bluuebunny/crossref_metadata_2025 huggingface dataset:
Sortilin exhibits tumor suppressor-like activity by limiting EGFR transducing function
Authors: Lapeyronnie E. , Granet C. , Tricard J. , Gallet F. , Yassine M. , Chermat A. , Jauberteau MO , Bertin F. , Melloni B. , Vincent F. , Naves T. , Lalloué F.
Published: May 2021

Lung cancer is the leading cause of cancer deaths worldwide and remains one of the most incurable. Tyrosine kinase receptors, such as the epidermal growth factor receptor (EGFR), are often aberrantly activated and drive tumor growth. Monotherapy with tyrosine kinase inhibitors to deactivate EGFR has shown initial efficacy, but their benefits tend to decline over time. EGFR acts as a transcriptional factor promoting the expression of co-oncogenic drivers, which, in turn, interact with canonical EGFR mutations to induce therapeutic relapse. This study reports that sortilin, a crucial regulator of cytoplasmic EGFR, attenuates its transducing function. Genome-wide chromatin binding revealed that sortilin interacts with gene regulatory elements occupied by EGFR. These results suggest a model, in which sortilin exhibits potential tumor suppressor-like activity by concurrently binding to regulatory elements of cMYC. Sortilin expression in lung adenocarcinoma may be predictive of the efficacy of anti-EGFR strategies.
Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis
Authors: Ewald Jan , Rivieccio Flora , Radosa Lukáš , Schuster Stefan , Brakhage Axel A. , Kaleta Christoph
Published: May 2021

Aspergillus fumigatusis an important human fungal pathogen and its conidia are constantly inhaled by humans. In immunocompromised individuals, conidia can grow out as hyphae that damage lung epithelium. The resulting invasive aspergillosis is associated with devastating mortality rates. Since infection is a race between the innate immune system and the outgrowth ofA. fumigatusconidia, we use dynamic optimization to obtain insight into the recruitment and depletion of alveolar macrophages and neutrophils. Using this model, we obtain key insights into major determinants of infection outcome on host and pathogen side. On the pathogen side, we predictin silicoand confirmin vitrothat germination speed is a key virulence trait of fungal pathogens due to the vulnerability of conidia against host defense. On the host side, we find that epithelial cells play a so far underappreciated role in fungal clearance and are potent mediators of cytokine release which we confirmex vivo. Further, our model affirms the importance of neutrophils in invasive aspergillosis and underlines that the role of macrophages remains elusive. We expect that our model will contribute to improvement of treatment protocols by focusing on the critical components of immune response to fungi but also fungal virulence.
Reverting the mode of action of the mitochondrial FOF1-ATPase by Legionella pneumophila preserves its replication niche
Authors: Escoll Pedro , Platon Lucien , Dramé Mariatou , Sahr Tobias , Schmidt Silke , Rusniok Christophe , Buchrieser Carmen
Published: May 2021

Legionella pneumophila, the causative agent of Legionnaires’ disease, a severe pneumonia, injects via a type-IV-secretion-system (T4SS) more than 300 proteins into macrophages, its main host cell in humans. Certain of these proteins are implicated in reprogramming the metabolism of infected cells by reducing mitochondrial oxidative phosphorylation (OXPHOS) early after infection. Here we show that despite reduced OXPHOS, the mitochondrial membrane potential (Δψm) is maintained during infection of primary human monocyte-derived macrophages (hMDMs). We reveal that L. pneumophila reverses the ATP-synthase activity of the mitochondrial FOF1-ATPase to ATP-hydrolase activity in a T4SS-dependent manner, which leads to a conservation of the Δψm, preserves mitochondrial polarization and prevents macrophage cell death. Analyses of T4SS effectors known to target mitochondrial functions revealed that LpSpl is partially involved in conserving the Δψm, but not LncP and MitF. The inhibition of the L. pneumophila-induced “reverse mode” of the FOF1-ATPase collapsed the Δψm and caused cell death in infected cells. Single-cell analyses suggested that bacterial replication occurs preferentially in hMDMs that conserved the Δψm and showed delayed cell death. This direct manipulation of the mode of activity of the FOF1-ATPase is a newly identified feature of L. pneumophila allowing to delay host cell death and thereby to preserve the bacterial replication niche during infection.
Wnt signaling mediates acquisition of blood-brain barrier properties in naïve endothelium derived from human pluripotent stem cells
Authors: Gastfriend Benjamin D. , Nishihara Hideaki , Canfield Scott G. , Foreman Koji L. , Engelhardt Britta , Palecek Sean P. , Shusta Eric V.
Published: May 2021

Endothelial cells (ECs) in the central nervous system (CNS) acquire their specialized blood-brain barrier (BBB) properties in response to extrinsic signals, with Wnt/β-catenin signaling coordinating multiple aspects of this process. Our knowledge of CNS EC development has been advanced largely by animal models, and human pluripotent stem cells (hPSCs) offer the opportunity to examine BBB development in anin vitrohuman system. Here we show that activation of Wnt signaling in hPSC-derived naïve endothelial progenitors, but not in matured ECs, leads to robust acquisition of canonical BBB phenotypes including expression of GLUT-1, increased claudin-5, and decreased PLVAP. RNA-seq revealed a transcriptome profile resembling ECs with CNS-like characteristics, including Wnt-upregulated expression ofLEF1,APCDD1, andZIC3. Together, our work defines effects of Wnt activation in naïve ECs and establishes an improved hPSC-based model for interrogation of CNS barriergenesis.
Face identity selectivity in the deep neural network and human brain
Authors: Wang Jinge , Cao Runnan , Brandmeir Nicholas J , Li Xin , Wang Shuo
Published: May 2021

