. To address these challenges, we built The Two Frontiers Project Handbook and OpenTools Resource, which aggregates our expertise in high-throughput sampling, sequencing, and culturing of microbes from thousands of samples. We provide our full suite of fieldwork methods as well as relevant software and hardware. We lay our standards for team roles and construction, general expedition planning, sample transport, permitting, and numerous other key aspects of executing a successful field campaign. The version-controlled resource is available at https://two-frontiers-project.github.io/ and is open for non-commercial use.

microbiology↗

bioRxiv2025

Modular metagenomic analysis of pan-domain symbioses with MAGUS

Metagenomic analysis of deeply sequenced, eukaryotic-dominant symbiotic communities can be difficult for many metagenomic workflows. Here, we present MAGUS, a bioinformatic toolkit that uses a suite of custom bioinformatic methods for iterative genome assembly and filtering of pan-domain communities, where eukaryotes, bacteria, viruses, and functionally annotated gene catalogs are resolved and analyzed over a series of interconnected, modular software components. We evaluated MAGUS using deeply sequenced (median depth: 579 million reads) ten samples of hard corals, soft corals, and hydrozoans, which comprise complex, eukaryote-dominated symbiotic communities. We successfully resolved phylogenetically comparable host (N = 10), algal (N = 6), bacterial (N = 55), and viral (N = 160,925) genomes, as well as a gene catalog comprising 15,369,684 non-redundant genes (7.6% functionally annotated). MAGUS is available on GitHub (https://github.com/two-frontiers-project/2FP_MAGUS/).

bioinformatics↗

bioRxiv2025

Electroporation-Based Gene Delivery and Whole-Organoid Imaging in Human Retinal Organoids

Human retinal organoids (hRetOrg) derived from human induced pluripotent stem cells (hiPSCs) have emerged as powerful in vitro systems for studying retinal development, modeling retinal diseases, and evaluating therapeutic strategies. However, current genetic manipulation approaches, such as stable hiPSC line generation and viral transduction, are laborious, costly, and inefficient, with limited spatial specificity and high variability. Here, we report a rapid, scalable, and spatially precise electroporation-based platform for efficient plasmid-based gene delivery in early-stage hRetOrg. This method enables tunable and region-specific transfection of retinal progenitor cells without viral vectors or clonal selection. Coupled with resonant-scanning two-photon microscopy, this approach allows fast live cell imaging of whole organoids with subcellular resolution. This versatile system supports high-throughput genetic manipulation and imaging in intact hRetOrg, advancing studies of human retinal development, gene function, and disease. MotivationhRetOrgs offer an unprecedented platform for functional genetic studies of human retinal development and disease. However, existing methods for gene manipulation in hRetOrg are limited by low throughput, inefficiency, and lack of scalability, hindering systematic analysis of gene function and regulatory elements. To address these limitations, we developed a streamlined, high-efficiency pipeline that enables spatially targeted electroporation of hRetOrg during early retinogenesis, combined with fast, high-resolution imaging of whole organoids using two-photon microscopy, allowing studies at both tissue and subcellular scales.

developmental biology↗

bioRxiv2025

Promiscuous endosymbionts in deep-sea corals and crinoids are shaped by nitrogen cycling

Crinoids are commonly associated with corals, but whether they physiologically interact is unclear. Like corals, crinoids host symbiotic microorganisms but little is known about the crinoid microbiome. Here, we reveal the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and, notably, their associated feather star crinoid, Koehlermetra (of the family Thalassometridae) in the Campos Basin, Brazil. We showed that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae interchangeably inhabit the internal and external structures of the corals and crinoid, indicating promiscuity in symbioses. The metagenome-assembled genome of the novel and dominant Endozoicomonas promiscua sp. nov. suggest that these symbionts may drive dissimilatory nitrate reduction to ammonia, which could be a source of energy for ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae. Thus, nitrogen cycling may determine the microorganisms that are hosted by deep-sea corals, which may be provided by their associated crinoids. These findings provide important insight about the complex ecological interactions that could lead to promiscuous symbiosis. TeaserDeep-sea corals and crinoids share symbiotic microbes that cycle nitrogen, potentially supporting each other in the nutrient-poor deep sea.

