bluuebunny/crossref_metadata_2025 huggingface dataset:
Arthritis Flares Mediated by Tissue Resident Memory T Cells in the Joint
Authors: Chang Margaret H , Levescot Anaïs , Nelson-Maney Nathan , Blaustein Rachel B , Winden Kellen D , Morris Allyn , Wactor Alexandra , Balu Spoorthi , Grieshaber-Bouyer Ricardo , Wei Kevin , Henderson Lauren A , Iwakura Yoichiro , Clark Rachael A , Rao Deepak A , Fuhlbrigge Robert C , Nigrovic Peter A
Published: June 2021

Although rheumatoid arthritis is a systemic disease, flares typically occur in a subset of joints that is distinctive for each patient. Pursuing this intriguing pattern, we show that arthritis recurrence is mediated by long-lived synovial resident memory T cells (TRM). In three murine models, CD8+ cells bearing TRM markers remain in previously inflamed joints during remission. These cells are bona fide TRM, exhibiting failure to migrate from joint to joint, preferential uptake of fatty acids, and long-term residency. Disease flares result from TRM activation by antigen, leading to CCL5-mediated recruitment of circulating effector cells. Correspondingly, TRM depletion ameliorates recurrence in a site-specific manner. Human rheumatoid arthritis joint tissues contain a comparable CD8+-predominant TRM population, most evident in late-stage non-inflamed synovium, exhibiting limited T cell receptor diversity and a pro-inflammatory transcriptomic signature. Together, these findings establish synovial TRM cells as a targetable mediator of disease chronicity in autoimmune arthritis.
Prenatal cadmium exposure alters proliferation in mouse CD4+ T cells via LncRNA Snhg7
Authors: McCall Jamie L. , Varney Melinda E. , Dziadowicz Sebastian A. , Hall Casey , Blethen Kathryn , Hu Gangqing , Barnett John B. , Martinez Ivan
Published: June 2021

Objective

Prenatal cadmium (Cd) exposure leads to immunotoxic phenotypes in the offspring affecting coding and non-coding genes. Recent studies have shown that long non-coding RNAs (lncRNAs) are integral to T cell regulation. Here, we investigated the role of long non-coding RNA small nucleolar RNA hostgene 7 (lncSnhg7) in T cell proliferation.

Methods

RNA sequencing was used to analyze the expression of lncRNAs in splenic CD4+ T cells with and without CD3/CD28 stimulation. Next, T cells isolated from offspring exposed to control or Cd water throughout mating and gestation were analyzed with and without stimulation with anti-CD3/CD28 beads. Quantitative qPCR and western blotting were used to detect RNA and protein levels of specific genes. Overexpression of a miR-34a mimic was achieved using nucleofection. Apoptosis was measured using flow cytometry and luminescence assays. Flow cytometry was also used to measure T cell proliferation in culture.

Results

We identified 23 lncRNAs that were differentially expressed in stimulated versus unstimulated T cells, including lncSnhg7. LncSnhg7 and a downstream protein, GALNT7, are upregulated in T cells from offspring exposed to Cd during gestation. Overexpression of miR-34a, a regulator of lncSnhg7 and GALNT7, suppresses GALNT7 protein levels in primary T cells, but not in a mouse T lymphocyte cell line. The T cells isolated from Cd-exposed offspring exhibit increased proliferation after activation in vitro, but Treg suppression and CD4+ T cell apoptosis are not affected by prenatal Cd exposure.

Conclusion

Prenatal Cd exposure alters the expression of lncRNAs during T cell activation. The induction of lncSnhg7 is enhanced in splenic T cells from Cd offspring resulting in the upregulation of GALNT7 protein and increased proliferation following activation. miR-34a overexpression decreased GALNT7 expression suggesting that the lncSnhg7/miR-34a/GALNT7 is an important pathway in primary CD4+ T cells. These data highlight the need to understand the consequences of environmental exposures on lncRNA functions in non-cancerous cells as well as the effects in utero.
Physical basis for distinct basal and mechanically-gated activity of the human K+ channel TRAAK
Authors: Rietmeijer Robert A. , Sorum Ben , Li Baobin , Brohawn Stephen G.
Published: June 2021

TRAAK is a mechanosensitive two-pore domain K+ (K2P) channel localized to nodes of Ranvier in myelinated neurons. TRAAK deletion in mice results in mechanical and thermal allodynia and gain-of-function mutations cause the human neurodevelopmental disorder FHEIG. TRAAK displays basal and stimulus-gated activities typical of K2Ps, but the mechanistic and structural differences between these modes are unknown. Here, we demonstrate that basal and mechanically-gated openings are distinguished by their conductance, kinetics, and structure. Basal openings are low conductance, short duration, and occur through a channel with an interior cavity exposed to the surrounding membrane. Mechanically-gated openings are high conductance, long duration, and occur through a channel that is sealed to the surrounding membrane. Our results explain how dual modes of activity are produced by a single ion channel and provide a basis for the development of state-selective pharmacology with the potential to treat disease.
High-throughput, label-free and slide-free histological imaging by computational microscopy and unsupervised learning
Authors: Zhang Yan , Kang Lei , Li Xiufeng , Wong Ivy H. M. , Wong Terence T. W.
Published: June 2021