A central challenge in face perception research is to understand how neurons encode various face identities. However, this challenge has not been met largely due to the lack of simultaneous access to the activity of the entire face processing neural network as well as the lack of a comprehensive multifaceted model that is able to characterize a large number of facial features. In this study, we address this challenge by conducting in silico experiments using a deep neural network (DNN) capable of face recognition with a diverse array of stimuli. We identified a subset of DNN neurons selective to face identities, and these identity-selective neurons demonstrated generalized discriminability to novel faces not involved in the training and in many different styles. Visualization of the network explained the response of the DNN neurons and manipulation of the network confirmed the importance of identity-selective neurons in face recognition. Importantly, using our human single-neuron recordings, we directly compared the response of artificial neurons with 490 real human neurons to the same stimuli and found that artificial neurons did share a similar representation of facial features as human neurons. We also observed a novel region-based feature coding mechanism in DNN neurons as in human neurons, which may explain how the DNN performs face recognition. Together, by directly linking between artificial and human neurons, our results shed light on how human neurons encode face identities.
Membrane phase separation drives organization at B cell receptor clusters
Authors: Shelby Sarah A. , Castello-Serrano Ivan , Wisser Kathleen C. , Levental Ilya , Veatch Sarah L.
Published: May 2021

Heterogeneity in intact cell plasma membranes has been explained by analogy to coexisting liquid-ordered and liquid-disordered phases, although models based on this idea fall short of describing the rich structure within cell membranes. Here, a new framework of lipid-driven plasma membrane heterogeneity is presented, drawing on quantitative measurements of protein partitioning and dynamics within B cell receptor clusters in live B lymphocyte plasma membranes, compared to coexisting phases in isolated plasma membranes. We propose that membrane domains in cells integrate the thermodynamic state of the membrane and the magnitude of the applied stimulus to give rise to a tunable response. This framework is supported through functional observations of B cell receptor phosphorylation in perturbed systems.
Sperm cryopreservation impacts the early development of equine embryos by downregulating specific transcription factors
Authors: Ortiz-Rodríguez José M , Martín-Cano FE Francisco E. , Gaitskell-Phillips Gemma , Barrientos A Álvarez , Rodríguez-Martínez Heriberto , Gil Maria C. , Ortega-Ferrusola C , Peña Fernando J.
Published: May 2021

Equine embryos were obtained by insemination with either fresh or frozen-thawed spermatozoa at 8, 10 and 12 h post spontaneous ovulation, maintaining the pairs mare-stallion for the type of semen used. Next generation sequencing (NGS) was performed in all embryos and bioinformatic and enrichment analysis performed on the 21,058 identified transcripts. A total of 165 transcripts were downregulated in embryos obtained with cryopreserved spermatozoa respect embryos resulting from an insemination with fresh spermatozoa (p=0.021, q=0.1). The enrichment analysis using human orthologs using g:profiler on the downregulated transcripts marked an enrichment in transcription factors (TFs) in mRNAs downregulated in embryos obtained after insemination with cryopreserved spermatozoa. The 12 mRNAs (discriminant variables) most significantly downregulated in these embryos included among others, the chromatin-remodeling ATPase INO80, Lipase maturation factor 1 LMF1, the mitochondrial mRNA pseudouridine synthase RPUSD3, LIM and cysteine-rich domains protein 1, LMCD1. Sperm cryopreservation also caused a significant impact on the embryos at 8 to 10 days of development, but especially in the transition from 10 to 12 days. Overall, our findings provide strong evidence that insemination with cryopreserved spermatozoa poses a major impact in embryo development that may compromise its growth and viability, probably due to modifications in sperm proteins induced by cryopreservation. Identification of specific factors in the spermatozoa causing these changes may improve cryopreservation.
Evaluation of BOLD effects in the rat cortex
Authors: Just Nathalie
Published: May 2021

Purpose

This study aimed to characterize Blood oxygen level-dependent (BOLD) effects in1H-MR spectra obtained during optogenetic activation of the rat forelimb cortex for the correction and estimation of accurate metabolite concentration changes.

Methods

T2*-induced effects were characterized by linewidth changes and amplitude changes of water, NAA and tCr spectral peaks during the stimulation paradigm. Spectral linewidth-matching procedures were used to correct for the line-narrowing effect induced by BOLD. For an increased understanding of spectroscopic BOLD effects and the optimized way to correct them, a 1 Hz line-narrowing effect was also simulated on mouseproton MR spectrum

1H-fMRS data acquired using STEAM acquisitions at 9.4T in rats (n=8) upon optogenetic stimulation of the primary somatosensory cortex were used. Data were analyzed with MATLAB routines and LCModel. Uncorrected and corrected1H-MR spectra of simulated and in-vivo data were quantified and compared. BOLD-corrected difference spectra were also calculated and analyzed.

