Recent QBI publications

  • Dysfunction in nonsense-mediated decay, protein homeostasis, mitochondrial function, and brain connectivity in ALS-FUS mice with cognitive deficits

    Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) represent two ends of the same disease spectrum of adult-onset neurodegenerative diseases that affect the motor and cognitive functions, respectively. Multiple common genetic loci such as fused in sarcoma (FUS) have been identified to play a role in ALS and FTD etiology. Current studies indicate that FUS mutations incur gain-of-toxic functions to drive ALS pathogenesis. However, how the disease-linked mutations of FUS affect cognition remains elusive. Using a mouse model expressing an ALS-linked human FUS mutation (R514G-FUS) that mimics endogenous expression patterns, we found that FUS proteins showed an age-dependent accumulation of FUS proteins despite the downregulation of mouse FUS mRNA by the R514G-FUS protein during aging. Furthermore, these mice developed cognitive deficits accompanied by a reduction in spine density and long-term potentiation (LTP) within the hippocampus. At the physiological expression level, mutant FUS is distributed in the nucleus and cytosol without apparent FUS aggregates or nuclear envelope defects. Unbiased transcriptomic analysis revealed a deregulation of genes that cluster in pathways involved in nonsense-mediated decay, protein homeostasis, and mitochondrial functions. Furthermore, the use of in vivo functional imaging demonstrated widespread reduction in cortical volumes but enhanced functional connectivity between hippocampus, basal ganglia and neocortex in R514G-FUS mice. Hence, our findings suggest that disease-linked mutation in FUS may lead to changes in proteostasis and mitochondrial dysfunction that in turn affect brain structure and connectivity resulting in cognitive deficits.
  • Modulatory effects of autophagy on app processing as a potential treatment target for Alzheimer’s disease

    Alzheimer’s disease (AD) is characterized by the formation of intracellular aggregate com-posed of heavily phosphorylated tau protein and extracellular deposit of amyloid-β (Aβ) plaques derived from proteolysis cleavage of amyloid precursor protein (APP). Autophagy refers to the lysosomal-mediated degradation of cytoplasmic constituents, which plays a critical role in maintaining cellular homeostasis. Importantly, recent studies reported that dysregulation of autophagy is associated in the pathogenesis of AD, and therefore, autophagy modulation has gained attention as a promising approach to treat AD pathogenesis. In AD, both the maturation of autolysosomes and its retrograde transports have been obstructed, which causes the accumulation of autophagic vacuoles and eventually leads to degenerating and dystrophic neurites function. However, the mechanism of autophagy modulation in APP processing and its pathogenesis have not yet been fully elucidated in AD. In the early stage of AD, APP processing and Aβ accumulation-mediated autophagy facilitate the removal of toxic protein aggregates via mTOR-dependent and-independent pathways. In addition, a number of autophagy-related genes (Atg) and APP are thought to influence the development of AD, providing a bidirectional link between autophagy and AD pathology. In this review, we summarized the current observations related to autophagy regulation and APP processing in AD, focusing on their modulation associated with the AD progression. Moreover, we emphasizes the application of small molecules and natural compounds to modulate autophagy for the removal and clearance of APP and Aβ deposits in the pathological condition of AD.
  • Identification of specific gene modules and candidate signatures in necrotizing enterocolitis disease: Networkbased gene co-expression approach

    Necrotizing enterocolitis (NEC) is a serious disease of the gastrointestinal systems that primarily affects premature newborns' intestine in neonatal intensive care units. The present study aimed to detect NEC molecular signatures and pathways from comprehensive bioinformatics analysis of NEC's RNA-seq transcriptomics. We performed systems biology analysis of RNA-seq transcriptomics data (with accession GSE64801) of NEC from nine NEC and five healthy controls. Differential expression of gene expression was performed using a combination of three R packages "DESeq2", "edgeR", “edger robust”. Gene co-expression analysis was performed using a weighted WGCNA package to identify gene modules, Gene Ontology (GO), pathway analysis, protein-protein interaction, gene-transcription factor, and gene-microRNA interaction analysis was performed. The differential expression analysis identified 966 differentially expressed genes (DEGs) in NEC from the RNA-seq dataset related to corresponding controls. The WGCNA showed the presence of three key gene modules. The GO analysis showed genes are enriched in metabolic processes, regulation of immune response and immune systems, cell communication, and cellular process. The immune and complement pathways are related to co-expressed key modules that were detected. The protein-protein interactions analysis showed the presence of key hub genes related to the modules. Integration of these co-expressed gene modules with regulatory networks showed the presence of significant key transcription factors and microRNAs as hub molecules. The present study's findings suggested the immune systems and complement cascade are key mechanisms of NEC pathogenesis. The comprehensive network analysis showed several key hub molecules that might be potential biomarkers and drug targets in NEC.
  • Cholinergic regulation of adult hippocampal neurogenesis and hippocampus-dependent functions

    The production and circuit integration of new neurons is one of the defining features of the adult mammalian hippocampus. A wealth of evidence has established that adult hippocampal neurogenesis is exquisitely sensitive to neuronal activity-mediated regulation. How these signals are interpreted and contribute to neurogenesis and hippocampal functions has been a subject of immense interest. In particular, neurotransmitters, in addition to their synaptic roles, have been shown to offer important trophic support. Amongst these, acetylcholine, which has a prominent role in cognition, has been implicated in regulating neurogenesis. In this review, we appraise the evidence linking the contribution of cholinergic signalling to the regulation of adult hippocampal neurogenesis and hippocampus-dependent functions. We discuss open questions that need to be addressed to gain a deeper mechanistic understanding of the role and translational potential of acetylcholine and its receptors in regulating this form of cellular neuroplasticity.
  • Bilateral visual projections exist in non-teleost bony fish and predate the emergence of tetrapods

    In most vertebrates, camera-style eyes contain retinal ganglion cell neurons that project to visual centers on both sides of the brain. However, in fish, ganglion cells were thought to innervate only the contralateral side, suggesting that bilateral visual projections appeared in tetrapods. Here we show that bilateral visual projections exist in non-teleost fishes and that the appearance of ipsilateral projections does not correlate with terrestrial transition or predatory behavior. We also report that the developmental program that specifies visual system laterality differs between fishes and mammals, as the Zic2 transcription factor, which specifies ipsilateral retinal ganglion cells in tetrapods, appears to be absent from fish ganglion cells. However, overexpression of human ZIC2 induces ipsilateral visual projections in zebrafish. Therefore, the existence of bilateral visual projections likely preceded the emergence of binocular vision in tetrapods.
  • De novo proteomic methods for examining the molecular mechanisms underpinning long-term memory

    Memory formation is a fundamental function of the nervous system that enables the experience-based adaptation of behaviour. The formation, recall and updating of long-term memory (LTM) requires new protein synthesis through its direct involvement in neuronal processes, such as long-term potentiation (LTP), long-term depression (LTD) and synaptic scaling. We discuss the advantages and limitations of several emerging techniques which enable the tagging of newly synthesised proteins, including stable isotope labelling with amino acids in cell culture (SILAC), puromycin labelling, and non-canonical amino acid (NCAA) labelling. We further present how these methods allow for the identification and visualisation of proteins which are newly synthesised during different stages of memory formation. These emerging techniques will continue to expand our understanding of how memories are formed, consolidated and retrieved.
  • Tau antibody isotype induces differential effects following passive immunisation of tau transgenic mice

    One of the main pathological hallmarks of Alzheimer's disease (AD) is the intraneuronal accumulation of hyperphosphorylated tau. Passive immunotherapy is a promising strategy for the treatment of AD and there are currently a number of tau-specific monoclonal antibodies in clinical trials. A proposed mechanism of action is to engage and clear extracellular, pathogenic forms of tau. This process has been shown in vitro to be facilitated by microglial phagocytosis through interactions between the antibody-tau complex and microglial Fc-receptors. As this interaction is mediated by the conformation of the antibody's Fc domain, this suggests that the antibody isotype may affect the microglial phagocytosis and clearance of tau, and hence, the overall efficacy of tau antibodies. We therefore aimed to directly compare the efficacy of the tau-specific antibody, RN2N, cloned into a murine IgG1/κ framework, which has low affinity Fc-receptor binding, to that cloned into a murine IgG2a/κ framework, which has high affinity Fc-receptor binding. Our results demonstrate, for RN2N, that although enhanced microglial activation via the IgG2a/κ isotype increased extracellular tau phagocytosis in vitro, the IgG1/κ isoform demonstrated enhanced ability to reduce tau pathology and microgliosis following passive immunisation of the P301L tau transgenic pR5 mouse model.
  • Association of antihypertensive drug target genes with psychiatric disorders: a Mendelian randomization study

    Observational studies have reported associations between antihypertensive medication and psychiatric disorders, although the reported direction of association appears to be dependent on drug class.

