bluuebunny/crossref_metadata_2025 huggingface dataset:
Axisymmetric diffusion kurtosis imaging with Rician bias correction: A simulation study
Authors: Oeschger Jan Malte , Tabelow Karsten , Mohammadi Siawoosh
Published: March 2022

Purpose: To compare the estimation accuracy of axisymmetric diffusion kurtosis imaging (DKI) and standard DKI in combination with Rician bias correction (RBC) under the influence of noise. Methods: Axisymmetric DKI is more robust against noise-induced variation in the measured signal than standard DKI because of its reduced parameter space. However, its susceptibility to Rician noise bias at low signal-to-noise ratios (SNRs) is unknown. Here, we investigate two main questions: first, does Rician bias correction improve estimation accuracy of axisymmetric DKI?; second, is the estimation accuracy of axisymmetric DKI increased compared to standard DKI? Estimation accuracy was investigated on the five axisymmetric DKI tensor metrics (AxTM): the parallel and perpendicular diffusivity and kurtosis and the mean kurtosis, using a simulation study based on synthetic and in-vivo data. Results: We found that RBC was most effective for increasing accuracy of the parallel AxTM in highly to moderately aligned white matter. For the perpendicular AxTM, axisymmetric DKI without RBC performed slightly better than with RBC. However, the combination of axisymmetric DKI with RBC was the overall best performing algorithm across all five AxTM and the axisymmetric DKI framework itself substantially improved accuracy in tissues with low fiber alignment. Conclusion: The combination of axisymmetric DKI with RBC facilitates accurate DKI parameter estimation at unprecedented low SNRs (approx 15), possibly making it a valuable tool for neuroscience and clinical research studies where scan time is a limited resource. The tools used in this paper are publicly available in the open-source ACID toolbox for SPM.
Arginine 65 methylation of Neurogenin 3 by PRMT1 is a prerequisite for development of hESCs into pancreatic endocrine cells
Authors: Cho Gahyang , Hyun Kwangbeom , Choi Jieun , Shin Eunji , Kim Bumsoo , Kim Jaehoon , Kim Hail , Han Yong-Mahn
Published: March 2022

In the developing pancreas, Neurogenin 3 (NGN3) is a key transcription factor in the cell fate determination of endocrine progenitors (EPs). Although the activation and stability of NGN3 are regulated by phosphorylation, the role of arginine methylation of NGN3 is poorly understood. Here, we report arginine 65 methylation of NGN3 is absolutely required for the pancreatic lineage development of human embryonic stem cells (hESCs) in vitro. First, we found inducible protein arginine methyltransferase 1 (PRMT1)-knockout (P-iKO) hESCs did not differentiate from EPs to endocrine cells (ECs) in the presence of doxycycline. Loss of PRMT1 caused an accumulation of NGN3 in the cytoplasm of EPs and blocked NGN3’s transcriptional activity in PRMT1-KO EPs. We also found that PRMT1 specifically methylates NGN3 arginine 65, and this modification is a prerequisite for ubiquitin-mediated NGN3 degradation. Our findings indicate arginine 65 methylation of NGN3 is a key molecular switch in hESCs in vitro permitting the differentiation into pancreatic endocrine lineages.
Health service research definition builder: An R Shiny application for exploring diagnosis codes associated with services reported in routinely collected health data
Authors: Chalmers Kelsey , Gopinath Valérie , Elshaug Adam G
Published: March 2022

Many administrative health data-based studies define patient cohorts using procedure and diagnosis codes. The impact these criteria have on a study’s final cohort is not always transparent to co-investigators or other audiences if access to the research data is restricted. We developed a SAS and R Shiny interactive research support tool which generates and displays the diagnosis code summaries associated with a selected medical service or procedure. This allows non-analyst users to interrogate claims data and groupings of reported diagnosis codes. The SAS program uses a tree classifier to find associated diagnosis codes with the service claims compared against a matched, random sample of claims without the service. Claims are grouped based on the overlap of these associated diagnosis codes. The Health Services Research (HSR) Definition Builder Shiny application uses this input to create interactive table and graphics, which updates estimated claim counts of the selected service as users select inclusion and exclusion criteria. This tool can help researchers develop preliminary and shareable definitions for cohorts for administrative health data research. It allows an additional validation step of examining frequency of all diagnosis codes associated with a service, reducing the risk of incorrect included or omitted codes from the final definition. In our results, we explore use of the application on three example services in 2016 US Medicare claims for patients aged over 65: knee arthroscopy, spinal fusion procedures and urinalysis. Readers can access the application at https://kelsey209.shinyapps.io/hsrdefbuilder/ and the code at https://github.com/kelsey209/hsrdefbuilder.
Validation of a rapid potency assay for cord blood stem cells using phospho flow cytometry: the IL-3-pSTAT5 assay
Authors: Simard Carl , Fournier Diane , Trépanier Patrick
Published: March 2022

Public cord blood banks (CBBs) are required to measure cord blood units (CBUs) potency before their release, allowing for the identification of units that may be unsuitable for hematopoietic transplantation. We have developed a rapid flow cytometry assay based on the measurement of STAT-5 phosphorylation of CD34+ stem cells in response to IL-3 stimulation: the IL-3-pSTAT5 assay.

