Biology subjects

Kim, H.

Publications and source records attributed to Kim, H..

At least 433 records · Page 24Linked to original sources

bioRxiv2021

Widespread false gene gains caused by duplication errors in genome assemblies

False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in previous genome assemblies and their new counterparts of the same species (platypus, zebra finch, Annas hummingbird) generated by the Vertebrate Genomes Project (VGP). Whole genome alignments revealed that 4 to 16% of the sequences were falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These led to overestimated gene family expansions. The main source of the false duplications was heterotype duplications, where the haplotype sequences were more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source was sequencing errors. Although present in a smaller proportion, we observed false duplications remaining in the VGP assemblies that can be identified and purged. This study highlights the need for more advanced assembly methods that better separates haplotypes and sequence errors, and the need for cautious analyses on gene gains.

genomics↗

bioRxiv2021

Differential effects of cerebellar degeneration on feedforward versus feedback control across speech and reaching movements

Errors that result from a mismatch between predicted movement outcomes and sensory afference are used to correct ongoing movements through feedback control and to adapt feedforward control of future movements. The cerebellum has been identified as a critical part of the neural circuit underlying implicit adaptation across a wide variety of movements (reaching, gait, eye movements, and speech). The contribution of this structure to feedback control is less well understood: although it has recently been shown in the speech domain that individuals with cerebellar degeneration produce even larger online corrections for sensory perturbations than control participants, similar behavior has not been observed in other motor domains. Currently, comparisons across domains are limited by different population samples and potential ceiling effects in existing tasks. To assess the relationship between changes in feedforward and feedback control associated with cerebellar degeneration across motor domains, we evaluated adaptive (feedforward) and compensatory (feedback) responses to sensory perturbations in reaching and speech production in human participants of both sexes with cerebellar degeneration and neurobiologically healthy controls. As expected, the cerebellar group demonstrated impaired adaptation in both reaching and speech. In contrast, the groups did not differ in their compensatory response in either domain. Moreover, compensatory and adaptive responses in the cerebellar group were not correlated within or across motor domains. These results point to a general impairment in feedforward control with spared feedback control in cerebellar degeneration. However, the magnitude of feedforward impairments and potential changes in feedback-based control manifest in a domain-specific manner across individuals. Significance StatementThe cerebellum contributes to feedforward updating of movement in response to sensory errors, but its role in feedback control is less understood. Here, we tested individuals with cerebellar degeneration (CD), using sensory perturbations to assess adaptation of feedforward control and feedback gains during reaching and speech production tasks. The results confirmed that CD leads to reduced adaption in both domains. However, feedback gains were unaffected by CD in either domain. Interestingly, measures of feedforward and feedback control were not correlated across individuals within or across motor domains. Together, these results indicate a general impairment in feedforward control with spared feedback control in CD. However, the magnitude of feedforward impairments manifests in a domain-specific manner across individuals.

neuroscience↗

bioRxiv2021

JAG1 intracellular domain acts as a transcriptional cofactor that forms an oncogenic transcriptional complex with DDX17/SMAD3/TGIF2

Jagged1 (JAG1) is a Notch ligand that contact-dependently activates Notch receptors and regulates cancer progression. The JAG1 intracellular domain (JICD1) is generated from JAG1, such as the formation of NOTCH1 intracellular domain (NICD1), however, the role of JICD1 in tumorigenicity has not been comprehensively elucidated. Herein, we revealed that JICD1 induced astrocytes to acquire several cancer stem cell properties, including tumor formation, invasiveness, stemness, and resistance to chemotherapy and radiotherapy. The transcriptome, ChIP-sequencing, and proteomic analyses revealed that JICD1 increased SOX2 expression by forming a transcriptional complex with DDX17, SMAD3, and TGIF2. Furthermore, JICD1-driven tumorigenicity was directly regulated by SOX2. Therefore, our results demonstrated that, like NICD1, JICD1 acts as a transcriptional cofactor in the formation of the DDX17/SMAD3/TGIF2 transcriptional complex, leading to oncogenic transformation.