Rapid and high-resolution histological imaging with minimal tissue preparation has long been a challenging and yet captivating medical pursue. Here, we propose a promising and transformative histological imaging method, termed computational high-throughput autofluorescence microscopy by pattern illumination (CHAMP). With the assistance of computational microscopy, CHAMP enables high-throughput and label-free imaging of thick and unprocessed tissues with large surface irregularity at an acquisition speed of 10 mm2/10 seconds with 1.1-µm lateral resolution. Moreover, the CHAMP image can be transformed into a virtually stained histological image (Deep-CHAMP) through unsupervised learning within 15 seconds, where significant cellular features are quantitatively extracted with high accuracy. The versatility of CHAMP is experimentally demonstrated using mouse brain/kidney tissues prepared with various clinical protocols, which enables a rapid and accurate intraoperative/postoperative pathological examination without tissue processing or staining, demonstrating its great potential as an assistive imaging platform for surgeons and pathologists to provide optimal adjuvant treatment.
Peroxidasin protein expression and enzymatic activity in metastatic melanoma cell lines are associated with invasive potential
Authors: Paumann-Page Martina , Kienzl Nikolaus F. , Motwani Jyoti , Bathish Boushra , Paton Louise N. , Magon Nick J. , Sevcnikar Benjamin , Furtmüller Paul G. , Traxlmayr Michael W. , Obinger Christian , Eccles Mike R. , Winterbourn Christine C.
Published: June 2021

Peroxidasin, a heme peroxidase, has been shown to play a role in cancer progression. mRNA expression has been reported to be upregulated in metastatic melanoma cell lines and connected to the invasive phenotype, but little is known about how peroxidasin acts in cancer cells. We have analyzed peroxidasin protein expression and activity in eight metastatic melanoma cell lines using an ELISA developed with an in-house peroxidasin binding protein. RNAseq data analysis confirmed high peroxidasin mRNA expression in the five cell lines classified as invasive and low expression in the three non-invasive cell lines. Protein levels of peroxidasin were higher in the cell lines with an invasive phenotype. Active peroxidasin was secreted to the cell culture medium, where it accumulated over time, and peroxidasin protein levels in the medium were also much higher in invasive than non-invasive cell lines. The only well-established physiological role of peroxidasin is in the formation of a sulfilimine bond, which cross-links collagen IV in basement membranes via catalyzed oxidation of bromide to hypobromous acid. We found that peroxidasin secreted from melanoma cells formed sulfilimine bonds in uncross-linked collagen IV, confirming peroxidasin activity and hypobromous acid formation. Moreover, 3-bromotyrosine, a stable product of hypobromous acid reacting with tyrosine residues, was detected in invasive melanoma cells, substantiating that their expression of peroxidasin generates hypobromous acid, and showing that it does not exclusively react with collagen IV, but also with other biomolecules.
Spatial cell type mapping of the oligodendrocyte lineage in the mouse juvenile and adult CNS with in situ sequencing
Authors: Hilscher Markus M. , Langseth Christoffer Mattsson , Kukanja Petra , Yokota Chika , Nilsson Mats , Castelo-Branco Gonçalo
Published: June 2021

Oligodendrocytes show transcriptional heterogeneity but the regional and functional implications of this heterogeneity are less clear. Here, we applyin situsequencing (ISS) to simultaneously probe the expression of 124 marker genes of distinct oligodendrocyte populations, providing comprehensive maps of corpus callosum, cingulate, motor and somatosensory cortex in the brain, as well as gray (GM) and white matter (WM) regions in the spinal cord, at juvenile and adult stages. We systematically compare abundances of these populations and investigate the neighboring preference of distinct oligodendrocyte populations. As previously described, we observed that oligodendrocyte lineage progression is more advanced in the juvenile spinal cord compared to the brain. Additionally, myelination is ongoing in the adult corpus callosum while it is mostly completed in the cortex. Interestingly, we found a medial-to-lateral gradient of oligodendrocyte lineage progression in the juvenile cortex, which could be linked to arealization, as well as a deep-to-superficial gradient with mature oligodendrocytes preferentially accumulating in the deeper layers of the cortex. We observed differences in abundances and population dynamics over time between GM and WM regions in the brain and spinal cord, indicating regional differences within GM and WM. We also found that oligodendroglia populations’ neighboring preferences are altered from the juvenile to the adult CNS. Thus, our ISS dataset reveals spatial heterogeneity of the oligodendrocyte lineage progression in the brain and spinal cord, which could be relevant to further investigate functional heterogeneity of oligodendroglia.
Cytotoxic and micronuclei inducing effects of petroleum ether fraction of leaf aqueous extract of Clerodendrum viscosum Vent. in Allium cepa root tip cells
Authors: Roy Sujit , Kundu Lalit Mohan , Roy Gobinda Chandra , Barman Manabendu , Ray Sanjib
Published: June 2021

