title: The developmental hourglass model is applicable to the spinal cord

abstract: The developmental hourglass model predicts that embryonic morphology is most conserved at the mid-embryonic stage and diverges at the early and late stages. This model is generally considered by whole embryonic level. Here, we demonstrate that the hourglass model is also applicable to a reduced element, the spinal cord. In the middle of spinal cord development, dorsoventrally arrayed neuronal progenitor domains are established, which are conserved among vertebrates. We found that, by comparing the single-cell transcriptomes between mice and zebrafish, V3 interneurons, a subpopulation of the post-mitotic spinal neurons, display divergent molecular profiles. We also found non-conservation of cis-regulatory elements located around the progenitor fate determinants, indicating the rewiring of the upstream gene regulatory network. These results demonstrate that, despite the conservation of the progenitor domains, processes before and after the progenitor domain specification diverged. This study may help understand the molecular basis of the developmental hourglass model.

category: evolutionary biology


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes

abstract: Insulator proteins located at the boundaries of topological associated domains (TAD) are involved in regulating chromatin loops. Yet, how chromatin loops contribute to transcription regulation is still not clear. Here we show that Relative-of-WOC (ROW) is essential for the long-range transcription regulation mediated by the Boundary Element-Associated Factor of 32kD (BEAF-32). We found that ROW physically interacts with heterochromatin proteins (HP1b and HP1c) and the insulator protein BEAF-32. The co-localization happens at TAD boundaries where ROW, through its AT-hooks motifs, binds AT-rich sequences flanked by BEAF-32 binding sites and motifs. Knockdown of row resulted in downregulation of genes that are long-range targets of BEAF-32 and bound indirectly by ROW (without binding motif). Analysis of high- throughput chromosome conformation capture (Hi-C) data revealed long-range interactions between promoters of housekeeping genes bound directly by ROW and promoters of developmental genes bound indirectly by ROW. Thus, our results show cooperation between BEAF-32 and the ROW complex, which includes HP1 proteins, to regulate the transcription of developmental and inducible genes by chromatin loops.

category: genomics


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes


title: Multichromatic Near-Infrared Imaging to Assess Interstitial Lymphatic and Venous Uptake In Vivo

abstract:
SignificanceChanges in interstitial fluid clearance are implicated in many diseases. Using NIR imaging with properly sized tracers could enhance our understanding of how venous and lymphatic drainage are involved in disease progression or enhance drug delivery strategies.

AimWe investigated multichromatic NIR imaging with multiple tracers to assess in vivo microvascular clearance kinetics and pathways in different tissue spaces.

ApproachWe used a chemically inert IR Dye 800CW (free dye) to target venous capillaries and a purified conjugate of IR Dye 680RD with a 40 kDa PEG (PEG) to target lymphatic capillaries in vivo. Optical imaging settings were validated and tuned in vitro using tissue phantoms. We investigated multichromatic NIR imagings utility in two in vivo tissue beds - the mouse tail and rat knee joint. We then tested the ability of the approach to detect interstitial fluid perturbations due to exercise.

ResultsIn an in vitro simulated tissue environment, free dye and PEG mixture allowed for simultaneous detection without interference. Co-injected NIR tracers cleared from the interstitial space via distinct routes allowed assessment lymphatic and venous uptake in the mouse tail. We determined that exercise after injection transiently increased lymphatic drainage as measured by lower normalized intensity immediately after exercise, while exercise pre-injection exhibited a transient delay in clearance from the joint

ConclusionsNIR imaging enables of simultaneous imaging of lymphatic and venous-mediated fluid clearance with great sensitivity and can be used to measure transient changes in clearance rates and pathways.

category: bioengineering


title: An Investigation into Patient-Specific 3D Printed Titanium Stents and the use of Etching to Overcome Selective Laser Melting Design Constraints.

abstract:
There is currently a clear clinical need in the area of stenting for paediatric patients, whereby currently commercially available adult stents are often required to be used off-label for paediatric patients resulting in less than optimal outcomes. The increasingly widespread use of CT and/or MR imaging for pre-surgical assessment, and the emergence of additive manufacturing processes such as 3D printing, could enable bespoke devices to be produced efficiently and cost-effectively. However, 3D printed metallic stents need to be self-supporting leading to limitations in the design of stents available through additive manufacturing. In this study we investigate the use of etching to overcome these design constraints and improve stent surface finish. Furthermore, using a combination of experimental bench testing and finite element methods we investigate how etching influences stent performance and using an inverse finite element approach the material properties of the printed and etched stents were calibrated and compared. Finally, using patient-specific finite element models the stent performance was tested to assess patient outcomes. Within this study, etching is confirmed as a means to create open-cell stent designs whilst conforming to additive manufacturing  rules and concomitantly improving stent surface finish. Additionally, the feasibility of using an in-vivo imaging to product development pipeline is demonstrated that enables patient-specific stents to be produced for varying anatomies to achieve optimum device performance.

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title: A network regularized linear model to infer spatial expression pattern for singlecells

abstract: Spatial gene-expression is a crucial determinant of cell fate and behavior. Recent imaging and sequencing-technology advancements have enabled scientists to develop new tools that use spatial information to measure gene-expression at close to single-cell levels. Yet, while Fluorescence In-situ Hybridization (FISH) can quantify transcript numbers at single-cell resolution, it is limited to a small number of genes. Similarly, slide-seq was designed to measure spatial-expression profiles at the single-cell level but has a relatively low gene-capture rate. And although single-cell RNA-seq enables deep cellular gene-expression profiling, it loses spatial information during sample-collection. These major limitations have stymied these methods broader application in the field. To overcome spatio-omics technologys limitations and better understand spatial patterns at single-cell resolution, we designed a computation algorithm that uses glmSMA to predict cell locations by integrating scRNA-seq data with a spatialomics reference atlas. We treated cell-mapping as a convex optimization problem by minimizing the differences between cellular-expression profiles and location-expression profiles with a L1 regularization and graph Laplacian based L2 regularization to ensure a sparse and smooth mapping. We validated the mapping results by reconstructing spatial-expression patterns of well-known marker genes in complex tissues, like the mouse cerebellum and hippocampus. We used the biological literature to verify that the reconstructed patterns can recapitulate cell-type and anatomy structures. Our work thus far shows that, together, we can use glmSMA to accurately assign single cells to their original reference-atlas locations.

category: bioinformatics


title: Dissecting Transition Cells from Single-Cell Transcriptome Data through Multiscale Stochastic Dynamics

abstract: Advances of single-cell technologies allow scrutinizing of heterogeneous cell states, however, analyzing transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique for the underlying stochastic dynamical systems that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transition, and distinguishes meta-stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using the coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. Mathematical analysis reveals consistency of the method with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms and benchmarking with seven existing tools, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.


title: GraphBreak: Network Community detection and annotation in biomedical regulatory informatics context

abstract: Graph network science is becoming increasingly popular, notably in big-data perspective where understanding individual entities for individual functional roles is complex and time consuming. It is likely when a set of genes are regulated by a set of genetic variants, the genes set is recruited for a common or related functional purpose. Grouping and extracting communities from network of associations becomes critical to understand system complexity, thus prioritizing genes for disease and functional associations. Workload is reduced when studying entities one at a time. For this, we present GraphBreak, a suite of tools for community detection application, such as for gene co-expression, protein interaction, regulation network, etc.Although developed for use case of eQTLs regulatory genomic network community study- results shown with our analysis with sample eQTL data-Graphbreak can be deployed for other studies if input data has been fed in requisite format, including but not limited to gene co-expression networks, protein-protein interaction network, signaling pathway and metabolic network. GraphBreak showed critical use case value in its downstream analysis for disease association of communities detected. If all independent steps of community detection and analysis are a step-by-step sub-part of the algorithm, GraphBreak can be considered a new algorithm for community based functional characterization. Combination of various algorithmic implementation modules into a single script for this purpose illustrates GraphBreaks novelty. Compared to other similar tools, with GraphBreak we can better detect communities with overrepresentation of its member genes for statistical association with diseases, therefore target genes which can be prioritized for drug-positioning or drug-repositioning as the case be.


title: Temperature-dependent Self assembly of biofilaments during red blood cell sickling

abstract: Molecular self-assembly plays vital role in various biological functions. However, when aberrant molecules self-assemble to form large aggregates, it can give rise to various diseases. For example, the sickle cell disease and Alzheimers disease are caused by self-assembled hemoglobin fibers and amyloid plaques, respectively. Here we study the assembly kinetics of such fibers using kinetic Monte-Carlo simulation. We focus on the initial lag time of these highly stochastic processes, during which self-assembly is very slow. The lag time distributions turn out to be similar for two very different regimes of polymerization, namely, a) when polymerization is slow and depolymerization is fast, and b) the opposite case, when polymerization is fast and depolymerization is slow. Using temperature dependent on- and off-rates for hemoglobin fiber growth, reported in recent in-vitro experiments, we show that the mean lag time can exhibit non-monotonic behaviour with respect to change of temperature.

