bluuebunny/crossref_metadata_2025 huggingface dataset:
Bodily ownership of an independent supernumerary limb: An exploratory study
Authors: Umezawa Kohei , Suzuki Yuta , Ganesh Gowrishankar , Miyawaki Yoichi
Published: September 2021

Can our brain perceive a sense of ownership towards an independent supernumerary limb; one that can be moved independently of any other limb and provides its own independent movement feedback? Following the rubberhand illusion experiment, a plethora of studies has shown that the human representation of ‘self’ is very plastic. But previous studies have almost exclusively investigated ownership towards ‘substitute’ artificial limbs, which are controlled by the movements of a real limb and/or limbs from which non-visual sensory feedback is provided on an existing limb. Here, to investigate whether the human brain can own an independent artificial limb, we first developed a novel independent robotic ‘sixth finger.’ We allowed participants to train using the finger and examined whether it induced changes in the body representation using behavioral as well as cognitive measures. Our results suggest that unlike a substituted artificial limb (like in the rubber hand experiment), it is more difficult for humans to perceive a sense of ownership towards an independent limb. However, ownership does seem possible, as we observed clear tendencies of changes in the body representation that correlated with the cognitive reports of the sense of ownership. Our results provide the first evidence to show that an independent supernumerary limb can be embodied by the human brain.
The secrets to domestic bliss – Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years
Authors: Hu Yi , D’Amelio Catherine L. , Béchade Benoît , Cabuslay Christian S. , Sanders Jon G. , Price Shauna , Fanwick Emily , Powell Scott , Moreau Corrie S. , Russell Jacob A.
Published: September 2021

Background

Gut microbiomes can vary across development, a pattern often found for insects with complete metamorphosis. With varying nutritional need and distinct opportunities for microbial acquisition, questions arise as to how such ‘holometabolous’ insects retain helpful microbes at larval and adult stages. Ants are an intriguing system for such study. In a number of lineages adults digest only liquid food sources, while larvae digest solid foods. Like some other social insects, workers and soldiers of some ant species engage in oral-anal trophallaxes, enabling microbial transfer among siblings. But do queens, the typical colony founding caste, obtain symbionts through such transfer? Does this enable transgenerational symbiont passage? And does the resulting partner fidelity promote the evolution of beneficial symbionts? Furthermore, how might such adult-centric biology shape larval microbiomes? To address these questions, we characterized symbiotic gut bacteria across 13 species of Cephalotes turtle ants, with up to 40-million years of divergence. Adding to the prior focus on workers we, here, study underexplored castes and stages including queens, soldiers, and larvae, by performing 16S rRNA qPCR, amplicon sequencing, and phylogenetic classification.

Results

We show that adult microbiomes are conserved across species and largely across castes. Nearly 95% of the bacteria in adults have, thus far, been found only in Cephalotes ants. Furthermore, the microbiomes from most adults exhibit phylosymbiosis, a trend in which microbiome community similarity recapitulates patterns of host relatedness. Additionally, an abundant, adult-enriched symbiont cospeciates with some Cephalotes. Evidence here suggests that these partner fidelity patterns extend from transgenerational symbiont transfer through alate gyne dispersal and subsequent colony-founding by queens. Like adults, larvae of Cephalotes species exhibit strong microbiome conservation. Phylosymbiosis patterns are weaker, however, with further evidence elevating environmental filtering as a primary mechanism behind such conservation. Specifically, while adult-enriched symbionts are found in most larvae, symbionts of older larvae are highly related to free-living bacteria from the Enterobacteriaceae, Lactobacillales, and Actinobacteria.

Conclusions

Our findings suggest that both partner fidelity and conserved environmental filtering drive stable, stage-specific, social insect symbioses. We discuss the implications for our broader understanding of insect microbiomes, and the means of sustaining a beneficial microbiome.
Insertive vaginal sex has a profound impact on the penile immune correlates of HIV susceptibility
Authors: Mohammadi Avid , Bagherichimeh Sareh , Choi Yoojin , Fazel Azadeh , Tevlin Elizabeth , Huibner Sanja , Shao Eric , Zuanazzi David , Prodger Jessica , Good Sara V , Tharao Wangari , Kaul Rupert
Published: September 2021

The penis is the primary site of HIV acquisition in heterosexual men. Elevated penile inflammatory cytokines increase sexual acquisition risk, and topically applied cytokines enhance foreskin HIV susceptibility in an explant model. However, the impact of penile-vaginal sex on these immune parameters is undefined. Heterosexual couples were recruited to the Sex, Couples and Science (SECS) Study, with the collection of penile swabs, semen, cervico-vaginal secretions, and blood after a period of abstinence, and repeated sampling up to 72 hours after either condomless (n=30) or condom-protected (n=8) penile-vaginal sex. Soluble immune parameters were quantified by multiplex immunoassay. Co-primary immune endpoints were penile levels of IL-8 and MIG, cytokines previously linked to penile HIV acquisition. One hour after sex there were dramatic increases in penile IL-8 and MIG levels, regardless of condom use, with a gradual return to baseline by 72 hours; similar patterns were observed for other chemoattractant chemokines. Penile cytokine changes were similar in circumcised and uncircumcised men, and repeated measures ANOVA and ANCOVA models demonstrated that the degree of change after condomless sex was explained by cytokine levels in their partners’ cervico-vaginal secretions. This may have important implications for the biology of penile HIV acquisition.