Clerodendrum viscosum is a traditionally used medicinal plant. The present study aimed to analyze a detailed cytotoxic effect of the nonpolar petroleum ether fraction (AQPEF) of leaf aqueous extract of C. viscosum Vent. (LAECV) in Allium cepa root tip cells. The LAECV was fractionated with petroleum ether and tested for A. cepa toxicity at early hours (2 and 4 h treatment) at concentrations 0, 50, 100, 150 and 200 µg mL-1. The highest aberrant cell percentage (10.45±0.46%) was scored from 150 µg mL-1 followed by100 µg mL-1 (8.75±0.26%) concentration at 4 h treated samples. The AQPEF treatment induced a significant (p<0.0001) increase in micronuclei frequency; 4.31±0.33, 5.08±0.13, 5.05±0.22 and 3.05±0.37% respectively at concentrations 50, 100, 150, and 200 µg mL-1. The highest polyploid frequency (20.14±0.68 %) induced with 100 µg mL-1 of AQPEF at 16 h recovery. 150 µg mL-1 is the most effective concentration of AQPEF to decipher its activity similar to colchicine (150 µg mL-1). In summary, the present study indicates petroleum ether is suitable for extraction of the active phytochemicals of LAECV having cytotoxic effects on A. cepa root tip cells. The AQPEF has colchicine like micronuclei, polyploidy, and mitotic abnormality inducing potentials in A. cepa root apical meristem cells.
Effect of differences in mechanical stress in vivo on the onset and progression of knee osteoarthritis
Authors: Arakawa Kohei , Takahata Kei , Oka Yuichiro , Ozone Kaichi , Nakagaki Sumika , Enomoto Saaya , Murata Kenji , Kanemura Naohiko , Kokubun Takanori
Published: June 2021

Objective

The effect of the type of mechanical stress on OA onset has not been clarified. The aim of this study was to establish a new model that reproduces the type and increase and decrease of mechanical stress in vivo and to clarify the differences in the mechanism of knee OA onset and progression among the models.

Design

To reproduce the difference in mechanical stress, we used the anterior cruciate ligament transection (ACL-T) model and the destabilization of the medial meniscus (DMM) model. In addition, we created a controlled abnormal tibial translation (CATT) model and a controlled abnormal tibial rotation (CATR) model that suppressed the joint instability of the ACL-T and DMM model, respectively. These four models reproduced the increase and decrease in shear force due to joint instability and compressive stress due to meniscal dysfunction. We performed joint instability analysis with soft X-ray, micro computed tomography analysis, histological analysis, and immunohistological analysis in 4 and 6 weeks.

Results

Joint instability decreased in the CATT and CATR groups. The meniscus deviated in the DMM and CATR groups. Chondrocyte hypertrophy increased in the ACL-T and DMM groups with joint instability. In the subchondral bone, bone resorption was promoted in the ACL-T and CATT groups, and bone formation was promoted in the DMM and CATR groups.

Conclusions

Increased shear force causes articular cartilage degeneration and osteoclast activation in the subchondral bone. In contrast, increased compressive stress promotes bone formation in the subchondral bone earlier than articular cartilage degeneration occurs.
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads
Authors: De Rop Florian V. , Ismail Joy N. , González-Blas Carmen Bravo , Hulselmans Gert J. , Flerin Christopher C. , Janssens Jasper , Theunis Koen , Christiaens Valerie M. , Wouters Jasper , Marcassa Gabriele , de Wit Joris , Poovathingal Suresh , Aerts Stein
Published: June 2021

Single-cell RNA-seq and single-cell ATAC-seq technologies are being used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases, lower the cost, and allow for more specialized multi-ome assays, custom droplet microfluidics may provide complementary solutions to commercial setups. We developed HyDrop, a flexible and generic droplet microfluidic platform encompassing three protocols. The first protocol involves creating dissolvable hydrogel beads with custom oligos that can be released in the droplets. In the second protocol, we demonstrate the use of these beads for HyDrop-ATAC, a low-cost non-commercial scATAC-seq protocol in droplets. After validating HyDrop-ATAC, we applied it to flash-frozen mouse cortex and generated 8,502 high-quality single-cell chromatin accessibility profiles in a single run. In the third protocol, we adapt both the reaction chemistry and the capture sequence of the barcoded hydrogel bead to capture mRNA, and demonstrate a significant improvement in throughput and sensitivity compared to previous open-source droplet-based scRNA-seq assays (Drop-seq and inDrop). Similarly, we applied HyDrop-RNA to flash-frozen mouse cortex and generated 9,508 single-cell transcriptomes closely matching reference single-cell gene expression data. Finally, we leveraged HyDrop-RNA’s high capture rate to analyse a small population of FAC-sorted neurons from the Drosophila brain, confirming the protocol’s applicability to low-input samples and small cells. HyDrop is currently capable of generating single-cell data in high throughput and at a reduced cost compared to commercial methods, and we envision that HyDrop can be further developed to be compatible with novel (multi-) omics protocols.
Long-term culture of fetal monocyte precursorsin vitroallowing the generation ofbona fidealveolar macrophagesin vivo
Authors: Li Fengqi , Okreglicka Katarzyna Maria , Pohlmeier Lea Maria , Schneider Christoph , Kopf Manfred
Published: June 2021