molecular biology↗

bioRxiv2021

Influence of substrate stiffness on barrier function in an iPSC-derived in vitro blood-brain barrier model

IntroductionVascular endothelial cells respond to a variety of biophysical cues such as shear stress and substrate stiffness. In peripheral vasculature, extracellular matrix (ECM) stiffening alters barrier function, leading to increased vascular permeability in atherosclerosis and pulmonary edema. The effect of ECM stiffness on blood-brain barrier (BBB) endothelial cells, however, has not been explored. To investigate this topic, we incorporated hydrogel substrates into an in vitro model of the human BBB. MethodsInduced pluripotent stem cells were differentiated to brain microvascular endothelial-like (BMEC-like) cells and cultured on hydrogel substrates of varying stiffness. Cellular changes were measured by imaging, functional assays such as transendothelial electrical resistance (TEER) and p-glycoprotein efflux activity, and bulk transcriptome readouts. ResultsThe magnitude and longevity of TEER in iPSC-derived BMEC-like cells is enhanced on compliant substrates. Quantitative imaging shows that BMEC-like cells form fewer intracellular actin stress fibers on substrates of intermediate stiffness (20 kPa relative to 1 kPa and 150 kPa). Chemical induction of actin polymerization leads to a rapid decline in TEER, agreeing with imaging readouts. P-glycoprotein activity is unaffected by substrate stiffness. Modest differences in RNA expression corresponding to specific signaling pathways were observed as a function of substrate stiffness. ConclusionsiPSC-derived BMEC-like cells exhibit differences in passive but not active barrier function in response to substrate stiffness. These findings may provide insight into BBB dysfunction during neurodegeneration, as well as aid in the optimization of more complex threedimensional neurovascular models utilizing compliant hydrogels.

bioengineering↗

bioRxiv2021

Style Transfer Using Generative Adversarial Networks for Multi-Site MRI Harmonization

Large data initiatives and high-powered brain imaging analyses require the pooling of MR images acquired across multiple scanners, often using different protocols. Prospective cross-site harmonization often involves the use of a phantom or traveling subjects. However, as more datasets are becoming publicly available, there is a growing need for retrospective harmonization, pooling data from sites not originally coordinated together. Several retrospective harmonization techniques have shown promise in removing cross-site image variation. However, most unsupervised methods cannot distinguish between image-acquisition based variability and cross-site population variability, so they require that datasets contain subjects or patient groups with similar clinical or demographic information. To overcome this limitation, we consider cross-site MRI image harmonization as a style transfer problem rather than a domain transfer problem. Using a fully unsupervised deep-learning framework based on a generative adversarial network (GAN), we show that MR images can be harmonized by inserting the style information encoded from a reference image directly, without knowing their site/scanner labels a priori. We trained our model using data from five large-scale multi-site datasets with varied demographics. Results demonstrated that our styleencoding model can harmonize MR images, and match intensity profiles, successfully, without relying on traveling subjects. This model also avoids the need to control for clinical, diagnostic, or demographic information. Moreover, we further demonstrated that if we included diverse enough images into the training set, our method successfully harmonized MR images collected from unseen scanners and protocols, suggesting a promising novel tool for ongoing collaborative studies.

neuroscience↗

bioRxiv2021

The Arabidopsis ORA59 coordinates jasmonic acid- and ethylene-responsive gene expression to regulate plant immunity

Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, among which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. Here, we identified the ERELEE4 as an ORA59-binding cis-element, in addition to the well-characterized GCC box, demonstrating that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in the gene promoters. Notably, ORA59 exhibited differential preference for the GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.

plant biology↗

bioRxiv2021

Cyto/myeloarchitectural changes of cortical gray matter and superficial white matter in early neurodevelopment: Multimodal MRI study of preterm neonates