category: biophysics


title: Nanoscale organization of Actin Filaments in the Red Blood Cell Membrane Skeleton

abstract: Red blood cell (RBC) shape and deformability are supported by a planar network of short actin filament (F-actin) nodes interconnected by long spectrin molecules at the inner surface of the plasma membrane. Spectrin-F-actin network structure underlies quantitative modelling of forces controlling RBC shape, membrane curvature and deformation, yet the nanoscale organization of F-actin nodes in the network in situ is not understood. Here, we examined F-actin distribution in RBCs using fluorescent-phalloidin labeling of F-actin imaged by multiple microscopy modalities. Total internal reflection fluorescence (TIRF) and Zeiss Airyscan confocal microscopy demonstrate that F-actin is concentrated in multiple brightly stained F-actin foci [~]200-300 nm apart interspersed with dimmer F-actin staining regions. Live cell imaging reveals dynamic lateral movements, appearance and disappearance of F-actin foci. Single molecule STORM imaging and computational cluster analysis of experimental and synthetic data sets indicate that individual filaments are non-randomly distributed, with the majority as multiple filaments, and the remainder sparsely distributed as single filaments. These data indicate that F-actin nodes are non-uniformly distributed in the spectrin-F-actin network and necessitate reconsideration of current models of forces accounting for RBC shape and membrane deformability, predicated upon uniform distribution of F-actin nodes and associated proteins across the micron-scale RBC membrane.


title: Label free sensing with Terahertz multiple ring resonators

abstract: Apart from their relevance for spectroscopy and imaging, terahertz signals have attracted a lot of interest for sensing. In this paper, a label free terahertz sensor is proposed, which can be employed to detect the presence of molecules in the environment. The proposed sensor consists of an array of ring resonators, resonating at the frequency of f=1.2 THz. By providing full-wave numerical simulations, it is shown that the proposed sensor is able to sense the variation of the refractive index in the environment. The proposed structure is found to show larger sensitivity compared to previous reports. Our findings provide a novel platform to realize label free terahertz sensors with extremely large sensitivity.


title: Combined MEK and STAT3 inhibition reprograms the tumor microenvironment to overcome immunotherapy resistance in pancreatic cancer

abstract: Pancreatic ductal adenocarcinoma (PDAC) is characterized by immune exclusion, pro-inflammatory polarization of cancer-associated fibroblasts (CAF), and resistance to immune checkpoint inhibition (ICI). We have previously demonstrated that reciprocally activated RAS/MEK/ERK and JAK/STAT3 pathways mediate therapeutic resistance, while combined MEK and STAT3 inhibition (MEKi+STAT3i) overcomes such resistance in preclinical models. We now show that combined MEKi+STAT3i not only alters stromal architecture but also uncovers stromal plasticity by revealing a substantial attenuation of Il6/Cxcl1-expressing secretory and Lrrc15-expressing myofibroblastic CAF phenotypes with a concomitant enrichment of Ly6a/Cd34-expressing CAF phenotypes exhibiting mesenchymal progenitor-like properties via single-cell RNA sequencing in Ptf1acre/+;LSL-KrasG12D/+;Tgfbr2flox/flox(PKT) mice. This remodeling of CAF heterogeneity is associated with reprogramming of immunosuppressive myeloid populations and enhanced trafficking of CD8+ T-cells which exhibit a distinct effector transcriptional program. These MEKi+STAT3i-mediated repercussions are in part CAF-dependent, since CRISPR/Cas9 genetic silencing of CAF-restricted Mek1/Stat3 mitigates inflammatory CAF polarization and myeloid infiltration in vivo. Addition of MEKi+STAT3i to PD-1 blockade overcomes ICI resistance by significantly augmenting anti-tumor responses and dramatically improving survival in PKT mice compared with anti-PD-1 monotherapy. The addition of MEKi+STAT3i to PD-1 blockade not only augments the recruitment of activated and memory T-cell populations, but also improves their degranulating capacity and functional cytotoxicity compared to PD-1 blockade alone. Importantly, treatment of a patient with chemotherapy-refractory metastatic PDAC with MEKi (Trametinib), STAT3i (Ruxolitinib), and PD-1 inhibitor (Nivolumab) was well-tolerated and yielded clinical benefit. These data uncover a novel paradigm in which combined MEKi+STAT3i reprograms stromal inflammation and immune tolerance to overcome immunotherapy resistance in PDAC.

category: cancer biology


title: Combined MEK and STAT3 inhibition reprograms stromal inflammation to overcome immunotherapy resistance in pancreatic cancer


title: The effects of insecticide seed treatments on green peach aphid Myzus persicae (Sulzer) (Homoptera: Aphididae) parasitism by Aphidius colemani Viereck (Hymenoptera: Aphidiidae) and predation by Mallada signatus (Schneider) (Neuroptera: Chrysopidae)

abstract: The green peach aphid, Myzus persicae (Sulzer) (Homoptera: Aphididae), is a major pest of Brassica L. species in Australia, where it can transmit >100 viruses. Globally, this species has evolved resistance to 74 insecticides from numerous chemical groups. Although Integrated Pest Management (IPM) strategies are being implemented, chemical treatment remains the predominant method used to control aphids. Insecticide seed treatments are viewed as a softer alternative to chemical sprays and are widely used in Australian canola fields. The effects of imidacloprid, thiamethoxam, and a mixture of thiamethoxam & lambda-cyhalothrin canola seed treatments were investigated on the parasitoid, Aphidius colemani Viereck (Hymenoptera: Aphidiidae) and the predator, the green lacewing Mallada signatus (Schneider) (Neuroptera: Chrysopidae); both important natural enemies of M. persicae. The number of mummies formed by A. colemani on the untreated plants was lower than those formed on the thiamethoxam & lambda-cyhalothrin and imidacloprid treated plants. The number of A. colemani reared from mummies on thiamethoxam & lambda-cyhalothrin plants was higher than those reared from thiamethoxam and untreated plants. Significant effects of insecticide seed treatments were only noted for mummies produced while the parent parasitoids were on the plants, not for those mummies produced after their removal. This suggests seed treatment effects were immediate but not long lasting. Based on cumulative parasitoid survival days for two generations, A. colemani exposed to thiamethoxam & lambda-cyhalothrin and imidacloprid treatments had a greater fitness than those exposed to the thiamethoxam and untreated controls, possibly due to the phenomenon of insecticide hormoligosis. Despite the treatment effects observed, we did not detect any behavioural differences in M. persicae or A. colemani. Mallada signatus were not negatively affected by feeding on M. persicae on insecticide seed treated plants, suggesting they are more tolerant of seed treatments than A. colemani. The findings from this study provide a useful platform for further experimentation on the effects of seed treatments on natural enemies of M. persicae.

category: zoology


title: Is galactose a hormetic sugar? Evidence from rat hippocampal redox regulatory network

abstract: Galactose is a ubiquitous simple monosaccharide with yet incompletely understood biochemical and physiological role. Most of what we currently know about galactose is based on induction from the research on inherited disorders of galactose metabolism and animal models that exploit galactose-induced oxidative stress to model aging in rodents, however, recent evidence also demonstrates unique properties of galactose to conserve cellular function during the periods of starvation, and prevent and alleviate cognitive deficits in a rat model of sporadic Alzheimers disease. Here, we try to understand the molecular background of both detrimental and beneficial effects of galactose by exploring the acute systemic and hippocampal biochemical changes upon oral administration of galactose solution focusing primarily on the components of the redox regulatory network (RRN). Although orogastric gavage of galactose solution (200 mg/kg) was insufficient to induce systemic RRN disbalance in the first two hours upon administration, analysis of hippocampal RRN revealed a mild pro-oxidative shift accompanied by a paradoxical increase in tissue reductive capacity, suggesting overcompensation of endogenous antioxidant systems in the response to the pro-oxidative stimulus. The more thorough analysis revealed that galactose-induced increment of reductive capacity was accompanied by inflation of the hippocampal pool of nicotinamide adenine dinucleotide phosphates indicating ROS detoxification through disinhibition of the oxidative pentose phosphate pathway flux, reduced neuronal activity, and upregulation of Leloir pathway gatekeeper enzyme galactokinase-1. Based on the observed findings, and in the context of previous work on galactose, we propose a hormetic hypothesis of galactose action suggesting that the protective effects of galactose might be inseparable from its pro-oxidative effects at the biochemical level.

category: neuroscience


title: Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization

abstract:
Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 {micro}m) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine novel spatially and molecularly defined subregions. EASI-FISH also facilitates iterative re-analysis of scRNA-Seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

Highlights- EASI-FISH enables robust gene expression profiling in thick brain slices
- A turnkey analysis pipeline for facile analysis of large EASI-FISH image datasets
- EASI-FISH reveals novel subregions of the lateral hypothalamus
- Identification of rare cell types based on morphological and spatial heterogeneity


title: Probing adaptation and spontaneous firing in human auditory-nerve fibers with far-field peri-stimulus time responses

abstract: Information in sound stimuli is conveyed from sensory hair cells to the cochlear nuclei by the firing of auditory nerve fibers (ANFs). For obvious ethical reasons, single unit recordings from the cochlear nerve have never been performed in human, thus functional hallmarks of ANFs are unknown. By filtering and rectifying the electrical signal recorded at the round window of gerbil cochleae, we reconstructed a peri-stimulus time response (PSTR), with a waveform similar to the peri-stimulus time histograms (PSTHs) recorded from single ANFs. Pair-by-pair analysis of simultaneous PSTR and PSTH recordings in gerbil provided a model to predict the rapid adaptation and spontaneous discharge rates (SR) in a population of ANFs according to their location in the cochlea. We then probed the model in the mouse, in which the SR-based distribution of ANFs differs from the gerbil. We show that the PSTR-based predictions of the rapid adaptation time constant and mean SR across frequency again matched those obtained by recordings from single ANFs. Using PSTR recorded from the human cochlear nerve in 8 normal-hearing patients who underwent cerebellopontine angle surgeries for a functional cranial-nerve disorders (trigeminal neuralgia or hemifacial spasm), we predicted a rapid adaptation of about 3 milliseconds and a mean SR of 23 spikes/s in the 4 kHz frequency range in human ANFs. Together, our results support the use of PSTR as a promising diagnostic tool to map the auditory nerve in humans, thus opening new avenues to better understanding neuropathies, tinnitus, and hyperacusis.