    To estimate the potential effect of different antihypertensive drug classes on schizophrenia, bipolar disorder, and major depressive disorder.

    This 2-sample mendelian randomization study assessed the association between a single-nucleotide variant (SNV) and drug target gene expression derived from existing expression quantitative trait loci (eQTL) data in blood (sample 1) and the SNV-disease association from published case-control genome-wide association studies (sample 2). Significant associations were corroborated using published brain eQTL and protein QTL data. Participants included 40 675 patients with schizophrenia and 64 643 controls, 20 352 patients with bipolar disorder and 31 358 controls, and 135 458 patients with major depressive disorder and 344 901 controls. Blood eQTL levels were measured in 31 684 individuals from 37 cohorts (eQTLGen consortium); prefrontal cortex eQTLs were measured from the PsychENCODE resource in 1387 individuals; and protein QTLs were measured in cerebral spinal fluid from 544 individuals and plasma from 818 individuals. Data were collected from October 4, 2019, to June 1, 2020, and analyzed from October 14, 2019, to June 6, 2020.

    Expression levels of antihypertensive drug target genes as proxies for drug exposure, and genetic variants robustly associated with the expression of these genes as mendelian randomization instruments.

    Risk for schizophrenia, bipolar disorder, and major depressive disorder.

    A 1-SD lower expression of the angiotensin-converting enzyme (ACE) gene in blood was associated with lower systolic blood pressure of 4.0 (95% CI, 2.7-5.3) mm Hg, but increased risk of schizophrenia (odds ratio [OR], 1.75; 95% CI, 1.28-2.38; P = 3.95 × 10-4). A concordant direction of association was also observed between ACE expression in prefrontal cortex (OR, 1.33; 95% CI, 1.13-1.56) and ACE protein levels in cerebral spinal fluid (OR per 1-SD decrease, 1.12; 95% CI, 1.05-1.19) and plasma (OR per 1-SD decrease, 1.04; 95% CI, 1.01-1.07). We found no evidence for an association between genetically estimated SBP and schizophrenia risk.

    Findings suggest an adverse association of lower ACE messenger RNA and protein levels with schizophrenia risk. These findings warrant greater pharmacovigilance and further investigation into the effect of ACE inhibitors, particularly those that are centrally acting, on psychiatric symptoms in patients with schizophrenia, as well as the role of ACE inhibitor use in late-onset schizophrenia.
  • A brief executive language screen for frontal aphasia

    Aphasia assessment tools have primarily focused on classical aphasia type and severity, with minimal incorporation of recent findings that suggest a significant role of executive control operations in language generation. Assessment of the interface between language and executive functions is needed to improve detection of spontaneous speech difficulties. In this study we develop a new Brief Executive Language Screen (BELS), a brief tool specifically designed to assess core language and executive functions shown to be involved in spontaneous generation of language. Similar to other measures of aphasia, the BELS assesses articulation and core language skills (repetition, naming and comprehension). Unique additions to the BELS include assessments of spontaneous connected speech, word fluency (phonemic/semantic) and sentence completion (verbal initiation, inhibition and selection). One‐hundred and eight healthy controls and 136 stroke patients were recruited. Confirmatory factor analysis was used to determine construct validity and logistic regression was used to evaluate the discriminative validity, informing the final version of the BELS. The results showed that the BELS is sensitive for articulation and nominal language deficits, and it measures executive aspects of spontaneous language generation, which is a hallmark of frontal dynamic aphasia. The results have encouraging theoretical and practical implications.
  • A unique C2 domain at the C terminus of Munc13 promotes synaptic vesicle priming

    Neurotransmitter release during synaptic transmission comprises a tightly orchestrated sequence of molecular events, and Munc13-1 is a cornerstone of the fusion machinery. A forward genetic screen for defects in neurotransmitter release in Caenorhabditis elegans identified a mutation in the Munc13-1 ortholog UNC-13 that eliminated its unique and deeply conserved C-terminal module (referred to as HC2M) containing a Ca-insensitive C2 domain flanked by membrane-binding helices. The HC2M module could be functionally replaced in vivo by protein domains that localize to synaptic vesicles but not to the plasma membrane. HC2M is broadly conserved in other Unc13 family members and is required for efficient synaptic vesicle priming. We propose that the HC2M domain evolved as a vesicle/endosome adaptor and acquired synaptic vesicle specificity in the Unc13ABC protein family.
  • New trajectory of clinical and biomarker changes in sporadic Alzheimer’s disease

    Identifying dynamic changes in biomarkers and clinical profiles is essential for understanding the progression of Alzheimer’s disease (AD). The relevant studies have primarily relied on patients with autosomal dominant AD; however, relevant studies in sporadic AD are poorly understood. Here, we analyzed longitudinal data from 665 participants (mean follow-up 4.90 ± 2.83 years). By aligning normal cognition (CN) baseline with a clinical diagnosis of mild cognitive impairment (MCI) or AD, we studied the progression of AD using a linear mixed model to estimate the clinical and biomarker changes from stable CN to MCI to AD. The results showed that the trajectory of hippocampal volume and fluorodeoxyglucose (FDG) was consistent with the clinical measures in that they did not follow a hypothetical sigmoid curve but rather showed a slow change in the initial stage and accelerated changes in the later stage from MCI conversion to AD. Dramatic hippocampal atrophy and the ADAS13 increase were, respectively, 2.5 and 1 years earlier than the MCI onset. Besides, cognitively normal people with elevated and normal amyloid showed no significant differences in clinical measures, hippocampal volume, or FDG. These results reveal that pre-MCI to pre-AD may be a better time window for future clinical trial design.
  • Broad frequency sensitivity and complex neural coding in the larval zebrafish auditory system

    Most animals have complex auditory systems that identify salient features of the acoustic landscape to direct appropriate responses. In fish, these features include the volume, frequency, complexity, and temporal structure of acoustic stimuli transmitted through water. Larval fish have simple brains compared to adults but swim freely and depend on sophisticated sensory processing for survival. Zebrafish larvae, an important model for studying brain-wide neural networks, have thus far been found to possess a rudimentary auditory system, sensitive to a narrow range of frequencies and without evident sensitivity to acoustic features that are salient and ethologically important to adult fish. Here, we have combined a novel method for delivering water-borne sounds, a diverse assembly of acoustic stimuli, and whole-brain calcium imaging to describe the responses of individual auditory-responsive neurons across the brains of zebrafish larvae. Our results reveal responses to frequencies ranging from 100 Hz to 4 kHz, with evidence of frequency discrimination from 100 Hz to 2.5 kHz. Frequency-selective neurons are located in numerous regions of the brain, and neurons responsive to the same frequency are spatially grouped in some regions. Using functional clustering, we identified categories of neurons that are selective for a single pure-tone frequency, white noise, the sharp onset of acoustic stimuli, and stimuli involving a gradual crescendo. These results suggest a more nuanced auditory system than has previously been described in larval fish and provide insights into how a young animal's auditory system can both function acutely and serve as the scaffold for a more complex adult system.
  • Co‐morbidity between mood and anxiety disorders: A systematic review and meta‐analysis