The developing cerebral cortex undergoes rapid microstructural and morphological changes throughout the third trimester. Recently, increased attention has been focused on the identification of imaging features that represent the underlying cortical cyto/myeloarchitecture driving intracortical myelination and the maturation of cortical gray matter (GM) and its adjacent superficial white matter (sWM). However, the characterization and spatiotemporal pattern of complex cyto/myeloarchitectural changes in this critical time period remain incompletely understood. Using 92 MRI scans from 78 preterm neonates (baseline: n{square}={square}78, postmenstrual age=33.1{+/-}1.8 weeks; follow-up: n=14, 37.3{+/-}1.3), the current study leveraged combined T1/T2 intensity ratio and diffusion tensor imaging (DTI) measurements, including fractional anisotropy (FA) and mean diffusivity (MD), to characterize the cyto/myeloarchitectural architecture of cortical GM and its adjacent sWM in preterm neonates. DTI metrics during these weeks showed an overall linear developmental trajectory: FA decreased along with time in GM but increased in sWM; MD decreased in both GM and sWM. In contrast, T1/T2 measurements showed a distinctive parabolic developmental trajectory, revealing additional cyto/myeloarchitectural signature inferred. Furthermore, the spatiotemporal courses of T1/T2 ratio and DTI parameters were found to be regionally heterogeneous across the cerebral cortex, suggesting these imaging features specific relationship to regional cyto/myeloarchitectural maturation: faster T1/T2 ratio changes were found in the central, ventral, and temporal regions of GM and sWM, faster FA increases in anterior sWM areas, and faster MD decreases in GM and sWM central and cingulate areas. Taken together, our results may offer an explanation of the novel pattern of cyto/myeloarchitectural processes observed throughout the third trimester, including dendritic arborization, synaptogenesis, glial proliferation, as well as radial glial cell organization and apoptosis. Finally, T1/T2 ratio and DTI measurements were significantly associated with 1 year outcome scores of language and cognitive performance as well as perinatal clinical conditions, including intraventricular hemorrhage and chronic lung disease, demonstrating their potential as imaging biomarkers characterizing microstructural deviation in atypical neurodevelopment. Ultimately, with combined properties of cortical T1/T2 and DTI measurements, this study provides unique insights into the cellular processes and associated developmental mechanisms during the critical development of the third trimester.

neuroscience↗

bioRxiv2021

Sod1 Integrates Oxygen Availability to Redox Regulate NADPH Production and the Thiol Redoxome

Cu/Zn superoxide dismutase (Sod1) is a highly conserved and abundant antioxidant enzyme that detoxifies superoxide (O2-) by catalyzing its conversion to dioxygen (O2) and hydrogen peroxide (H2O2). Using Saccharomyces cerevisiae and mammalian cells, we discovered that a major new aspect of the antioxidant function of Sod1 is to integrate O2 availability to promote NADPH production. The mechanism involves Sod1-derived H2O2 oxidatively inactivating the glycolytic enzyme, glyceraldehyde phosphate dehydrogenase (GAPDH), which in turn re-routes carbohydrate flux to the oxidative phase of the pentose phosphate pathway (oxPPP) to generate NADPH. The aerobic oxidation of GAPDH is exclusively dependent on and rate-limited by Sod1. Thus, Sod1 senses O2 via O2- to balance glycolytic and oxPPP flux, through control of GAPDH activity, for adaptation to life in air. Importantly, this new mechanism for Sod1 antioxidant activity requires the bulk of cellular Sod1, unlike for its role in protection against O2- toxicity, which only requires < 1% of total Sod1. Using mass spectrometry, we identified proteome-wide targets of Sod1-dependent redox signaling, including numerous metabolic enzymes. Altogether, Sod1-derived H2O2 is important for antioxidant defense and a master regulator of metabolism and the thiol redoxome. Significance StatementCu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress, metabolic defects, and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2-) in a manner that produces an oxidant as a byproduct, hydrogen peroxide (H2O2). While much is known about the necessity of scavenging O2-, it is less clear what the physiological roles of Sod1-derived H2O2 are. Herein, we discovered that Sod1-derived H2O2 plays a very important role in antioxidant defense by stimulating the production of NADPH, a vital cellular reductant required for ROS scavenging enzymes, as well as redox regulating a large network of enzymes.