title: Hypothalamic perineuronal nets are regulated by sex and dietary interventions

abstract: Perineuronal nets (PNNs) are widely present in the hypothalamus, and are thought to provide physical protection and ion buffering for neurons, and regulate their synaptic plasticity and intracellular signaling. Recent evidence indicates that PNNs in the mediobasal hypothalamus plays an important role in the regulation of glucose homeostasis. However, whether and how hypothalamic PNNs are regulated are not fully understood. In the present study, we examined whether PNNs in various hypothalamic regions in mice can be regulated by sex, gonadal hormones, dietary interventions, or their interactions. We demonstrated that gonadal hormones are required to maintain normal PNNs in the arcuate nucleus of hypothalamus in both male and female mice. In addition, PNNs in the terete hypothalamic nucleus display a sexual dimorphism with females higher than males, and high-fat diet feeding increases terete PNNs only in female mice but not in male mice. On the other hand, PNNs in other hypothalamic regions are not influenced by sex, gonadal hormones or dietary interventions. In summary, we demonstrated that hypothalamic PNNs are regulated in a region-specific manner and these results provide a framework to further investigate the potential functions of PNNs in regulating energy/glucose homeostasis at the interplay of sex, gonadal hormones and diets.


title: In vitro neuronal networks show bidirectional axonal conduction with antidromic action potentials effectively depolarizing the soma

abstract: Recent technological advances are revealing the complex physiology of the axon and challenging long-standing assumptions. Namely, while most action potential (AP) initiation occurs at the axon initial segment in central nervous system neurons, initiation in distal parts of the axon has been shown to occur in both physiological and pathological conditions. However, such ectopic action potential (EAP) activity has not been reported yet in studies using neuronal cultures and its functional role, if exists, is still not clear. Here, we show the spontaneous occurrence of EAPs and effective antidromic conduction in hippocampal neuronal cultures. We also observe a significant fraction of bidirectional axonal conduction in dorsal root ganglia neuronal cultures. We investigate and characterize this antidromic propagation via a combination of microfluidics, microelectrode arrays, advanced data analysis and in silico studies. We show that EAPs and antidromic conduction can occur spontaneously, and after distal axotomy or physiological changes in the axon biochemical environment. Conduction velocity is asymmetrical, with antidromic conduction being slower than orthodromic. Importantly, EAPs may carry information and can have a functional impact on the neuron, as they consistently depolarize the soma. Thus, plasticity or gene transduction mechanisms triggered by soma depolarization can also be affected by these antidromic APs. Altogether these findings have important implications for the study of neuronal function in vitro, reshaping our understanding on how information flows in neuronal cultures.


title: Neuronal cultures show bidirectional axonal conduction with antidromic action potentials depolarizing the soma


title: Medulla glutamatergic neurons control wake-sleep transitions

abstract: Sleep is a ubiquitous behavior in animal species. Yet, brain circuits controlling sleep remain poorly understood. Previous studies have identified several brain structures that promote sleep, but whether these structures are involved in sleep initiation or sleep maintenance remains largely unknown. Here we identified a population of glutamatergic neurons in the medulla that project to the preoptic area (POA), a prominent sleep-promoting region. Chemogenetic silencing of POA-projecting medulla neurons disrupts the transitions from wakefulness to Non-Rapid Eye Movement (NREM) sleep, whereas chemogenetic activation of these neurons promotes NREM sleep. Moreover, we show that optogenetic activation of medulla glutamatergic neurons or their projections in the POA reliably initiates long-lasting NREM sleep in awake mice. Together, our findings uncover a novel excitatory brainstem-hypothalamic circuit that controls the wake-sleep transitions.


title: Prospective Identification of Ictal Electroencephalogram

abstract:
BackgroundElectroencephalogram (EEG) monitoring and objective seizure identification is an essential clinical investigation for some patients with epilepsy. Accurate annotation is done through a time-consuming process by EEG specialists. Computer-assisted systems for seizure detection currently lack extensive clinical utility due to retrospective, patient-specific, and/or irreproducible studies that result in low sensitivity or high false positives in clinical tests. We aim to significantly reduce the time and resources on data annotation by demonstrating a continental generalization of seizure detection that balances sensitivity and specificity.

MethodsThis is a prospective inference test of artificial intelligence on nearly 14,590 hours of adult EEG data from patients with epilepsy between 2011 and 2019 in a hospital in Sydney, Australia. The inference set includes patients with different types and frequencies of seizures across a wide range of ages and EEG recording hours. The artificial intelligence (AI) is a convolutional long short-term memory network that is trained on a USA-based dataset. The Australian set is about 16 times larger than the US training dataset with very long interictal periods (between seizures), which is way more realistic than the training set and makes our false positives highly reliable. We validated our inference model in an AI-assisted mode with a human expert arbiter and a result review panel of expert neurologists and EEG specialists on 66 sessions to demonstrate achievement of the same performance with over an order-of-magnitude reduction in time.

FindingsOur inference on 1,006 EEG recording sessions on the Australian dataset achieved 76.68% with nearly 56 [0, 115] false alarms per 24 hours on average, against legacy ground-truth annotations by human experts, conducted independently over nine years. Our pilot test of 66 sessions with a human arbiter, and reviewed ground truth by a panel of experts, confirmed an identical human performance of 92.19% with an AI-assisted system, while the time requirements reduce significantly from 90 to 7.62 minutes on average.

InterpretationAccurate and objective seizure counting is an important factor in epilepsy. An AI-assisted system can help improve efficiency and accuracy alongside human experts, particularly in low and middle-income countries with limited expert human resources.

FundingsSOAR Fellowship from The University of Sydney, a Microsoft AI for Accessibility grant, and a Research Training Program (RTP) support provided by the Australian Government.

Research in contextO_ST_ABSEvidence before this studyC_ST_ABSDuring the development of our artificial intelligence (AI) system, we did a systematic review of the scientific literature with search via PubMed for research articles published on seizure detection with the following inclusion criteria: (1) Tests or inference evaluation is conducted on large-scale clinical EEG data; (2) Generalization is attempted or potentials for generalization is considered, e.g., in commercialized tools; (3) Seizure detection delay and real-time (aka. online) operation were not considered critical in this context as long as the test was conducted on raw EEG data. Note that ICU seizure detection or portable seizure alert systems are relying on detection delay and real-time needs. Our keywords include "prospective seizure detection", "automated seizure detection", "non-patient specific seizure detection", "seizure detection on continuous EEG", and "deep learning-based seizure detection" and "machine learning-based seizure detection". We found that the only two categories of works meet our criteria: two research papers published in 2020 and works published by commercial tools developers. We cited a recent review of 89 deep learning-based seizure detection, all of which are retrospective. One work from Stanford reported seizure detection on all ages (pediatric to adult ages) using post-acquisition EEG recordings and provided an avenue for independent evaluation by providing a test on a publicly available Temple University Hospital (TUH) EEG dataset. The other work pivoted on algorithmic-assisted real-time seizure risk monitoring in continuous EEG in neonatal intensive care unit (NICU) with 128 neonates (32 with seizures) showing about 20% improvement in seizure identification over 130 neonates (38 with seizures) with no algorithmic assistance.

Commercial tools we studied are Encevis (EpiScan), Besa, and Persyst. There is a recent comparative study on these tools on 81 patients. Encevis is reported as the best performing tool, and hence we provided a comparative study with Encevis ver. 1.9.2. Encevis is also the only tool that provided an avenue for comparative study on publicly available EEG data. The Stanford work, published in 2020, confirms many false positives with Persyst 13. We excluded our tests on Persyst 14 as it highly under-performed relative to Encevis. Only Stanfords work provides code availability. We compared our results with Stanfords work outcome and provided pilot test results with the Encevis (EpiScan) tool on the Australian dataset, which shows a considerably lower sensitivity.

Added value of this studyTo the best of our knowledge, the current study is the first continental generalization that demonstrates the potential to achieve an expert human-level seizure recognition rate in a clinical setting and in just a fraction of time. The two datasets used in this study are recorded with different infrastructure, which adds to the independence of inference from hardware types and improves clinical utility. This is particularly important as 80% of patients with epilepsy live in low and middle-income countries with limited resources, particularly EEG specialists and neurologists.