    There is consistent evidence that mood disorders often co-occur with anxiety disorders, however, the strength of the association of these two broad groups of disorders has been challenging to summarize across different studies. The aim was to conduct a meta-analysis of publications reporting on the pairwise comorbidity between mood and anxiety disorders after sorting into comparable study types. We searched MEDLINE, Embase, CINAHL, Web of Science, and the grey literature for publications between 1980 and 2017 regardless of geographical locations and languages. We meta-analyzed estimates from original articles after sorting by: (a) broad or narrow diagnostic criteria, (b) study time-frame, and (c) estimates with or without covariate adjustments. Over 43 000 unique studies were identified through electronic searches, of which 391 were selected for full-text review. Finally, 171 studies were eligible for inclusion, including 53 articles from additional snowball searching. In general, regardless of variations in diagnosis type, study time-frame, temporal order, or use of adjustments, there was substantial comorbidity between mood and anxiety disorders. Based on the entire 90 separate meta-analyses, the median OR was 6.1 (range 1.5-18.7). Of these estimates, all 90 were above 1, and 87 were significantly greater than 1 (i.e., the 95% confidence intervals did not include 1). Fourteen of the 90 pooled estimates had ORs that were greater than 10. This systematic review found robust and consistent evidence of comorbidity between broadly defined mood and anxiety disorders. Clinicians should be vigilant for the prompt identification and treatment of this common type of comorbidity.
  • Positive symptom phenotypes appear progressively in “EDiPS”, a new animal model of the schizophrenia prodrome

    An increase in dopamine (DA) synthesis capacity in the dorsal striatum (DS) during the prodromal stage of schizophrenia becomes more pronounced as patients progress to the full disorder. Understanding this progression is critical to intervening in disease course. We developed an animal model—Enhanced Dopamine in Prodromal Schizophrenia (EDiPS)—which uses a genetic construct to increase DA synthesis capacity in the DS of male rats. We assessed pre-pulse inhibition (PPI) and amphetamine (AMPH)-induced locomotion (0.6 mg/kg) in EDiPS animals longitudinally after post-natal day 35 (when the EDiPS construct is administered). We also assessed their response to repeated acute restraint stress. In adult EDiPS animals, we measured baseline and evoked extracellular DA levels, and their stereotyped responses to 5 mg/kg AMPH. AMPH-induced hyperlocomotion was apparent in EDiPS animals 6-weeks after construct administration. There was an overall PPI deficit in EDiPS animals across all timepoints, however the stress response of EDiPS animals was unaltered. Adult EDiPS animals show normal baseline and potassium-evoked DA release in the DS. These findings suggest that key behavioural phenotypes in EDiPS animals show a progressive onset, similar to that demonstrated by patients as they transition to schizophrenia. The EDiPS model could therefore be used to investigate the molecular mechanisms underlying the prodrome of schizophrenia.
  • L-lactate exerts a pro-proliferative effect on adult hippocampal precursor cells in vitro

    L-lactate has energetic and signaling properties and its availability is modulated by activitydependent stimuli, which also regulate adult hippocampal neurogenesis. Studying the effects of L-lactate on neural precursor cells (NPCs) in vitro, we found that L-lactate is proproliferative and that this effect is dependent on the active lactate transport by monocarboxylate transporters. Increased proliferation was not linked to amplified mitochondrial respiration. Instead, L-lactate deviated glucose metabolism to the pentose phosphate pathway, indicated by increased glucose-6-phosphate dehydrogenase activity while glycolysis decreased. Knockout of Hcar1 revealed that the pro-proliferative effect of Llactate was not dependent on receptor activity although phosphorylation of ERK1/2 and Akt was increased following L-lactate treatment. Together, we show that availability of L-lactate is linked to the proliferative potential of NPCs and add evidence to the hypothesis that lactate influences cellular homeostatic processes in the adult brain, specifically in the context of adult hippocampal neurogenesis.
  • GWAS of peptic ulcer disease implicates Helicobacter pylori infection, other gastrointestinal disorders and depression

    Genetic factors are recognized to contribute to peptic ulcer disease (PUD) and other gastrointestinal diseases, such as gastro-oesophageal reflux disease (GORD), irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Here, genome-wide association study (GWAS) analyses based on 456,327 UK Biobank (UKB) individuals identify 8 independent and significant loci for PUD at, or near, genes MUC1, MUC6, FUT2, PSCA, ABO, CDX2, GAST and CCKBR. There are previously established roles in susceptibility to Helicobacter pylori infection, response to counteract infection-related damage, gastric acid secretion or gastrointestinal motility for these genes. Only two associations have been previously reported for duodenal ulcer, here replicated trans-ancestrally. The results highlight the role of host genetic susceptibility to infection. Post-GWAS analyses for PUD, GORD, IBS and IBD add insights into relationships between these gastrointestinal diseases and their relationships with depression, a commonly comorbid disorder.
  • Widespread signatures of natural selection across human complex traits and functional genomic categories

    Understanding how natural selection has shaped genetic architecture of complex traits is of importance in medical and evolutionary genetics. Bayesian methods have been developed using individual-level GWAS data to estimate multiple genetic architecture parameters including selection signature. Here, we present a method (SBayesS) that only requires GWAS summary statistics. We analyse data for 155 complex traits (n = 27k–547k) and project the estimates onto those obtained from evolutionary simulations. We estimate that, on average across traits, about 1% of human genome sequence are mutational targets with a mean selection coefficient of ~0.001. Common diseases, on average, show a smaller number of mutational targets and have been under stronger selection, compared to other traits. SBayesS analyses incorporating functional annotations reveal that selection signatures vary across genomic regions, among which coding regions have the strongest selection signature and are enriched for both the number of associated variants and the magnitude of effect sizes.
  • Phenotypic covariance across the entire spectrum of relatedness for 86 billion pairs of individuals

    Attributing the similarity between individuals to genetic and non-genetic factors is central to genetic analyses. In this paper we use the genomic relationship (ππ) among 417,060 individuals to investigate the phenotypic covariance between pairs of individuals for 32 traits across the spectrum of relatedness, from unrelated pairs through to identical twins. We find linear relationships between phenotypic covariance and ππ that agree with the SNP-based heritability (h^2SNPh^SNP2) in unrelated pairs (π<0.02π<0.02), and with pedigree-estimated heritability in close relatives (π>0.05π>0.05). The covariance increases faster than πh^2SNPπh^SNP2 in distant relatives (0.02>π>0.050.02>π>0.05), and we attribute this to imperfect linkage disequilibrium between causal variants and the common variants used to construct ππ. We also examine the effect of assortative mating on heritability estimates from different experimental designs. We find that full-sib identity-by-descent regression estimates for height (0.66 s.e. 0.07) are consistent with estimates from close relatives (0.82 s.e. 0.04) after accounting for the effect of assortative mating.
  • Inflammatory mechanisms in Parkinson’s disease: from pathogenesis to targeted therapies

    Inflammation is a critical factor contributing to the progressive neurodegenerative process observed in Parkinson's disease (PD). Microglia, the immune cells of the central nervous system, are activated early in PD pathogenesis and can both trigger and propagate early disease processes via innate and adaptive immune mechanisms such as upregulated immune cells and antibody-mediated inflammation. Downstream cytokines and gene regulators such as microRNA (miRNA) coordinate later disease course and mediate disease progression. Biomarkers signifying the inflammatory and neurodegenerative processes at play within the central nervous system are of increasing interest to clinical teams. To be effective, such biomarkers must achieve the highest sensitivity and specificity for predicting PD risk, confirming diagnosis, or monitoring disease severity. The aim of this review was to summarize the current preclinical and clinical evidence that suggests that inflammatory processes contribute to the initiation and progression of neurodegenerative processes in PD. In this article, we further summarize the data about main inflammatory biomarkers described in PD to date and their potential for regulation as a novel target for disease-modifying pharmacological strategies.
  • A systematic review of apathy and depression in progressive supranuclear palsy

    Depression and apathy can be significant problems in progressive supranuclear palsy (PSP). Using PRISMA guidelines, this systematic review examined prevalence estimates for depression and apathy in PSP, and, how different methods of definition may influence results. 29 studies meeting inclusion/exclusion criteria were identified: 12 on depression, 9 on apathy, and 8 on both. Studies were stratified according to whether a diagnostic criteria, rating scale or screening question methodology was employed. The weighted mean prevalence was 59.7% for depression (sample size = 473) and 58.3% for apathy (sample size = 858). Results for depression using diagnostic criteria or rating scales were similar whereas screening questions were associated with considerable inconsistency. Depression prevalence appeared to be influenced by apathy but not somatic symptoms. Most apathy studies relied only on a screening question method. Depression and apathy are common in PSP but there is a need for consensus on how they are defined (both tools and cut-off scores). In particular, more studies probing apathy in greater detail than a simple screening question are required.
  • A novel dual Ca2+ sensor system regulates Ca2+-dependent neurotransmitter release

