Biology subjects

Costa, M.

Publications and source records attributed to Costa, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗

bioRxiv2024

Placentas from SARS-CoV-2 infection during pregnancy exhibit foci of oxidative stress and DNA damage

ProblemCOVID-19 during pregnancy is linked to increased maternal morbidity and a higher incidence of preterm births, yet the underlying mechanisms remain unclear. Cellular senescence, characterized by the irreversible cessation of cell division, is a critical process in placental function and its dysregulation has been implicated in pregnancy complications like preterm birth. Senescence can be induced by various stressors, including oxidative stress, DNA damage, and viral infections. Method of StudyIn this study, we determined whether COVID-19 had an impact on placental senescence. We examined placentas from women infected with SARS-CoV-2 (n=10 term, 4 preterm) compared to uninfected controls (n=10 term, 3 preterm). The placentas were analyzed for SARS-CoV-2 infection/replication (Spike and Nucleocapsid viral proteins), markers of DNA damage ({gamma}H2AX) and oxidative stress (ROS), and senescence (telomere length; cell cycle regulators, SASP). ResultsWhile no overall differences in cellular senescence markers were observed between the COVID-19 positive and negative groups, we found increased secreted SASP markers and confocal microscopy revealed localized areas of oxidative stress and DNA damage in the placentas from COVID-19 positive cases. ConclusionsThese findings indicate that SARS-CoV-2 infection induces localized placental damage, warranting further investigation into its impact on maternal and perinatal outcomes.

microbiology↗

bioRxiv2024

Comparative connectomics of the descending and ascending neurons of the Drosophila nervous system: stereotypy and sexual dimorphism

In most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains most of the final motor outputs necessary for behaviour, and the brain. In insects, the neck connective is both a physical and information bottleneck connecting the brain and the ventral nerve cord (VNC, spinal cord analogue) and comprises diverse populations of descending (DN), ascending (AN) and sensory ascending neurons, which are crucial for sensorimotor signalling and control. Integrating three separate EM datasets, we now provide a complete connectomic description of the ascending and descending neurons of the female nervous system of Drosophila and compare them with neurons of the male nerve cord. Proofread neuronal reconstructions have been matched across hemispheres, datasets and sexes. Crucially, we have also matched 51% of DN cell types to light level data defining specific driver lines as well as classifying all ascending populations. We use these results to reveal the general architecture, tracts, neuropil innervation and connectivity of neck connective neurons. We observe connected chains of descending and ascending neurons spanning the neck, which may subserve motor sequences. We provide a complete description of sexually dimorphic DN and AN populations, with detailed analysis of circuits implicated in sex-related behaviours, including female ovipositor extrusion (DNp13), male courtship (DNa12/aSP22) and song production (AN hemilineage 08B). Our work represents the first EM-level circuit analyses spanning the entire central nervous system of an adult animal.

neuroscience↗

bioRxiv2024

Intensifying marine heatwaves and limited protection threaten global kelp forests

Kelp forests are one of the earths most productive ecosystems and are at the greatest risk from climate change, yet little is known regarding their future threats and current conservation status. By combining a global remote sensing dataset of floating kelp forests with climate data and projections, we find that exposure to projected marine heatwaves will increase [~]8 times compared to contemporary (2001-2020) exposure for intermediate climate scenarios. While exposure will intensify for all forests, climate refugia emerge for some southern hemisphere kelp forests, which have lower exposure to contemporary and projected marine heatwaves. Under these escalating threats, less than 3% of global kelp forests are currently within highly restrictive marine protected areas, the most effective conservation measure for providing climate resilience. Our findings emphasize the urgent need to increase the global protection of kelp forests and set bolder climate adaptation goals.