To adapt the assay from a research setting to its implementation within our CBB regulated operations, we proceeded with a full method validation and a correlation comparison of the IL-3-pSTAT5 assay results with the colony-forming unit assay (CFU) results. A total of 60 CBUs cryopreserved in vials were analyzed by flow cytometry to determine the sensitivity, specificity, intra-assay precision, robustness, reproducibility and inter-laboratory agreement of the assay. The CFU assay was also done on the same samples for comparison purposes.

The assay threshold was established at 50% CD34+CD45+pSTAT5+, which provides a 100% sensitivity and a 98.3% specificity. An average intra-assay CV of 7.3% was determined. All results met our qualitative results acceptance criteria regarding the inter-user and inter-laboratory agreements, IL-3 stimulation time, post-thaw incubation delay and staining time. The IL-3-pSTAT5 assay results correlated well with the total CFU determined using the CFU assay (r2 = 0.82, n = 56).

This study shows that our rapid flow cytometry assay can be successfully validated and that the potency data obtained display good sensitivity, specificity and robustness. These results demonstrate the feasibility of implementing this assay within CBB operations, as a validated CB potency assay.
Estimation of time-varying causal effects with multivariable Mendelian randomization: some cautionary notes
Authors: Tian Haodong , Burgess Stephen
Published: March 2022

Introduction

For many exposures present across the lifecourse, the effect of the exposure may vary over time. Multivariable Mendelian randomization (MVMR) is an approach that can assess the effects of related risk factors using genetic variants as instrumental variables. Recently, multivariable Mendelian randomization has been used to estimate the effects of an exposure during distinct time periods.

Methods

We investigated the behaviour of estimates from MVMR in a simulation study for different time-varying causal scenarios. We also performed an applied analysis to consider how MVMR estimates of body mass index on systolic blood pressure vary depending on the time periods considered.

Results

Estimates from MVMR in the simulation study were close to the true values when the outcome model was correctly specified: that is, when the outcome was a discrete function of the exposure at the precise timepoints at which the exposure was measured. However, in more realistic cases, MVMR estimates were not only incorrect, but misleading. For example, in one scenario MVMR estimates for early life were clearly negative despite the true causal effect being constant and positive. In the applied example, estimates were highly variable depending on the time period in which genetic associations with the exposure were estimated.

Conclusions

The poor performance of MVMR to study time-varying causal effects can be attributed to model misspecification and violation of the exclusion restriction assumption. We would urge caution about quantitative conclusions from such analyses and even qualitative interpretations about the direction, or presence or absence of a causal effect during a given time period.
Humoral and cellular immune responses to CoronaVac assessed up to one year after vaccination
Authors: Costa Priscilla Ramos , Correia Carolina Argondizo , Marmorato Mariana Prado , Dias Juliana Zanatta de Carvalho , Thomazella Mateus Vailant , da Silva Amanda Cabral , Oliveira Ana Carolina Soares de , Gusmão Arianne Fagotti , Ferrari Lilian , Freitas Angela Carvalho , Patiño Elizabeth González , Grifoni Alba , Weiskopf Daniela , Sette Alessandro , Scharf Rami , Kallas Esper Georges , Silveira Cássia Gisele Terrassani
Published: March 2022

Background

The Sinovac SARS-CoV-2 inactivated vaccine (CoronaVac) has been demonstrated to be safe, well tolerated, and efficacious in preventing mild and severe Covid-19. Although different studies have demonstrated its short-term immunogenicity, long-term cellular and humoral response evaluations are still lacking.

Methods

Cellular and humoral responses were assessed after enrollment of volunteers in the PROFISCOV phase 3 double-blind, randomized, placebo-controlled clinical trial to evaluate CoronaVac. Assays were performed using flow cytometry to evaluate cellular immune response and an antigen binding electrochemiluminescence assay to detect antigen-specific antibodies to the virus.

Results

Fifty-three volunteers were selected for long term assessment of their SARS-CoV-2-specific immune responses. CD4+ T cell responses (including circulating follicular helper (cTfh, CD45RA- CXCR5+) expressing CD40L, as well as non-cTfh cells expressing CXCR3) were observed early upon the first vaccine dose, increased after the second dose, remaining stable for 6-months. Memory CD4+ T cells were detected in almost all vaccinees, the majority being central memory T cells. IgG levels against Wuhan/WH04/2020 N, S and receptor binding domain (RBD) antigens and the variants of concern (VOCs, including B.1.1.7/Alpha, B.1.351/Beta and P.1/Gamma) S and RBD antigens peaked 14 days after the second vaccine shot, and were mostly stable for a 1-year period.

Conclusions

CoronaVac two-doses regimen is able to induce a potent and durable SARS-CoV-2 specific cellular response. The cellular reaction is part of a coordinated immune response that includes high levels of specific IgG levels against parental and SARS-CoV-2 VOC strains, still detected after one year.