    Ca2+-dependent neurotransmitter release requires synaptotagmins as Ca2+ sensors to trigger synaptic vesicle (SV) exocytosis via binding of their tandem C2 domains-C2A and C2B-to Ca2+. We have previously demonstrated that SNT-1, a mouse synaptotagmin-1 (Syt1) homologue, functions as the fast Ca2+ sensor in Caenorhabditis elegans. Here, we report a new Ca2+ sensor, SNT-3, which triggers delayed Ca2+-dependent neurotransmitter release. snt-1;snt-3 double mutants abolish evoked synaptic transmission, demonstrating that C. elegans NMJs use a dual Ca2+ sensor system. SNT-3 possesses canonical aspartate residues in both C2 domains, but lacks an N-terminal transmembrane (TM) domain. Biochemical evidence demonstrates that SNT-3 binds both Ca2+ and the plasma membrane. Functional analysis shows that SNT-3 is activated when SNT-1 function is impaired, triggering SV release that is loosely coupled to Ca2+ entry. Compared with SNT-1, which is tethered to SVs, SNT-3 is not associated with SV. Eliminating the SV tethering of SNT-1 by removing the TM domain or the whole N terminus rescues fast release kinetics, demonstrating that cytoplasmic SNT-1 is still functional and triggers fast neurotransmitter release, but also exhibits decreased evoked amplitude and release probability. These results suggest that the fast and slow properties of SV release are determined by the intrinsically different C2 domains in SNT-1 and SNT-3, rather than their N-termini-mediated membrane tethering. Our findings therefore reveal a novel dual Ca2+ sensor system in C. elegans and provide significant insights into Ca2+-regulated exocytosis.
  • Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

    Autism spectrum disorder (ASD) is a complex neurodevelopmental condition whose biological basis is yet to be elucidated. The Australian Autism Biobank (AAB) is an initiative of the Cooperative Research Centre for Living with Autism (Autism CRC) to establish an Australian resource of biospecimens, phenotypes and genomic data for research on autism.

    Genome-wide single-nucleotide polymorphism genotypes were available for 2,477 individuals (after quality control) from 546 families (436 complete), including 886 participants aged 2 to 17 years with diagnosed (n = 871) or suspected (n = 15) ASD, 218 siblings without ASD, 1,256 parents, and 117 unrelated children without an ASD diagnosis. The genetic data were used to confirm familial relationships and assign ancestry, which was majority European (n = 1,964 European individuals). We generated polygenic scores (PGS) for ASD, IQ, chronotype and height in the subset of Europeans, and in 3,490 unrelated ancestry-matched participants from the UK Biobank. We tested for group differences for each PGS, and performed prediction analyses for related phenotypes in the AAB. We called copy-number variants (CNVs) in all participants, and intersected these with high-confidence ASD- and intellectual disability (ID)-associated CNVs and genes from the public domain.

    The ASD (p = 6.1e-13), sibling (p = 4.9e-3) and unrelated (p = 3.0e-3) groups had significantly higher ASD PGS than UK Biobank controls, whereas this was not the case for height-a control trait. The IQ PGS was a significant predictor of measured IQ in undiagnosed children (r = 0.24, p = 2.1e-3) and parents (r = 0.17, p = 8.0e-7; 4.0% of variance), but not the ASD group. Chronotype PGS predicted sleep disturbances within the ASD group (r = 0.13, p = 1.9e-3; 1.3% of variance). In the CNV analysis, we identified 13 individuals with CNVs overlapping ASD/ID-associated CNVs, and 12 with CNVs overlapping ASD/ID/developmental delay-associated genes identified on the basis of de novo variants.

    This dataset is modest in size, and the publicly-available genome-wide-association-study (GWAS) summary statistics used to calculate PGS for ASD and other traits are relatively underpowered.

    We report on common genetic variation and rare CNVs within the AAB. Prediction analyses using currently available GWAS summary statistics are largely consistent with expected relationships based on published studies. As the size of publicly-available GWAS summary statistics grows, the phenotypic depth of the AAB dataset will provide many opportunities for analyses of autism profiles and co-occurring conditions, including when integrated with other omics datasets generated from AAB biospecimens (blood, urine, stool, hair).
  • Preventing brain injury in the preterm infant — current controversies and potential therapies

    Preterm birth is associated with a high risk of morbidity and mortality including brain damage and cerebral palsy. The development of brain injury in the preterm infant may be influenced by many factors including perinatal asphyxia, infection/inflammation, chronic hypoxia and exposure to treatments such as mechanical ventilation and corticosteroids. There are currently very limited treatment options available. In clinical trials, magnesium sulfate has been associated with a small, significant reduction in the risk of cerebral palsy and gross motor dysfunction in early childhood but no effect on the combined outcome of death or disability, and longer-term follow up to date has not shown improved neurological outcomes in school-age children. Recombinant erythropoietin has shown neuroprotective potential in preclinical studies but two large randomized trials, in extremely preterm infants, of treatment started within 24 or 48 h of birth showed no effect on the risk of severe neurodevelopmental impairment or death at 2 years of age. Preclinical studies have highlighted a number of promising neuroprotective treatments, such as therapeutic hypothermia, melatonin, human amnion epithelial cells, umbilical cord blood and vitamin D supplementation, which may be useful at reducing brain damage in preterm infants. Moreover, refinements of clinical care of preterm infants have the potential to influence later neurological outcomes, including the administration of antenatal and postnatal corticosteroids and more accurate identification and targeted treatment of seizures.
  • The influence of tDCS intensity on decision-making training and transfer outcomes

    Transcranial direct current stimulation (tDCS) has been shown to improve single- and dual-task performance in healthy participants and enhance transferable training gains following multiple sessions of combined stimulation and task practice. However, it has yet to be determined what the optimal stimulation dose is for facilitating such outcomes. We aimed to test the effects of different tDCS intensities, with a commonly used electrode montage, on performance outcomes in a multisession single/dual-task training and transfer protocol. In a preregistered study, 123 participants, who were pseudorandomized across four groups, each completed six sessions (pre- and posttraining sessions and four combined tDCS and training sessions) and received 20 min of prefrontal anodal tDCS at 0.7, 1.0, or 2.0 mA or 15-s sham stimulation. Response time and accuracy were assessed in trained and untrained tasks. The 1.0-mA group showed substantial improvements in single-task reaction time and dual-task accuracy, with additional evidence for improvements in dual-task reaction times, relative to sham performance. This group also showed near transfer to the single-task component of an untrained multitasking paradigm. The 0.7- and 2.0-mA intensities varied in which performance measures they improved on the trained task, but in sum, the effects were less robust than for the 1.0-mA group, and there was no evidence for the transfer of performance. Our study highlights that training performance gains are augmented by tDCS, but their magnitude and nature are not uniform across stimulation intensity. Using techniques such as transcranial direct current stimulation to modulate cognitive performance is an alluring endeavor. However, the optimal parameters to augment performance are unknown. Here, in a preregistered study with a large sample (123 subjects), three different stimulation dosages (0.7, 1.0, and 2.0 mA) were applied during multitasking training. Different cognitive training performance outcomes occurred across the dosage conditions, with only one of the doses (1.0 mA) leading to training transfer.
  • The NLRP3 inflammasome triggers sterile neuroinflammation and Alzheimer’s disease

    To maintain homeostasis, an organism must detect and resolve sterile tissue damage. The NLRP3 inflammasome coordinates such processes to clear tissue damage and induce repair. Dysregulated NLRP3 inflammasome activity, however, drives many conditions including Alzheimer's disease (AD). Recent reports posit that β-amyloid and tau aggregates trigger destructive NLRP3 inflammasome signalling in the brain, leading to AD pathophysiology and cognitive decline. Other endogenous molecules (e.g. TNF, ATP, serum amyloid A), as well as dysbiosis, can induce peripheral or central inflammation and thereby promote microglial NLRP3 inflammasome signalling and resultant AD. The NLRP3 inflammasome is thus emerging as a critical driver of sterile neuroinflammation and the resultant pathogenesis and progression of AD.
  • A salience misattribution model for addictive-like behaviors