biochemistry↗

bioRxiv2021

Volumetric Calcium Imaging of 1 Million Neurons Across Cortical Regions at Cellular Resolution Using Light Beads Microscopy

Two-photon microscopy together with genetically encodable calcium indicators has emerged as a standard tool for high-resolution imaging of neuroactivity in scattering brain tissue. However, its various realizations have not overcome the inherent tradeoffs between speed and spatiotemporal sampling in a principled manner which would be necessary to enable, amongst other applications, mesoscale volumetric recording of neuroactivity at cellular resolution and speed compatible with resolving calcium transients. Here, we introduce Light Beads Microscopy (LBM), a scalable and spatiotemporally optimal acquisition approach limited only by fluorescence life-time, where a set of axially-separated and temporally-distinct foci record the entire axial imaging range near-simultaneously, enabling volumetric recording at 1.41 x 108 voxels per second. Using LBM, we demonstrate mesoscopic and volumetric imaging at multiple scales in the mouse cortex, including cellular resolution recordings within ~3x5x0.5 mm3 volumes containing >200,000 neurons at ~5 Hz, recording of populations of ~1 million neurons within ~5.4x6x0.5 mm3 volumes at ~2Hz as well as higher-speed (9.6 Hz) sub-cellular resolution volumetric recordings. LBM provides an unprecedented opportunity for discovering the neurocomputations underlying cortex-wide encoding and processing of information in the mammalian brain.

neuroscience↗

bioRxiv2021

Analysis of the blood microbiome in a porcine model of fecal-induced peritonitis

BackgroundRecent studies have proposed the existence of a blood microbiome, even in the healthy host. However, we do not know how the blood microbiome changes when a bloodstream infection (BSI) occurs. Here, we analyzed the dynamics of the blood microbiome in a porcine model of polymicrobial bacteremia induced by fecal peritonitis. Serial blood samples were taken over 12 hours post-induction of fecal peritonitis, and BSI was validated by conventional blood culture and assessment of clinical symptoms. ResultsThe bacterial populations in the blood microbiome were retained throughout the experimental period. However, there were significant taxonomic differences between the profile in the fecal and blood microbiomes, reflecting tropism for the blood environment. We also confirmed that the microbiota we detected was not contaminated by low mass bacteria in the bloodstream. However, at the same time, we noted a slight increase in Bacteroidetes, which is a major component of the gut microbiome, as sepsis developed. Comparison of the functional pathways in the blood and fecal microbiomes revealed upregulation of pathways involved in environmental interactions, and downregulation of those related to cell proliferation, in the former. Based on the enriched biological pathways, we concluded that communication and stress management pathways are essential for the survival of the blood microbiome under harsh conditions. ConclusionThis study suggests that the microbiota can be stably retained in the bloodstream over time. Although further investigation in humans is required, we suggest that the blood microbiome may be another factor to be considered in the context of BSI and subsequent sepsis.

microbiology↗

bioRxiv2021

Promoting axon regeneration by enhancing the non-coding function of the injury-responsive coding gene Gpr151

Gene expression profiling in response to nerve injury has been mainly focused on protein functions of coding genes to understand mechanisms of axon regeneration and to identify targets of potential therapeutics for nerve repair. However, the protein functions of several highly injury-induced genes including Gpr151 for regulating the regenerative ability remain unclear. Here we present an alternative approach focused on non-coding functions of the coding genes, which led to the identification of the non-coding function of Gpr151 RNA interacting with RNA- binding proteins such as CSDE1. Gpr151 promotes axon regeneration by the function of its 5- untranslated region (5UTR) and expression of an engineered form of the 5UTR improves regenerative capacity in vitro and in vivo in both sciatic nerve and optic nerve injury models. Our data suggest that searching injury-induced coding genes potentially functioning by their non- coding regions is required for the RNA-based gene therapy for improving axon regeneration.