Results

Significant mean increases in water and NAA peak heights (+ 1.1% and +4.5%, respectively) were found accompanied by decreased linewidths (−0.5 Hz and −2.8%) upon optogenetic stimulation. These estimates were used for further definition of an accurate line-broadening factor (lb). Usage of an erroneous lb introduced false-positive errors in metabolite concentration change estimates thereby altering the specificity of findings. Using different water scalings within LCModel, the water and metabolite BOLD contributions were separated.

Conclusion

The linewidth-matching procedure using a precise lb factor remains the most performant approach for the accurate quantification of small (±0.3 μmol/g) metabolic changes in1H-fMRS studies. A simple and preliminary compartmentation of BOLD effects was proposed, which will require validation.
All-atom Simulations Uncover the Molecular Terms of NKCC1 Transport Mechanism
Authors: Janoš Pavel , Magistrato Alessandra
Published: May 2021

The secondary-active Na-K-Cl Cotransporter 1 (NKCC1), member of the Cation Chloride Cotransporters (CCC) family, ensures the electroneutral movement of Cl-, Na+, K+ ions across cellular membranes. NKCC1 regulates Cl- homeostasis and cell volume, handling a pivotal role in transepithelial water transport and neuronal excitability. Aberrant NKCC1 transport is hence implicated in a variety of human diseases (hypertension, renal disorders, neuropathies, cancer). Building on the newly-resolved NKCC1 cryo-EM structure, all-atom enhanced sampling simulations unprecedentedly unlock the mechanism of NKCC1-mediated ions transport, assessing the order and the molecular basis of its interdependent ions translocation. Our outcomes strikingly advance the understanding of the physiological mechanism of CCCs transporters and disclose a key role of CCC-conserved asparagine residues, whose side-chain promiscuity ensures the transport of both negatively and positively charged ions along the same translocation route. This study sets a conceptual basis to devise NKCC-selective inhibitors to treat diseases linked to Cl- dishomeostasis.

Abstract Figure
Wiring logic of the early rodent olfactory system revealed by high-throughput sequencing of single neuron projections
Authors: Chen Yushu , Chen Xiaoyin , Baserdem Batuhan , Zhan Huiqing , Li Yan , Davis Martin B. , Kebschull Justus M. , Zador Anthony M. , Koulakov Alexei A. , Albeanu Dinu F.
Published: May 2021

The structure of neuronal connectivity often provides insights into the relevant stimulus features, such as spatial location, orientation, sound frequency, etc1–6. The olfactory system, however, appears to lack structured connectivity as suggested by reports of broad and distributed connections both from the olfactory bulb to the piriform cortex7–22 and within the cortex23–25. These studies have inspired computational models of circuit function that rely on random connectivity26–33. It remains, nonetheless, unclear whether the olfactory connectivity contains spatial structure. Here, we use high throughput anatomical methods (MAPseq and BARseq)34–38 to analyze the projections of 5,309 bulb and 30,433 piriform cortex output neurons in the mouse at single-cell resolution. We identify previously unrecognized spatial organization in connectivity along the anterior-posterior axis (A-P) of the piriform cortex. We find that both the bulb projections to the cortex and the cortical outputs are not random, but rather form gradients along the A-P axis. Strikingly, these gradients are matched: bulb neurons targeting a given location within the piriform cortex co-innervate extra-piriform regions that receive strong inputs from neurons within that piriform locus. We also identify signatures of local connectivity in the piriform cortex. Our findings suggest an organizing principle of matched direct and indirect olfactory pathways that innervate extra-piriform targets in a coordinated manner, thus supporting models of information processing that rely on structured connectivity within the olfactory system.
ADP-ribose triggers neuronal ferroptosis by rewiring purine and pyrimidine metabolism
Authors: Ni Haoqi , He Yingying , Cui Peng , Chen Hebing , Lv Guoqing , Lei Huiyan , Wang Feng , ZhuGe Qichuan , Chen Baodong , Liang Ling , Zhang Yong , You Fuping , Yuan Lin
Published: May 2021

Hyperactivation of NAD+-consuming pathways frequently occurs in neurological diseases, however therapies replenishing NAD+levels show limited therapeutic efficacy, indicating more complex underlying pathophysiology. Here, we delineate a pathogenic link between ADP-ribose —a product of NAD+consumption—and a metabolic rewiring-dependent form of neuronal ferroptosis. We demonstrate that oxidative stress induces neurons to produce ADP-ribose through the PARP1-PARG axis. ADP-ribose directly binds and inhibits the equilibrative nucleoside transporter ENT2, remodelingde novopurine and pyrimidine synthesis by hyperactivating the inosine-hypoxanthine-xanthine oxidase and glutamine-dihydroorotate-dihydroorotate dehydrogenase axes. This overproduces superoxide radicals and drives lipid peroxidation and neuronal ferroptosis. Elevated ADP-ribose levels were observed in neurological disease models, and acute ADP-ribose exposure severely reduced mouse brain neuronsin vivo. Critically, interventions blocking ADP-ribose signaling alleviated cognitive decline in mouse intracerebral hemorrhage models. Our findings characterize ADP-ribose signaling as linking NAD+consumption to neuronal ferroptosis, and provide a theraputic strategy for neuropathologies involving NAD+consumption and oxidative stress.
Metagenomic sequencing for rapid identification of Xylella fastidiosa from leaf samples
Authors: Roman-Reyna Veronica , Dupas Enora , Cesbron Sophie , Marchi Guido , Campigli Sara , Hansen Mary Ann , Bush Elizabeth , Prarat Melanie , Shiplett Katherine , Ivey Melanie L. Lewis , Pierzynski Joy , Miller Sally A. , Hand Francesca Peduto , Jacques Marie-Agnes , Jacobs Jonathan M.
Published: May 2021