Author summary

In heterosexual men, the penis is the primary site of Human Immunodeficiency Virus (HIV) acquisition. Levels of inflammatory cytokines in the coronal sulcus are associated with an increased HIV risk, and we hypothesized that these may be altered after insertive penile sex. Therefore, we designed the Sex, Couples and Science Study (SECS study) to define the impact of penile-vaginal sex on the penile immune correlates of HIV susceptibility. We found that multiple coronal sulcus cytokines increased dramatically and rapidly after sex, regardless of condom use, with a return to baseline levels by 72 hours. The changes observed after condomless sex were strongly predicted by cytokine concentrations in the vaginal secretions of the female partner, and were similar in circumcised and uncircumcised men. We believe that these findings have important implications for understanding the immunopathogenesis of penile HIV acquisition; in addition, they have important implications for the design of clinical studies of penile HIV acquisition and prevention.
Size-selective mortality fosters ontogenetic changes in collective risk-taking behaviour in zebrafish,Danio rerio
Authors: Roy Tamal , Arlinghaus Robert
Published: September 2021

Size-selective mortality is common in fish populations and can operate either in a positive size-selective fashion or be negatively size-selective. Through various mechanisms (like genetic correlations among behaviour and life-history traits or direct selection on behaviour co-varying with growth rate or size-at-maturation), both positive- and negative size-selection can result in evolutionary changes in behavioural traits. Theory suggests that size-selection alone favours boldness, but little experimental evidence exists about whether and to what extent size-selection can trigger its evolution. Here we investigated the impact of size-selective mortality on boldness across ontogeny using three experimental lines of zebrafish (Danio rerio) generated through positive (large-harvested), negative (small-harvested) and random (control line) size-selective mortality for five generations. We measured risk-taking during feeding (boldness) under simulated aerial predation threat and in presence of a live cichlid. We found that boldness decreased with ontogenetic age under aerial predation threat, and the small-harvested line was consistently bolder than controls. Collective personality emerged post larval stages among the selection lines. In presence of a cichlid, the large-harvested line was bolder at the highest risk of predation. The large-harvested line showed higher variability and plasticity in boldness across life stages and predation risks. Collectively, our results demonstrate that size-selective harvesting may evolutionarily alter risk-taking tendency. Size-selection alone favours boldness when selection acts on small fish. Selection typical of fisheries operating on large fish favours boldness at the highest risk of predation and increases behavioural variability and plasticity. There was no evidence for positive size-selection favouring evolution of shyness.
Potential Key Genes Associated with Stroke types and its subtypes: A Computational Approach
Authors: Das Gourab , Kumar Pradeep
Published: September 2021

To investigate prospective key genes and pathways associated with the pathogenesis and prognosis of stroke types along with subtypes. Human genes using genome assembly build 38 patch release 13 with known gene symbols through NCBI gene database (https://www.ncbi.nlm.nih.gov/gene) were fetched. PubMed advanced queries were constructed using stroke-related keywords and associations were calculated using Normalized pointwise mutual information (nPMI) between each gene symbol and queries. Genes related with stroke risk within their types and subtypes were investigated in order to discover genetic markers to predict individuals who are at the risk of developing stroke with their subtypes. A total of 2,785 (9.4%) genes were found to be linked to the risk of stroke. Based on stroke types, 1,287 (46.2%) and 376 (13.5%) genes were found to be related with IS and HS respectively. Further stratification of IS based on TOAST classification, 86 (6.6%) genes were confined to Large artery atherosclerosis; 131 (10.1%) and 130 (10%) genes were related with the risk of small vessel disease and Cardioembolism subtypes of IS. Besides, a prognostic panel of 9 genes signature consisting of CYP4A11, ALOX5P, NOTCH, NINJ2, FGB, MTHFR, PDE4D, HDAC9, and ZHFX3 can be treated as a diagnostic marker to predict individuals who are at the risk of developing stroke with their subtypes.
Dysregulation of the Tweak/Fn14 pathway in skeletal muscle of spinal muscular atrophy mice
Authors: Meijboom Katharina E. , McFall Emily , Anthony Daniel , Edwards Benjamin , Kubinski Sabrina , Hazell Gareth , Ahlskog Nina , Claus Peter , Davies Kay E. , Kothary Rashmi , Wood Matthew J.A. , Bowerman Melissa
Published: September 2021