neuroscience↗

bioRxiv2021

Daily caffeinated soda intake is associated with impaired working memory and higher impulsivity in children

Background and ObjectivesUse of psychotropic substances in childhood has been associated with both impulsivity and other manifestations of poor executive function as well as escalation over time to use of progressively stronger substances. However, how this relationship may start in earlier childhood has not been well explored. Here, we investigated the neurobehavioral correlates of daily caffeinated soda consumption in preadolescent children and examined whether caffeinated soda intake is associated with a higher risk of subsequent alcohol initiation. MethodsUsing Adolescent Brain Cognitive Development study data, we first investigated cross-sectional relationships between frequent caffeinated soda intake and well-known risk factors of substance misuse: impaired working memory, high impulsivity, and aberrant reward processing. We then examined whether caffeinated soda intake at baseline predicts more alcohol sipping at 12 months follow-up using a machine learning algorithm. ResultsDaily consumption of caffeinated soda was cross-sectionally associated with neurobehavioral risk factors for substance misuse such as higher impulsivity scores and lower working memory performance. Furthermore, caffeinated soda intake predicted greater alcohol sipping after 12 months even after controlling for rates of baseline alcohol sipping; children who drink caffeinated soda daily are twice as likely to start sipping alcohol after one year compared to those who do not drink caffeinated soda at all. ConclusionsThese findings suggest that previous linkages between caffeine and substance use in adolescence also extend to younger initiation, and may stem from core neurocognitive features thought conducive to substance initiation.

neuroscience↗

bioRxiv2021

Scaling laws in enzyme function reveal a new kind of biochemical universality

All life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to currently observed biochemistry and does not allow quantitative predictions about examples not yet observed. Here we introduce a more generalizable concept of biochemical universality, more akin to the kind of universality discussed in physics. Using annotated genomic datasets including an ensemble of 11955 metagenomes and 1282 archaea, 11759 bacteria and 200 eukaryotic taxa, we show how four of the major enzyme functions - the oxidoreductases, transferases, hydrolases and ligases - form universality classes with common scaling behavior in their relative abundances observed across the datasets. We verify these universal scaling laws are not explained by the presence of compounds, reactions and enzyme functions shared across all known examples of life. We also demonstrate how a consensus model for the last universal common ancestor (LUCA) is consistent with predictions from these scaling laws, with the exception of ligases and transferases. Our results establish the existence of a new kind of biochemical universality, independent of the details of the component chemistry, with implications for guiding our search for missing biochemical diversity on Earth, or other for any biochemistries that might deviate from the exact chemical make-up of life as we know it, such as at the origins of life, in alien environments, or in the design of synthetic life.

systems biology↗

bioRxiv2021

Systematic analysis of brain lactate and pH levels in 65 animal models related to neuropsychiatric conditions

Increased levels of lactate, an end-product of glycolysis, have been proposed as a potential surrogate marker for metabolic changes during neuronal excitation. These changes in lactate levels can result in decreased brain pH, which has been implicated in patients with various neuropsychiatric disorders. We previously demonstrated that such alterations are commonly observed in five mouse models of schizophrenia, bipolar disorder, and autism, suggesting a shared endophenotype among these disorders rather than mere artifacts due to medications or agonal state. However, there is still limited research on this phenomenon in animal models, leaving its generality across other disease animal models uncertain. Moreover, the association between changes in brain lactate levels and specific behavioral abnormalities remains unclear. To address these gaps, the International Brain pH Project Consortium investigated brain pH and lactate levels in 109 strains/conditions of 2,294 animals with genetic and other experimental manipulations relevant to neuropsychiatric disorders. Systematic analysis revealed that decreased brain pH and increased lactate levels were common features observed in multiple models of depression, epilepsy, Alzheimers disease, and some additional schizophrenia models. While certain autism models also exhibited decreased pH and increased lactate levels, others showed the opposite pattern, potentially reflecting subpopulations within the autism spectrum. Furthermore, utilizing large-scale behavioral test battery, a multivariate cross-validated prediction analysis demonstrated that poor working memory performance was predominantly associated with increased brain lactate levels. Importantly, this association was confirmed in an independent cohort of animal models. Collectively, these findings suggest that altered brain pH and lactate levels, which could be attributed to dysregulated excitation/inhibition balance, may serve as transdiagnostic endophenotypes of debilitating neuropsychiatric disorders characterized by cognitive impairment, irrespective of their beneficial or detrimental nature.