Xylella fastidiosa (Xf) is a globally distributed plant pathogenic bacterium. The primary control strategy for Xf diseases is eradicating infected plants; therefore, timely and accurate detection is necessary to prevent crop losses and further pathogen dispersal. Conventional Xf diagnostics primarily relies on quantitative PCR (qPCR) assays. However, these methods do not consider new or emerging variants due to pathogen genetic recombination and sensitivity limitations. We developed and tested a metagenomics pipeline using in-house short-read sequencing as a complementary approach for affordable, fast, and highly accurate Xf detection. We used metagenomics to identify Xf to strain level in single and mixed infected plant samples at concentrations as low as one picogram of bacterial DNA per gram of tissue. We also tested naturally infected samples from various plant species originating from Europe and the United States. We identified Xf subspecies in samples previously considered inconclusive with real-time PCR (Cq > 35). Overall, we showed the versatility of the pipeline by using different plant hosts and DNA extraction methods. Our pipeline provides taxonomic and functional information for Xf diagnostics without extensive knowledge of the disease. We hope this pipeline can be used for early detection of Xf and incorporated as a tool to inform disease management strategies.

IMPORTANCE

Xylella fastidiosa (Xf) destructive outbreaks in Europe highlight this pathogen’s capacity to expand its host range and geographical distribution. The current disease diagnostic approaches are limited by a multiple-step process, biases to known sequences, and detection limits. We developed a low-cost, user-friendly metagenomic sequencing tool for Xf detection. In less than three days, we were able to identify Xf subspecies and strains in field-collected samples. Overall, our pipeline is a diagnostics tool that could be easily extended to other plant-pathogen interactions and implemented for emerging plant threat surveillance.
ABCDEF Bundle Implementation: The influence of access to bundle-enhancing supplies and equipment
Authors: Jeffery Alvin D. , Werthman Jennifer A. , Danesh Valerie , Dietrich Mary S. , Mion Lorraine C. , Boehm Leanne M.
Published: May 2021

Importance

The ABCDEF bundle is a guideline-recommended framework for implementing evidence-based practices in the Intensive Care Unit (ICU), but it is underutilized across the world.

Objective

Describe the physical environment factors (i.e., availability, accessibility) of bundle-enhancing items in units implementing the bundle and the influence of physical environment on bundle adherence.

Design, Setting, and Participants

This multicenter, exploratory, cross-sectional study used data from two ICU-based randomized controlled trials (RCTs) (NCT01211522 and NCT01739933) that measured daily bundle adherence. The study included 10 medical and surgical ICUs in 6 academic medical centers in the continental United States. Adults with qualifying respiratory failure and/or septic shock (e.g., mechanical ventilation, vasopressor use) were included in the RCTs. Unit- and patient-level data collection occurred between 2011 and 2016. We conducted hierarchical logistic regression models using Frequentist and Bayesian frameworks.

Exposure

The ABCDE bundle (Awakening and Breathing trial Coordination, Delirium assessment/management, Early mobility) was recommended standard of care for RCT patients and adherence tracked daily.

Measure(s)

The primary outcome was adherence to the full bundle and the early mobility bundle component as identified from daily adherence documentation (n=751 patient observations). Unit-level measures included minimum and maximum distances to 25 bundle-enhancing items and the relationship to bundle adherence.

Results

In all cases, mechanical ventilation was associated with decreased bundle adherence. Some of the models suggested the following variables were also influential: age (older associated with decreased adherence), unit size (larger associated with decreased adherence), and a standard walker (presence associated with increased adherence).

Conclusions and Relevance

Both unit- and patient-level barriers influenced full bundle and early mobility implementation. There is potential benefit of physical proximity to essential items for ABCDEF bundle and early mobility adherence. Future studies with larger sample sizes should explore how equipment location and availability influences practice.

Key Points

Question

Does the physical environment, specifically the availability and accessibility of ABCDEF bundle-enhancing items, influence bundle adherence?

Findings

In this cross-sectional study in 10 units evaluating ABCDEF bundle adherence across 751 patient observations, units with access to a standard walker were significantly more likely to provide bundled care. Across all models, patients who were on the ventilator or older were significantly less likely to received bundled care.

Meaning

Both unit- and patient-level factors influence ABCDEF bundle implementation and amenable targets for implementation strategy development.
Tyrosine Kinase Inhibitor Family of Drugs as Prospective Targeted Therapy for COVID-19 Based on In Silico And 3D-Human Vascular Lung Model Studies
Authors: Saxena Shalini , Meher Kranti , Rotella Madhuri , Vangala Subhramanyam , Chandran Satish , Malhotra Nikhil , Palakodeti Ratnakar , Voleti Sreedhara R , Saxena Uday
Published: May 2021

COVID-19 pandemic has ravaged the world and vaccines have been rapidly developed as preventive measures. But there is no target-based therapy which can be used if infection sets in. Remdesiver and dexamethasone were not designed to combat COVID-19 but are used clinically till better targeted therapies are available. Given this situation target based therapies that intervene in the disease pathway are urgently needed.