    Adapting to the changing environment is a key component of optimal decision-making. Internal-models that accurately represent and selectively update from behaviorally relevant/salient stimuli may facilitate adaptive behaviors. Anterior cingulate cortex (ACC) and dopaminergic systems may produce these adaptive internal-models through selective updates from behaviorally relevant stimuli. Dysfunction of ACC and dopaminergic systems could therefore produce misaligned internal-models where updates are disproportionate to the salience of the cues. An aspect of addictive-like behaviors is reduced adaptation and, ACC and dopaminergic systems typically exhibit dysfunction in drug-dependents. We argue that ACC and dopaminergic dysfunction in dependents may produce misaligned internal-models such that drug-related stimuli are misattributed with a higher salience compared to non-drug related stimuli. Hence, drug-related rewarding stimuli generate over-weighted updates to the internal-model, while negative feedback and non-drug related rewarding stimuli generate down-weighted updates. This misaligned internal-model may therefore incorrectly reinforce maladaptive drug-related behaviors. We use the proposed framework to discuss ways behavior may be made more adaptive and how the framework may be supported or falsified experimentally.
  • Identification of common pathogenetic processes between schizophrenia and diabetes mellitus by systems biology analysis

    Schizophrenia (SCZ) is a psychiatric disorder characterized by both positive symptoms (i.e., psychosis) and negative symptoms (such as apathy, anhedonia, and poverty of speech). Epidemi-ological data show a high likelihood of early onset of type 2 diabetes mellitus (T2DM) in SCZ patients. However, the molecular processes that could explain the epidemiological association between SCZ and T2DM have not yet been characterized. Therefore, in the present study, we aimed to identify underlying common molecular pathogenetic processes and pathways between SCZ and T2DM. To this aim, we analyzed peripheral blood mononuclear cell (PBMC) transcriptomic data from SCZ and T2DM patients, and we detected 28 differentially expressed genes (DEGs) commonly modulated between SCZ and T2DM. Inflammatory-associated processes and membrane trafficking pathways as common biological processes were found to be in common between SCZ and T2DM. Analysis of the putative transcription factors involved in the regulation of the DEGs revealed that STAT1 (Signal Transducer and Activator of Transcription 1), RELA (v-rel reticuloendotheliosis viral oncogene homolog A (avian)), NFKB1 (Nuclear Factor Kappa B Subunit 1), and ERG (ETS-related gene) are involved in the expression of common DEGs in SCZ and T2DM. In conclusion, we provide core molecular signatures and pathways that are shared between SCZ and T2DM, which may contribute to the epidemiological association between them.
  • Endocannabinoid reactivity to acute stress: investigation of the relationship between salivary and plasma levels

    The endogenous cannabinoid (eCB) system has been shown in animal models to regulate the initiation and termination of central nervous responses to stress. In human studies, the role of peripherally measured eCBs is much less clear and the effect in salivary eCBs has not been studied. In this study, we use a novel method to quantify cortisol and eCBs arachidonoyl ethanolamide (AEA) and 2-arachidonoyl glycerol (2-AG) in human saliva, as well as in plasma samples. Forty-five females and 32 males completed a mixed physiological/psychosocial stress-induction study where saliva, and blood samples in males, were collected at baseline, immediately following, 30-minutes following, and 45-minutes following stress induction. Cortisol significantly increased after stress, but there were sex differences in the cortisol response to stress, with females having higher cortisol after stress compared to males. There was a significant increase in salivary levels of 2-AG immediately following stress induction, but no effect of AEA. Salivary AEA was higher in males compared to females. Surprisingly, there was no effect of stress on plasma AEA or 2-AG levels in the male cohort, though small effect sizes for 2-AG were observed, which is consistent with most other human literature. This study is the first to show that the eCB system is active in human saliva and is responsive to acute stress, possibly as part of the sympathetic nervous system response.
  • 16Up: Outline of a study investigating wellbeing and information and communication technology use in adolescent twins

    The '16Up' study conducted at the QIMR Berghofer Medical Research Institute from January 2014 to December 2018 aimed to examine the physical and mental health of young Australian twins aged 16-18 years (N = 876; 371 twin pairs and 18 triplet sets). Measurements included online questionnaires covering physical and mental health as well as information and communication technology (ICT) use, actigraphy, sleep diaries and hair samples to determine cortisol concentrations. Study participants generally rated themselves as being in good physical (79%) and mental (73%) health and reported lower rates of psychological distress and exposure to alcohol, tobacco products or other substances than previously reported for this age group in the Australian population. Daily or near-daily online activity was almost universal among study participants, with no differences noted between males and females in terms of frequency or duration of internet access. Patterns of ICT use in this sample indicated that the respondents were more likely to use online information sources for researching physical health issues than for mental health or substance use issues, and that they generally reported partial levels of satisfaction with the mental health information they found online. This suggests that internet-based mental health resources can be readily accessed by adolescent Australians, and their computer literacy augurs well for future access to online health resources. In combination with other data collected as part of the ongoing Brisbane Longitudinal Twin Study, the 16Up project provides a valuable resource for the longitudinal investigation of genetic and environmental contributions to phenotypic variation in a variety of human traits.
  • Vitamin D and schizophrenia: 20 years on

    Many epidemiological studies have highlighted the link between vitamin D deficiency and schizophrenia. In particular, two prominent studies report an association between neonatal vitamin D deficiency and an increased risk of schizophrenia. In parallel, much has been learnt about the role of vitamin D in the developing central nervous system over the last two decades. Studies in rodent models of developmental vitamin D (DVD)-deficiency describe how brain development is altered leading to a range of neurobiological and behavioral phenotypes of interest to schizophrenia. While glutamate and gamma aminobutyric acid (GABA) systems have been little investigated in these models, alterations in developing dopamine systems are frequently reported. There have been far more studies reporting patients with schizophrenia have an increased risk of vitamin D deficiency compared to well controls. Here we have conducted a systematic review and meta-analysis that basically confirms this association and extends this to first-episode psychosis. However, patients with schizophrenia also have poorer general health, poorer diets, are frequently less active and also have an increased risk of other medical conditions, all factors which reduce circulating vitamin D levels. Therefore, we would urge caution in any causal interpretation of this association. We also summarize the inconsistent results from existing vitamin D supplementation trials in patients with schizophrenia. In respect to animal models of adult vitamin D deficiency, such exposures produce subtle neurochemical alterations and effects on cognition but do not appear to produce behavioral phenotypes of relevance to schizophrenia. We conclude, the hypothesis that vitamin D deficiency during early life may increase the risk of schizophrenia remains plausible and warrants ongoing research.
  • Caveolin-1 and cavin1 act synergistically to generate a unique lipid environment in caveolae

    Caveolae are specialized domains of the vertebrate cell surface with a well-defined morphology and crucial roles in cell migration and mechanoprotection. Unique compositions of proteins and lipids determine membrane architectures. The precise caveolar lipid profile and the roles of the major caveolar structural proteins, caveolins and cavins, in selectively sorting lipids have not been defined. Here, we used quantitative nanoscale lipid mapping together with molecular dynamic simulations to define the caveolar lipid profile. We show that caveolin-1 (CAV1) and cavin1 individually sort distinct plasma membrane lipids. Intact caveolar structures composed of both CAV1 and cavin1 further generate a unique lipid nano-environment. The caveolar lipid sorting capability includes selectivities for lipid headgroups and acyl chains. Because lipid headgroup metabolism and acyl chain remodeling are tightly regulated, this selective lipid sorting may allow caveolae to act as transit hubs to direct communications among lipid metabolism, vesicular trafficking, and signaling.
  • A 5‐channel LED display to investigate UV perception