microbiology↗

bioRxiv2024

Bacterial inoculation manipulates the coral epigenome

Environmental shifts can cause epigenetic modifications in corals, which are associated with changes in gene expression and physiology, though it remains unclear if associated bacteria can also induce such changes. Here, we inoculated nubbins of the coral Pocillopora verrucosa with an opportunistic pathogen, Vibrio coralliilyticus, and/or a coral probiotic, Cobetia sp., and subjected the nubbins to heat stress. We show that pathogen exposure led to distinct DNA methylation changes compared to the control, probiotic, and co-inoculation groups. We also demonstrate that DNA methylation correlates with coral gene expression and highlight genes altered by pathogen inoculation that showed similar responses in their expression and methylation. Notably, the coral probiotic was able to mitigate specific epigenetic changes, which correlated with increased stress resilience and higher coral survival rates. Thus, bacterial-induced changes to the coral epigenome may instigate long-term changes in host resilience.

molecular biology↗

bioRxiv2024

Striatal output regulates the postnatal maturation of cortical circuits

The dorsomedial prefrontal cortex (dmPFC) is interconnected with the basal ganglia (BG) through large-scale circuit loops that regulate critical motor and cognitive functions. In mice, these circuits undergo extensive postnatal maturation with marked changes in neural activity and expansion of synaptic connectivity. While cortical activity is known to regulate the development of downstream striatal circuits, the role of the basal ganglia in cortical maturation remains unknown. Here, we used mesoscale two-photon microscopy and whole-cell electrophysiology to examine whether striatal output during early postnatal development impacts the activity and maturation of upstream dmPFC circuits. We found that ablating spiny projection neurons of the direct or indirect pathways of the striatum during the first two postnatal weeks causes bidirectional changes in dmPFC neural activity, similar to observations in mature circuits. In addition, these manipulations alter the maturation of synaptic connectivity of dmPFC layer 2/3 pyramidal neurons, shifting the balance of excitation and inhibition of cortical circuits. These findings demonstrate that striatal output modulates the activity of cortical circuits during early postnatal development and suggest a regulatory role of the basal ganglia in the establishment of cortical circuits.

neuroscience↗

bioRxiv2023

Late onset and regional heterogeneity of synaptic deficits in cortical PV interneurons of Shank3B-/- mice

Epilepsy and epileptiform patterns of cortical activity are highly prevalent in autism spectrum disorders (ASDs), but the neural substrates and pathophysiological mechanisms underlying the onset of cortical dysfunction in ASD remains elusive. Reduced cortical expression of Parvalbumin (PV) has been widely observed in ASD mouse models and human postmortem studies, suggesting a crucial role of PV interneurons (PVINs) in ASD pathogenesis. Shank3B-/- mice carrying a {Delta}13-16 deletion in SHANK3 exhibit cortical hyperactivity during postnatal development and reduced sensory responses in cortical GABAergic interneurons in adulthood. However, whether these phenotypes are associated with PVIN dysfunction is unknown. Using whole-cell electrophysiology and a viral-based strategy to label PVINs during postnatal development, we performed a developmental characterization of AMPAR miniature excitatory postsynaptic currents (mEPSCs) in PVINs and pyramidal (PYR) neurons of layer (L) 2/3 mPFC in Shank3B-/- mice. Surprisingly, reduced mEPSC frequency was observed in both PYR and PVIN populations, but only in adulthood. At P15, when cortical hyperactivity is already observed, both neuron types exhibited normal mEPSC amplitude and frequency, suggesting that glutamatergic connectivity deficits in these neurons emerge as compensatory mechanisms. Additionally, we found normal mEPSCs in adult PVINs of L2/3 somatosensory cortex, revealing region-specific phenotypic differences of cortical PVINs in Shank3B-/- mice. Together, these results demonstrate that loss of Shank3 alters PVIN function but suggest that PVIN glutamatergic synapses are a suboptimal therapeutic target for normalizing early cortical imbalances in SHANK3-associated disorders. More broadly, these findings underscore the complexity of interneuron dysfunction in ASDs, prompting further exploration of region and developmental stage specific phenotypes for understanding and developing effective interventions.

neuroscience↗

bioRxiv2023

Groundwater redox dynamics across the terrestrial-aquatic interface of Lake Erie coastal ecosystems