Tissue-resident macrophage-based immune therapies have been proposed for various diseases. However, generation of sufficient numbers that possess tissue-specific functions remains a major handicap. Here, we show that fetal liver monocytes (FLiMo) cultured with GM-CSF (also known as CSF2) rapidly differentiate into a long-lived, homogeneous alveolar macrophage (AM)-like populationin vitro. CSF2-cultured FLiMo remain the capacity to develop intobona fideAM upon transfer intoCsf2ra-/-neonates and prevent development of alveolar proteinosis and efferocytosis of apoptotic cells for at least 1 yearin vivo. Compared to transplantation of AM-like cells derived from bone marrow macrophages (BMM), CSF2-cFliMo more efficiently engraft empty AM niches in the lung and protect mice from respiratory viral infection. Harnessing the potential of this approach for gene therapy, we restored a disrupted Csf2ra gene in FLiMo and their capacity to develop into AMin vivo. Together, we provide a novel platform for generation of immature AM-like precursors amenable for genetic manipulation, which will be useful to study to dissect AM development and function and pulmonary transplantation therapy.
Heterogeneous mutation rates and spectra in yeast hybrids
Authors: Fijarczyk Anna , Hénault Mathieu , Marsit Souhir , Charron Guillaume , Landry Christian R.
Published: June 2021

Mutation rates and spectra vary between species and among populations. Hybridization can contribute to this variation, but its role remains poorly understood. Estimating mutation rates requires controlled conditions where the effect of natural selection can be minimized. One way to achieve this is through mutation accumulation experiments coupled with genome sequencing. Here we investigate 400 mutation accumulation lines initiated from 11 genotypes spanning intra-lineage, inter-lineage and interspecific crosses of the yeasts Saccharomyces paradoxus and S. cerevisiae and propagated for 770 generations. We find significant differences in mutation rates and spectra among crosses, which are not related to the level of divergence of parental strains but are specific to some genotype combinations. Differences in number of generations and departures from neutrality play a minor role, whereas polyploidy and loss of heterozygosity impact mutation rates in some of the hybrid crosses in an opposite way.
Presynaptic Gq-coupled receptors drive biphasic dopamine transporter trafficking that modulates dopamine clearance and motor function
Authors: Kearney Patrick J. , Kahuno Elizabeth , Conklin Tucker L. , Martin Gilles E. , Lubec Gert , Melikian Haley E.
Published: June 2021

Extracellular dopamine (DA) levels are constrained by the presynaptic DA transporter (DAT), a major psychostimulant target. Despite its necessity for DA neurotransmission, DAT regulation in situ is poorly understood, and it is unknown whether regulated DAT trafficking impacts dopaminergic signaling and/or behaviors. Leveraging chemogenetics and conditional gene silencing, we found that activating presynaptic Gq-coupled receptors, either hM3Dq or mGluR5, drove rapid biphasic DAT membrane trafficking, with region-specific differences in ventral and dorsal striata. DAT insertion required DRD2 autoreceptors and intact retromer, whereas DAT retrieval required PKC activation and Rit2. Ex vivo voltammetry revealed that DAT trafficking impacts DA clearance. Importantly, dopaminergic mGluR5 silencing elevated surface DAT, which abolished motor learning and was rescued by inhibiting DAT. We found that presynaptic DAT trafficking is complex, multimodal, and region-specific, and identify cell autonomous mechanisms governing presynaptic DAT tone. Importantly, the findings suggest regulated DAT trafficking impacts both DA clearance and motor function.
Learning and organization of memory for evolving patterns
Authors: Schnaack Oskar H , Peliti Luca , Nourmohammad Armita
Published: June 2021

Storing memory for molecular recognition is an efficient strategy for responding to external stimuli. Biological processes use different strategies to store memory. In the olfactory cortex, synaptic connections form when stimulated by an odor, and establish distributed memory that can be retrieved upon re-exposure. In contrast, the immune system encodes specialized memory by diverse receptors that recognize a multitude of evolving pathogens. Despite the mechanistic differences between the olfactory and the immune memory, these systems can still be viewed as different information encoding strategies. Here, we present a theoretical framework with artificial neural networks to characterize optimal memory strategies for both static and dynamic (evolving) patterns. Our approach is a generalization of the energy-based Hopfield model in which memory is stored as a network’s energy minima. We find that while classical Hopfield networks with distributed memory can efficiently encode a memory of static patterns, they are inadequate against evolving patterns. To follow an evolving pattern, we show that a distributed network should use a higher learning rate, which in turn, can distort the energy landscape associated with the stored memory attractors. Specifically, narrow connecting paths emerge between memory attractors, leading to misclassification of evolving patterns. We demonstrate that compartmentalized networks with specialized subnetworks are the optimal solutions to memory storage for evolving patterns. We postulate that evolution of pathogens may be the reason for the immune system to encoded a focused memory, in contrast to the distributed memory used in the olfactory cortex that interacts with mixtures of static odors.
Parallel valence processing alterations associated with compulsive behavior in SAPAP3 knockout mice and human OCD
Authors: Kajs Bridget L. , van Roessel Peter J. , Davis Gwynne L. , Williams Leanne M. , Rodriguez Carolyn I. , Gunaydin Lisa A.
Published: June 2021