Spinal muscular atrophy (SMA) is a childhood neuromuscular disorder caused by depletion of the survival motor neuron (SMN) protein. SMA is characterized by the selective death of spinal cord motor neurons, leading to progressive muscle wasting. Loss of skeletal muscle in SMA is a combination of denervation-induced muscle atrophy and intrinsic muscle pathologies. Elucidation of the pathways involved is essential to identify the key molecules that contribute to and sustain muscle pathology. The tumor necrosis factor-like weak inducer of apoptosis (TWEAK)/TNF receptor superfamily member fibroblast growth factor inducible 14 (Fn14) pathway has been shown to play a critical role in the regulation of denervation-induced muscle atrophy as well as muscle proliferation, differentiation and metabolism in adults. However, it is not clear whether this pathway would be important in highly dynamic and developing muscle. We thus investigated the potential role of the TWEAK/Fn14 pathway in SMA muscle pathology, using the severe Taiwanese Smn-/-;SMN2 and the less severe Smn2B/- SMA mice, which undergo a progressive neuromuscular decline in the first three post-natal weeks. Here, we report significantly dysregulated expression of the TWEAK/Fn14 pathway during disease progression in skeletal muscle of the two SMA mouse models. In addition, siRNA-mediated Smn knockdown in C2C12 myoblasts suggests a genetic interaction between Smn and the TWEAK/Fn14 pathway. Further analyses of SMA, Tweak-/- and Fn14-/- mice revealed dysregulated myopathy, myogenesis and glucose metabolism pathways as a common skeletal muscle feature, and providing further evidence in support of a relationship between the TWEAK/Fn14 pathway and Smn. Finally, a pharmacological intervention (Fc-TWEAK) to upregulate the activity of the TWEAK/Fn14 pathway improved disease phenotypes in the two SMA mouse models. Our study provides novel mechanistic insights into the molecular players that contribute to muscle pathology in SMA and into the role of the TWEAK/Fn14 pathway in developing muscle.
Identification of a discrete neuronal circuit that relays insulin signaling into the brain to regulate glucose homeostasis
Authors: Mehdi Mouna El , Takhlidjt Saloua , Devère Mélodie , Arabo Arnaud , Le Solliec Marie-Anne , Maucotel Julie , Bénani Alexandre , Nedelec Emmanuelle , Duparc Céline , Lefranc Benjamin , Leprince Jérôme , Anouar Youssef , Prévost Gaëtan , Chartrel Nicolas , Picot Marie
Published: September 2021

26RFa (QRFP) is a biologically active peptide that regulates glucose homeostasis by acting as an incretin and by increasing insulin sensitivity at the periphery. 26RFa is also produced by a neuronal population localized in the hypothalamus. In the present study, we have investigated whether the 26RFa neurons may be involved in the hypothalamic regulation of glucose homeostasis. Our data indicate that 26RFa, i.c.v. injected, induces a robust antihyperglycemic effect associated with an increase of insulin production by the pancreatic islets. In addition, we found that insulin strongly stimulates 26RFa expression and secretion by the hypothalamus. RNAscope experiments revealed that neurons expressing 26RFa in the lateral hypothalamic area and the ventromedial hypothalamic nucleus also express the insulin receptor and that insulin induces the expression of 26RFa in these neurons. Concurrently, we show that the central antihyperglycemic effect of insulin is abolished in presence of a 26RFa receptor (GPR103) antagonist as well as in mice deficient for 26RFa. Finally, our data indicate that the hypothalamic 26RFa neurons are not involved in the central inhibitory effect of insulin on hepatic glucose production, but mediate the central effects of the hormone on its own peripheral production.

To conclude, in the present study we have identified a novel actor of the hypothalamic regulation of glucose homeostasis, the 26RFa/GPR103 system and we provide the evidence that this neuronal peptidergic system is a key relay for the central regulation of glucose metabolism by insulin.
Blood-based untargeted metabolomics in Relapsing-Remitting Multiple Sclerosis revealed the testable therapeutic target
Authors: Zahoor Insha , Suhail Hamid , Datta Indrani , Ahmed Mohammad Ejaz , Poisson Laila M , Waters Jeffrey , Bin Rui , Singh Jaspreet , Cerghet Mirela , Kumar Ashok , Hoda Md Nasrul , Rattan Ramandeep , Mangalam Ashutosh K , Giri Shailendra
Published: September 2021

Metabolic aberrations impact the pathogenesis of multiple sclerosis (MS) and possibly can provide clues for new treatment strategies. Using untargeted metabolomics, we measured serum metabolites from 35 relapsing-remitting patients and 14 healthy age-matched controls. Out of 632 known metabolites detected, 60 were significantly altered in relapsing-remitting MS (RRMS). Bioinformatics analysis identified an altered “metabotype” in RRMS patients, represented by 4 changed metabolic pathways of glycerophospholipid, citrate cycle, sphingolipid, and pyruvate metabolism. Interestingly, the common upstream metabolic pathway feeding these 4 pathways is the glycolysis pathway. Real-time bioenergetic analysis of the patient derived peripheral blood mononuclear cells, showed enhanced glycolysis, supporting the altered metabolic state of immune cells. Experimental autoimmune encephalomyelitis mice treated with the glycolytic inhibitor, 2-deoxy-D-glucose ameliorated the disease progression and inhibited the disease pathology significantly by promoting the anti-inflammatory phenotype of monocytes/macrophage in the central nervous system. Our study suggests that targeting glycolysis offers a potential target for MS.
Multiphase Organization Is a Second Phase Transition Within Multi-Component Biomolecular Condensates
Authors: Mazarakos Konstantinos , Zhou Huan-Xiang
Published: September 2021