Since COVID-19 genesis is driven by uncontrolled inflammation/thrombosis and protein kinases are critical in mounting this response, we explored if available tyrosine kinase inhibitors (TKI’s) can be used as intervention. We profiled four TKI’s namely; Lapatinib, Dasatinib, Pazopanib and Sitravatinib which inhibit tyrosine kinases but are completely distinct in their chemical structures.

We demonstrate using in silico and an in vitro 3D-human vascular lung model which profiles anti-inflammatory and anti-thrombogenic properties that all four TKI’s are active in varying degrees. Our findings that chemically different TKI’s which share kinase inhibition as the common mechanism of action are active, strongly indicates that it’s a tyrosine kinase target-based activity and not off-target arbitrary effect. We propose that TKI’s, approved for human use and widely available, can be rapidly deployed as specific target-based therapy for COVID-19.
The compound of baicalein, wogonin, and oroxylin-A inhibiting EMT in A549 cell line via PI3K/AKT-TWIST1- glycolysis pathway
Authors: Cao Hui-Juan , Zhou Wei , Xian Xiao-Le , Sun Shu-Jun , Ding Pei-Jie , Tian Chun-Yu , Tian Fu-Ling , Jiang Chun-Hua , Fu Ting-Ting , Zhao Shu , Dai Jian-Ye
Published: May 2021

Non-small cell lung cancer (NSCLC) is a worldwide disease with high morbidity and mortality, which is most derived from its metastasis. Some researches show that the epithelial-mesenchymal transition (EMT) process promotes lung cancer cells migration and invasion, leading to NSCLC metastasis. Total Flavonoid Aglycones Extract (TFAE) isolated from Scutellaria baicalensis was reported to inhibit tumor growth and induce apoptosis. In this study, we found that baicalein, wogonin, and oroxylin-A were the active compounds of TFAE. After reconstructing with these three compounds (baicalein (65.8%), wogonin (21.2%), and oroxylin-A (13.0%)), the reconstructed TFAE (reTFAE) present inhibitory effect on the EMT process of A549 cells. Then, bioinformatic technology was employed to elucidate the potential pharmacodynamic mechanism network of reTFAE. We identified the relationship between reTFAE and PI3K/Akt signaling pathways, with TWIST1 as the key protein. LY294002, the inhibitor of PI3K/Akt signaling pathway, and knock-down TWIST1 could significantly enhance the efficacy of reTFAE, with increasing expression of epithelial markers and decreasing expression of mesenchymal markers in A549 cells at the same time. Furthermore, stable isotope dimethyl-labeled proteomics technology was conducted to complement the follow-up mechanism that the EMT-inhibition process may be realized through glycolysis pathway. In conclusion, we claim that TWIST1-targeted flavonoids could provide a new strategy to inhibit EMT progress for the treatment of NSCLC.
Reversal of the adipostat control of torpor during migration in hummingbirds
Authors: Eberts Erich R. , Guglielmo Christopher G. , Welch Kenneth C.
Published: May 2021

Many small endotherms use torpor to reduce metabolic rate and manage daily energy balance. However, the physiological “rules” that govern torpor use are unclear. We tracked torpor use and body composition in ruby-throated hummingbirds (Archilochus colubris), a long-distance migrant, throughout the summer using respirometry and quantitative magnetic resonance. During the mid-summer, birds entered torpor at consistently low fat stores (∼5% of body mass), and torpor duration was negatively related to evening fat load. Remarkably, this energy-emergency strategy was abandoned in the late summer when birds accumulated fat for migration. Migrating birds were more likely to enter torpor on nights when they had higher fat stores, and fat gain was positively correlated with the amount of torpor used. These findings demonstrate the versatility of torpor throughout the annual cycle and suggest a fundamental change in physiological feedback between adiposity and torpor during migration. Moreover, this study highlights the underappreciated importance of facultative heterothermy in migratory ecology.
Distinct Alterations in Cerebellar Connectivity with Substantia Nigra and Ventral Tegmental Area in Parkinson’s Disease
Authors: O’Shea Ian M. , Popal Haroon S. , Olson Ingrid R. , Murty Vishnu P. , Smith David V.
Published: May 2021

In Parkinson’s disease (PD), neurodegeneration of dopaminergic neurons occurs in the midbrain, specifically targeting the substantia nigra (SN), while leaving the ventral tegmental area (VTA) relatively spared in early phases of the disease. Although the SN and VTA are known to be functionally dissociable in healthy adults, it remains unclear how this dissociation is altered in PD. To examine this issue, we performed a whole-brain analysis to compare functional connectivity in PD to healthy adults using resting-state functional magnetic resonance imaging (rs-fMRI) data compiled from three independent datasets. Our analysis showed that across the sample, the SN had greater connectivity with the precuneus, anterior cingulate gyrus, and areas of the occipital cortex, partially replicating our previous work in healthy young adults. Notably, we also found that, in PD, VTA-right cerebellum connectivity was higher than SN-right cerebellum connectivity, whereas the opposite trend occurred in healthy controls. This double dissociation may reflect a compensatory role of the cerebellum in PD and could provide a potential target for future study and treatment.
Neuronal NADPH oxidase 2 in Parkinson’s disease pathogenesis
Authors: Keeney Matthew T. , Hoffman Eric K. , Farmer Kyle , Bodle Christopher R. , Fazzari Marco , Zharikov Alevtina , Castro Sandra L. , Kofler Julia K. , Cifuentes-Pagano Eugenia , Pagano Patrick J. , Burton Edward A. , Hastings Teresa G. , Greenamyre J. Timothy , Di Maio Roberto
Published: May 2021