Abnormalities in valence processing – the processing of aversive or appetitive stimuli – may be an underrecognized component of obsessive-compulsive disorder (OCD). Independent experimental paradigms have suggested disturbance of emotional valence systems in OCD, yet no standardized assay has been employed to assess both negative and positive valence processing in clinical studies of OCD patients, either at baseline or in response to therapeutic interventions. Additionally, preclinical rodent models are critical for treatment discovery in OCD, yet investigations examining whether rodent models of compulsive behavior similarly show alterations in valence systems have been limited. We sought to establish paradigms for assessing valence processing across both human OCD patients and in a preclinical rodent model: in OCD patients, we used validated behavioral tests to assess explicit and implicit processing of fear-related facial expressions (negative valence) and socially-rewarding happy expressions (positive valence); in the SAPAP3 knockout (KO) mouse model of compulsive behavior, we used auditory fear conditioning and extinction (negative valence) and reward-based operant conditioning (positive valence). We find that OCD patients show enhanced negative and impaired positive valence processing, and that performance on valence processing tasks correlates with clinical measures of OCD severity. We further find that SAPAP3 KO mice show heightened negative and impaired positive valence processing alterations similar to those of OCD patients. Our results show parallel valence processing abnormalities in OCD patients and a preclinical rodent model of compulsive behavior, and suggest valence processing alterations as novel therapeutic targets across a translational research spectrum.
Drosophila melanogaster females prioritise dietary sterols for producing high quality eggs
Authors: Zanco Brooke , Rapley Lisa , Johnstone Joshua N , Dedman Amy , Mirth Christen K , Sgrò Carla M , Piper Matthew DW
Published: June 2021

Limiting calories or specific nutrients without malnutrition, otherwise known as dietary restriction (DR), has been shown to extend lifespan across a broad range of taxa. Our recent findings in Drosophila melanogaster show that supplementing flies on macronutrient-rich diets with additional cholesterol can extend lifespan to the same extent as DR. Macronutrient-rich diets drive high levels of egg production and in doing so deplete the mothers of somatic sterols that are essential for survival. Thus, DR may be beneficial for lifespan because it reduces egg production which in turn reduces the mother’s demand for sterols. If this is true, mothers must be prioritising their available sterols, whether from the diet or from their own bodies, to sustain high quality egg production. To test this, we measured the quality of eggs laid by mothers fed either cholesterol-sufficient or cholesterol-depleted diets. We found that even when the mother’s diet was completely devoid of cholesterol, high quality egg production persisted. Furthermore, we show that sterol-supplemented flies with long lives continue to lay high quality eggs that give rise to healthy offspring. Thus, in our assays, long life does not require a fecundity cost.
Federated analysis of BRCA1 and BRCA2 variation in a Japanese cohort
Authors: Casaletto James , Parsons Michael , Markello Charles , Iwasaki Yusuke , Momozawa Yukihide , Spurdle Amanda B. , Cline Melissa
Published: June 2021

More than 40% of the germline variants in ClinVar today are variants of uncertain significance (VUS). These variants remain unclassified in part because the patient-level data needed for their interpretation is siloed. Federated analysis can overcome this problem by “bringing the code to the data”: analyzing the sensitive patient-level data computationally within its secure home institution and providing researchers with valuable insights from data that would not otherwise be accessible. We tested this principle with a federated analysis of breast cancer clinical data at RIKEN, derived from the BioBank Japan repository. We were able to analyze these data within RIKEN’s secure computational framework, without the need to transfer the data, gathering evidence for the interpretation of several variants. This exercise represents an approach to help realize the core charter of the Global Alliance for Genomics and Health (GA4GH): to responsibly share genomic data for the benefit of human health.
RT-QuIC amplification of CWD prions in winter ticks (Dermacentor albipictus) collected from North American elk (Cervus canadensis) in a CWD-endemic area
Authors: Haley NJ , Henderson DM , Senior K , Miller M , Donner R
Published: June 2021

Chronic wasting disease (CWD) is a progressive and fatal spongiform encephalopathy of deer and elk species, caused by a misfolded variant of the normal prion protein. Horizontal transmission of the misfolded CWD prion between animals is thought to occur through shedding in saliva and other forms of excreta. The role of blood in CWD transmission is less clear, though infectivity has been demonstrated in various blood fractions. Blood-feeding insects, including ticks, are known vectors for a range of bacterial and viral infections in animals and humans, though to date there has been no evidence for their involvement in prion disease transmission. In the present study, we evaluated winter ticks (Dermacentor albipictus) collected from 136 North American elk (Cervus canadensis) in a CWD-endemic area for evidence of CWD prion amplification using the real time quaking-induced conversion assay (RT-QuIC). Although 30 elk were found to be CWD-positive (22%) postmortem, amplifiable prions were found in just a single tick collected from an elk in advanced stages of CWD infection, with some evidence for prions in ticks collected from elk in mid-stage infection. These findings suggest that further investigation of ticks as reservoirs for prion disease may be warranted.