We present a mean-field theory for the multiphase organization of multi-component biomolecular condensates and validate the theory by molecular dynamics simulations of model mixtures. A first phase transition results in the separation of the dense phase from the bulk phase. In a second phase transition, the components in the dense phase demix to localize in separate regions that attach to each other. The second phase transition occurs when the strength of cross-species attraction goes below the mean strength of the self-attraction of the individual species and reaches a critical value. At a given strength of cross-species attraction, both of the phase transitions can be observed by decreasing temperature, leading first to phase separation and then to demixing of the dense phase. The theory and simulations establish the disparity in strength between self and cross-species attraction as a main driver for the multiphase organization of multi-component biomolecular condensates.

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Active sensing in bees through antennal movements is independent of odor molecule
Authors: Claverie Nicolas , Buvat Pierrick , Casas Jérôme
Published: September 2021

When sampling odors, many insects are moving their antennae in a complex but repeatable fashion. Previous works with bees have tracked antennal movements in only two dimensions, with a low sampling rate and with relatively few odorants. A detailed characterization of the multimodal antennal movement patterns as function of olfactory stimuli is thus wanting. The aim of this study is to test for a relationship between the scanning movements and the properties of the odor molecule.

We tracked several key locations on the antennae of 21 bumblebees at high frequency (up to 1200 fps) and in three dimensions while submitting them to puffs of 11 common odorants released in a low-speed continuous flow. To cover the range of diffusivity and molecule size of most odors sampled by bees, compounds as different as butanol and farnesene were chosen, with variations of 200% in molar masses. Water and paraffin were used as negative controls. Movement analysis was done on the tip, the scape and the base of the antennae tracked with the neural network Deeplabcut.

Bees use a stereotypical motion of their antennae when smelling odors, similar across all bees, independently of the identity of the odors and hence their diffusivity. The variability in the movement amplitude among odors is as large as between individuals. The first oscillation mode at low frequencies and large amplitude (ca. 1-3 Hz, ca. 100°) is triggered by the presence of an odor and is in line with previous work, as is the speed of movement. The second oscillation mode at higher frequencies and smaller amplitude (40 Hz, ca. 0.1°) is constantly present. Antennae are quickly deployed when a stimulus is perceived, decorrelate their movement trajectories rapidly and oscillate vertically with a large amplitude and laterally with a smaller one. The cone of air space thus sampled was identified through the 3D understanding of the motion patterns.

The amplitude and speed of antennal scanning movements seem to be function of the internal state of the animal, rather than determined by the odorant. Still, bees display an active olfaction strategy. First, they deploy their antennae when perceiving an odor rather than let them passively encounter it. Second, fast vertical scanning movements further increase the flow speed experienced by an antenna and hence the odorant capture rate. Finally, lateral movements might enhance the likelihood to locate the source of odor, similarly to the lateral scanning movement of insects at odor plume boundaries. Definitive proofs of this function will require the simultaneous 3D recordings of antennal movements with both the air flow and odor fields.
Convergent transcriptomic targets of propranolol and primidone identify potential biomarkers for essential tremor
Authors: Castonguay Charles-Etienne , Liao Calwing , Khayachi Anouar , Houle Gabrielle , Ross Jay P , Dion Patrick A , Rouleau Guy A
Published: September 2021

Essential tremor (ET) is one of the most common movement disorders, affecting nearly 5% of individuals over 65 years old. Despite its high heritability, few genetic risk loci for ET have been identified. Recent advances in pharmacogenomics have generated a wealth of data that led to the identification of molecular signatures in response to hundreds of chemical compounds. Among the different forms of data, gene expression has proven to be quite successful for the inference of drug response in cell models. We sought to leverage this approach in the context of ET where many patients are responsive two drugs: propranolol and primidone. Propranolol- and primidone-specific transcriptomic drug targets, as well as convergent gene targets across both drugs, could provide insights into the pathogenesis of ET and identify possible targets of interest for future treatments. In this study, cerebellar DAOY and neural progenitor cells were treated for 5 days with clinical concentrations of propranolol and primidone, after which RNA-sequencing was used to identify differentially expressed genes. The expression of genes previously implicated in genetic and transcriptomic studies of ET and other movement disorders, such as TRAPPC11, were significantly upregulated by propranolol. Pathway enrichment analysis identified multiple terms related to calcium signalling, endosomal sorting, axon guidance, and neuronal morphology. Convergent differentially expressed genes across all treatments and cell types were also found to be significantly more mutationally constrained, implying that they might harbour rare deleterious variants implicated in disease. Furthermore, these genes were enriched within cell types having high expression of ET related genes in both cortical and cerebellar tissues. Altogether, our results highlight potential cellular and molecular mechanisms associated with tremor reduction and identify relevant genetic biomarkers for drug-responsiveness in ET.
Development of anin-situprinting system with human platelet lysate-based bio-adhesive to treat corneal perforation
Authors: You Jingjing , Frazer Hannah , Sayyar Sepidar , Chen Zhi , Liu Xiao , Taylor Adam , Filippi Benjamin , Beirne Stephen , Wise Innes , Hodge Chris , Wallace Gordon , Sutton Gerard
Published: September 2021