    The ability to see ultraviolet (UV) light (<400 nm) may have importance for foraging, communication or navigation in many taxa including insects, crustaceans, fishes, amphibians, reptiles, birds and mammals. Behavioural experiments reveal how vision mediates such behaviour; however, our knowledge of UV perception is constrained by the challenge of creating and calibrating stimuli that reflect or emit UV. Commonly used technologies for displaying visual stimuli-such as computer screens and printers-are designed for human vision and thus are unsuitable for testing UV perception.To overcome this limitation, we designed and constructed a display with five spectral channels with peak wavelengths as follows: red at 629 nm, green at 526 nm, blue at 466 nm, violet at 395 nm and UV at 367 nm. Each pixel of the display consists of five LEDs with a baffle to prevent crosstalk from adjacent pixels and a diffuser to promote uniform colour mixing. The LEDs are driven by high-performance pulse-width-modulated constant-current drivers with a maximum flicker rate of 64 kHz and a maximum frame rate of 6.5 kHz. This method allows colour mixing with wavelengths as low as 350 nm to be calibrated and tested rapidly and concurrently.To demonstrate the utility of this display, we conducted colour detection tests using the anemonefish, Amphiprion ocellaris, a species known to have UV-sensitive cones. Fish were able to associate pecking all target colours ('Blue', 'UV-grey' and 'UV') with a food reward, demonstrating for the first time, UV perception in A. ocellaris.The RGB-V-UV LED display is a useful device for behavioural tests of colour vision across a broad spectrum (350-650 nm) visible to many animals and can be used to investigate various questions concerning animal perception, including colour discrimination and categorisation. We include design documents and source code so this system can be further developed and modified to investigate other visual behaviours in a variety of taxa.
  • From circuits to chromatin: the emerging role of epigenetics in mental health

    A central goal of neuroscience research is to understand how experiences modify brain circuits to guide future adaptive behavior. In response to environmental stimuli, neural circuit activity engages gene regulatory mechanisms within each cell. This activity-dependent gene expression is governed, in part, by epigenetic processes that can produce persistent changes in both neural circuits and the epigenome itself. The complex interplay between circuit activity and neuronal gene regulation is vital to learning and memory, and, when disrupted, is linked to debilitating psychiatric conditions, such as substance use disorder. To develop clinical treatments, it is paramount to advance our understanding of how neural circuits and the epigenome cooperate to produce behavioral adaptation. Here, we discuss how new genetic tools, used to manipulate neural circuits and chromatin, have enabled the discovery of epigenetic processes that bring about long-lasting changes in behavior relevant to mental health and disease.
  • Exosomes induce endolysosomal permeabilization as a gateway by which exosomal tau seeds escape into the cytosol

    The microtubule-associated protein tau has a critical role in Alzheimer’s disease and other tauopathies. A proposed pathomechanism in the progression of tauopathies is the trans-synaptic spreading of tau seeds, with a role for exosomes which are secretory nanovesicles generated by late endosomes. Our previous work demonstrated that brain-derived exosomes isolated from tau transgenic rTg4510 mice encapsulate tau seeds with the ability to induce tau aggregation in recipient cells. We had also shown that exosomes can hijack the endosomal pathway to spread through interconnected neurons. Here, we reveal how tau seeds contained within internalized exosomes exploit mechanisms of lysosomal degradation to escape the endosome and induce tau aggregation in the cytosol of HEK293T-derived ‘tau biosensor cells’. We found that the majority of the exosome-containing endosomes fused with lysosomes to form endolysosomes. Exosomes induced their permeabilization, irrespective of the presence of tau seeds, or whether the exosomal preparations originated from mouse brains or HEK293T cells. We also found that permeabilization is a conserved mechanism, operating in both non-neuronal tau biosensor cells and primary neurons. However, permeabilization of endolysosomes only occurred in a small fraction of cells, which supports the notion that permeabilization occurs by a thresholded mechanism. Interestingly, tau aggregation was only induced in cells that exhibited permeabilization, presenting this as an escape route of exosomal tau seeds into the cytosol. Overexpression of RAB7, which is required for the formation of endolysosomes, strongly increased tau aggregation. Conversely, inhibition of lysosomal function with alkalinizing agents, or by knocking-down RAB7, decreased tau aggregation. Together, we conclude that the enzymatic activities of lysosomes permeabilize exosomal and endosomal membranes, thereby facilitating access of exosomal tau seeds to cytosolic tau to induce its aggregation. Our data underscore the importance of endosomal membrane integrity in mechanisms of cellular invasion by misfolded proteins that are resistant to lysosomal degradation.
  • Genome-wide analyses of behavioural traits are subject to bias by misreports and longitudinal changes

    Genome-wide association studies (GWAS) have discovered numerous genetic variants associated with human behavioural traits. However, behavioural traits are subject to misreports and longitudinal changes (MLC) which can cause biases in GWAS and follow-up analyses. Here, we demonstrate that individuals with higher disease burden in the UK Biobank (n = 455,607) are more likely to misreport or reduce their alcohol consumption levels, and propose a correction procedure to mitigate the MLC-induced biases. The alcohol consumption GWAS signals removed by the MLC corrections are enriched in metabolic/cardiovascular traits. Almost all the previously reported negative estimates of genetic correlations between alcohol consumption and common diseases become positive/non-significant after the MLC corrections. We also observe MLC biases for smoking and physical activities in the UK Biobank. Our findings provide a plausible explanation of the controversy about the effects of alcohol consumption on health outcomes and a caution for future analyses of self-reported behavioural traits in biobank data.
  • Stronger top-down and weaker bottom-up frontotemporal connections during sensory learning are associated with severity of psychotic phenomena

    Recent theories in computational psychiatry propose that unusual perceptual experiences and delusional beliefs may emerge as a consequence of aberrant inference and disruptions in sensory learning. The current study investigates these theories and examines the alterations that are specific to schizophrenia spectrum disorders vs those that occur as psychotic phenomena intensify, regardless of diagnosis. We recruited 66 participants: 22 schizophrenia spectrum inpatients, 22 nonpsychotic inpatients, and 22 nonclinical controls. Participants completed the reversal oddball task with volatility manipulated. We recorded neural responses with electroencephalography and measured behavioral errors to inferences on sound probabilities. Furthermore, we explored neural dynamics using dynamic causal modeling (DCM). Attenuated prediction errors (PEs) were specifically observed in the schizophrenia spectrum, with reductions in mismatch negativity in stable, and P300 in volatile, contexts. Conversely, aberrations in connectivity were observed across all participants as psychotic phenomena increased. DCM revealed that impaired sensory learning behavior was associated with decreased intrinsic connectivity in the left primary auditory cortex and right inferior frontal gyrus (IFG); connectivity in the latter was also reduced with greater severity of psychotic experiences. Moreover, people who experienced more hallucinations and psychotic-like symptoms had decreased bottom-up and increased top-down frontotemporal connectivity, respectively. The findings provide evidence that reduced PEs are specific to the schizophrenia spectrum, but deficits in brain connectivity are aligned on the psychosis continuum. Along the continuum, psychotic experiences were related to an aberrant interplay between top-down, bottom-up, and intrinsic connectivity in the IFG during sensory uncertainty. These findings provide novel insights into psychosis neurocomputational pathophysiology.
  • Calcium imaging and the curse of negativity

    The imaging of neuronal activity using calcium indicators has become a staple of modern neuroscience. However, without ground truths, there is a real risk of missing a significant portion of the real responses. Here, we show that a common assumption, the non-negativity of the neuronal responses as detected by calcium indicators, biases all levels of the frequently used analytical methods for these data. From the extraction of meaningful fluorescence changes to spike inference and the analysis of inferred spikes, each step risks missing real responses because of the assumption of non-negativity. We first show that negative deviations from baseline can exist in calcium imaging of neuronal activity. Then, we use simulated data to test three popular algorithms for image analysis, CaImAn, suite2p, and CellSort, finding that suite2p may be the best suited to large datasets. We also tested the spike inference algorithms included in CaImAn, suite2p, and Cellsort, as well as the dedicated inference algorithms MLspike and CASCADE, and found each to have limitations in dealing with inhibited neurons. Among these spike inference algorithms, FOOPSI, from CaImAn, performed the best on inhibited neurons, but even this algorithm inferred spurious spikes upon the return of the fluorescence signal to baseline. As such, new approaches will be needed before spikes can be sensitively and accurately inferred from calcium data in inhibited neurons. We further suggest avoiding data analysis approaches that, by assuming non-negativity, ignore inhibited responses. Instead, we suggest a first exploratory step, using k-means or PCA for example, to detect whether meaningful negative deviations are present. Taking these steps will ensure that inhibition, as well as excitation, is detected in calcium imaging datasets.
  • A roadmap of brain recovery in a mouse model of concussion: insights from neuroimaging