Funding

Fundação Butantan, Instituto Butantan and São Paulo Research Foundation (FAPESP) (grants 2020/10127-1 and 2020/06409-1). This work has also been supported by NIH contract 75N93019C00065 (A.S, D.W). PATH facilitated reagent donations for this work with support by the Bill & Melinda Gates Foundation (INV-021239). Under the grant conditions of the foundation, a Creative Commons Attribution 4.0 generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission.
Adaptive Magnetic Resonance
Authors: Beracha Inbal , Seginer Amir , Tal Assaf
Published: March 2022

Nuclear magnetic resonance is one of the cornerstones of modern medicine and biomedical research. Over the past several decades, the speed and precision of in-vivo magnetic resonance imaging (MRI) and spectroscopy (MRS) have increased by leaps and bounds, by utilizing sophisticated excitation and acquisition techniques, from parallel imaging and compressed sensing to magnetic resonance fingerprinting. However, these approaches have all been static in nature, fixing measurement parameters in advance, in anticipation of a wide range of expected tissue parameter values, and are therefore sub-optimal for any given subject. We depart from the conventional framework of magnetic resonance and propose a new approach - termed adaptive magnetic resonance - which binds acquisition and excitation, by using the measured signal to update and fine-tune the measurement parameters in real time. This targets the specific tissue characteristics of the subject while they are being scanned. Adaptive magnetic resonance provides a completely new and previously-untapped avenue for improving the sensitivity and specificity of in-vivo magnetic resonance across all tissue contrast mechanisms. Equivalently, it can accelerate data acquisition compared to non-adaptive schemes, by obtaining the same precision using fewer, optimally tuned excitations. We demonstrate that an adaptive pulse sequence for measuring the transverse relaxation time (T2) of metabolites in-vivo improves upon the precision of static approaches by a factor of ≈ 1.7 - or, alternatively, accelerates acquisition 2.5-fold.
Saturated reconstruction of living brain tissue
Authors: Velicky Philipp , Miguel Eder , Michalska Julia M. , Wei Donglai , Lin Zudi , Watson Jake F. , Troidl Jakob , Beyer Johanna , Ben-Simon Yoav , Sommer Christoph , Jahr Wiebke , Cenameri Alban , Broichhagen Johannes , Grant Seth G. N. , Jonas Peter , Novarino Gaia , Pfister Hanspeter , Bickel Bernd , Danzl Johann G.
Published: March 2022

Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full in-silico reconstruction1–5, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches6–12 facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy6,13 in extracellularly labelled tissue14 for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue.
Sst+ GPi output neurons provide direct feedback to key nodes of the basal ganglia and drive behavioral flexibility
Authors: Weglage M. , Ährlund-Richter S. , Fuzik J. , Skara V. , Lazaridis I. , Meletis K.
Published: March 2022

The GPi-LHb pathway is the main output of the basal ganglia suggested to shape motivated behaviors. We show here that Sst+ GPi-LHb neurons send direct feedback to key nodes of the basal ganglia: the GPe, the striatal striosomes, and dopamine neurons in the SNc. Chronic silencing of this pathway did not affect learning or execution of value-guided choices, but severely disrupted the ability to adapt choice-behavior and seek an alternative reward location after task reversal. Calcium imaging revealed that Sst+ GPi neurons did not signal outcome value or value updates during reversal learning. Instead, progressive suppression of the Sst+ GPi activity was linked to increased commitment to one choice, and activity increased during exploration of alternative choices. We propose that GPi Sst+ neurons drive behavioral flexibility through a direct feedback signal to balance the activity of key nodes in the basal ganglia.
Microglial P2Y12 mediates chronic stress-induced synapse loss in the prefrontal cortex and associated behavioral consequences in male mice
Authors: Bollinger J.L. , Dadosky D.T. , Flurer J.K. , Rainer I.L. , Woodburn S.C. , Wohleb E.S.
Published: March 2022

Recent studies demonstrate that chronic unpredictable stress (CUS) drives microglia-mediated neuronal remodeling, contributing to synapse loss in the prefrontal cortex (PFC) and cognitive-behavioral dysfunction. Nonetheless, it remains unclear what mechanisms guide microglia-neuron interactions in stress. Evidence indicates that neuronal activity-dependent purinergic signaling directs microglial processes and microglia-synapse interaction via P2Y12, a purinergic receptor exclusively expressed by microglia in the brain. Stress exposure alters excitatory neurotransmission in the PFC, thus we aimed to determine if P2Y12 signaling promotes functional changes in microglia in the context of chronic stress. Using an activating DREADD, our initial studies showed that PFC microglia adopt a CUS-associated phenotype after repeated pyramidal neuronal activation. To further investigate the role of purinergic signaling, we used genetic (P2ry12-/-) or pharmacological (clopidogrel, ticagrelor) approaches to block P2Y12 in the context of CUS. Various behavioral, physiological, and cytometric endpoints were analyzed. Both P2Y12-deletion and treatment with clopidogrel prevented increases in forced swim test immobility and attenuated deficits in temporal object recognition following CUS. Flow cytometry of PFC microglia revealed that both P2ry12-/- mice and those treated with clopidogrel have significantly different phenotypes (independent of CUS); with diminished P2Y12 expression and altered surface levels of CX3CR1, CSF1R, and CD11b. Immunohistology in Thy1-GFP(M) mice demonstrated that pharmacological blockade of P2Y12 prevented stress-induced increases in the proportion of microglia with GFP+ neuronal inclusions and limited dendritic spine loss in the PFC. Together, these findings indicate that microglial P2Y12 is a critical mediator of stress-induced neuronal remodeling in the PFC and subsequent behavioral deficits.
Estimating consensus proteomes and metabolic functions from taxonomic affiliations
Authors: Belcour Arnaud , Hamon-Giraud Pauline , Mataigne Alice , Ruiz Baptiste , Le Cunff Yann , Got Jeanne , Awhangbo Lorraine , Lebreton Mégane , Frioux Clémence , Dittami Simon , Dabert Patrick , Siegel Anne , Blanquart Samuel
Published: March 2022