Purpose

Corneal perforation is a clinical emergency. Tissue glue to seal the perforation, and supplementary topical medication represents existing standard treatment. Previously, our group developed a transparent human platelet lysate (hPL)-based biomaterial that showed good cell compatibility and accelerated corneal epithelial cells healingin-vitro.This study aims to develop a novel treatment method for corneal perforation using this biomaterial.

Methods

Rheometry was used to measure the hPL-based biomaterial behaviour at room and corneal surface temperatures. Its adhesiveness to porcine skin and burst pressure limit were also measured. Based on rheological behaviour, a hand-held biopen was developed to extrude it onto the cornea. An animal trial (5 New Zealand white rabbits) to compare impact of the biomaterial and cyanoacrylate glue (control group) on a 2mm perforation was conducted to evaluate safety and efficacy.

Results

The hPL-based biomaterial showed higher adhesiveness compared to commercial fibrin glue and withstood burst pressure approximately 6.4× higher than routine intraocular pressure. Treatment rabbits had lower pain scores and faster recovery, despite generating similar scar-forming structure compared to controls. No secondary corneal ulcer was generated in rabbits treated with the bio-adhesive.

Conclusions

This study reports a novelin-situprinting system capable of delivering a hPL-based, transparent bio-adhesive and successfully treating small corneal perforations. Bio-adhesive-treated rabbits recovered faster and required no additional analgesia. Both groups showed scarred corneal tissue after healing, however no infection and inflammation was observed by 3 weeks. The delivery system was easy to use and may represent an alternative treatment for corneal perforation.

Highlights

This study presents a novelin situprinting system to treat corneal perforation

The system is comprised of a human platelet lysate-based bio-adhesive and a pen-like hand held delivery system

Mechanical tests showed our transparent bio-adhesive has a higher adhesiveness compared to existing treatments and burst pressure threshold approximately 6.4 times higher than normal intraocular pressure.

In vivo rabbit trial showed that compared to cyanoacrylate glue, the bio-adhesive was safer, faster healing and led to less pain in rabbits.
Performance of the sea turtleLepidochelys olivaceahatchlings from a hatchery on the Pacific coast of Guatemala
Authors: Morales-Mérida B. Alejandra , Contreras-Mérida María Renee , Cortés-Gómez Adriana , Godfrey Matthew H. , Girondot Marc
Published: September 2021

Sea turtles are marine species that are generally in danger of extinction. The conservation strategies in the different countries are attempting to preserve these species and should be constantly updating their policies according to research results taking place on site. The most abundant and frequent species of sea turtle that nest in the Pacific Coast of Guatemala isLepidochelys olivacea(Eschscholtz, 1829), therefore human predation has been historically high. The solution to this predation, since the 1970s, as a conservation strategy was to place eggs in enclosed protected spaces called hatcheries, where collectors must give 20% of the nest as a conservation quota. Since this program leads to no natural nests (in situ) remaining on the beaches, the good functioning of the hatcheries plays a fundamental role in the conservation process to work. To understand and predict the fitness of the hatchlings being produced in Guatemalan hatcheries, crawling performance and self-righting performance were measured in 210 hatchlings of the Multiple Uses Area of Hawaii, in the Pacific Coast of Guatemala. The results of the performance were contrasted with incubation conditions to provide an insight into how the management may influence it. We found that self-righting may be a more meaningful measure of variable behavior than crawling performance, showing that there was little variation due to the homogeneous environment of the hatcheries. We can conclude that a greater number of eggs result in faster self-righting, while deeper nests produce hatchlings with slower rates of self-righting.

Summary statement

When hatcheries are the only sea turtle conservation strategy, and their well-functioning is vital to achieve this purpose, performance can provide information of hatchlings’ fitness in response to management conditions.
Optimization of long-term human iPSC-derived spinal motor neuron culture using a dendritic polyglycerol amine-based substrate
Authors: Thiry Louise , Clément Jean-Pierre , Haag Rainer , Kennedy Timothy E , Stifani Stefano
Published: September 2021