Importance

This study reports the first finding of detectable levels of prions linked to chronic wasting disease in a tick collected from a clinically infected elk. Using the real time quaking-induced conversion assay (RT-QuIC), evidence of amplifiable CWD prions was also found in ticks collected from elk in earlier stages of disease. Observed levels were at the lower end of our detection limits, though our findings suggest that additional research evaluating ticks collected from animals in late-stage disease may be warranted to further evaluate the role of ticks as potential vectors of chronic wasting disease.
Measuring Integrated Novel Dimensions in Neurodevelopmental and Stress-related Mental Disorders (MIND-Set): a cross-sectional comorbidity study from an RDoC perspective
Authors: van Eijndhoven Philip F.P. , Collard Rose M. , Vrijsen Janna N. , Geurts Dirk G.M. , Arias-Vasquez Alejandro , Schellekens Arnt F.A. , van den Munckhof Eva , Brolsma Sophie C.A. , Duyser Fleur A. , Bergman M. Annemiek , van Oort Jasper , Tendolkar Indira , Schene Aart H.
Published: June 2021

Background

It is widely acknowledged that comorbidity between psychiatric disorders is common. Shared and diverse underpinnings of psychiatric disorders cannot be systematically understood on the basis of symptom-based categories of mental disorders, which map poorly onto pathophysiological mechanisms. In the MIND-Set study, we make use of current concepts of comorbidity that transcend the current diagnostic categories. We test this approach to psychiatric problems in patients with frequently occurring psychiatric disorders and their comorbidities (excluding psychosis). The main objective of the MIND-Set project is to determine the shared and specific mechanisms of neurodevelopmental and stress-related psychiatric disorders at different observational levels.

Methods

This is an observational, cross-sectional study. Data from different observational levels as defined in the research domain criteria (RDoC; genetics, physiology, neuropsychology, system level neuroimaging, behavior, self-report and experimental neurocognitive paradigms) are collected over four time points. Included are adult (≥ 18 years), non-psychotic, psychiatric patients with a clinical diagnosis of a stress-related disorder (mood disorder, anxiety disorder and/or addiction disorder) and/or a neurodevelopmental disorder (ASD and/or ADHD). Individuals with no current or past psychiatric diagnosis are included as controls. Data collection started in June 2016 with the aim to include a total of 650 patients and 150 healthy controls by 2021. The data collection procedure includes online questionnaires and three subsequent sessions with 1) Standardized clinical examination, physical examination, and blood sampling; 2) Psychological constructs, neuropsychological tests, and biological marker sampling; 3) Neuroimaging measures.

Discussion

The MIND-Set study enables us to investigate the mechanistic underpinnings of non-psychotic psychiatric disorders transdiagnostically. We will identify both shared and disorder-specific markers at different observational levels that can be used as targets for future diagnostic and treatment approaches.
Insect-specific viruses regulate vector competence in Aedes aegypti mosquitoes via expression of histone H4
Authors: Olmo Roenick P. , Todjro Yaovi M. H. , Aguiar Eric R. G. R. , de Almeida João Paulo P. , Armache Juliana N. , de Faria Isaque J. S. , Ferreira Flávia V. , Silva Ana Teresa S. , de Souza Kátia P. R. , Vilela Ana Paula P. , Tan Cheong H. , Diallo Mawlouth , Gaye Alioune , Paupy Christophe , Obame-Nkoghe Judicaël , Visser Tessa M. , Koenraadt Constantianus J. M. , Wongsokarijo Merril A. , Cruz Ana Luiza C. , Prieto Mariliza T. , Parra Maisa C. P. , Nogueira Maurício L. , Avelino-Silva Vivian , Mota Renato N. , Borges Magno A. Z. , Drumond Betânia P. , Kroon Erna G. , Sedda Luigi , Marois Eric , Imler Jean-Luc , Marques João T.
Published: June 2021

Aedes aegypti and Aedes albopictus are major mosquito vectors for arthropod-borne viruses (arboviruses) such as dengue (DENV) and Zika (ZIKV) viruses. Mosquitoes also carry insect-specific viruses (ISVs) that may affect the transmission of arboviruses. Here, we analyzed the global virome in urban Aedes mosquitoes and observed that two insect-specific viruses, Phasi Charoen-like virus (PCLV) and Humaita Tubiacanga virus (HTV), were the most prevalent in A. aegypti worldwide except for African cities, where transmission of arboviruses is low. Spatiotemporal analysis revealed that presence of HTV and PCLV led to a 200% increase in the chances of having DENV in wild mosquitoes. In the laboratory, we showed that HTV and PCLV prevented downregulation of histone H4, a previously unrecognized proviral host factor, and rendered mosquitoes more susceptible to DENV and ZIKV. Altogether, our data reveals a molecular basis for the regulation of A. aegypti vector competence by highly prevalent ISVs that may impact how we analyze the risk of arbovirus outbreaks.
Quantification of Antisense Oligonucleotides by Splint Ligation and Quantitative Polymerase Chain Reaction
Authors: Shin Minwook , Krishnamurthy Pranathi Meda , Watts Jonathan K.
Published: June 2021

Reliable detection and quantification of antisense oligonucleotides (ASOs) in experimental and clinical specimens is essential to understand the biological function of novel oligonucleotide-based therapeutics. In this study, we describe a method to detect and quantify ASOs in biological samples, whereby the ASO acts as a splint to direct the ligation of complementary probes and quantitative real-time PCR was used to monitor ligation products. Low levels of 2′-O-MOE gapmer ASO in serum, liver, kidney, lung, heart, muscle, and brain tissues can be detected over a 6-log linear range for detection using this method. This method allows quantification of various types of chemically modified ASOs, including PS linkage, 2′-OMe, 2′-O-MOE, locked nucleic acid (LNA), and siRNA. This method does not require probe modifications, and can be performed using standard laboratory equipment; making it a fast, sensitive, and reliable technique that can be widely applied. This detection method may find potential applications in detection of therapeutic oligonucleotides in biological samples.
Sustained post-developmental T-bet expression is critical for the maintenance of type one innate lymphoid cells in vivo
Authors: Schroeder J-H , Roberts LB , Meissl K , Lo JW , Hromadová D , Hayes K , Zabinski T , Read E , Heliodoro C Moreira , Reis R , Howard JK , Grencis RK , Neves J F , Strobl B , Lord GM
Published: June 2021