Purpose

Metabarcoding, and metagenomic sequencing have enabled the characterization of highly diverse environmental communities. The challenge of estimating the metabolic functions carried out by these communities has led to the development of several state-of-the-art methods, most of which are tailored to a specific gene marker. However, the increasing diversity of approaches resulting from advances in sequencing technologies drives the need for methods capable of handling heterogeneous microbial community data. Moreover, predictions often depend on their internal analysis pipelines and are influenced by the underlying databases, which link marker genes to specific functional annotations. This limits users’ ability to evaluate the quality of predictions by tracing internal data and processes. Finally, users are constrained by the specific annotations provided by these methods (e.g. EC numbers), limiting their ability to conduct further specialized analyses based on intermediate results.

Methods

EsMeCaTa predicts consensus proteomes and their associated functions from taxonomic affiliations. A key feature of EsMeCaTa is its explainability and flexibility. To support the flexible integration of heterogeneous sequencing data, EsMeCaTa utilizes taxonomic affiliations obtained through analyses of diverse sequencing datasets. To provide insight into the knowledge available for each taxonomic affliation and to interpret the relevance of predicted functions, EsMeCaTa identifies a taxonomic rank within a given affliation that is suffciently represented by documented proteomes in the UniProt database. The proteins of the UniProt proteomes are clustered and filtered according to a threshold to create consensus proteomes. These consensus proteomes are automatically annotated with functional information (e.g., EC numbers, GO terms) but they are also designed to be used in further customized annotation workflows. Functional annotations are reported in a functional table, which can be enriched with taxon abundances to generate comprehensive functional profiles.

Results

EsMeCaTa predictions have been validated using multiple datasets and compared to a state-of-the-art method. Additionally, it was applied to a novel metabarcoding dataset from a methanogenic reactor, characterizing the microbial community and biogas production across different time points and intake condition. Our results demonstrate the link between biogas production, intake condition and the dynamics of the metabolic functions predicted by EsMeCaTa in the microbial communities.
Tuning of motor outputs produced by spinal stimulation during voluntary control of torque directions in monkeys
Authors: Kaneshige Miki , Obara Kei , Suzuki Michiaki , Tazoe Toshiki , Nishimura Yukio
Published: March 2022

Spinal stimulation is a promising method to restore motor function after impairment of descending pathways. While paresis, a weakness of voluntary movements driven by surviving descending pathways, can benefit from spinal stimulation, the effects of descending commands on motor outputs produced by spinal stimulation are unclear. Here, we show that descending commands amplify stimulus-evoked joint torque and the function of intraspinal elements. During the wrist torque tracking task, optimized currents of spinal stimulation over the cervical enlargement facilitated and/or suppressed activities of forelimb muscles. Magnitudes of these effects were dependent on directions of voluntarily-produced torque and positively correlated with levels of voluntary muscle activity. Furthermore, the directions of evoked wrist torque corresponded to the directions of voluntarily-produced torque. These results suggest that spinal stimulation is beneficial in cases of partial lesion of descending pathways by compensating for reduced descending commands through activation of excitatory and inhibitory synaptic connections to motoneurons.
Comparable theta phase coding dynamics along the transverse axis of CA1
Authors: Bishnoi Aditi , Deshmukh Sachin S.
Published: March 2022

Topographical projection patterns from the entorhinal cortex to area CA1 of the hippocampus have led to a hypothesis that proximal CA1 (pCA1, closer to CA2) is spatially more selective than distal CA1 (dCA1, closer to the subiculum). While earlier studies have shown evidence supporting this hypothesis, we recently showed that this difference does not hold true under all experimental conditions. In a complex environment with distinct local texture cues on a circular track and global visual cues, pCA1 and dCA1 display comparable spatial selectivity. Correlated with the spatial selectivity differences, the earlier studies also showed differences in theta phase coding dynamics between pCA1 and dCA1 neurons. Here we show that there are no differences in theta phase coding dynamics between neurons in these two regions under the experimental conditions where pCA1 and dCA1 neurons are equally spatially selective. We also show that dCA1 local field potentials (LFPs) show higher power in theta range compared to pCA1 LFPs. These findings challenge the established notion of dCA1 being inherently less spatially selective and theta modulated than pCA1 and suggest that theta-mediated activation of the CA1 sub-networks to represent space is task-dependent.
Xanthomonas indicasp. nov., a non-pathogenic bacterium isolated from healthy rice(Oryza sativa)seeds from India
Authors: Rana Rekha , Madhavan Vishnu Narayanan , Saroha Tanu , Bansal Kanika , Kaur Amandeep , Sonti Ramesh V. , Patel Hitendra K. , Patil Prabhu B.
Published: March 2022