Human induced pluripotent stem cells (h-iPSCs) derived from healthy and diseased individuals can give rise to many cell types, facilitating the study of mechanisms of development, human disease modeling, and early drug target validation. In this context, experimental model systems based on h-iPSC-derived motor neurons (MNs) have been used to study MN diseases such as spinal muscular atrophy and amyotrophic lateral sclerosis. Modeling MN disease using h-iPSC-based approaches requires culture conditions that can recapitulate in a dish the events underlying differentiation, maturation, aging, and death of MNs. Current h-iPSC-derived MN-based applications are often hampered by limitations in our ability to monitor MN morphology, survival, and other functional properties over a prolonged timeframe, underscoring the need for improved long-term culture conditions. Here we describe a cytocompatible dendritic polyglycerol amine (dPGA) substrate-based method for prolonged culture of h-iPSC-derived MNs. We provide evidence that MNs cultured on dPGA-coated dishes are more amenable to long-term study of cell viability, molecular identity, and spontaneous network electrophysiological activity. The present study has the potential to improve iPSC-based studies of human MN biology and disease.
EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling
Authors: Randzavola Lyra O. , Mortimer Paige M. , Garside Emma , Dufficy Elizabeth R. , Schejtman Andrea , Roumelioti Georgia , Yu Lu , Pardo Mercedes , Spirohn Kerstin , Tolley Charlotte , Brandt Cordelia , Harcourt Katherine , Nichols Esme , Nahorski Mike , Woods Geoff , Williamson James C. , Suresh Shreehari , Sowerby John M. , Matsumoto Misaki , Santos Celio X.C. , Kiar Cher Shen , Mukhopadhyay Subhankar , Rae Will M. , Dougan Gordon J. , Grainger John , Lehner Paul J. , Calderwood Michael , Choudhary Jyoti , Clare Simon , Speak Anneliese , Santilli Giorgia , Bateman Alex , Smith Kenneth G. C. , Magnani Francesca , Thomas David C.
Published: September 2021

EROS (Essential for Reactive Oxygen Species) protein is indispensable for expression of gp91phox, the catalytic core of the phagocyte NADPH oxidase. EROS deficiency in humans is a novel cause of the severe immunodeficiency, chronic granulomatous disease (CGD), but its mechanism of action was unknown until now. We elucidate the role of EROS, showing it acts at the earliest stages of gp91phox maturation. It binds the immature 58kDa gp91phox directly, preventing gp91phox degradation and allowing glycosylation via the oligosaccharyltransferase (OST) machinery and the incorporation of the heme prosthetic groups essential for catalysis. EROS also regulates the purine receptors P2X7 and P2X1 through direct interactions and P2X7 is almost absent in EROS deficient mouse and human primary cells. Accordingly, lack of EROS results in markedly abnormal P2X7 signalling, inflammasome activation and T cell responses. The loss of both ROS and P2X7 signalling leads to resistance to influenza infection. Our work identifies EROS as a highly selective chaperone for key proteins in innate and adaptive immunity and a rheostat for immunity to infection. It has profound implications for our understanding of immune physiology, ROS dysregulation and possibly gene therapy.
Synthetic amyloid beta does not induce a robust transcriptional response in innate immune cell culture systems
Authors: Quiroga I.Y. , Cruikshank A.E. , Reed K. S. M. , Bond M.L. , Evangelista B.A. , Tseng J.H. , Ragusa J. V. , Meeker R. B. , Won H. , Cohen S. , Cohen T.J. , Phanstiel D.H.
Published: September 2021

Alzheimer’s disease (AD) is a progressive neurodegenerative disease that impacts nearly 400 million people worldwide. The accumulation of amyloid beta (Aβ) in the brain has historically been associated with AD, and recent evidence suggests that neuroinflammation plays a central role in its origin and progression. These observations have given rise to the theory that Aβ is the primary trigger of AD, and induces proinflammatory activation of immune brain cells (i.e. microglia), which culminates in neuronal damage and cognitive decline. In order to test this hypothesis, many in vitro systems have been established to study Aβ-mediated activation of innate immune cells. Nevertheless, the transcriptional resemblance of these models to the microglia in the AD brain has never been comprehensively studied on a genome-wide scale. To address this, we used bulk RNA-seq to assess the transcriptional differences between in vitro cell types used to model neuroinflammation in AD, including several established, primary and iPSC-derived immune cell lines (macrophages, microglia and astrocytes) and their similarities to primary cells in the AD brain. We then analyzed the transcriptional response of these innate immune cells to synthetic Aβ. We found that human induced pluripotent stem cell (hIPSC)-derived microglia (IMGL) are the in vitro cell model that best resembles primary microglia. Surprisingly, synthetic Aβ does not trigger a robust transcriptional response in any of the cellular models analyzed, despite testing a wide variety of Aβ formulations, concentrations, and treatment conditions. Finally, we found that bacterial LPS and INFγ activate microglia and induce transcriptional changes similar to those observed in disease associated microglia present in the AD brain, suggesting the potential suitability of this model to study AD-related neuroinflammation.
ToxoNet: A high confidence map of protein-protein interactions inToxoplasma gondiireveals novel virulence factors implicated in host cell invasion
Authors: Swapna Lakshmipuram S. , Stevens Grant C. , da Silva Aline Sardinha , Hu Lucas Zhongming , Brand Verena , Fusca Daniel D. , Xiong Xuejian , Boyle Jon P. , Grigg Michael E. , Emili Andrew , Parkinson John
Published: September 2021