    Concussion or mild traumatic brain injury is the most common form of traumatic brain injury with potentially long-term consequences. Current objective diagnosis and treatment options are limited to clinical assessment, cognitive rest, and symptom management, which raises the real danger of concussed patients being released back into activities where subsequent and cumulative injuries may cause disproportionate damages. This study conducted a cross-sectional multi-modal examination investigation of the temporal changes in behavioural and brain changes in a mouse model of concussion using magnetic resonance imaging. Sham and concussed mice were assessed at day 2, day 7, and day 14 post-sham or injury procedures following a single concussion event for motor deficits, psychological symptoms with open field assessment, T2-weighted structural imaging, diffusion tensor imaging (DTI), neurite orientation density dispersion imaging (NODDI), stimulus-evoked and resting-state functional magnetic resonance imaging (fMRI). Overall, a mismatch in the temporal onsets and durations of the behavioural symptoms and structural/functional changes in the brain was seen. Deficits in behaviour persisted until day 7 post-concussion but recovered at day 14 post-concussion. DTI and NODDI changes were most extensive at day 7 and persisted in some regions at day 14 post-concussion. A persistent increase in connectivity was seen at day 2 and day 14 on rsfMRI. Stimulus-invoked fMRI detected increased cortical activation at day 7 and 14 post-concussion. Our results demonstrate the capabilities of advanced MRI in detecting the effects of a single concussive impact in the brain, and highlight a mismatch in the onset and temporal evolution of behaviour, structure, and function after a concussion. These results have significant translational impact in developing methods for the detection of human concussion and the time course of brain recovery.
  • Chemical synthesis and characterisation of the complement C5 inhibitory peptide zilucoplan

    The complement component C5 inhibitory peptide zilucoplan is currently in phase III clinical trials for myasthenia gravis (MG). Despite being at an advanced stage of clinical development, there have been no published reports in the literature detailing its chemical synthesis. In this work, we describe an approach for the chemical synthesis of zilucoplan and validate that the synthesised compound blocks LPS-induced C5a production from human blood.
  • On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain

    The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic regulation of protein-coding gene expression, recent findings indicate that activity-induced lncRNAs also regulate neural plasticity. In this review, we discuss how lncRNAs may exert molecular control over brain function beyond their known roles in the nucleus. We propose that subcellular localization is a critical feature of experience-dependent lncRNA activity in the brain, and that lncRNA-mediated control over RNA metabolism at the synapse serves to regulate local mRNA stability and translation, thereby influencing neuronal function, learning and memory.
  • A meta-analysis of the relationship between subjective sleep and depressive symptoms in adolescence

    Adolescence is a risk period for the development of mental illness, as well as a time for pronounced change in sleep behaviour. While prior studies, including several meta-analyses show a relationship between sleep and depressive symptoms, there were many inconsistences found in the literature.

    To investigate the relationship between subjective sleep and depressive symptoms.

    Following PRISMA guidelines, we conducted a literature search that yielded forty-nine recent studies (2014-2020) with adolescent samples aged 9 to 25-year-olds, and more than double the sample size of previous meta-analyses (N = 318,256).

    In a series of meta-analyses, we show that while several common categories of subjective sleep are associated with depressive symptoms in adolescents, the strength of this relationship varies. Measures of sleep perception: poor sleep quality (r = 0.41), insomnia (r = 0.37), sleep disturbances (r = 0.36), wake after sleep onset (r = 0.31), and daytime sleepiness (r = 0.30) correlated more strongly with depressive symptoms, than measures of sleep behaviour: sleep latency (r = 0.22), and sleep duration (r = -0.19).

    These findings suggest that in studies of depressive symptoms it may be important to assess an adolescent's perception about their sleep, in addition to their sleep/wake behaviours.
  • Combining single molecule super-resolution imaging techniques to unravel the nanoscale organization of the presynapse

    The fusion of synaptic vesicles with the plasma membrane underpins neurotransmission. A number of presynaptic proteins play a critical role in overcoming the energy barrier inherent to the fusion of the negatively charged vesicular and plasma membranes. Emerging concepts suggest that this process is hierarchical and dependent on rapid and transient reorganization of proteins in and out of small nanoclusters located in the active zones of nerve terminals. Examining the nanoscale organization of presynaptic molecules requires super-resolution microscopy to overcome the limits of conventional light microscopy. In this chapter, we describe three super-resolution techniques that allow for the examination of the nanoscale organization of proteins within live hippocampal nerve terminals. We used (1) single-particle tracking photoactivated localization microscopy (sptPALM) to resolve the mobility and clustering of syntaxin1A (STX1A), (2) universal Point Accumulation Imaging in Nanoscale Topography (uPAINT) to study the mobility of a pool of vesicular-associated membrane protein 2 (VAMP2) transiting on the plasma membrane, and (3) subdiffractional Tracking of Internalized Molecules (sdTIM) to track VAMP2-positive recycling synaptic vesicles in conjunction with Cholera Toxin subunit B (CTB), which has recently been shown to be trafficked retrogradely from the presynapse to the cell body via signaling endosomes.
  • Reduced effective connectivity between right parietal and inferior frontal cortex during audiospatial perception in neglect patients with a right-hemisphere lesion: Reduced effective connectivity in neglect syndrome

    A lesion to the right hemisphere of the brain in humans commonly leads to perceptual neglect of the left side of the sensorium. The clinical observation that lesions to disparate cortical and subcortical areas converge upon similar behavioural symptoms points to neglect as a dysconnection syndrome that may result from the disruption of a distributed network, rather than aberrant computations in any particular brain region. To test this hypothesis, we used Bayesian analysis of effective connectivity based on electroencephalographic recordings in ten patients (6 male, 4 female; age range 41–68) with left-sided neglect following a right-hemisphere lesion. In line with previous research, age-matched healthy controls showed a contralateral increase in connection strength between parietal and frontal cortex with respect to the laterality of audiospatial oddball stimuli. Neglect patients, however, showed a dysconnection between parietal and frontal cortex in the right hemisphere when oddballs appeared on their left side, but preserved connectivity in the left hemisphere when stimuli appeared on their right. This preserved fronto-parietal connectivity was associated with lower neglect severity. Moreover, we saw ipsilateral fronto-temporal connectivity increases for oddballs appearing on the neglected side, which might be a compensatory mechanism for residual left side awareness. No group differences were found in intrinsic (within-region) connectivity. While further validation is required in a bigger sample, our findings are in keeping with the idea that neglect results from the disruption of a distributed network, rather than a lesion to any single brain region. Significance statement: Lesions to the right hemisphere of the brain commonly lead to neglect syndrome, characterized by perceptual deficits where patients are unaware of the left side of their body and environment. Using analysis of non-invasive electrophysiological recordings, we provide evidence that patients with left-sided neglect have reduced connectivity between the right parietal and frontal cortex during audiospatial stimuli, but preserved connectivity between regions in the non-lesioned left hemisphere. Moreover, for these intact connections we observed an ipsilateral fronto-temporal increase in connectivity during oddballs appearing on the neglected side, which might be a compensatory mechanism for residual perception. Crucially, we found that patients with more severe neglect symptoms had reduced connectivity between parietal and frontal cortex in the left hemisphere. This suggests that neglect may be caused by the disruption of a distributed network in the brain, rather than a lesion to any particular brain region.
  • Risk in relatives, heritability, SNP-based heritability and genetic correlations in psychiatric disorders: a review

    The genetic contribution to psychiatric disorders is observed through the increased rates of disorders in the relatives of those affected. These increased rates are observed to be non-specific, for example children of those with schizophrenia have increased rates of schizophrenia, but also a broad range of other psychiatric diagnoses. While many factors contribute to risk, epidemiological evidence suggest that the genetic contribution carries the highest risk burden. The patterns of inheritance are consistent with a polygenic architecture of many contributing risk loci. The genetic studies of the last decade have provided empirical evidence identifying thousands of DNA variants associated with psychiatric disorders. Here, we describe how these latest results are consistent with observations from epidemiology. We provide an R tool (CHARRGe) to calculate genetic parameters from epidemiological parameters and vice versa. We discuss how the SNP-based estimates of heritability and genetic correlation relate to those estimated from family records.
  • From basic science to clinical application of polygenic risk scores : a primer

    Polygenic risk scores (PRS) are predictors of the genetic susceptibilities of individuals to diseases. All individuals have DNA risk variants for all common diseases, but genetic susceptibility differences between people reflect the cumulative burden of these. Polygenic risk scores for an individual are calculated as weighted counts of thousands of risk variants that they carry, where the risk variants and their weights have been identified in genome-wide association studies. Here, we review the underlying basic science of PRS, providing a foundation for understanding the potential clinical utility and limitations of PRS.