Two yellow pigmented bacterial strains were isolated from healthy rice seeds. The strains designated as PPL560Tand PPL568 were identified as members of genusXanthomonasbased on analysis of biochemical and 16S rRNA gene sequence retrieved from whole genome sequence. Isolates formed a distinct monophyletic lineage withX. sontiiandX. saccharias the closest relatives in the phylogenetic tree based on core gene content shared by reported species in genusXanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridisation values calculated against other species ofXanthomonaswere below their respective cut-offs.In plantastudies revealed that PPL560Tand PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. Absence of type III secretion system related genes and effectors further supported their non-pathogenic status. Herein, we proposeXanthomonas indicasp. nov. as novel species of genusXanthomonaswith PPL560T=MTCC13185 as its type strain and PPL568 as another constituent member.
A flexible and versatile system for multicolor fiber photometry and optogenetic manipulation
Authors: Formozov Andrey , Dieter Alexander , Wiegert J. Simon
Published: March 2022

Fiber photometry is a technique of growing popularity in neuroscientific research. It is widely used to infer brain activity by recording calcium dynamics in genetically defined populations of neurons. Aside from the wide variety of calcium indicators, other genetically encoded biosensors have recently been engineered to measure membrane potential, neurotransmitter release, pH, or various cellular metabolites, such as ATP or cAMP. Due to the spectral characteristics of these molecular tools, different assemblies of optical hardware are usually needed to reveal the full potential of different biosensors. In addition, the combination of multiple biosensors in one experiment often requires the investment in more complex equipment, which limits the flexibility of the experimental design. Such constraints often hamper a straightforward implementation of new molecular tools, evaluation of their performance in vivo, and design of new experimental paradigms - especially if the financial budget is a limiting factor. Here, we propose a novel approach for fiber photometry recordings, based on a multimode optical fused-fiber coupler (FFC) for both light delivery and collection. Recordings can readily be combined with optogenetic manipulations in a single device without the requirement for dichroic beam-splitters. In combination with a multi-color light source and appropriate emission filters, our approach offers remarkable flexibility in experimental design and facilitates the implication of new molecular tools in vivo at minimal cost. The ease of assembly, operation, characterization, and customization of this platform holds the potential to foster the development of experimental strategies for multicolor fused fiber photometry (FFP) combined with optogenetics far beyond its current state.

Abstract Figure

Highlights

Fused Fiber Photometry (FFP) enables straightforward monitoring and manipulation of brain activity

FFP allows monitoring of indicators with virtually any spectral characteristics

FFP is compatible with simultaneous optogenetic manipulation

Easy assembly, characterization, and customization
Dual blockade of misfolded alpha-sarcoglycan degradation by bortezomib and givinostat combination
Authors: Hoch Lucile , Bourg Nathalie , Degrugillier Fanny , Bruge Céline , Benabides Manon , Pellier Emilie , Tournois Johana , Mahé Gurvan , Maignan Nicolas , Dawe Jack , Georges Maxime , Papazian David , Subramanian Nik , Simon Stéphanie , Fanen Pascale , Delevoye Cédric , Richard Isabelle , Nissan Xavier
Published: March 2022

Limb-girdle muscular dystrophy type R3 (LGMD R3) is a rare genetic disorder characterized by a progressive proximal muscle weakness and caused by mutations in the SGCA gene encoding alpha-sarcoglycan (α-SG). Here, we report the results of a mechanistic screening ascertaining the molecular mechanisms involved in the degradation of the most prevalent misfolded R77C-α-SG protein. We performed a combinatorial study to identify drugs potentializing the effect of a low dose of the proteasome inhibitor bortezomib on the R77C-α-SG degradation inhibition. Analysis of the screening associated to artificial intelligence-based predictive ADMET characterization of the hits led to identification of the HDAC inhibitor givinostat as potential therapeutical candidate. Functional characterization revealed that givinostat effect was related to autophagic pathway inhibition, unveiling new theories concerning degradation pathways of misfolded SG proteins. Beyond the identification of a new therapeutic option for LGMD R3 patients, our results shed light on the potential repurposing of givinostat for the treatment of other genetic diseases sharing similar protein degradation defects such as LGMD R5 and cystic fibrosis.
Brain-wide screen of prelimbic cortex inputs reveals a functional shift during early fear memory consolidation
Authors: Dixsaut Lucie , Gräff Johannes
Published: March 2022