ecology↗

bioRxiv2024

Accelerated growth increases the somatic epimutation rate in trees

Trees are critical components of ecosystems and of major economic importance. Due to their extraordinary longevity and well-defined modular architecture they have also emerged as model systems to study the long-term accumulation of somatic mutations in plants. Coupled with retrospective life-history and environmental data, trees can offer unique insights into mutational processes that would be difficult to obtain with prospective studies. In addition to genetic mutations, somatic epimutations in the form of stochastic gains and losses of DNA cytosine methylation have been shown to accumulate rapidly during ontogeny. One hypothesis is that somatic epimutations originate from DNA methylation maintenance errors during mitotic cell divisions, which would predict that their rate of accumulation scales with growth rate, rather than with age. Here we test this hypothesis in European beech. We analyzed one of the oldest continuously measured experimental plots in the world. The plot contains an even-aged beech stand that was established in 1822 and monitored for growth at regular intervals until the present. Starting [~]150 years ago, alternative thinning strategies were applied to subplots of this experiment, resulting in differential stem growth rates among trees. We show that accelerated growth significantly increased the per-year somatic epimutation rate at CG dinucleotides, and that this effect is accompanied by differences in cell division rates. Hence, faster growth elevates the chances for methylation maintenance errors during DNA replication per unit time. As somatic CG epimutations can be stably inherited to subsequent generations in plants, our insights have direct ecological and evolutionary implications.

genomics↗

bioRxiv2024

Systematic perturbation screens decode regulators of inflammatory macrophage states and identify a role for TNF mRNA m6A modification

Macrophages adopt dynamic cell states with distinct effector functions to maintain tissue homeostasis and respond to environmental challenges. During chronic inflammation, macrophage polarization is subverted towards sustained inflammatory states which contribute to disease, but there is limited understanding of the regulatory mechanisms underlying these disease-associated states. Here, we describe a systematic functional genomics approach that combines genome-wide phenotypic screening in primary murine macrophages with transcriptional and cytokine profiling of genetic perturbations in primary human monocyte-derived macrophages (hMDMs) to uncover regulatory circuits of inflammatory macrophage states. This process identifies regulators of five distinct inflammatory states associated with key features of macrophage function. Among these, the mRNA m6A writer components emerge as novel inhibitors of a TNF-driven cell state associated with multiple inflammatory pathologies. Loss of m6A writer components in hMDMs enhances TNF transcript stability, thereby elevating macrophage TNF production. A PheWAS on SNPs predicted to impact m6A installation on TNF revealed an association with cystic kidney disease, implicating an m6A-mediated regulatory mechanism in human disease. Thus, systematic phenotypic characterization of primary human macrophages describes the regulatory circuits underlying distinct inflammatory states, revealing post-transcriptional control of TNF mRNA stability as an immunosuppressive mechanism in innate immunity.

immunology↗

bioRxiv2024

Seed sequences mediate off-target activity in the CRISPR-interference (CRISPRi) system

The CRISPR interference (CRISPRi) system is a powerful tool that is widely used to selectively and efficiently silence genes in functional genomics research applications. However, the extent of off-target activity associated with the CRISPRi system has not been systematically investigated. Here, we utilized a genome-wide CRISPRi Cas9 single guide RNA (sgRNA) library to investigate the presence of off-target activity and its effects on gene expression. Our findings suggest that off-target effects in CRISPRi are quite pervasive and have direct and indirect impact on gene expression. Most of the identified off-target activities can be accounted for by complementarity of the PAM-proximal genomic sequence with the 3 half of the sgRNA spacer sequence, the seed sequence. We also report that not all PAM proximal positions are equally important for binding of sgRNA to the DNA and that mismatches in the PAM-proximal regions can be tolerated depending on the sequence context.

bioinformatics↗

bioRxiv2024

A blueprint for national assessments of the blue carbon capacity of kelp forests applied to Canadas coastline

Kelp forests offer substantial carbon fixation, with the potential to contribute to natural climate solutions (NCS). However, to be included in national NCS inventories, governments must first quantify the kelp-derived carbon stocks and fluxes leading to carbon sequestration. Here, we present a blueprint for assessing the national carbon sequestration capacity of kelp forests in which data synthesis and Bayesian hierarchical modelling enable estimates of kelp forest carbon production, storage, and export capacity from limited data. Applying this blueprint to Canadas extensive coastline, we find kelp forests store an estimated 1.4 Tg C in short-term biomass and produce 3.1 Tg C yr-1 with modest carbon fluxes to the deep ocean. Arctic kelps had the highest carbon stocks and production capacity, while Pacific kelps had greater carbon fluxes overall due to their higher productivity and export rates. Our transparent, reproducible blueprint represents an important step towards accurate carbon accounting for kelp forests.

ecology↗

bioRxiv2024

Retrieval of human aversive memories involves reactivation of gamma activity patterns in the hippocampus that originate in the amygdala during encoding