The apicomplexan intracellular parasiteToxoplasma gondiiis a major food borne pathogen with significant impact in children and during pregnancy. The majority of theT. gondiiproteome remains uncharacterized and the organization of proteins into complexes is unclear. To overcome this knowledge gap, we utilize a biochemical fractionation strategy coupled with mass spectrometry to predict interactions by correlation profiling. Key to this approach is the integration of additional datasets based on gene co-expression as well as phylogenetic profiles that eliminate poorly supported interactions and reduce the number of false positive interactions. In addition to a supervised machine learning strategy, we employed an unsupervised approach in data integration, based on similarity network fusion, to overcome the deficit of high-quality training data in non-model organisms. The resulting high confidence network, we term ToxoNet, comprises 2,063 interactions connecting 652 proteins. Clustering of this network identifies 93 protein complexes, predicting both novel complexes as well as new components for previously known complexes. In particular, we identified clusters enriched in mitochondrial machinery that include previously uncharacterized proteins that likely represent novel adaptations to oxidative phosphorylation. Furthermore, complexes enriched in proteins localized to secretory organelles and the inner membrane complex, predict additional novel components representing novel targets for detailed functional characterization. We present ToxoNet as a publicly available resource with the expectation that it will help drive future hypotheses within the research community.
Interpreting sensory and cognitive signals in the cortical reading network
Authors: Lerma-Usabiaga Garikoitz , Le Rosemary , Gafni Chen , Ben-Shachar Michal , Wandell Brian
Published: September 2021

Voxels in the visual cortex contain neurons that are responsive to small regions of the visual field; these regions can be quantified using population receptive field (pRF) analysis. We measured pRFs using several types of patterns: words, visually matched false-fonts, and visually dissimilar checker patterns. In visual field maps pRF estimates using words and false-fonts are similar, but pRF estimates using checkers differ substantially. The pattern of results in the contiguous ventral occipito-temporal reading circuitry is different: word pRF estimates differ from false-fonts and checkers. These findings were replicated at two research sites. We explain these results with a qualitative model, where the response differences in the visual field maps arise from sensory signals, and the differences in the reading circuitry arise from the integration of sensory and cognitive signals.
The future impact of climate and land-use changes on Anatolian ground squirrels under different scenarios
Authors: Gür Hakan
Published: September 2021

Climate and land-use changes are among the most important drivers of biodiversity loss and, moreover, their impacts on biodiversity are expected to increase further in the 21st century. In this study, the future impact of climate and land-use changes on Anatolian ground squirrels was assessed. Accordingly, a hierarchical approach with two steps was used. First, ecological niche modelling was used to assess the impact of climate change in areas accessible to Anatolian ground squirrels through dispersal (i.e. the impact of climate change). Second, based on the habitat preferences of ground squirrels, land-use data were used to assess the impact of land-use change in suitable bioclimatic areas for Anatolian ground squirrels under present and future conditions (i.e. the combined impact of both changes). Also, priority areas for the conservation of Anatolian ground squirrels were identified based onin-situclimate change refugia. This study represents a first attempt to combine niche modelling and land-use data for a species in Anatolia, one of the most vulnerable regions to the drivers of biodiversity loss, because it is the region where three of biodiversity hotspots meet, and interact. Habitat availability (i.e. suitable habitats across suitable bioclimatic areas) was projected to decline by 19-69% in the future (depending on the scenario), mainly due to the loss of suitable bioclimatic areas (47-77%, depending on the scenario) at lower elevations and in the western part of the central Anatolia and in the eastern Anatolia, suggesting that Anatolian ground squirrels will contract their range in the future, mainly due to climate change. Thus,in-situclimate change refugia were projected mainly in the eastern and southeastern parts of the central Anatolia, suggesting these regions as priority areas for the conservation of Anatolian ground squirrels.
Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania
Authors: Cuypers B. , Meysman P. , Erb I. , Bittremieux W. , Valkenborg D. , Baggerman G. , Mertens I. , Sundar Shyam , Khanal Basudha , Notredame C. , Dujardin J-C. , Domagalska M.A. , Laukens K.
Published: September 2021

Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, protein complex subunits and non-cytoplasmic proteins, showed dosage compensation, responding less or even not at all to aneuploidy-induced dosage changes. In contrast to other Eukaryotes, we did not observe the widespread regulation at the transcript level that typically modulates some of the negative effects of aneuploidy. Further, the majority of differentially expressed proteins between aneuploid strains were encoded by non-aneuploid chromosomes and were not driven by a significant underlying transcript change, suggesting that aneuploidy is accompanied by extensive post-transcriptional protein-level modulation. This makes Leishmania a unique Eukaryotic model for elucidating post-transcriptional protein-abundance modulation in the context of aneuploidy.
Long-termin vivoimaging of mouse spinal cord through an optically cleared intervertebral window
Authors: Wu Wanjie , He Sicong , Wu Junqiang , Chen Congping , Li Xuesong , Liu Kai , Qu Jianan Y.
Published: September 2021