Innate lymphoid cells (ILC) play a significant role in the intestinal immune response and T-bet+ CD127+ group 1 cells (ILC1) have been linked to the pathogenesis of human inflammatory bowel disease (IBD). However, the functional importance of ILC1 in the context of an intact adaptive immune response has been controversial. In this report we demonstrate that induced depletion of T-bet using a Rosa26-Cre-ERT2 model resulted in the loss of intestinal ILC1, pointing to a post-developmental requirement of T-bet expression for these cells. In contrast, neither colonic lamina propria (cLP) ILC2 nor cLP ILC3 abundance were altered upon induced deletion of T-bet. Mechanistically, we report that STAT1 or STAT4 are not required for intestinal ILC1 development and maintenance. Mice with induced deletion of T-bet and subsequent loss of ILC1 were protected from the induction of severe colitis in vivo. Hence, this study provides support for the clinical development of an IBD treatment based on ILC1 depletion via targeting T-bet or its downstream transcriptional targets.
A marginal habitat, but not a sink: Ecological genetics reveal a diversification hotspot for marine invertebrates in the brackish Baltic Sea
Authors: Geburzi Jonas C. , Heuer Nele , Homberger Lena , Kabus Jana , Moesges Zoe , Ovenbeck Kira , Brandis Dirk , Ewers-Saucedo Christine
Published: June 2021

Aim

Environmental gradients have emerged as important barriers structuring populations and species distributions. We set out to test whether a strong salinity gradient from marine to brackish, represented in a marginal northern European sea, should be considered a diversification hotspot or a population sink, and to identify life history traits that correlate with either evolutionary trajectory.

Location

The Baltic Sea, the North Sea and their transition zone.

Methods

We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data and data on the distribution, salinity tolerance and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta and Gastrotricha, including seven non-native species. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times and migration rates between North and Baltic Sea populations, and analysed correlations between genetic and life history data.

Results

The majority of investigated species is either genetically differentiated and/or is adapted to the lower salinity conditions of the Baltic Sea. Moreover, the species exhibiting population structure have a range of patterns of genetic diversity in comparison to the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea.

Main conclusions

Our results indicate that the Baltic Sea should be considered a diversification hotspot: The diversity of genetic patterns points towards independent trajectories in the Baltic compared to the North Sea. At the same time, we found limited evidence for the traditional scenario of the Baltic Sea as a population sink with lower diversity and strong gene flow. The North Sea - Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non-native species.
Carboxypeptidase E is efficiently secreted and internalized via lysosomes
Authors: Armoza-Eilat Shir , Caspi Michal , Shomron Olga , Hirschberg Koret , Rosin-Arbesfeld Rina
Published: June 2021

Carboxypeptidase E (CPE) a key factor in the biosynthesis of most peptide hormones and neuropeptides, is predominantly expressed in endocrine tissues and the nervous system. This highly conserved enzyme cleaves the C-terminal basic residues of the peptide precursors to generate their bioactive form. CPE is a secreted protein; however, the Intracellular pathways leading to its secretion are still obscure. We combined live-cell microscopy and molecular analysis to examine the intracellular distribution and secretion dynamics of fluorescently tagged CPE. CPE was found to be a soluble luminal protein as it traffics from the ER via the Golgi apparatus to lysosomes. Moreover, CPE is efficiently secreted and reinternalized to lysosomes of neighboring cells. The C-terminal amphipathic helix of CPE is essential for its efficient targeting to, and secretion from lysosomes. Fluorescence resonance energy transfer demonstrated that CPE and its substrate neuropeptide Y (NPY) interact in the Golgi apparatus and Immunoprecipitation analysis demonstrated that both CPE and NPY are co-secreted. The implications of the well-defined CPE intra and extracellular routes are discussed.
The ciliary gene INPP5E confers dorsal telencephalic identity to human cortical organoids by negatively regulating Sonic Hedgehog signalling
Authors: Schembs Leah , Willems Ariane , Hasenpusch-Theil Kerstin , Cooper James D. , Whiting Katie , Burr Karen , Bøstrand Sunniva M.K. , Selvaraj Bhuvaneish T. , Chandran Siddharthan , Theil Thomas
Published: June 2021

Defects in primary cilia, cellular antennas that controls multiple intracellular signalling pathways, underlie several neurodevelopmental disorders, but how cilia control essential steps in human brain formation remains elusive. Here, we show that cilia are present on the apical surface of radial glial cells in human foetal forebrain. Interfering with cilia signalling in human organoids by mutating the INPP5E gene leads to the formation of ventral telencephalic cell types instead of cortical progenitors and neurons. INPP5E mutant organoids also showed increased SHH signalling and cyclopamine treatment partially rescued this ventralisation. In addition, ciliary expression of SMO was increased and the integrity of the transition zone was compromised. Overall, these findings establish the importance of primary cilia for dorsal/ventral patterning in human corticogenesis, indicate a tissue specific role of INPP5E as a negative regulator of SHH signalling and have implications for the emerging roles of cilia in the pathogenesis of neurodevelopmental disorders.
Generative replay for compositional visual understanding in the prefrontal-hippocampal circuit
Authors: Schwartenbeck Philipp , Baram Alon , Liu Yunzhe , Mark Shirley , Muller Timothy , Dolan Raymond , Botvinick Matthew , Kurth-Nelson Zeb , Behrens Timothy
Published: June 2021