Groundwater biogeochemistry in coastal areas is spatially and temporally dynamic because fluctuations in groundwater level may cause alternate redox between distinct hydrological conditions. Recent studies have proposed connections between biogeochemistry and large-scale hydrological processes, specifically focusing on the role of redox-active compounds in changing the oxidation state during flooding and draining events. While water saturation generally results in a shift of redox-active compounds from electron donors to acceptors, the specific mechanisms underlying the transition of groundwater between oxidizing and reducing conditions in response to water level fluctuations are uncertain. To determine the effects of groundwater levels on redox dynamics, we monitored groundwater redox potential across the terrestrial-aquatic interface in Lake Erie coastal areas throughout the high and low-water seasons. In contrast to previously observed responses to flooding in soils, our results revealed patterns of oxidizing redox potentials during high-water and reducing during low-water periods. Furthermore, short-term fluctuations in water table levels significantly impacted the redox potential of groundwater when dissolved oxygen increased, and redox dynamics displayed voltage hysteresis in most events. Based on these findings, we propose that for improved predictions of microbial functions and biogeochemical cycles, redox-informed models should incorporate the antagonistic changes in groundwater redox balance compared to soils and consider the time lags in redox fluctuations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/544684v1_figu1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4d7a19org.highwire.dtl.DTLVardef@8b2b92org.highwire.dtl.DTLVardef@d9bc11org.highwire.dtl.DTLVardef@ca3e13_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractConceptual diagram of groundwater redox fluctuations in coastal ecosystems. Large redox fluctuations are derived by dissolved oxygen inputs and smaller more frequent redox fluctuations are led by redox sensitive species leaching from topsoil. C_FIG

ecology↗

bioRxiv2020

Integrated tapered fibertrode for simultaneous control and readout of neural activity over small brain volumes with reduced light-induced artefacts

Recognizing the neural patterns underlying different brain functions is essential to achieve a more comprehensive view on how small sets of neurons organize in complex 3D networks to determine different behaviours. In this framework, optogenetic techniques have been successfully proven as a powerful tool to control brain functions achieving millisecond temporal resolution and cell-type specificity, by combining the use of light-gated opsins and ad-hoc light delivery optoelectronic devices. However, targeting small brain volumes with simultaneous electrical recording results in the introduction of photoelectric artefacts, in particular when light emission and recoding sites are very close one to each other. In this work we take advantage of the photonic properties of tapered fibers to present a fully integrated fibertrode to target small brain volumes with abated photoelectric noise. The device hosts a light emitting window just below a recording pad, and exploits the angled light emission from the window to achieve simultaneous activation and electrical readout of small groups of cells with no photoelectric artifacts in vivo. Despite the highly non-planar surface of the fiber taper, windows size, shape and electrodes impedance can be modulated by controlling the fabrication parameters during focused ion beam milling and deposition, thus resulting in a versatile, integrated and customizable optogenetic tool for neurobiology studies in closed-loop configuration over small brain volumes.

neuroscience↗

bioRxiv2019

Transcriptional regulation of MGE progenitor proliferation by PRDM16 controls cortical GABAergic interneuron production

The mammalian cortex is populated by neurons derived from neural progenitors located throughout the embryonic telencephalon. Excitatory neurons are derived from progenitors located in the dorsal telencephalon, while inhibitory interneurons are generated by ventral telencephalic progenitors. The transcriptional regulator PRDM16 is expressed by radial glia, neural progenitors present in both regions; however, its mechanisms of action are still not fully understood. It is unclear if PRDM16 functions plays a role in neurogenesis in both dorsal and ventral progenitor lineages, and if so, whether it does so by regulating common or unique networks of genes. Here, we show that Prdm16 expression in MGE progenitors is required for maintaining their proliferative capacity and for the production of proper numbers of pallial GABAergic interneurons. PRDM16 binds to cis-regulatory elements and represses the expression of region-specific neuronal differentiation genes, thereby controlling the timing of neuronal maturation. Our results highlight the importance of PRDM16 for the development of both excitatory and inhibitory cortical circuits. We demonstrate the existence of convergent developmental gene expression programs regulated by PRDM16, which utilize both common and region-specific sets of genes in the cortex and the MGE to control the proliferative capacity of neural progenitors, ensuring the generation of correct numbers of cortical neurons.

neuroscience↗