Implications of all the available evidenceOur results support the potential benefits of deep learning AI in clinical settings for seizure recognition and its contribution to significant sensitivity over available solutions. Our AI-assisted system achieves more than a ten-fold increase in time efficiency and reports identical performance to human experts for EEG interpretation with access to great neurophysiology support and auxiliary data. Our findings, particularly our tests on an available commercial tool, recommend that the evaluation, test, or inference in AI systems be performed on different datasets, with diverse infrastructures, and on large-scale and realistic sets with long interictal periods.


title: Continental generalization of an AI system for clinical seizure recognition


title: Structured Modulations of Ongoing Variability by Task and Development

abstract: In carefully designed experiments, cognitive scientists interpret the mean event-related potentials (ERP) in terms of cognitive operations. However, the huge signal variability from one trial to the next, questions the representability of such mean events. We explored here whether this variability is an unwanted noise, or an informative part of the neural response. We took advantage of the rapid changes in the visual system during human infancy and analyzed the variability of visual responses to central and lateralized faces in 2-to 6-month-old infants and adults using high-density electroencephalography (EEG). We observed that neural trajectories of individual trials always remain very far from ERP components, only moderately bending their direction with a substantial temporal jitter across trials. However, single trial trajectories displayed characteristic patterns of acceleration and deceleration when approaching ERP components, as if they were under the active influence of steering forces causing transient attraction and stabilization. These dynamic events could only partly be accounted for by induced microstate transitions or phase reset phenomena. Furthermore, these structured modulations of response variability, both between and within trials, had a rich sequential organization, which, in infants, was modulated by the task difficulty. Our approaches to characterize Event Related Variability (ERV) expand and reinterpret classic ERP analyses, making them compliant with pervasive neural variability and providing a more faithful description of neural events following stimulus presentation.


title: Event-Related Variability is Modulated by Task and Development


title: Aberrant Temporal-spatial Patterns to Sad expressions in Major Depressive Disorders via Hidden Markov Model

abstract:
BackgroundThe pathological mechanisms of Major depressive disorders (MDD) is associated with over-expressing of negative emotions, and the overall temporal-spatial patterns underlying over-representation in depression still remained to be revealed to date. We hypothesized that the aberrant spatio-temporal attributes of the process of sad expressions relate to MDD and help to detect depression severity.

MethodsWe enrolled a total of 96 subjects including 47 MDDs and 49 healthy controls (HCs), and recorded their Magnetoencephalography data under a sad expressions recognition task. A hidden Markov model (HMM) was applied to separate the whole neural activity into several brain states, then to characterize the dynamics. To find the disrupted spatial-temporal features, power estimations and fractional occupancy of each state were contrasted between MDDs and HCs.

ResultsThree states were found over the period of emotional stimuli processing procedure. The visual state was mainly distributed in early stage (0 - 270ms) and the limbic state in middle and later stage (270ms - 600ms) of the task, while the fronto-parietal state remained a steady proportion across the whole period. MDDs activated statistically more in limbic system during limbic state (p = 0.0045) and less in frontoparietal control network during fronto-parietal state (p = 5.38*10-5) relative to HCs. Hamilton-Depression-Rating Scale scores was significantly correlated with the predicted severity value using the state descriptors (p = 0.0062, r = 0.3933).

DiscussionAs human brain exhibited varied activation patterns under the negative stimuli, MDDs expressed disrupted temporal-spatial activated patterns across varied stages involving the primary visual perception and emotional contents processing compared to HCs, indicting disordered regulation of brain functions. Furthermore, descriptors built by HMM could be potential biomarkers for identifying the severity of depression disorders.


title: A rapid CRISPR competitive assay for in vitro and in vivo discovery of potential drug targets affecting the hematopoietic system

abstract:
CRISPR/Cas9 can be used as an experimental tool to inactivate genes in cells. However, a CRISPR-targeted cell population will not show a uniform genotype of the targeted gene. Instead, a mix of genotypes is generated - from wild type to different forms of insertions and deletions. Such mixed genotypes complicate analyzing the role of the targeted gene in the studied cell population. Here, we present a rapid experimental approach to functionally analyze a CRISPR-targeted cell population that does not involve generating clonal cell lines. As a simple readout, we leverage the CRISPR-induced genetic heterogeneity and use sequencing to identify how different genotypes are enriched or depleted related to the studied cellular behavior or phenotype. The approach uses standard PCR, Sanger sequencing, and a simple sequence deconvoluting software, enabling laboratories without specific in-depth knowledge to also perform these experiments. As proof of principle, we present examples studying the role of different genes for various aspects related to hematopoietic cells (T cell development in vivo and activation in vitro, macrophage phagocytosis, and a leukemia-like phenotype induced by overexpressing a proto-oncogene). In conclusion, we present a rapid experimental approach to identify potential drug targets related to mature immune cells, as well as normal and malignant hematopoiesis.

Highlights- CRISPR generates genetic heterogeneity at the targeted site.
- Genetic heterogeneity complicates identifying the role of a targeted gene.
- Heterogeneity can be quantified by Sanger sequencing with sufficient sensitivity.
- Enrichment of specific genotypes can be used to identify roles for targeted genes.
- Competitive experiments show the potential of genotype enrichment as a discovery tool.

Graphical representation

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category: immunology


title: Impaired Cx43 gap junction endocytosis causes cardiovascular defects in zebrafish

abstract: Gap junction proteins, termed connexins (Cx), mediate direct cell-to-cell communication by forming channels that physically couple cells, thereby linking their cytoplasm, permitting exchange of molecules, ions, and electrical impulses. The most ubiquitously expressed gap junction protein, connexin43 (Cx43) has been implicated in cardiovascular diseases including arrhythmias, cardiomyopathies, hypertension and diabetes. The Cx43 C-terminal (CT) domain serves as the regulatory hub of the protein affecting all aspects of gap junction function. Here, deletion within the Cx43 CT (amino acids 256-289), a region known to encode key residues regulating gap junction turnover is employed to examine the effects of dysregulated Cx43 gap junction endocytosis using cultured cells (Cx43{Delta}256-289) and zebrafish model (cx43lh10). We report that this CT deletion causes defective gap junction endocytosis as well as increased gap junction intercellular communication (GJIC). Increased Cx43 protein content in cx43lh10 zebrafish, specifically in the cardiac tissue, larger gap junction plaques and longer Cx43 protein half-lives coincide with severely impaired cardiovascular development. These findings suggest that normal, unimpaired Cx43 gap junction endocytosis and turnover is an essential aspect of gap junction function as demonstrated here for cardiovascular development that when impaired can give rise to arrhythmias, heart malformations and aberrant vasculature structure and function.

category: cell biology


title: Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle

abstract: Moniliophthora perniciosa and Moniliophthora roreri are hemibiotrophic fungi that harbor a large number of Pathogenesis-Related 1 genes, many of which are induced in the biotrophic interaction with Theobroma cacao. Here, we provide evidence that the evolution of PR-1 in Moniliophthora was adaptive and potentially related to the emergence of the parasitic lifestyle in this genus. Phylogenetic analysis revealed conserved PR-1 genes, shared by many Agaricales saprotrophic species, that have diversified in new PR-1 genes putatively related to pathogenicity in Moniliophthora, as well as in recent specialization cases within both species. PR-1 families in Moniliophthora with higher evolutionary rates exhibit induced expression in the biotrophic interaction and positive selection clues, supporting the hypothesis that these proteins accumulated adaptive changes in response to host-pathogen arm race. Furthermore, we show that the highly diversified MpPR-1 genes are not induced by two phytoalexins, suggesting detoxification might not be their main function as proposed before.


title: Hibernation slows epigenetic aging in yellow-bellied marmots

abstract: Species that hibernate live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor-arousal cycles occur multiple times during hibernation, and it has been suggested that processes controlling the transition between torpor and arousal states cause aging suppression. Metabolic rate is also a known correlate of longevity, we thus proposed the  hibernation-aging hypothesis whereby aging is suspended during hibernation. We tested this hypothesis in a well-studied population of yellow-bellied marmots (Marmota flaviventer), which spend 7-8 months per year hibernating. We used two approaches to estimate epigenetic age: the epigenetic clock and the epigenetic pacemaker. Variation in epigenetic age of 149 samples collected throughout the life of 73 females were modeled using generalized additive mixed models (GAMM), where season (cyclic cubic spline) and chronological age (cubic spline) were fixed effects. As expected, the GAMM using epigenetic ages calculated from the epigenetic pacemaker was better able to detect nonlinear patterns in epigenetic age change over time. We observed a logarithmic curve of epigenetic age with time, where the epigenetic age increased at a higher rate until females reached sexual maturity (2-years old). With respect to circannual patterns, the epigenetic age increased during the summer and essentially stalled during the winter. Our enrichment analysis of age-related CpG sites revealed pathways related to development and cell differentiation, while the season-related CpGs enriched pathways related to central carbon metabolism, immune system, and circadian clock. Taken together, our results are consistent with the hibernation-aging hypothesis and may explain the enhanced longevity in hibernators.