Spinal cord, as part of the central nervous system, accounts for the main communication pathway between the brain and the peripheral nervous system. Spinal cord injury is a devastating and largely irreversible neurological trauma, and can result in lifelong disability and paralysis with no available cure.In vivospinal cord imaging in mouse models without introducing immunological artifacts is critical to understand spinal cord pathology and discover effective treatments. We developed a minimal-invasive intervertebral window by retaining ligamentum flavum to protect the underlying spinal cord. By introducing an optical clearing method, we achieved repeated two-photon fluorescence and stimulated Raman scattering imaging at subcellular resolution with up to 16 imaging sessions over 167 days and observed no inflammatory response. Using this optically cleared intervertebral window, we studied the neuron-glia dynamics following laser axotomy and observed strengthened contact of microglia with the nodes of Ranvier during axonal degeneration. By enabling long-term, repetitive, stable, high-resolution and inflammation-free imaging of mouse spinal cord, our method provides a reliable platform in the research aiming at understanding and treatment of spinal cord pathology.
Environmental and molecular modulation of motor individuality in larval zebrafish
Authors: Hageter John , Waalkes Matthew , Starkey Jacob , Copeland Haylee , Price Heather , Bays Logan , Showman Casey , Laverty Sean , Bergeron Sadie A. , Horstick Eric J.
Published: September 2021

Innate behavioral biases such as human handedness are a ubiquitous form of inter-individual variation that are not strictly hardwired into the genome and are influenced by diverse internal and external cues. Yet, genetic and environmental factors modulating behavioral variation remain poorly understood, especially in vertebrates. To identify genetic and environmental factors that influence behavioral variation, we take advantage of larval zebrafish light-search behavior. During light-search, individuals preferentially turn in leftward or rightward loops, in which directional bias is sustained and non-heritable, and maintained by a habenula-rostral PT circuit. Here we use a medium-throughput recording strategy and unbiased analysis to show that significant individual to individual variation exists in wildtype larval zebrafish turning preference. We classify stable left, right, and unbiased turning types, with most individuals exhibiting a directional preference. Raising larvae at elevated temperature selectively reduces the leftward turning type and impacts rostral PT neurons, specifically. Exposure to conspecifics, variable salinity, environmental enrichment, and physical disturbance does not significantly impact inter-individual turning bias. Pharmacological manipulation of Notch signaling and carrying a mutant allele of a known Notch pathway affecter gene, gsx2, disrupted turn bias individuality in a dose-dependent manner. These results establish that larval zebrafish is a powerful vertebrate model for inter-individual variation with sensitivity to specific environmental perturbations and gene dosage.
Crocin inhibited amyloid-beta (Aβ) generation via promoting non-amyloidogenic APP processing and suppressed ER stress UPR signaling in N2a/APP cells
Authors: Lin Crystal Cuijun , Yue Erin Qian , Liang Zirong , Yuen Lee Simon Ming , Zhang Zaijun , Man Hoi Maggie Pui
Published: September 2021

Background

Crocin is a major active component of saffron (Crocus sativus) with many beneficial effects. More recently, crocin has been proposed for management of neurodegenerative diseases such as Alzheimer’s disease (AD). Here, we demonstrated for the first time that crocin reduced amyloid-beta (Aβ) generation through promoting α-cleavage of APP processing and inhibited ER stress by attenuating UPR signaling in N2a/APP cells.

Methodology

Mouse neuroblastoma N2a cells stably transfected with the Swedish mutant APP (N2a/APP) was used as a cellular model for AD pathogenesis. Vector transfected cells (N2a/vector) were employed to serve as control. The toxicity of crocin was first evaluated and non-toxic treatment of crocin (>30 µM for 24 h) was used for further investigations. Aβ levels were determined by ELISA. Expression levels of UPR signaling proteins were determined by using Western blot.

Results

Crocin significantly inhibited the protein expression of total APP in N2a/APP cells and promoted α-cleavage of APP processing to increase sAPPα generation, but only modestly reduced BACE-1 and PS1, suggesting Aβ reduction by crocin was mainly associated with the non-amyloidogenic APP processing. Further investigation on ER stress related protein expressions showed that GRP78, CHOP, p-PERK, p-eIF2α, p-IRE1α, XBP1, ATF6α and PDI were all significantly elevated in N2a/APP cells compared to N2a/vector. Crocin effectively reduced the levels of GRP78 and CHOP, and significantly inhibited p-PERK/p-eIF2α amd AT6α while slightly reduced p-IRE1α.

Conclusion

The present study showed that crocin was effective at blocking Aβ generation and inhibiting ER stress associated overactivation of UPR signaling in AD cell model N2a/APP. The results provided evidence for crocin as useful natural product for the treatment of AD.
Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes
Authors:   The CRyPTIC Consortium, Earle Sarah G , Wilson Daniel J
Published: September 2021

The emergence of drug resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of twofold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased heritability for the new and repurposed drugs by 26-37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p<10-7.7). We observed that artefactual signals of cross resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.