Memory formation and storage rely on multiple interconnected brain areas, the contribution of which varies during memory consolidation. The medial prefrontal cortex, in particular the prelimbic cortex (PL), was traditionally found to be involved in remote memory storage, but recent evidence points towards its implication in early consolidation as well. Nevertheless, the inputs to the PL governing these dynamics remain unknown. Here, we first performed a brain-wide, rabies-based retrograde tracing screen of PL engram cells activated during contextual fear memory formation to identify relevant PL input regions. Next, we assessed the specific activity pattern of these inputs across different phases of memory consolidation, from fear memory encoding to recent and remote memory recall. Using projection-specific chemogenetic inhibition, we then tested their functional role in memory consolidation, which revealed a hitherto unknown contribution of claustrum to PL inputs at encoding, and of insular cortex to PL inputs at recent memory recall. Both of these inputs further impacted how PL engram cells were reactivated at memory recall, testifying to their relevance for establishing a memory trace in the PL. Collectively, this data identify a spatiotemporal shift in PL inputs important for early memory consolidation, and thereby help to refine the working model of memory formation.
Reproductive tradeoffs govern sexually dimorphic tubular lysosome induction in C. elegans
Authors: Ramos Cara D. , Bohnert K. Adam , Johnson Alyssa E.
Published: March 2022

Animals of different sexes often exhibit unique behaviors that benefit their specific reproductive interests. In the nematode Caenorhabditis elegans, self-fertilizing hermaphrodites can reproduce without a mate and thus prioritize feeding to satisfy the high energetic costs of reproduction. However, males, which rely on finding potential mates for reproduction, sacrifice feeding and instead prioritize exploratory behavior. Here, we demonstrate that these differences in behavior are linked to sexual dimorphism at the cellular level; young males raised on a rich food source show constitutive induction of gut tubular lysosomes, a non-canonical lysosome morphology that typically forms in the gut of young hermaphrodites only when food is limited. We find that male-specific induction of gut tubular lysosomes on abundant food is due to self-imposed dietary restriction through daf-7/TGFβ signaling, which promotes mate-searching at the cost of feeding. While gut tubular lysosomes are largely absent from well-fed hermaphrodites at the start of adulthood, their induction accelerates in hermaphrodites in early aging, dependent on the presence of sperm and, partly, on embryo production. These findings identify tubular lysosome induction as a sexually dimorphic cellular event that may integrate animal physiology with sex-specific behavioral differences important for reproductive success.
Comparison of the 2021 COVID-19 Roadmap Projections against Public Health Data in England
Authors: Keeling Matt J. , Dyson Louise , Tildesley Michael J. , Hill Edward M. , Moore Samuel
Published: March 2022

Control and mitigation of the COVID-19 pandemic in England has relied on a combination of vaccination and non-pharmaceutical interventions (NPIs). Some of these NPIs are extremely costly (economically and socially), so it was important to relax these promptly without overwhelming already burdened health services. The eventual policy was a Roadmap of four relaxation steps throughout 2021, taking England from lock-down to the cessation of all restrictions on social interaction. In a series of six Roadmap documents generated throughout 2021, models assessed the potential risk of each relaxation step. Here we show that the model projections generated a reliable estimation of medium-term hospital admission trends, with the data points up to September 2021 generally lying within our 95% prediction intervals. The greatest uncertainties in the modelled scenarios came from vaccine efficacy estimates against novel variants, and from assumptions about human behaviour in the face of changing restrictions and risk.
Detection of Bourbon virus specific serum neutralizing antibodies in human serum in Missouri, USA
Authors: Bamunuarachchi Gayan , Harastani Houda , Rothlauf Paul W. , Dai Ya-nan , Ali Ellebedy , Fremont Daved , Whelan Sean P.J. , Wang David , Boon Adrianus C. M.
Published: March 2022

Bourbon virus (BRBV) was first discovered in 2014 in a fatal human case. Since then it has been detected in the Amblyomma americanum tick in the states of Missouri and Kansas in the United States. Despite the high prevalence of BRBV in ticks in these states, very few human cases have been reported, and the true infection burden of BRBV in the community is unknown. Here, we developed two virus neutralization assays, a VSV-BRBV pseudotyped rapid assay, and a BRBV focus reduction neutralization assay, to assess the seroprevalence of BRBV neutralizing antibodies in human sera collected in 2020 in St. Louis, Missouri. Out of 440 human serum samples tested, three (0.7%) were able to potently neutralize both VSV-BRBV and wild type BRBV. These findings suggest that human infections with BRBV are more common than previously recognized.