title: U5 snRNA interactions with exons ensure splicing precision

abstract: Imperfect conservation of human pre-mRNA splice sites is necessary to produce alternative isoforms. This flexibility is combined with precision of the message reading frame. Apart from intron-termini GU_AG and the branchpoint A, the most conserved are the exon-end guanine and +5G of the intron-start. Association between these guanines cannot be explained solely by base-pairing with U1snRNA in the early spliceosome complex. U6 succeeds U1 and pairs +5G in the pre-catalytic spliceosome, while U5 binds the exon-end. Current U5snRNA reconstructions by CryoEM cannot explain the conservation of the exon-end G. Conversely, human mutation analyses show that guanines of both exon-termini can suppress splicing mutations. Our U5 hypothesis explains the mechanism of splicing precision and the role of these conserved guanines in the pre-catalytic spliceosome. We propose: 1) Optimal binding register for human exons and U5 - the exon junction positioned at U5Loop1 C39|C38. 2) Common mechanism of base pairing of human U5snRNA with diverse exons and bacterial Ll.LtrB intron with new loci in retrotransposition - guided by base pair geometry. 3) U5 plays a significant role in specific exon recognition in the pre-catalytic spliceosome. Our statistical analyses show increased U5 Watson-Crick pairs with the 5exon in the absence of +5G at the intron-start. In 5exon positions -3 and -5 this effect is specific to U5snRNA rather than U1snRNA of the early spliceosome. Increased U5 Watson-Crick pairs with 3exon position +1 coincide with substitutions of the conserved -3C at the intron 3end. Based on mutation and X-ray evidence we propose that -3C pairs with U2 G31 juxtaposing the branchpoint and the 3intron-end. The intron-termini pair, formed in the pre-catalytic spliceosome to be ready for transition after branching, and the early involvement of the 3intron-end ensure that the 3exon contacts U5 in the pre-catalytic complex. We suggest that splicing precision is safeguarded cooperatively by U5, U6 and U2snRNAs that stabilise the pre-catalytic complex by Watson-Crick base pairing. In addition, our new U5 model explains the splicing effect of exon-start +1G mutations: U5 Watson-Crick pairs with exon +2C/+3G strongly promote exon inclusion. We discuss potential applications for snRNA-therapeutics and gene repair by reverse splicing.

category: genetics


title: Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

abstract: The accuracy of the identification of unknown specimens using DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. A rampant growth in barcode data led to a stringent need for data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data deposited in the Barcode of Life Data Systems (BOLD) has been undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). For practical reasons, only major taxonomic groups were reviewed and annotated (crustaceans, echinoderms, molluscs, and polychaetes). The congruence of Linnean names with Barcode Index Numbers (BINs) was investigated, and the records deemed uncertain were annotated with four tags: a) MIS-ID (misidentified, mislabeled or contaminated records), b) AMBIG (ambiguous records unresolved with the current data), c) COMPLEX (species occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. This high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross -contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is crucial for barcode applications, such manual efforts of reviewing large datasets are not sustainable and the implementation of automated solutions to the furthest possible extent is hi ghly desirable.


title: Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo's Paradox

abstract: Temperate bacteriophages lyse or lysogenize the host cells depending on various parameters of infection, a key one being the host population density. However, the effect of different propensities of phages for lysis and lysogeny on phage fitness is an open problem. We explore a nonlinear dynamic evolution model of competition between two phages, one of which is disadvantaged in both the lytic and lysogenic phases. We show that the disadvantaged phage can win the competition by alternating between the lytic and lysogenic phases, each of which individually is a "loser". This counter-intuitive result recapitulates Parrondos paradox in game theory, whereby individually losing strategies can combine to produce a winning outcome. The results suggest that evolution of phages optimizes the ratio between the lysis and lysogeny propensities rather than the phage reproduction rate in any individual phase. These findings are expected to broadly apply to the evolution of host-parasite interactions.


title: Clustering-based time series analysis on insulin response in the blood-brain barrier

abstract:
BackgroundCritical functions of the blood-brain barrier (BBB), including cerebral blood flow and vascular response, are regulated by insulin signaling pathways. Therefore, endothelial insulin resistance could lead to vascular dysfunction, which is associated with neurodegenerative diseases such as Alzheimers disease (AD).

ObjectiveThe objective of the current study is to map the dynamics of insulin-responsive pathways in polarized human cerebral microvascular endothelial cells (hCMEC/D3) cell monolayers, a widely used BBB cell culture model, to identify molecular mechanisms underlying BBB dysfunction in AD.

MethodsRNA-Sequencing (RNA-Seq) was performed on hCMEC/D3 cell monolayers with and without insulin treatment at various time points. The Short Time-series Expression Miner (STEM) method was used to identify clusters of genes with distinct and representative patterns. Functional annotation and pathway analysis of the genes from top clusters were conducted using the Webgestalt and Ingenuity Pathway Analysis (IPA) software, respectively.

ResultsQuantitative expression differences of 19,971 genes between the insulin-treated and control monolayers at five-time points were determined. STEM software identified 11 clusters with 3061 genes across that displayed various temporal patterns. Gene ontology enrichment analysis performed using the top 5 clusters demonstrated that these genes were enriched in various biological processes associated with AD pathophysiology. The IPA analyses revealed that signaling pathways exacerbating AD pathology such as inflammation were downregulated after insulin treatment (clusters 1 to 3). In contrast, pathways attenuating AD pathology were upregulated, including synaptogenesis and BBB repairment (clusters 4 and 5).

ConclusionsThese findings unravel the dynamics of insulin action on the BBB endothelium and inform about downstream signaling cascades that potentially regulate neurovascular unit (NVU) functions that are disrupted in AD.


title: AN INTEGRATIVE APPROACH DISCOVERS A NOVEL ANTI-LEUKEMIC PEPTIDE FROM HUMAN MILK

abstract:
Chemotherapy in childhood leukemia is associated with late morbidity in leukemic survivors, while certain patient subsets are relatively resistant to standard chemotherapy. It is therefore important to identify new agents with sensitivity and selectivity towards leukemic cells, while having less systemic toxicity. Peptide-based therapeutics has gained much attention during the last few years. Here, we used an integrative workflow combining mass spectrometric peptide library construction, in silico anticancer peptide screening, and in vitro leukemic cell studies to discover a novel anti-leukemic peptide having 3+charges and alpha-helical structure, namely HMP-S7, from human breast milk. HMP-S7 showed cytotoxic activity against four distinct leukemic cell lines in a dose-dependent manner but had no effect on solid malignancies or representative normal cells. HMP-S7 induced leukemic cell death by penetrating the plasma membrane to enter the cytoplasm and cause leakage of lactate dehydrogenase, thus acting in a membranolytic manner. Importantly, HMP-S7 exhibited anti-leukemic effect against patient-derived leukemic cells ex vivo. In conclusion, HMP-S7 is a selective anti-leukemic peptide with promise which requires further validation in preclinical and clinical studies.

TeaserIn silico screening of naturally occurring human milk peptides discovers a new anticancer peptide that kills leukemic cells in vitro and ex vivo.

category: pharmacology and toxicology


title: An integrative approach leads to the discovery of a novel anti-leukemic peptide from human milk


title: Knowledge, Attitude and Practices towards COVID-19 Guidelines among Students in Bangladesh

abstract:
This paper explores the level of knowledge, attitude and practices of COVID-19 guidelines among the students in Bangladesh. In achieving this objective, this paper uses primary data collected from 1822 students and three different Likert scales and a one-way ANOVA test are used to assess knowledge, attitudes, and practice (KAP) scores and mean differences with respect to different variables. The research reveals that the majority of students have a higher level of knowledge and a positive attitude towards the COVID-19 guidelines. In contrary, only 0.22 percent students show strong compliance towards COVID-19 guidelines while majority students (60.54 percent) have rather a poor adherence which is an alarming finding. Reopening the educational institutions in Bangladesh is, therefore, not advisable yet and reinforcing the preventive measures through campaigns and online discussion to persuade people to follow the preventive guidelines is highly recommended to contain this global disease.

What We Already KnowO_LIMajority papers revealed the KAP of general people or medical related people.
C_LIO_LIMajority people have moderate level of knowledge towards COVID-19.
C_LIO_LINo research is found on KAP of the students in Bangladesh.
C_LI

What This Article AddsO_LIThe KAP of COVID-19 guidelines among the students in Bangladesh.
C_LIO_LIMajority students have the higher level of knowledge towards COVID-19 guideline among students.
C_LIO_LIOnly 0.22 percent students show strong compliance towards COVID-19 guidelines which recommends not reopening educational institutions now.
C_LI

category: scientific communication and education


title: Differential Roles of Positive and Negative Valence Systems in the Development of Post-Traumatic Stress Psychopathology

abstract: Negative and positive valence systems (NVS and PVS) pertain to processing of aversive and rewarding stimuli, respectively. Post-Traumatic Stress Disorder (PTSD) has been typically associated with hyper-responsivity of the NVS, and more recently, with deficient PVS functionality. The respective roles of these systems in early PTSD development have yet to be resolved. Here, we assessed neurobehavioral indicators of PVS and NVS longitudinally among 171 adult civilians at 1-, 6-, and 14-months following trauma exposure (TP1, TP2, and TP3). Using the  Safe or Risky Domino Choice (SRDC) game during fMRI, NVS and PVS functionality (i.e., activity and connectivity) were indicated by the amygdala and ventral striatum (VS) responses to punishments and rewards, respectively. The complementary functionality of these systems was behaviorally assessed as the percentage of risky choices taken during the game. Results revealed that increased amygdala functionality at TP1 was associated with greater PTSD severity at TP1 and TP3, specifically with hyperarousal and intrusion. Decreased VS functionality at TP1 was associated with greater PTSD severity at TP3, specifically with avoidance. Explainable machine learning revealed the primacy of PVS over NVS functionality at TP1 in predicting PTSD severity at TP3. Behaviorally, fewer risky choices were associated with more severe symptoms at TP1, especially with intrusion and avoidance. Overall, these results suggest a differential and potentially complementary involvement of NVS and PVS in PTSD development following trauma. Early therapeutics for PTSD in the immediate aftermath of trauma may thus target both negative and positive valence processing.


title: Regulation of coordinated muscular relaxation by a pattern-generating intersegmental circuit

abstract: Typical patterned movements in animals are achieved through combinations of contraction and delayed relaxation of groups of muscles. However, how intersegmentally coordinated patterns of muscular relaxation are regulated by the neural circuits remain poorly understood. Here, we identify Canon, a class of higher-order premotor interneurons, that regulates muscular relaxation during backward locomotion of Drosophila larvae. Canon neurons are cholinergic interneurons present in each abdominal neuromere and show wave-like activity during fictive backward locomotion. Optogenetic activation of Canon neurons induces relaxation of body wall muscles, whereas inhibition of these neurons disrupts timely muscle relaxation. Canon neurons provide excitatory outputs to inhibitory premotor interneurons. Canon neurons also connect with each other to form an intersegmental circuit and regulate their own wave-like activities. Thus, our results demonstrate how coordinated muscle relaxation can be realized by an intersegmental circuit that regulates its own patterned activity and sequentially terminates motor activities along the anterior-posterior axis.


title: Development and pre-clinical evaluation of Newcastle disease virus-vectored SARS-CoV-2 intranasal vaccine candidate

abstract:
The COVID-19 pandemic has claimed the lives of millions of people worldwide and threatens to become an endemic problem, therefore the need for as many types of vaccines as possible is of high importance.