Mitochondrial dysfunction and oxidative stress are strongly implicated in the pathogenesis of Parkinson’s disease (PD) and there is evidence that mitochondrially-generated superoxide can activate NADPH oxidase 2 (NOX2), which is a major enzymatic generator of superoxide. Although NOX2 has been examined in the context of PD, previous studies have focused on microglial function; the role of neuronal NOX2 in PD pathogenesis remains to be defined. Here we devised and validated a proximity ligation assay for NOX2 activity and demonstrated that in human PD and 2 models thereof, neuronal NOX2 is highly active in substantia nigra dopamine neurons. Further, NOX2 activity is responsible for accumulation, post-translational modification and oligomerization of α-synuclein as well as activation of leucine-rich repeat kinase 2 (LRRK2). Administration of a brain-penetrant, specific NOX2 inhibitor prevented NOX2 activation and its downstream effectsin vivoin a rat model of PD. We conclude that neuronal NOX2 is a major contributor to oxidative stress in PD, to α-synuclein pathology and to LRRK2 activation in idiopathic PD. In this context, NOX2 inhibitors hold potential as a disease-modifying therapy in PD.

In dopamine neuron, NADPH oxidase isoform 2 amplifies the oxidative stress-related pathogenic cascade in Parkinson’s disease
Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
Authors: Gosavi Devadatta , Wower Iwona , Beckmann Irene K. , Hofacker Ivo L. , Wower Jacek , Wolfinger Michael T. , Sztuba-Solinska Joanna
Published: May 2021

The Internal Ribosome Entry Site (IRES) RNA of Bovine viral diarrhea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modeling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA forms in solution a modular architecture composed of three distinct structural domains (I-III). Two regions within domain III are engaged in tertiary interactions to form an H-type pseudoknot. Computational modeling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
Pseudomonas arenae sp. nov., Pseudomonas glycinis sp. nov. and Pseudomonas harudinis sp. nov., three novel bacterial species and plant endophytes
Authors: Seaton Sarah , Lemaire Jacqueline , Inderbitzin Patrik , Knight-Connoni Victoria , White James F. , Trujillo Martha E.
Published: May 2021

Three novel Pseudomonas species associated with healthy plants are described from the United States. They are Pseudomonas arenae sp. nov. from soybean in Missouri and Phragmites sp. in New Jersey; Pseudomonas glycinis sp. nov. from Vaccinium macrocarpon fruit in Massachusetts, groundwater in Tennessee and soybean in Indiana; and Pseudomonas harudinis sp. nov. from Phragmites sp. in New Jersey. No pathogenic strains are known for any of the novel species based on genome comparisons to assemblies in GenBank.
The conserved endocannabinoid anandamide modulates olfactory sensitivity to induce hedonic feeding in C. elegans
Authors: Levichev Anastasia , Faumont Serge , Berner Rachel Z. , Purcell Zhifeng , Lockery Shawn R.
Published: May 2021

The ability of cannabis to increase consumption of food has been known for centuries. In addition to producing hyperphagia, cannabinoids can amplify existing preferences for calorically dense, palatable food sources, a phenomenon called hedonic feeding. These effects result from the action of plant-derived cannabinoids on brain receptors where they mimic natural ligands called endocannabinoids. The high degree of conservation of cannabinoid signaling at the molecular level across the animal kingdom suggests hedonic feeding may also be widely conserved. Here we show that exposure of C. elegans to anandamide, an endocannabinoid common to nematodes and mammals, shifts both appetitive and consummatory responses toward nutritionally superior food, an effect analogous to hedonic feeding. We find that anandamide’s effect on feeding requires the C. elegans cannabinoid receptor NPR-19 but it can also be mediated by the human CB1 cannabinoid receptor, indicating functional conservation between the nematode and mammalian endocannabinoid systems for regulation of food preferences. Furthermore, the effect of anandamide in C. elegans is bidirectional, as it increases appetitive and consummatory responses to superior food but decreases these responses to inferior food. This bidirectionality is mirrored at the cellular level. Anandamide’s behavioral effects require the AWC chemosensory neurons, and anandamide renders these neurons more sensitive to superior food and less sensitive to inferior food. Our findings reveal a surprising degree of functional conservation in the effects of endocannabinoids on hedonic feeding across species and establish a new system in which to investigate the cellular and molecular basis of endocannabinoid system function in the regulation of food choice.
A recombinant rotavirus harboring a spike protein with a heterologous peptide reveals a novel role of VP4 in viroplasm stability
Authors: Papa Guido , Vetter Janine , Seyffert Michael , Gunasekera Kapila , De Lorenzo Giuditta , Wiesendanger Mahesa , Schraner Elisabeth M. , Reymond Jean-Louis , Fraefel Cornel , Burrone Oscar R. , Eichwald Catherine
Published: May 2021