neuroscience↗

bioRxiv2021

Spc1 regulates substrate selection for signal peptidase

Signal peptidase (SPase) cleaves the signal sequences (SSs) of secretory precursors. It contains an evolutionarily conserved membrane protein subunit, Spc1 that is dispensable for the catalytic activity of SPase, and its role remains elusive. In the present study, we investigated the function of yeast Spc1. First, we set up an in vivo SPase cleavage assay using secretory protein CPY variants with SSs modified in the n and h regions. When comparing the SS cleavage efficiencies of these variants in cells with or without Spc1, we found that signal-anchored sequences become more susceptible to cleavage by SPase without Spc1. Further, SPase-mediated processing of transmembrane (TM) segments in model membrane proteins was reduced upon overexpression of Spc1. Spc1 was co-immunoprecipitated with membrane proteins carrying uncleaved signal-anchored or TM segments. These results suggest a role of Spc1 in shielding TM segments from SPase action, thereby contributing to accurate substrate selection for SPase.

biochemistry↗

bioRxiv2021

PICASSO: Ultra-multiplexed fluorescence imaging of biomolecules through single-round imaging and blind source unmixing

Ultra-multiplexed fluorescence imaging of biomolecules is essential to studying heterogeneous biological systems. However, this is challenging due to fluorophores spectral overlap and variation of the emission spectra. Here, we propose a strategy termed PICASSO, which enables more than 15-colour multiplexed imaging of thick tissue slices through a single imaging process and blind unmixing without reference spectra measurement. We show that PICASSO can be used to achieve a high multiplexing capability in diverse applications, such as 3D protein imaging, expansion microscopy, tissue clearing, imaging of clinical specimens, and cyclic immunofluorescence imaging. PICASSO only requires an equal number of images as the number of fluorophores, enabling such a high level of multiplexed imaging even with bandpass filter-based microscopy. As such, PICASSO would be a useful tool for the study of cancer, the immune system, and the brain, as well as for the diagnosis of cancer, as it enables ultra-multiplexed imaging of diverse specimens with minimum instrumental requirements and experimental processes.

neuroscience↗

bioRxiv2021

UNC-2 CaV2 channel localization at presynaptic active zones depends on UNC-10/RIM and SYD-2/Liprin-α in Caenorhabditis elegans.