Because of the millions of doses required, it is desirable that vaccines are not only safe and effective, but also easy to administer, store, and inexpensive to produce.

Newcastle Disease Virus (NDV) is responsible for a respiratory disease in chickens. It has no pathogenic homologue in humans. NDV is recognized as an oncolytic virus, and its use in humans for oncological treatment is being evaluated.

In the present work, we have developed two types of NDV-vectored candidate vaccines, which carry the surface-exposed RBD and S1 antigens of SARS-CoV-2, respectively. These vaccine candidates were produced in specific-pathogen-free embryonating chicken eggs, and purified from allantoic fluid before lyophilization. These vaccines were administered intranasally to three different animal models: mice, rats and hamsters, and evaluated for safety, toxicity, immunogenicity, stability and efficacy. Efficacy was evaluated in a challenge assay against active SARS-CoV-2 virus in the Golden Syrian hamster model.

The NDV-vectored vaccine based on the S1 antigen was shown to be safe and highly immunogenic, with the ability to neutralize SARS-CoV-2 in-vitro, even with an extreme dilution of 1/640. Our results reveal that this vaccine candidate protects the lungs of the animals, preventing cellular damage in this tissue. In addition, this vaccine reduces the viral load in the lungs, suggesting that it may significantly reduce the likelihood of transmission. Being lyophilized, this vaccine candidate is very stable and can be stored for several months at 4-8C.

In conclusion, our NDV-based vaccine candidate has shown a very favorable performance in the pre-clinical study, serving as evidence for a future evaluation in a Phase-I human clinical trial. This candidate represents a promising tool in the fight against COVID-19.


title: Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection

abstract: Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 66 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL collection (BActeriophage SElection for your Laboratory). This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside ten well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to eleven defense systems across different layers of bacterial immunity, and matched these results to the phages host range across a panel of pathogenic enterobacterial strains. Our results reveal clear patterns in the distribution of phage phenotypes and genomic features that highlight systematic differences in the potency of different immunity systems and point towards the molecular basis of receptor specificity in several phage groups. Strong trade-offs were detected between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

category: microbiology


title: Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies

abstract: Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.


title: A Peek into the Plasmidome of Global Sewage

abstract:
Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impact on the ecology and evolution of bacteria and can significantly influence the burden of infectious diseases. Insight about the identity and functions encoded on plasmids on the global scale are largely lacking. Here we investigate the plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project. We obtained 105 Gbp Oxford Nanopore and 167 Gbp Illumina DNA sequences from plasmid DNA preparations and assembled 165,302 contigs (159,322 circular). Of these, 58,429 encoded for genes with plasmid-related and 11,222 with virus/phage-related proteins. About 90% of the circular DNA elements did not have any similarity to known plasmids. Those that exhibited similarity, had similarity to plasmids whose hosts were previously detected in these sewage samples (e.g. Acinetobacter, Escherichia, Moraxella, Enterobacter, Bacteroides, and Klebsiella). Some AMR classes were detected at a higher abundance in plasmidomes (e.g. macrolide-lincosamide-streptogramin B, macrolide, and quinolone), as compared to the respective complex sewage samples. In addition to AMR genes, a range of functions were encoded on the candidate plasmids, including plasmid replication and maintenance, mobilization, and conjugation. In summary, we describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes. Moreover, the obtained data could provide further valuable insight into the ecology and evolution of microbiomes, knowledge about AMR transmission, and the discovery of novel functions.

ImportanceThis is, to the best of our knowledge, the first study to investigate plasmidomes at a global scale using long read sequencing from complex untreated domestic sewage. Previous metagenomic surveys have detected AMR genes in a variety of environments, including sewage. However, it is unknown whether the AMR genes were encoded on the microbial chromosome or are located on extrachromosomal elements, such as plasmids. Using our approach, we recovered a large number of plasmids, of which most appear novel. We identified distinct AMR genes that were preferentially located on plasmids, potentially contributing to their transmissibility. Overall, plasmids are of great importance for the biology of microorganisms in their natural environments (free-living and host-associated), as well as molecular biology, and biotechnology. Plasmidome collections may therefore be valuable resources for the discovery of fundamental biological mechanisms and novel functions useful in a variety of contexts.


title: Deletion disrupts a conserved antibody epitope in a SARS-CoV-2 variant of concern

abstract: Multiple SARS-CoV-2 variants with altered antigenicity have emerged and spread internationally. In one lineage of global concern, we identify a transmitted variant with a deletion in its receptor binding domain (RBD) that disrupts an epitope which is conserved across sarbecoviruses. Overcoming antigenic variation by selectively focusing immune pressure on this conserved site may, ultimately, drive viral resistance.


title: Drug development of an affinity enhanced, broadly neutralizing heavy chain only antibody that restricts SARS-CoV-2 in hamsters

abstract: We have identified camelid single-domain antibodies (VHHs) that cross-neutralize SARS-CoV-1 and -2, such as VHH72, which binds to a unique highly conserved epitope in the viral receptor-binding domain (RBD) that is difficult to access for human antibodies. Here, we establish a protein engineering path for how a stable, long-acting drug candidate can be generated out of such a VHH building block. When fused to human IgG1-Fc, the prototype VHH72 molecule prophylactically protects hamsters from SARS-CoV-2. In addition, we demonstrate that both systemic and intranasal application protects hACE-2-transgenic mice from SARS-CoV-2 induced lethal disease progression. To boost potency of the lead, we used structure-guided molecular modeling combined with rapid yeast-based Fc-fusion prototyping, resulting in the affinity-matured VHH72_S56A-Fc, with subnanomolar SARS-CoV-1 and -2 neutralizing potency. Upon humanization, VHH72_S56A was fused to a human IgG1 Fc with optimized manufacturing homogeneity and silenced effector functions for enhanced safety, and its stability as well as lack of off-target binding was extensively characterized. Therapeutic systemic administration of a low dose of VHH72_S56A-Fc antibodies strongly restricted replication of both original and D614G mutant variants of SARS-CoV-2 virus in hamsters, and minimized the development of lung damage. This work led to the selection of XVR011 for clinical development, a highly stable anti-COVID-19 biologic with excellent manufacturability. Additionally, we show that XVR011 is unaffected in its neutralizing capacity of currently rapidly spreading SARS-CoV-2 variants, and demonstrate its unique, wide scope of binding across the Sarbecovirus clades.

category: molecular biology


title: Drug development of an affinity enhanced, broadly neutralizing heavy chain-only antibody that restricts SARS-CoV-2 in rodents


title: Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3 and SIRT1

abstract: Mitosis comprises multiple changes, including chromatin condensation and transcription reduction. Intriguingly, while histone acetylation levels are reduced during mitosis, the mechanism of this reduction is unclear. We studied the mitotic regulation of H3K9ac by using inhibitors of histone deacetylases. We evaluated the involvement of the targeted enzymes in regulating H3K9ac during mitotic stages and cytokinesis by immunofluorescence and immunoblots. We identified HDAC2, HDAC3 and SIRT1 as modulators of the mitotic levels of H3K9ac. HDAC2 inhibition increased H3K9ac levels in prophase, whereas HDAC3 or SIRT1 inhibition, increased H3K9ac levels in metaphase. Next, we performed ChIP-seq in mitotic cells following targeted inhibition of these histone deacetylases. While the genomic areas impacted by HDAC2 and HDAC3 were mostly concordant, a subset of loci were unique to each enzyme. Interestingly, HDAC3-specific targets were enriched for genes involved in mitosis regulation. Our results support a model in which H3K9 deacetylation is a stepwise process - at prophase HDAC2 modulates most transcription-associated H3K9ac-marked loci and at metaphase HDAC3 maintains the reduced acetylation, whereas SIRT1 potentially regulates H3K9ac by impacting HAT activity.


title: The DMT and Psilocin Treatment Changes CD11b+ Activated Microglia Immunological Phenotype

abstract: Psychedelics are new, promising candidate molecules for clinical use in psychiatric disorders such as Treatment-Resistant Depression (TRD) and Post Traumatic Stress Disorder (PTSD). They were recently also proposed as molecules supporting neural tissue repair by anti-inflammatory properties. Here we reported that two classic psychedelics, DMT and psilocin, can influence microglial functions by reducing the level of TLR4, p65, CD80 proteins, which are markers of the immune response, and upregulat TREM2 neuroprotective receptor. Psilocin also secured neuronal survival in the neuron-microglia co-culture model by attenuating the phagocytic function of microglia. We conclude that DMT and psilocin regulate the immunomodulatory potential of microglia. Of note, psychedelics were previously reported as a relatively safe treatment approach. The demonstrated regulation of inflammatory molecules and microglia phagocytosis suggests that psychedelics or their analogs are candidates in the therapy of neurological disorders where microglia and inflammation significantly contribute to pathogenic disease mechanisms.