The rotavirus (RV) VP4 spike protrudes as a trimeric structure from the five-fold axes of the virion triple-layer. Infectious RV particles need to be proteolytically cleaved in VP4 into two subunits, VP8* and VP5*, constituting both the distal part and central body of the virus spike. Modification of VP4 has been challenging as it is involved in biological processes such as the interaction with sialic acid and integrins, cell tropism and hemagglutinin activity. Using RV reverse genetics, four loops in the lectin domain of the VP8* subunit were engineered independently to harbor a small biotin acceptor peptide (BAP) tag and then tested for their ability to rescue virus. Only a single recombinant virus, rRV/VP4-BAP, harboring VP4 with a modified loop at position K145-G150 was rescued. This rRV/VP4-BAP internalizes, replicates, and generates virus progeny, demonstrating that the VP4 spike of RV particles can be genetically manipulated by the incorporation of at least 15 exogenous amino acids. VP4-BAP had a similar distribution as VP4 in infected cells by localizing in the cytoskeleton and surrounding viroplasms. However, compared to wild-type RV, rRV/VP4-BAP featured a reduced replication fitness and impaired viroplasm stability. Upon treatment with 1,6-hexanediol, a drug disrupting liquid-liquid phase-separated condensates, the kinetic of rRV/VP4-BAP viroplasm recovery was delayed, and their size and numbers reduced when compared to viroplasms of wild type RV. Moreover, siRNA silencing of VP4 expression in RV strain SA11 showed similar recovery patterns as rRV/VP4-BAP, revealing a novel function of VP4 in viroplasm stability.
System characterization of dynamic biological cultivations through improved data analysis
Authors: Stouten Gerben Roelandt , Douwenga Sieze , Hogendoorn Carmen , Kleerebezem Robbert
Published: May 2021

Determining the functional development and dominant competitive strategy in microbial community enrichments is complicated by the extensive measurement campaigns required for off-line system analysis. This study demonstrates that detailed system characterization of aerobic pulse fed enrichments can be established using on-line measurements combined with automated data analysis. By incorporating the physicochemical processes in on-line data processing with a Particle Filter and kinetic process model, an accurate reconstruction of the dominant biological rates can be made. We hereby can differentiate between storage compound production and biomass growth in sequencing batch bioreactors. The method proposed allows for close monitoring of changes in functional behavior of long-running enrichment cultures, without the need for off-line samples, therewith enabling the identification of new insights in process dynamics with a minimal experimental effort. Even though a specific example application of the method proposed is described here, the approach can readily be extended to a wide range of dynamic experimental systems that can be characterized based on on-line measurements.
Population-level variation of enhancer expression identifies novel disease mechanisms in the human brain
Authors: Dong Pengfei , Hoffman Gabriel E. , Apontes Pasha , Bendl Jaroslav , Rahman Samir , Fernando Michael B. , Zeng Biao , Vicari James M. , Zhang Wen , Girdhar Kiran , Townsley Kayla G. , Misir Ruth ,   the CommonMind Consortium, Brennand Kristen J. , Haroutunian Vahram , Voloudakis Georgios , Fullard John F. , Roussos Panos
Published: May 2021

Identification of risk variants for neuropsychiatric diseases within enhancers underscores the importance of understanding the population-level variation of enhancers in the human brain. Besides regulating tissue- and cell-type-specific transcription of target genes, enhancers themselves can be transcribed. We expanded the catalog of known human brain transcribed enhancers by an order of magnitude by generating and jointly analyzing large-scale cell-type-specific transcriptome and regulome data. Examination of the transcriptome in 1,382 brain samples in two independent cohorts identified robust expression of transcribed enhancers. We explored gene-enhancer coordination and found that enhancer-linked genes are strongly implicated in neuropsychiatric disease. We identified significant expression quantitative trait loci (eQTL) for 25,958 enhancers which mediate 6.8% of schizophrenia heritability, mostly independent from standard gene eQTL. Inclusion of enhancer eQTL in transcriptome-wide association studies enhanced functional interpretation of disease loci. Overall, our study characterizes the enhancer-gene regulome and genetic mechanisms in the human cortex in both healthy and disease states.
Fast-spiking interneurons of the premotor cortex contribute to action planning
Authors: Giordano Nadia , Alia Claudia , Fruzzetti Lorenzo , Pasquini Maria , Mazzoni Alberto , Micera Silvestro , Fogassi Leonardo , Bonini Luca , Caleo Matteo
Published: May 2021