    Polygenic risk scores can be calculated for a wide range of diseases from a saliva or blood sample using genotyping technologies that are inexpensive. While genotyping only needs to be done once for each individual in their lifetime, the PRS can be recalculated as identification of risk variants improves. On their own, PRS will never be able to establish or definitively predict future diagnoses of common complex conditions because genetic factors only contribute part of the risk, and PRS will only ever capture part of the genetic contributions. Nonetheless, just as clinical medicine uses a multitude of other predictive measures, PRS either on their own or as part of multivariable predictive algorithms could play a role.

    Utility of PRS in clinical medicine and ethical issues related to their use should be evaluated in the context of realistic expectations of what PRS can and cannot deliver. For different diseases, PRS could have utility in community settings (stratification to better triage people into established screening programs) or could contribute to clinical decision-making for those presenting with symptoms but where formal diagnosis is unclear. In principle, PRS could contribute to treatment choices, but more data are needed to allow development of PRS in this context.
  • Quantitative Analysis of Renal Perfusion by Arterial Spin Labeling

    The signal intensity differences measured by an arterial-spin-labelling (ASL) magnetic resonance imaging (MRI) experiment are proportional to the local perfusion, which can be quantified with kinetic modeling. Here we present a step-by-step tutorial for the data post-processing needed to calculate an ASL perfusion map. The process of developing an analysis software is described with the essential program code, which involves nonlinear fitting a tracer kinetic model to the ASL data. Key parameters for the quantification are the arterial transit time (ATT), which is the time the labeled blood takes to flow from the labeling area to the tissue, and the tissue T. As ATT varies with vasculature, physiology, anesthesia and pathology, it is recommended to measure it using multiple delay times. The tutorial explains how to analyze ASL data with multiple delay times and a T map for quantification.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure.
  • Identifying the function of methylated genes in Alzheimer’s disease to determine epigenetic signatures: a comprehensive bioinformatics analysis

    Gene methylation is one means of controlling tissue gene expression, but it is unknown what pathways influencing Alzheimer’s disease (AD) are controlled this way. We compared normal and AD brain tissue data for gene expression (mRNAs) and gene methylation profiling. We identified methylated differentially expressed genes (MDEGs). Protein-protein interaction (PPI) of the MDEGs showed 18 hypermethylated low-expressed genes (Hyper-LGs) involved in cell signaling and metabolism; also 10 hypomethylated highly expressed (Hypo-HGs) were involved in regulation of transcription and development. Molecular pathways enriched in Hyper-LGs included neuroactive ligand-receptor interaction pathways. Hypo-HGs were notably enriched in pathways including hippo signaling. PPI analysis also identified both Hyper-LGs and Hypo-HGs, as hub proteins. Our analysis of AD datasets identified Hyper-LGs, Hypo-HGs, and transcription factors linked to these genes. These pathways, which may participate in Alzheimer’s disease development, may be affected by treatments that influence gene methylation patterns.
  • Genome-wide integrative analysis reveals common molecular signatures in blood and brain of alzheimer’s disease

    The currently utilized neuroimaging and cerebrospinal fluid-based detection of Alzheimer’s disease (AD) suffer several limitations, including sensitivity, specificity, and cost. Therefore, the identification of AD by analyzing blood gene expression may ameliorate the early diagnosis of the AD. We aimed to identify common genes commonly deregulated in blood and brain in AD. Comprehensive analysis of blood and brain gene expression datasets of AD, eQTL, and epigenetics data was analyzed by the integrative bioinformatics approach. The integrative analysis showed nine differentially expressed genes common to blood cells and brain (CNBD1, SUCLG2-AS1, CCDC65, PDE4D, MTMR1, C3, SLC6A15, LINC01806, and FRG1JP). Analysis of SNP and cis-eQTL data showed 18 genes; namely, HSD17B1, GAS5, RPS5, VKORC1, GLE1, WDR1, RPL12, MORN1, RAD52, SDR39U1, NPHP4, MT1E, SORD, LINC00638, MCM3AP-AS1, GSDMD, RPS9, and GNL2 were observed deregulated AD blood and brain tissues. Functional gene set enrichment analysis demonstrated a significant association of these genes in neurodegeneration-associated molecular pathways. Integrative biomolecular networks revealed dysregulation of several hub transcription factors and microRNAs in AD. Moreover, hub genes were observed associated with significant histone modification. This study detected common molecular biomarkers and pathways in blood and brain tissues in AD that may be potential biomarkers and therapeutic targets in AD.
  • Regional changes in muscle activity do not underlie the repeated bout effect in the human gastrocnemius muscle

    The repeated bout effect (RBE) confers protection following exercise-induced muscle damage. Typical signs of this protective effect are significantly less muscle soreness and faster recovery of strength after the second bout. The aim of this study was to compare regional changes in medial gastrocnemius (MG) muscle activity and mechanical hyperalgesia after repeated bouts of eccentric exercise. Twelve healthy male participants performed two bouts of eccentric heel drop exercise (separated by 7 days) while wearing a vest equivalent to 20% of their body weight. High-density MG electromyographic amplitude maps and topographical pressure pain sensitivity maps were created before, two hours (2H) and two days (2D) after both exercise bouts. Statistical parametric mapping was used to identify RBE effects on muscle activity and mechanical hyperalgesia, using pixel-level statistics when comparing maps. The results revealed a RBE, as a lower strength loss (17% less; P<0.01) and less soreness (50% less; P<0.01) were found after the second bout. However, different muscle regions were activated 2H and 2D after the initial bout but not following the repeated bout. Further, no overall changes in EMG distribution or mechanical hyperalgesia were found between bouts. These results indicate that muscle activation is unevenly distributed during the initial bout, possibly to maintain muscle function during localized mechanical fatigue. However, this does not reflect a strategy to confer protection during the repeated bout by activating undamaged/non-fatigued muscle areas.
  • Direct detection of neuronal activity using organic photodetectors

    Calcium- and voltage-sensitive indicators allow for the optical monitoring of neuronal activity at both cellular and population levels. However, conventional approaches for the optical detection of electrical activity in an intact brain typically involve a trade-off between tissue depth and resolution. Cameras of high temporal and spatial resolution can detect activity with single-cell resolution, but are restricted to more superficial structures such as the neocortex and require elaborate optical setups. In contrast, optical fibers can collect fluorescent neural activity from deeper brain areas, but with low spatial resolution. Here, we present a new class of high-resolution, light-sensing devices that are capable of detecting ultralow changes in fluorescent neuronal activity without the need for an optical setup. We show that organic photodetectors (OPDs) based on rubrene and fullerene feature a photovoltage responsivity of 2 V m W and that can directly detect changes in fluorescent neuronal activity as low as 2.3 nW cm. Primary cortical neurons were loaded with the fluorescent calcium indicator Cal-520, and neuronal activity was evoked with brief pulses of electrical field stimulation. During simultaneous sCMOS camera acquisition, the OPD was observed to reliably detect electrically evoked fluorescent activity with high fidelity and signal-to-noise ratio. The device also detected time-locked spontaneous fluorescent transients, demonstrating sufficient sensitivity for the detection of physiological events. Our results pave the way for a new class of subdermally implanted stereotactic sensors, representing a capacity for minimally invasive, high-resolution in vivo recordings, which are especially suited to record neuronal populations in behaving animals.