title: Simultaneous equations modelling of communities with interacting species networks

abstract: To understand community assembly, ecologists have long sought to extract the signal of biotic interactions from species co-occurrence patterns. These efforts face multiple difficulties such as confounding environmental effects, confounding indirect interactions between multiple species and asymmetry of interactions. To address these problems, we propose Simultaneous Community Equations Modelling (SCEM) as a framework to explicitly account for asymmetric interaction networks in community models. SCEM uses a system of equations to model the occurrence of each species as a function of measured and unmeasured (latent) environmental predictors, and the occurrence of potentially all the other species in the community. Biotic interactions most supported by the data are identified using heuristic optimization of a parsimony criterion, implemented as a Genetic Algorithm. Extensive simulations show that SCEM can recover interaction network topologies in virtual communities. We present a software to implement SCEM and illustrate its application with a case study.

category: ecology


title: In search of an honest butterfly: sexually selected wing coloration and reproductive traits from wild populations of the cabbage white butterfly

abstract: Sexual selection is central to many theories on mate selection and individual behavior. Relatively little is known, however, about the impacts that human-induced rapid environmental change are having on secondary sexually selected characteristics. Honest signals function as an indicator of mate quality when there are differences in nutrient acquisition and are thus potentially sensitive to anthropogenically-altered nutrient inputs. We used the cabbage white butterfly, Pieris rapae (L.), to investigate differences in color and testes size in a system that is often exposed to agricultural landscapes with nitrogen addition. We collected individuals from four sites in California and Nevada to investigate variation in key traits and the possibility that any relationship between wing color and a reproductive trait (testes size) could vary among locations in the focal butterfly. Coloration variables and testes size were positively albeit weakly associated across sites, consistent with the hypothesis that females could use nitrogen-based coloration in the cabbage white as an indicator for a male mating trait that has the potential to confer elevated mating success in progeny. However, variation in testes size and in the relationship between testes size and wing color suggest complexities that need exploration, including the possibility that the signal is not of equal value in all populations. Thus these results advance our understanding of complex relationships among environmental change and sexual selection in the wild.


title: GFI1 cooperates with IKAROS/IKZF1 to activate gene expression in T-cell acute lymphoblastic leukemia

abstract: Growth factor independence-1 (GFI1) is a transcriptional repressor and master regulator of normal and malignant hematopoiesis. Repression by GFI1 is attributable to recruitment of LSD1-containing protein complexes via its SNAG domain. However, the full complement of GFI1 partners in transcriptional control is not known. We show that in T-ALL cells, GFI1 and IKAROS are transcriptional partners that co-occupy regulatory regions of hallmark T cell development genes. Transcriptional profiling reveals a subset of genes directly transactivated through the GFI1--IKAROS partnership. Among these is NOTCH3, a key factor in T-ALL pathogenesis. Surprisingly, NOTCH3 transactivation by GFI1 and IKAROS requires the GFI1 SNAG domain but occurs independent of SNAG--LSD1 binding. GFI1 variants deficient in LSD1 binding fail to transactivate NOTCH3, but conversely, small molecules that disrupt the SNAG--LSD1 interaction while leaving the SNAG primary structure intact stimulate NOTCH3 expression. These results identify a non-canonical transcriptional control mechanism in T-ALL which supports GFI1-mediated transactivation in partnership with IKAROS and suggest competition between LSD1-containing repressive complexes and others favoring transactivation.

category: biochemistry


title: Ameliorating Emotional Attention through Modulation of Neural Oscillations with Transcranial Alternating Current Stimulation

abstract:
BackgroundNumerous clinical reports suggest that psychopathy like schizophrenia, anxiety and depressive disorder is accompanied by early attentional abnormalities in emotional information processing. In the past decade, the efficacy of transcranial alternating current stimulation (tACS) in changing emotional functioning has been repeatedly observed and has demonstrated a causal relationship between endogenous oscillations and emotional processing. However, tACS effects on emotional attention have not yet been tested.

MethodsA total of 53 healthy participants were randomized to 2 groups, and they were subjected to active or sham tACS at individual alpha frequency (IAF) in the bilaterally dorsolateral prefrontal cortex (dlPFC). Participants and received this treatment for 20 min durations daily for 7 consecutive days. On days 1 and 7, electroencephalogram (EEG) recording of 8 minute resting with eyes open and closed. Responses to a facial emotion identification task were also recorded to measure alpha changes and event-related potential (ERP) alterations.

ResultsOn day 7 after tACS, the active group showed a more clear elevation in alpha power at rest, especially in open state around stimulation area, compared to the sham group. ERPs revealed a significant larger P200 amplitude after active stimulation (p < 0.05), indicating attentional improvement in facial emotion processing. Additionally, a notable positive correlation (p < 0.05) between alpha power and P200 amplitude was found, providing an electrophysiological interpretation regarding the role of tACS in emotional attention modulation. In addition, the IAF-tACS showed an obvious advantage in alpha entrainment compared to an additional 10 Hz-tACS.

ConclusionsThese results support a seminal outcome for the effect of IAF-tACS on emotional attention modulation, demonstrating a feasible and individual-specific therapy for neuropsychiatric disorders related to emotion processing, especially regarding oscillatory disturbances.


title: A Macro-scale Comparison Algorithm for Analysis of TCR Repertoire Completeness

abstract:
Recent advances in biotechnology are beginning to generate whole immunome datasets, which will enable the comparison of immune repertoires between individuals, e.g., to assess immunocompetence. Existing algorithms cluster cell types based on the relative expression abundance of about 20 000 genes, but such algorithms have limited utility when comparing immunome datasets with many higher orders of magnitude (>1012) of variation, such as occurs in immunoreceptor sequences in highly polyclonal naive repertoires.

In this paper we present a method for comparing immune repertoires by identifying macro-level features that are conserved between similar individuals. Our method allows us to detect some blind spots in naive populations and to assess whether a repertoire is likely complete by examining only a sample of its sequences.

Author SummaryIn this paper we present a method for comparing the immune repertoire of different individuals. Repertoires are represented by a sample of genetic sequences. Our technique coarse grains each individuals data into groups, matches groups between individuals and finds significant differences.


title: Spatial patterns in functional brain connectomes reflect acute and chronic cannabis use.

abstract: Resting state fMRI has been employed to identify alterations in functional connectivity within or between brain regions following acute and chronic exposure to {Delta}9-tetrahydrocannabinol (THC), the psychoactive component in cannabis. Most studies focused a priori on a limited number of local brain areas or circuits, without considering the impact of cannabis on wholebrain network organization. The present study attempted to identify changes in the wholebrain human functional connectome as assessed with ultra-high field (7T) resting state scans of occasional (N=12) and chronic cannabis users (N=14) during placebo and following vaporization of cannabis. Two distinct data-driven methodologies, i.e. network-based statistics (NBS) and connICA, were used to identify changes in functional connectomes associated with acute cannabis intoxication and chronic cannabis use. Both methodologies revealed a broad state of hyperconnectivity within the entire range of major brain networks in chronic cannabis users compared to occasional cannabis users, which might be reflective of an adaptive network reorganization following prolonged cannabis exposure. The connICA methodology also extracted a distinct spatial connectivity pattern of hypoconnectivity involving the dorsal attention, limbic, subcortical and cerebellum networks and of hyperconnectivity between the default mode and ventral attention network, that was associated with the feeling of subjective high during THC intoxication across both user groups. Whole-brain network approaches identified spatial patterns in functional brain connectomes that distinguished acute from chronic cannabis use, and offer an important utility for probing the interplay between short and long-term alterations in functional brain dynamics when progressing from occasional to chronic use of cannabis.


title: Control of Parallel Hippocampal Output Pathways by Amygdalar Long-Range Inhibition

abstract: Projections from the basal amygdala (BA) to the ventral hippocampus (vH) are proposed to provide information about the rewarding or threatening nature of learned associations to support appropriate goal-directed and anxiety-like behaviour. Such behaviour occurs via the differential activity of multiple, parallel populations of pyramidal neurons in vH that project to distinct downstream targets, but the nature of BA input and how it connects with these populations is unclear. Using channelrhodopsin-2-assisted circuit mapping in mice, we show that BA input to vH consists of both excitatory and inhibitory projections. Excitatory input specifically targets BA- and nucleus accumbens-projecting vH neurons, and avoids prefrontal cortex-projecting vH neurons; while inhibitory input preferentially targets BA-projecting neurons. Through this specific connectivity, BA inhibitory projections gate place-value associations by controlling the activity of nucleus accumbens-projecting vH neurons. Our results define a parallel excitatory and inhibitory projection from BA to vH that can support goal-directed behaviour.