Presynaptic active zone proteins couple calcium influx with synaptic vesicle exocytosis. However, the control of presynaptic calcium channel clustering by active zone proteins is not completely understood. In a C. elegans forward genetic screen, we find that UNC-10/RIM (Rab3-interacting molecule) and SYD-2/Liprin- regulate presynaptic clustering of UNC-2, the CaV2 channel ortholog. We further quantitatively analyzed live animals using endogenously GFP-tagged UNC-2 and active zone components. Consistent with the interaction between RIM and CaV2 in mammals, the intensity and number of UNC-2 channel clusters at presynaptic terminals were greatly reduced in unc-10 mutant animals. To understand how SYD-2 regulates presynaptic UNC-2 channel clustering, we analyzed presynaptic localization of endogenous SYD-2, UNC-10, RIMB-1/RIM-BP (RIM binding protein), and ELKS-1. Our analysis revealed that while SYD-2 is the most critical for active zone assembly, loss of SYD-2 function does not completely abolish presynaptic localization of UNC-10, RIMB-1, and ELKS-1, suggesting an existence of SYD-2-independent active zone assembly. UNC-2 localization analysis in double and triple mutants of active zone components show that SYD-2 promotes UNC-2 clustering by partially controlling UNC-10 localization, and ELKS-1 and RIMB-1 also contribute to UNC-2 channel clustering. In addition, we find that core active zone proteins are unequal in their abundance. While the abundance of UNC-10 at the active zone is comparable to UNC-2, SYD-2 and ELKS-1 are twice more and RIMB-1 four times more abundant than UNC-2. Together our data show that UNC-10, SYD-2, RIMB-1, and ELKS-1 control presynaptic UNC-2 channel clustering in redundant yet distinct manners. Significance StatementPrecise control of neurotransmission is dependent on the tight coupling of the calcium influx through voltage-gated calcium channels (VGCCs) to the exocytosis machinery at the presynaptic active zones. However, how these VGCCs are tethered to the active zone is incompletely understood. To understand the mechanism of presynaptic VGCC localization, we performed a C. elegans forward genetic screen and quantitatively analyzed endogenous active zones and presynaptic VGCCs. In addition to RIM (Rab3-interacting molecule), our study finds that SYD-2/Liprin- is critical for presynaptic localization of VGCCs. Yet, the loss of SYD-2, the master active zone scaffolding protein, does not completely abolish the presynaptic localization of the VGCC, showing that the active zone is a resilient structure assembled by redundant mechanisms.

neuroscience↗

bioRxiv2021

Robust T1 MRI cortical surface pipeline for neonatal brain and systematic evaluation using multi-site MRI datasets

The human brain grows the most dramatically during the perinatal and early postnatal periods, during which preterm birth or perinatal injury that may alter brain structure and lead to developmental anomalies. Thus, characterizing cortical thickness of developing brains remains an important goal. However, this task is often complicated by inaccurate cortical surface extraction due to small-size brains. Here, we propose a novel complex framework for the reconstruction of neonatal WM and pial surfaces, accounting for large partial volumes due to small-size brains. The proposed approach relies only on T1-weighted images unlike previous T2-weighted image-based approaches while only T1-weighted images are sometimes available under the different clinical/research setting. Deep neural networks are first introduced to the neonatal MRI pipeline to address the mis-segmentation of brain tissues. Furthermore, this pipeline enhances cortical boundary delineation using combined models of the CSF/GM boundary detection with edge gradient information and a new skeletonization of sulcal folding where no CSF voxels are seen due to the limited resolution. We also proposed a systematic evaluation using three independent datasets comprising 736 preterm and 97 term neonates. Qualitative assessment for reconstructed cortical surfaces shows that 86.9% are rated as accurate across the three site datasets. In addition, our landmark-based evaluation shows that the mean displacement of the cortical surfaces from the true boundaries was less than a voxel size (0.532{+/-}0.035mm). Evaluating the proposed pipeline (namely NEOCIVET 2.0) shows the robustness and reproducibility across different sites and different age-groups. The mean cortical thickness measured positively correlated with postmenstrual age (PMA) at scan (p<0.0001); Cingulate cortical areas grew the most rapidly whereas the inferior temporal cortex grew the least rapidly. The range of the cortical thickness measured was biologically congruent (1.3mm at 28 weeks of PMA to 1.8mm at term equivalent). Cortical thickness measured on T1 MRI using NEOCIVET 2.0 was compared with that on T2 using the established dHCP pipeline. It was difficult to conclude that either T1 or T2 imaging is more ideal to construct cortical surfaces. NEOCIVET 2.0 has been open to the public through CBRAIN (https://mcin-cnim.ca/technology/cbrain/), a web-based platform for processing brain imaging data.

bioinformatics↗