Importance

Since the discovery of the Bourbon virus (BRBV) in 2014, a total of five human cases have been identified, including two fatal cases. BRBV is thought to be transmitted by the Lone Star tick, which is prevalent in the East, Southeast, and Midwest of the United States (US). BRBV has been detected in ticks in Missouri and Kansas and serological evidence suggests that it is also present in North Carolina. However, the true infection burden of BRBV in humans is not known. In the present study, we developed two virus neutralization assays to assess the seroprevalence of BRBV specific antibodies in human sera collected in 2020 in St. Louis, Missouri. We found that a small subset of individuals is seropositive for neutralizing antibodies against BRBV. Our data suggest that BRBV infection in humans is more common than previously thought.
A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance
Authors: Patchsung Maturada , Homchan Aimorn , Aphicho Kanokpol , Suraritdechachai Surased , Wanitchanon Thanyapat , Pattama Archiraya , Sappakhaw Khomkrit , Meesawat Piyachat , Wongsatit Thanakrit , Athipanyasilp Artittaya , Jantarug Krittapas , Athipanyasilp Niracha , Buahom Juthamas , Visanpattanasin Supapat , Niljianskul Nootaree , Chaiyen Pimchai , Tinikul Ruchanok , Wichukchinda Nuanjun , Mahasirimongkol Surakameth , Sirijatuphat Rujipas , Angkasekwinai Nasikarn , Crone Michael A. , Freemont Paul S. , Joung Julia , Ladha Alim , Abudayyeh Omar , Gootenberg Jonathan , Zhang Feng , Chewapreecha Claire , Chanarat Sittinan , Horthongkham Navin , Pakotiprapha Danaya , Uttamapinant Chayasith
Published: March 2022

Point-of-care (POC) nucleic acid detection technologies are poised to aid gold-standard technologies in controlling the COVID-19 pandemic, yet shortcomings in the capability to perform critically needed complex detection—such as multiplexed detection for viral variant surveillance—may limit their widespread adoption. Herein, we developed a robust multiplexed CRISPR-based detection using LwaCas13a and PsmCas13b to simultaneously diagnose SARS-CoV-2 infection and pinpoint the causative SARS-CoV-2 variant of concern (VOC)— including globally dominant VOCs Delta (B.1.617.2) and Omicron (B.1.1.529)—all while maintaining high levels of accuracy upon the detection of multiple SARS-CoV-2 gene targets. The platform has several attributes suitable for POC use: premixed, freeze-dried reagents for easy use and storage; convenient direct-to-eye or smartphone-based readouts; and a one-pot variant of the multiplexed detection. To reduce reliance on proprietary reagents and enable sustainable use of such a technology in low- and middle-income countries, we locally produced and formulated our own recombinase polymerase amplification reaction and demonstrated its equivalent efficiency to commercial counterparts. Our tool—CRISPR-based detection for simultaneous COVID-19 diagnosis and variant surveillance which can be locally manufactured—may enable sustainable use of CRISPR diagnostics technologies for COVID- 19 and other diseases in POC settings.
Single molecule imaging and modelling of mRNA decay dynamics in theDrosophilaembryo
Authors: Beadle Lauren Forbes , Love Jennifer C. , Shapovalova Yuliya , Artemev Artem , Rattray Magnus , Ashe Hilary L.
Published: March 2022

Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling. Here we use a non-invasive method for estimating half-lives for hundreds of mRNAs in the earlyDrosophilaembryo. This approach uses the intronic and exonic reads from a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs. We show how regulation of mRNA stability is used to establish a range of mature mRNA dynamics during embryogenesis, despite shared transcription profiles. Using single molecule imaging we provide evidence that, for the mRNAs tested, there is a correlation between short half-life and mRNA association with P-bodies. Moreover, we detect an enrichment of mRNA 3’ ends in P-bodies in the early embryo, consistent with 5’ to 3’ degradation occurring in P-bodies for at least a subset of mRNAs. We discuss our findings in relation to recently published data suggesting that the primary function of P-bodies in other biological contexts is mRNA storage.
Acute Cytomegalovirus Infection Modulates the Intestinal Microbiota and Targets Intestinal Epithelial Cells
Authors: Le-Trilling Vu Thuy Khanh , Ebel Jana-Fabienne , Baier Franziska , Wohlgemuth Kerstin , Pfeifer Kai Robin , Mookhoek Aart , Krebs Philippe , Determann Madita , Katschinski Benjamin , Adamczyk Alexandra , Lange Erik , Klopfleisch Robert , Lange Christian M. , Sokolova Viktoriya , Trilling Mirko , Westendorf Astrid M.
Published: March 2022

Primary and recurrent cytomegalovirus (CMV) infections frequently cause CMV colitis in immunocompromised as well as inflammatory bowel disease (IBD) patients. Additionally, colitis occasionally occurs upon primary CMV infection in patients who are apparently immunocompetent. In both cases, the underlying pathophysiologic mechanisms are largely elusive - in part due to the lack of adequate access to specimens. We employed the mouse cytomegalovirus (MCMV) model to probe into the association between CMV and colitis. During acute primary MCMV infection of immunocompetent mice, the gut microbial composition was affected within the first 5 days post-infection as manifested by an altered ratio of the Firmicutes to Bacteroidetes phyla. Interestingly, these microbial changes incited with high-titer MCMV replication in the colon, mild crypt necrosis and increased colonic pro-inflammatory cytokine levels. Further analyses revealed that murine and human intestinal epithelial cell line as well as primary intestinal crypt cells/ organoids represent direct targets of CMV accompanied by increased cell mortality upon infection. Accordingly, in vivo MCMV infection disrupted the intestinal epithelial barrier and increased apoptosis of intestinal epithelial cells. In summary, our data show that CMV induces colitis in immunocompetent hosts by altering the intestinal homeostasis.
Mesoaccumbal glutamate neurons drive reward via glutamate release, but aversion via dopamine co-release
Authors: Warlow Shelley M. , Zell Vivien , Hunker Avery C. , Zweifel Larry S. , Hnasko Thomas S.
Published: March 2022