Emotional memories require coordinated activity of the amygdala and hippocampus. Human intracranial recordings have shown that formation of aversive memories involves an amygdala theta-hippocampal gamma phase code. Yet, the mechanisms engaged during translation of aversive experiences into memories and subsequent retrieval remain unclear. Directly recording from human amygdala and hippocampus, here we show that hippocampal gamma activity increases for correctly remembered aversive scenes, while exerting unidirectional oscillatory influence within the theta/beta frequency range on the amygdala for previously seen aversive scenes. Crucially, patterns of amygdala high amplitude gamma activity at encoding are reactivated in the hippocampus, but not amygdala, during both aversive encoding and retrieval. Trial-specific hippocampal gamma patterns showing highest representational similarity with amygdala activity at encoding are replayed in the hippocampus during aversive retrieval. This reactivation process occurs against a background of gamma activity that is otherwise decorrelated between encoding and retrieval. Thus, retrieval of aversive memories is hippocampal-centered, with hippocampal activity patterns apparently entrained by the amygdala during encoding.

neuroscience↗

bioRxiv2023

Perception of butenolides by Bacillus subtilis via the α/β-hydrolase RsbQ

The regulation of behavioural and developmental decisions by small molecules is common to all domains of life. In plants, strigolactones and karrikins are butenolide growth regulators that influence several aspects of plant growth and development, as well as interactions with symbiotic fungi1-3. DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are homologous receptors that perceive strigolactones and karrikins, respectively, and that hydrolyse their ligands to effect signal transduction4-7. RsbQ, a homologue of D14 and KAI2 from the Gram-positive bacterium Bacillus subtilis, regulates growth responses to nutritional stress via the alternative transcription factor SigmaB ({sigma}B)8,9. However, the molecular function of RsbQ is unknown. Here we show that RsbQ perceives butenolide compounds that are bioactive in plants. RsbQ is thermally destabilised by the synthetic strigolactone GR24 and its desmethyl butenolide equivalent dGR24. We show that, like D14 and KAI2, RsbQ is a functional butenolide hydrolase that undergoes covalent modification of the catalytic histidine residue. Exogenous application of both GR24 and dGR24 inhibited the endogenous signalling function of RsbQ in vivo, with dGR24 being 10-fold more potent. Application of dGR24 to B. subtilis phenocopied loss-of-function rsbQ mutations and led to a significant down-regulation of {sigma}B-regulated transcripts. We also discovered that exogenous butenolides promoted the transition from planktonic to biofilm growth. Our results suggest that butenolides may serve as inter-kingdom signalling compounds between plants and bacteria to help shape rhizosphere communities.

microbiology↗

bioRxiv2023

JAGGER localization and function is dependent on GPI anchor addition

In flowering plants, successful double fertilization requires the correct delivery of two sperm cells to the female gametophyte inside the ovule. The delivery of a single pair of sperm cells is achieved by the entrance of a single pollen tube into one female gametophyte. To prevent polyspermy, Arabidopsis ovules avoid the attraction of multiples pollen tubes to one ovule - polytubey block. In Arabidopsis jagger mutants, a significant number of ovules attract more than one pollen tube to an ovule due to an impairment in synergid degeneration. JAGGER encodes a putative arabinogalactan protein (AGP) which is predicted to be anchored to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor. Here, we show that JAGGER fused to citrine yellow fluorescent protein (JAGGER-cYFP) is functional and localizes mostly to the periphery of ovule integuments and transmitting tract cells. We further investigated the importance of GPI-anchor addition domains for JAGGER localization and function. Different JAGGER proteins with deletions in predicted {omega}-site regions and GAS (GPI attachment signal) domain, expected to compromise the addition of the GPI anchor, led to disruption of JAGGER localization in the cell periphery. All JAGGER proteins with disrupted localization were also not able to rescue the polytubey phenotype, pointing to the importance of GPI-anchor addition to in vivo function of the JAGGER protein.

plant biology↗

bioRxiv2023

Network Statistics of the Whole-Brain Connectome of Drosophila

Brains comprise complex networks of neurons and connections. Network analysis applied to the wiring diagrams of brains can offer insights into how brains support computations and regulate information flow. The completion of the first whole-brain connectome of an adult Drosophila, the largest connectome to date, containing 130,000 neurons and millions of connections, offers an unprecedented opportunity to analyze its network properties and topological features. To gain insights into local connectivity, we computed the prevalence of two- and three-node network motifs, examined their strengths and neurotransmitter compositions, and compared these topological metrics with wiring diagrams of other animals. We discovered that the network of the fly brain displays rich club organization, with a large population (30% percent of the connectome) of highly connected neurons. We identified subsets of rich club neurons that may serve as integrators or broadcasters of signals. Finally, we examined subnetworks based on 78 anatomically defined brain regions or neuropils. These data products are shared within the FlyWire Codex and will serve as a foundation for models and experiments exploring the relationship between neural activity and anatomical structure.