Planning and execution of voluntary movement depend on the contribution of distinct classes of neurons in primary motor and premotor areas. However, the specific functional role of GABAergic cells remains only partly understood. Here, electrophysiological and computational analyses are employed to compare directly the response properties of putative pyramidal (PNs) and fast-spiking, GABAergic neurons (FSNs) during licking and forelimb retraction in mice. Recordings from anterolateral motor cortex and rostral forelimb area, reveal that FSNs fire earlier and for a longer duration than PNs, with the exception of a subset of early-modulated PNs in deep layers. Computational analysis reveals that FSNs carry vastly more information than PNs about the onset of movement. While PNs differently modulate their discharge during distinct motor acts, most FSNs respond with a stereotyped increase in firing rate. Accordingly, the informational redundancy was greater among FSNs than PNs. These data suggest that a global rise of inhibition contributes to early action planning.
Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic
Authors: Patrono Livia Victoria , Vrancken Bram , Budt Matthias , Düx Ariane , Lequime Sebastian , Boral Sengül , Gilbert M. Thomas P. , Gogarten Jan F. , Hoffmann Luisa , Horst David , Merkel Kevin , Morens David , Prepoint Baptiste , Schlotterbeck Jasmin , Schuenemann Verena , Suchard Marc A. , Taubenberger Jeffery K. , Tenkhoff Luisa , Urban Christian , Widulin Navena , Winter Eduard , Worobey Michael , Leendertz Fabian H. , Schnalke Thomas , Wolff Thorsten , Lemey Philippe , Calvignac-Spencer Sébastien
Published: May 2021

The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze the first 1918 IAV genomes from Europe and from the first, milder wave of the pandemic. 1918 IAV genomic diversity is consistent with local transmission and frequent long-distance dispersal events and in vitro polymerase characterization suggests potential phenotypic variability. Comparison of first and second wave genomes shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, phylogenetic estimates based on extended molecular clock modelling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of an intrasubtype reassortment origin.

One Sentence Summary

Much can be learned about past pandemics by uncovering their footprints in medical archives, which we here demonstrate for the 1918 flu pandemic.
Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity
Authors: Labavić Darka , Loverdo Claude , Bitbol Anne-Florence
Published: May 2021

The gut microbiota features important genetic diversity, and the specific spatial features of the gut may shape evolution within this environment. We investigate the fixation probability of neutral bacterial mutants within a minimal model of the gut that includes hydrodynamic flow and resulting gradients of food and bacterial concentrations. We find that this fixation probability is substantially increased compared to an equivalent well-mixed system, in the regime where the profiles of food and bacterial concentration are strongly spatially-dependent. Fixation probability then becomes independent of total population size. We show that our results can be rationalized by introducing an active population, which consists of those bacteria that are actively consuming food and dividing. The active population size yields an effective population size for neutral mutant fixation probability in the gut.

Significance statement

The human body harbors numerous and diverse bacteria, the vast majority of which are located in the gut. These bacteria can mutate and evolve within the gut, which is their natural environment. This can have important public health implications, e.g. when gut bacteria evolve antibiotic resistance. The gut features specific characteristics, including hydrodynamic flow and resulting gradients of food and bacterial concentrations. How do these characteristics impact the evolution and diversity of gut bacteria? We demonstrate that they can substantially increase the probability that neutral mutants reach high proportions and eventually take over the population. This is because only a fraction of gut bacteria is actively dividing. Thus, the specific environment of the gut enhances neutral bacterial diversity.
The diversification of Pterocarpus (Leguminosae: Papilionoideae) was influenced by biome-switching and infrequent long-distance dispersal
Authors: Schley Rowan J. , Qin Ming , Vatanparast Mohammad , Malakasi Panagiota , de la Estrella Manuel , Lewis Gwilym , Klitgård Bente
Published: May 2021

Aim

Phenotypes which evolved for dispersal over ecological timescales may lead to significant macroevolutionary consequences, such as infrequent long-distance dispersal and diversification in novel biomes. We aimed to reconstruct the phylogenetic history of Pterocarpus (Leguminosae/ Fabaceae) to assess whether seed dispersal phenotypes and biome switching explain the current biogeographical patterns of this group.

Location

Pantropical

Taxon

The Pterocarpus clade, particularly Pterocarpus (Leguminosae/Fabaceae)

Methods

We sequenced ~300 nuclear loci captured using Angiosperms-353, a genomic ‘bait set’ for flowering plants, from which we generated a time-calibrated phylogenomic tree. To corroborate this, we also generated a time-calibrated phylogenetic tree from data-mined Sanger-sequencing data. We then collated distribution data and fruit dispersal morphology traits to compare trait-dependent and trait-independent biogeographical models, allowing us to assess whether dispersal traits influenced the spatio-temporal evolution of Pterocarpus. Finally, using the results of these model tests, we estimated the ancestral ranges and biomes of Pterocarpus species to better understand their biogeographical history, and assessed the degree and direction of biome switching over the course of Pterocarpus’ diversification history.

Results

We recovered well-supported phylogenetic relationships within Pterocarpus, within which there were two subclades – one Neotropical and the other Palaeotropical. Our divergence date estimates suggested that Pterocarpus largely diversified from around 12 Ma, during the Miocene.

Trait-dependent biogeographical models were rejected for both range and biome evolution within Pterocarpus, but models parameterising dispersal were supported. Pterocarpus’ ancestral node shared a range across the new-world and old-world tropics, followed by divergence into two clades, one palaeotropical and one neotropical. Biome switching occurred most frequently into rainforest and grassland.

Main conclusions

Overall, our analyses suggest that Pterocarpus underwent infrequent cross-continental dispersal and establishment into novel biomes. While this was minimally impacted by fruit dispersal syndromes, biome switching precipitated by long-distance dispersal and environmental change have played an important role in diversification within Pterocarpus since the Miocene.