Ventral tegmental area (VTA) projections to the nucleus accumbens medial shell (NAc) drive reward-related motivation. Although dopamine neurons are predominant, a substantial glutamatergic projection is also present, and a subset of these populations can release both dopamine and glutamate. Optogenetic stimulation of VTA glutamate neurons supports self-stimulation, but can also induce place avoidance, even in the same assay. Here, we parsed the selective contribution of glutamate or dopamine co-release from VTA glutamate neurons to reinforcement and avoidance. We expressed Channelrhodopsin (ChR2) in VTA glutamate neurons, in combination with CRISPR/Cas9 to disrupt either the gene encoding vesicular glutamate transporter 2 (VGLUT2) or Tyrosine hydroxylase (Th). Selective disruption of VGLUT2 abolished optogenetic self-stimulation, but left real-time place avoidance intact, while CRISPR/Cas9 deletion of Th preserved optogenetic self-stimulation but abolished place avoidance. Our results demonstrate that glutamate release from VTA glutamate neurons is positively reinforcing, but that dopamine release from these same neurons can induce avoidance behavior.
Transcriptome analysis of alcohol dependence and stress interactions in the nucleus of the solitary tract
Authors: Grantham EK , Tiwari GR , Ponomereva O , Warden AS , DaCosta A , Mason S , Blednov YA , Harris RA , Lopez MF , Becker HC , Mayfield RD
Published: March 2022

Stress exposure contributes to the development of drug and alcohol use disorders. In animal models, stress exacerbates escalations in alcohol consumption in alcohol-dependent animals. The nucleus of the solitary tract (NTS) is a critical brainstem region for integrating and relaying peripheral signals to regulate stress responses. To define the molecular adaptions within this brain region that may contribute to stress-induced alcohol drinking, we exposed animals to chronic intermittent bouts of ethanol vapor (CIE), forced swim stress (FSS), or both (CIE + FSS) and then transcriptionally profiled the NTS at three different timepoints after the last vapor exposure (0-hr, 72-hr, and 186-hr). We identified interferon (IFN) signaling as a critical gene network correlated with alcohol consumption levels. Using a likelihood ratio test, we identified genes that were differentially expressed across time and between groups. Clustering analysis of these genes to identify unique expression patterns identified a subset of genes that fail to normalize in the CIE + FSS group, but not the others. These genes were enriched for cell-to-cell interaction and cellular movement pointing to long-term structural and functional changes in this brain region caused by the unique interaction of alcohol dependence and stress. Specific genes of interest identified in this group include Aqp4, Il16, Reln, Grm4, Gabrd, and Gabra6. We also compared gene expression changes in the NTS to the PFC and found a significant overlap of genes between the two brain regions. Overlapping NTS/PFC genes in the CIE + FSS group were enriched for type I IFN signaling. Finally, we tested the hypothesis that activation of type I IFN signaling increases alcohol consumption based on the three lines of evidence identifying type I IFN signaling as critical for escalations in alcohol intake. Mice treated with recombinant IFNβ showed significantly elevated levels of alcohol intake in a two-bottle choice procedure compared to saline-treated controls. Overall, these results define the transcriptomic changes across time in the NTS that may be critical to the development of stress-induced increases in alcohol consumption and alcohol dependence.
A brain-wide analysis maps structural evolution to distinct anatomical modules
Authors: Kozol Robert A. , Conith Andrew J. , Yuiska Anders , Cree-Newman Alexia , Tolentino Bernadeth , Banesh Kasey , Paz Alexandra , Lloyd Evan , Kowalko Johanna E. , Keene Alex C. , Albertson R. Craig , Duboue Erik R.
Published: March 2022

Brain anatomy is highly variable and it is widely accepted that anatomical variation impacts brain function and ultimately behavior. The structural complexity of the brain, including differences in volume and shape, presents an enormous barrier to define how variability underlies differences in function. In this study, we sought to investigate the evolution of brain anatomy in relation to brain region volume and shape across the brain of a single species with variable genetic and anatomical morphs. We generated a high-resolution brain atlas for the blind Mexican cavefish and coupled the atlas with automated computational tools to directly assess brain region shape and volume variability across all populations. We measured the volume and shape of every neuroanatomical region of the brain and assess correlations between anatomical regions in surface, cavefish and surface to cave F2 hybrids, whose phenotypes span the range of surface to cave. We find that dorsal regions of the brain are contracted in cavefish, while ventral regions have expanded. Interestingly, in hybrid fish the volume and shape of dorsal regions are inversely proportional to ventral regions. This trend is true for both volume and shape, suggesting that these two parameters share developmental mechanisms necessary for remodeling the entire brain. Given the high conservation of brain anatomy and function among vertebrate species, we expect these data to studies reveal generalized principles of brain evolution and show that Astyanax provides a system for functionally determining basic principles of brain evolution by utilizing the independent genetic diversity of different morphs, to test how genes influence early patterning events to drive brain-wide anatomical evolution.