neuroscience↗

bioRxiv2023

Neuronal wiring diagram of an adult brain

Connections between neurons can be mapped by acquiring and analyzing electron microscopic (EM) brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative, yet inadequate for understanding brain function more globally. Here, we present the first neuronal wiring diagram of a whole adult brain, containing 5x107 chemical synapses between [~]130,000 neurons reconstructed from a female Drosophila melanogaster. The resource also incorporates annotations of cell classes and types, nerves, hemilineages, and predictions of neurotransmitter identities. Data products are available by download, programmatic access, and interactive browsing and made interoperable with other fly data resources. We show how to derive a projectome, a map of projections between regions, from the connectome. We demonstrate the tracing of synaptic pathways and the analysis of information flow from inputs (sensory and ascending neurons) to outputs (motor, endocrine, and descending neurons), across both hemispheres, and between the central brain and the optic lobes. Tracing from a subset of photoreceptors all the way to descending motor pathways illustrates how structure can uncover putative circuit mechanisms underlying sensorimotor behaviors. The technologies and open ecosystem of the FlyWire Consortium set the stage for future large-scale connectome projects in other species.

neuroscience↗

bioRxiv2023

A consensus cell type atlas from multiple connectomes reveals principles of circuit stereotypy and variation

The fruit fly Drosophila melanogaster combines surprisingly sophisticated behaviour with a highly tractable nervous system. A large part of the flys success as a model organism in modern neuroscience stems from the concentration of collaboratively generated molecular genetic and digital resources. As presented in our FlyWire companion paper1, this now includes the first full brain connectome of an adult animal. Here we report the systematic and hierarchical annotation of this [~]130,000-neuron connectome including neuronal classes, cell types and developmental units (hemilineages). This enables any researcher to navigate this huge dataset and find systems and neurons of interest, linked to the literature through the Virtual Fly Brain database2. Crucially, this resource includes 4,552 cell types. 3,094 are rigorous consensus validations of cell types previously proposed in the "hemibrain" connectome3. In addition, we propose 1,458 new cell types, arising mostly from the fact that the FlyWire connectome spans the whole brain, whereas the hemibrain derives from a subvolume. Comparison of FlyWire and the hemibrain showed that cell type counts and strong connections were largely stable, but connection weights were surprisingly variable within and across animals. Further analysis defined simple heuristics for connectome interpretation: connections stronger than 10 unitary synapses or providing >1% of the input to a target cell are highly conserved. Some cell types showed increased variability across connectomes: the most common cell type in the mushroom body, required for learning and memory, is almost twice as numerous in FlyWire as the hemibrain. We find evidence for functional homeostasis through adjustments of the absolute amount of excitatory input while maintaining the excitation-inhibition ratio. Finally, and surprisingly, about one third of the cell types proposed in the hemibrain connectome could not yet be reliably identified in the FlyWire connectome. We therefore suggest that cell types should be defined to be robust to inter-individual variation, namely as groups of cells that are quantitatively more similar to cells in a different brain than to any other cell in the same brain. Joint analysis of the FlyWire and hemibrain connectomes demonstrates the viability and utility of this new definition. Our work defines a consensus cell type atlas for the fly brain and provides both an intellectual framework and open source toolchain for brain-scale comparative connectomics.

neuroscience↗

bioRxiv2023

Transforming descending input into behavior: The organization of premotor circuits in the Drosophila Male Adult Nerve Cord connectome