Understanding the visual world is a constructive process. Whilst a frontal-hippocampal circuit is known to be essential for this task, little is known about the associated neuronal computations. Visual understanding appears superficially distinct from other known functions of this circuit, such as spatial reasoning and model-based planning, but recent models suggest deeper computational similarities. Here, using fMRI, we show that representations of a simple visual scene in these brain regions are relational and compositional – key computational properties theorised to support rapid construction of hippocampal maps. Using MEG, we show that rapid sequences of representations, akin to replay in spatial navigation and planning problems, are also engaged in visual construction. Whilst these sequences have previously been proposed as mechanisms to plan possible futures or learn from the past, here they are used to understand the present. Replay sequences form constructive hypotheses about possible scene configurations. These hypotheses play out in an optimal order for relational inference, progressing from predictable to uncertain scene elements, gradually constraining possible configurations, and converging on the correct scene configuration. Together, these results suggest a computational bridge between apparently distinct functions of hippocampal-prefrontal circuitry, and a role for generative replay in constructive inference and hypothesis testing.
Whole-cell cryo-electron tomography of cultured and primary eukaryotic cells on micropatterned TEM grids
Authors: Sibert Bryan S. , Kim Joseph Y. , Yang Jie E. , Wright Elizabeth R.
Published: June 2021

Whole-cell cryo-electron tomography (cryo-ET) is a powerful technique that can provide nanometer-level resolution of biological structures within the cellular context and in a near-native frozen-hydrated state. It remains a challenge to culture or adhere cells on TEM grids in a manner that is suitable for tomography while preserving the physiological state of the cells. Here, we demonstrate the versatility of micropatterning to direct and promote growth of both cultured and primary eukaryotic cells on TEM grids. We show that micropatterning is compatible with and can be used to enhance studies of host-pathogen interactions using respiratory syncytial virus infected BEAS-2B cells as an example. We demonstrate the ability to use whole-cell tomography of primary Drosophila neuronal cells to identify organelles and cytoskeletal stuctures in cellular axons and the potential for micropatterning to dramatically increase throughput for these studies. During micropatterning, cell growth is targeted by depositing extra-cellular matrix (ECM) proteins within specified patterns and positions on the foil of the TEM grid while the other areas remain coated with an anti-fouling layer. Flexibility in the choice of surface coating and pattern design make micropatterning broadly applicable for a wide range of cell types. Micropatterning is useful for studies of structures within individual cells as well as more complex experimental systems such as host-pathogen interactions or differentiated multi-cellular communities. Micropatterning may also be integrated into many downstream whole-cell cryo-ET workflows including correlative light and electron microscopy (cryo-CLEM) and focused-ion beam milling (FIB-SEM).
Confronting assumptions about prey selection by lunge‐feeding whales using a process‐based model
Authors: Chenoweth Ellen M. , Boswell Kevin M. , Friedlaender Ari S. , McPhee Megan V. , Burrows Julia A. , Heintz Ron A. , Straley Jan M.
Published: June 2021

The relative energetic benefits of foraging on one type of prey rather than another are not easily measured, particularly for large free‐ranging predators. Nonetheless, assumptions about preferred and alternative prey are frequently made when predicting how a predator may impact its environment, adapt to environmental change or interact with human activities.

We developed and implemented a process‐based model to investigate the potential energetic benefit (PEB) of in situ foraging opportunities in rorqual whales. The model integrates and evaluates the energetic importance of measured prey patch characteristics (prey distribution, energy content and predator avoidance) and predator characteristics (morphometrics, foraging tactics and feeding rates). We applied the model to test the assumption that hatchery‐released juvenile salmon are an ‘easy meal’ for humpback whales compared to more common prey: herring and krill.

In 11 out of the 13 foraging situations considered, whales were found to be feeding in a manner where net energy gain was greater than the energetic costs of non‐foraging swimming. Humpback whale PEB for hatchery‐released juvenile salmon fell within the range of the PEB for krill and herring but varied by species, from relatively high PEB for chum salmon to relatively low for coho salmon. Our model provides behavioural insight as well, indicating that shallow feeding may be more important for reducing energy expenditure through slower lunge speeds than for increasing prey capture. The model also provides a means of identifying prey patch characteristics, with prey aggregation playing the largest role in determining PEB despite being a poor overall proxy for PEB, supporting the use of the complex model framework.

Modelling approaches are especially valuable where they can use reasonable assumptions to substitute for lack of reliable observations, thereby integrating a range of interacting factors into a single framework. Additionally, because process‐based models can be used to make predictions outside the range of previously observed conditions, they will be increasingly useful in a changing climate.

A free Plain Language Summary can be found within the Supporting Information of this article.