title: Pediatric nasal epithelial cells are less permissive to SARS-CoV-2 replication compared to adult cells

abstract: Children typically experience more mild symptoms of COVID-19 when compared to adults. There is a strong body of evidence that children are also less susceptible to SARS-CoV-2 infection with the ancestral viral isolate. However, the emergence of SARS-CoV-2 variants of concern (VOCs) has been associated with an increased number of pediatric infections. Whether this is the result of widespread adult vaccination or fundamental changes in the biology of SARS-CoV-2 remains to be determined. Here, we use primary nasal epithelial cells from children and adults, differentiated at an air-liquid interface to show that the ancestral SARS-CoV-2 replicates to significantly lower titers in the nasal epithelial cells of children compared to those of adults. This was associated with a heightened antiviral response to SARS-CoV-2 in the nasal epithelial cells of children. Importantly, the Delta variant also replicated to significantly lower titres in the nasal epithelial cells of children. This trend was markedly less pronounced in the case of Omicron. It is also striking to note that, at least in terms of viral RNA, Omicron replicated better in pediatric NECs compared to both Delta and the ancestral virus. Taken together, these data show that the nasal epithelium of children supports lower infection and replication of ancestral SARS-CoV-2, although this may be changing as the virus evolves.


title: Experimental susceptibility of North American raccoons (Procyon lotor) and striped skunks (Mephitis mephitis) to SARS-CoV-2

abstract:
Skunks and raccoons were intranasally inoculated or indirectly exposed to SARS-CoV-2. Both species are susceptible to infection; however, the lack of, and low quantity of infectious virus shed by raccoons and skunks, respectively, and lack of cage mate transmission in both species, suggest that neither species are competent SARS-CoV-2 reservoirs.

Article Summary LineExperimental SARS-CoV-2 inoculation of North American raccoons and striped skunks showed susceptibility to infection, but transient, low-level shedding suggests that neither species is likely to be a competent natural reservoir.


title: CBL-C E3 ubiquitin ligase acts as a host defense to mediate ubiquitin-proteasomal degradation of enteropathogenic Escherichia coli Tir protein

abstract:
Translocated intimin receptor (Tir) is an essential bacterial factor for enteropathogenic Escherichia coli (EPEC) to establish Tir-intimin interaction-mediated adherence to the epithelial cell and to form actin pedestal structures beneath the adherent bacteria. However, it remains unclear how the host cells eliminate Tir protein after infection. Here we show that intracellular translocated Tir is degraded via the host ubiquitin- proteasome system. We found that host CBL-C, an E3 ubiquitin-protein ligase, bound to and ubiquitinated the 454 tyrosine-phosphorylated Tir protein. Tir ubiquitination leads to proteasome-dependent degradation and attenuated EPEC colonization of the epithelial cell. Using Citrobacter rodentium, a mouse model for EPEC, we demonstrated that infection with C. rodentium mutant expressing a tyrosine- phenylalanine-substituted Tir (CBL-C resistant) showed increased bacterial loads in the colon and lethality compared with infection with C. rodentium expressing wild-type Tir. These results indicate that CBL-C is a critical host defense factor that determines the fate of cytosolic Tir and terminates bacterial colonization.

Graphical Abstracts

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title: Domain dependent orchestrated regulation of bacterial growth, persistence and chemotaxis by an essential GTPase, CgtA, in Vibrio cholerae

abstract: CgtA, an evolutionarily conserved GTPase, associated with the 50S ribosome controls a broad spectrum of physiological processes in bacteria. It has three structural domains, viz., N-terminal domain (NTD), GTPase domain and C-terminal domain (CTD). CgtA regulates expression of several of genes during nutritional stress in Vibrio cholerae. The mechanism of transcriptional regulation by CgtA is unknown, though the NTD concomitantly with the GTPase domain participates in the process. Here, we show that the in vivo deletion of the 57 amino acids long CTD of CgtA GTPase of V. cholerae is dispensable for viability, contrary to the complete knockdown of cgtA gene. Slower growth was observed in cgtA knockdown strain with intermittent diauxic lags in minimal media than the CTD deleted strain. Irreversible defect in colony morphology was observed in the cells with CTD deletion. Resuscitation of persister cells occurred when nutritionally deprived complete cgtA knockdown cells after growing for longer periods were transferred to nutritionally enriched media. The motility of the cgtA knockdown strain was significantly reduced than the wild type cells. Furthermore, CTD deleted cells were also found to be defective in motility, but comparatively lower than cgtA knockdown cells. Elongated and slender V. cholerae cells were observed by SEM imaging upon cgtA depletion, whereas, upon CTD deletion cellular elongation did not occur. Based on our study here, we propose that the CTD of CgtA perceives the nutritional stress response, to which the NTD and GTPase responds.


title: Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion

abstract:
BackgroundRecent studies have suggested that individual variants do not sufficiently explain the variable expressivity of phenotypes observed in complex disorders. For example, the 16p12.1 deletion is associated with developmental delay and neuropsychiatric features in affected individuals, but is inherited in >90% of cases from a mildly-affected parent. While children with the deletion are more likely to carry additional "second-hit" variants than their parents, the mechanisms for how these variants contribute to phenotypic variability are unknown.

MethodsWe performed detailed clinical assessments, whole-genome sequencing, and RNA sequencing of lymphoblastoid cell lines for 32 individuals in five large families with multiple members carrying the 16p12.1 deletion. We identified contributions of the 16p12.1 deletion and "second-hit" variants towards a range of expression changes in deletion carriers and their family members, including differential expression, outlier expression, alternative splicing, allele-specific expression, and expression-quantitative trait loci analyses.

ResultsWe found that the deletion dysregulates multiple autism and brain development genes such as FOXP1, ANK3, and MEF2. Carrier children also showed an average of 5,323 gene expression changes compared with one or both parents, which matched with 33/39 observed developmental phenotypes. We identified significant enrichments for 13/25 classes of "second-hit" variants in genes with expression changes, where 4/25 variant classes were only enriched when inherited from the non-carrier parent, including loss-of-function SNVs and large duplications. In 11 instances, including for ZEB2 and SYNJ1, gene expression was synergistically altered by both the deletion and inherited "second-hits" in carrier children. Finally, brain-specific interaction network analysis showed strong connectivity between genes carrying "second-hits" and genes with transcriptome alterations in deletion carriers.

ConclusionsOur results suggest a potential mechanism for how "second-hit" variants modulate expressivity of complex disorders such as the 16p12.1 deletion through transcriptomic perturbation of gene networks important for early development. Our work further shows that family-based assessments of transcriptome data are highly relevant towards understanding the genetic mechanisms associated with complex disorders.


title: Microfluidic Live-Imaging technology to perform research activities in 3D models

abstract: One of the most surprising differences observed when comparing cell cultures in 2D and 3D is morphological dissimilarity and their evolution over time. Cells grown in a monolayer tend to flatten in the lower part of the plate adhering to and spreading in the horizontal plane without expanding in the vertical dimension. The result is that cells grown in 2D have a forced apex-basal polarity. 3D cultures support co-cultivation and crosstalking between multiple cell types, which regulate development and formation in the in vivo counterpart. 3D models culture, with or without a scaffold matrix, can exhibit more in vivo-like morphology and physiology. 3D cultures recapitulate relevant physiological cellular processes, transforming into unique platforms for drug screening. To support and guarantee the functional maintenance of a 3D structure, one must consider the structures and dynamics of regulatory networks, increasingly studied with live-imaging microscopy. However, commercially available technologies that can be used for current laboratory needs are limited, although there is a need to facilitate the acquisition of cellular kinetics with a high spatial and temporal resolution, to elevate visual performance and consequently that of experimentation. The CELLviewer is a newly conceived and developed multi-technology instrumentation, combining and synchronizing the work of different scientific disciplines. This work aims to test the system with two models: the first model is a single Jurkat cell while the second is an MCF-7 spheroid. After having grown both models, the two models used are loaded into the microfluidic cartridge for each experiment and recorded in time-lapse for a total of 4 hours. After adaptive autofocus, when sliding inside the cartridge chamber, the samples used are tracked under the action of the optics and the 3D rotation was experimentally successfully obtained. A cell viability assessment was then used using the MitoGreen dye, a fluorescence marker selectively permeable to live cells. The ImageJ software was used to: calculate the model diameter, create fluorescence intensity graphs along a straight line passing through the cell, visualize the spatial fluorescence intensity distribution in 3D.


title: Retention Time Prediction Using Neural Networks Increases Identifications in Crosslinking Mass Spectrometry

abstract: Crosslinking mass spectrometry (Crosslinking MS) has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the spectra limits the numbers of protein-protein interactions (PPIs) that can be confidently identified. Here, we successfully leveraged chromatographic retention time (RT) information to aid the identification of crosslinked peptides from spectra. Our Siamese machine learning model xiRT achieved highly accurate RT predictions of crosslinked peptides in a multi-dimensional separation of crosslinked E. coli lysate. We combined strong cation exchange (SCX), hydrophilic strong anion exchange (hSAX) and reversed-phase (RP) chromatography and reached R2 0.94 in RP and a margin of error of 1 fraction for hSAX in 94%, and SCX in 85% of the predictions. Importantly, supplementing the search engine score with retention time features led to a 1.4-fold increase in PPIs at a 1% false discovery rate. We also demonstrate the value of this approach for the more routine analysis of a crosslinked multiprotein complexes. An increase of 1.7-fold in heteromeric crosslinked residue-pairs was achieved at 1% residue-pair FDR for Fanconi anaemia monoubiquitin ligase complex, solely using reversed-phase RT. Retention times are a powerful complement to mass spectrometric information to increase the sensitivity of Crosslinking MS analyses.