In most animals, a relatively small number of descending neurons (DNs) connect higher brain centers in the animals head to circuits and motor neurons (MNs) in the nerve cord of the animals body that effect movement of the limbs. To understand how brain signals generate behavior, it is critical to understand how these descending pathways are organized onto the body MNs. In the fly, Drosophila melanogaster, MNs controlling muscles in the leg, wing, and other motor systems reside in a ventral nerve cord (VNC), analogous to the mammalian spinal cord. In companion papers, we introduced a densely-reconstructed connectome of the Drosophila Male Adult Nerve Cord (MANC, (Takemura et al., 2024)), including cell type and developmental lineage annotation (Marin et al., 2024), which provides complete VNC connectivity at synaptic resolution. Here, we present a first look at the organization of the VNC networks connecting DNs to MNs based on this new connectome information. We proofread and curated all DNs and MNs to ensure accuracy and reliability, then systematically matched DN axon terminals and MN dendrites with light microscopy data to link their VNC morphology with their brain inputs or muscle targets. We report both broad organizational patterns of the entire network and fine-scale analysis of selected circuits of interest. We discover that direct DN-MN connections are infrequent and identify communities of intrinsic neurons linked to control of different motor systems, including putative ventral circuits for walking, dorsal circuits for flight steering and power generation, and intermediate circuits in the lower tectulum for coordinated action of wings and legs. Our analysis generates hypotheses for future functional experiments and, together with the MANC connectome, empowers others to investigate these and other circuits of the Drosophila ventral nerve cord in richer mechanistic detail.

neuroscience↗

bioRxiv2023

Structural Basis for the transmembrane signaling and antidepressant-induced activation of the receptor tyrosine kinase TrkB

Neurotrophin receptors of the Trk family are involved in the regulation of brain development and neuroplasticity, and therefore can serve as targets for anti-cancer and stroke-recovery drugs, antidepressants, and many others. The structures of Trk protein domains in various states upon activation need to be elucidated to allow rational drug design. However, little is known about the conformations of the transmembrane and juxtamembrane domains of Trk receptors. In the present study, we employed NMR spectroscopy to solve the structure of the TrkB dimeric transmembrane domain in the lipid environment. We verified the structure using mutagenesis and confirmed that the conformation corresponds to the active state of the receptor. Subsequent study of TrkB interaction with the antidepressant drug fluoxetine, and the antipsychotic drug chlorpromazine, provided a clear self-consistent model, describing the mechanism by which fluoxetine activates the receptor by binding to its transmembrane domain.

biochemistry↗

bioRxiv2023

Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation

Nervous systems function as ensembles of neurons communicating via synaptic connections, and a functional understanding of nervous systems requires extensive knowledge of their connectomes. In a companion paper (Takemura et al., 2023), we describe the acquisition of a complete fruit fly nerve cord connectome, the first for an animal that can walk or fly. Here, to efficiently navigate and to appreciate the biological significance of this connectome, we categorise and name nearly all neurons systematically and link them to the experimental literature. We employ a system of hierarchical coarse annotations and group similar neurons across the midline and across segments, then define systematic cell types for sensory neurons, intrinsic neurons, ascending neurons, and non-motor efferent neurons. Stereotyped arrays of neuroblasts generate related neuron populations called hemilineages that repeat across the segments of the nerve cord. We confirm that larval-born neurons from a given hemilineage generally express the same neurotransmitter but find that earlier born neurons often express a different one. We match over 35% of intrinsic, ascending, and non-motor efferent neurons across segments, defining serial sets which were crucial for systematic typing of motor neurons and sensory neurons. We assign a sensory modality to over 5000 sensory neurons, cluster them by connectivity, and identify serially homologous cell types and a layered organisation likely corresponding to peripheral topography. Finally, we present selected examples of sensory circuits predicated on programmatic analysis of a complete VNC connectome. Our annotations are critical for analysing the structure of descending input to the nerve cord and of motor output, both described in a third companion paper (Cheong et al., 2023). These annotations are being released as part of the neuprint.janelia.org and clio.janelia.org web applications and also serve as the basis for programmatic analysis of the connectome through dedicated tools that we describe in this paper.

neuroscience↗

bioRxiv2023

A Connectome of the Male Drosophila Ventral Nerve Cord

Animal behavior is principally expressed through neural control of muscles. Therefore understanding how the brain controls behavior requires mapping neuronal circuits all the way to motor neurons. We have previously established technology to collect large-volume electron microscopy data sets of neural tissue and fully reconstruct the morphology of the neurons and their chemical synaptic connections throughout the volume. Using these tools we generated a dense wiring diagram, or connectome, for a large portion of the Drosophila central brain. However, in most animals, including the fly, the majority of motor neurons are located outside the brain in a neural center closer to the body, i.e. the mammalian spinal cord or insect ventral nerve cord (VNC). In this paper, we extend our effort to map full neural circuits for behavior by generating a connectome of the VNC of a male fly.

neuroscience↗