bluuebunny/crossref_metadata_2025 huggingface dataset:
Synaptotagmins Maintain Diacylglycerol Homeostasis at Endoplasmic Reticulum-Plasma Membrane Contact Sites during Abiotic Stress
Authors: Ruiz-Lopez Noemi , Pérez-Sancho Jessica , del Valle Alicia Esteban , Haslam Richard P. , Vanneste Steffen , Catalá Rafael , Perea-Resa Carlos , Van Damme Daniël , García-Hernández Selene , Albert Armando , Vallarino José , Lin Jinxing , Friml Jir□í , Macho Alberto P. , Salinas Julio , Rosado Abel , Napier Johnathan A. , Amorim-Silva Vitor , Botella Miguel A.
Published: July 2020

Endoplasmic Reticulum-Plasma Membrane contact sites (ER-PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis mutants lacking the ER-PM protein tether synaptotagmin1 (SYT1) exhibit decreased plasma membrane (PM) integrity under multiple abiotic stresses such as freezing, high salt, osmotic stress and mechanical damage. Here, we show that, together withSYT1, the stress-inducedSYT3is an ER-PM tether that also functions in maintaining PM integrity. The ER-PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in asyt1/3double mutant relative to WT while the levels of most glycerolipid species remain unchanged. Additionally, SYT1-GFP preferentially binds diacylglycerolin vivowith little affinity for polar glycerolipids. Our work uncovers a crucial SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.
Disrupting the biodiversity – ecosystem function relationship: response of shredders and leaf breakdown to urbanization in Andean streams
Authors: Zúñiga-Sarango Wilson , Gaona Fernando P. , Reyes-Castillo Valeria , Iñiguez-Armijos Carlos
Published: July 2020

Urbanization is a major driver of stream ecosystems impairment and often associated with multiple stressors and species loss. A challenge is to understand how those stressors alter the relationship between biodiversity and ecosystem functioning (B-EF). In Andean streams of southern Ecuador, we assessed the response of shredder diversity and organic matter breakdown (OMB) to urbanization and identified the urban-associated stressors disrupting the B-EF relationship. A leaf-litter bag experiment during stable flow conditions in 2016 was carried out to quantify total OMB and shredder-mediated OMB, which was estimated to represent the B-EF relationship. We calculated the taxonomic and functional diversity of shredder invertebrates associated with leaf packs. Also, a suite of physicochemical and habitat stressors was weekly measured during the field experiment. Along the urbanization gradient, both taxonomic and functional diversity of shredders declined while OMB rates decayed. Shredders were absent and their contribution to OMB was null at the most urbanized sites. The B-EF relationship was interrupted through nutrient enrichment and physical habitat homogenization as a consequence of urbanization. These results demonstrate how species loss propagates to ecosystem functions in urbanized streams and how environmental stressors alter the B-EF relationship. Better land-use practices are crucial in Andean catchments to guarantee ecosystem services which are the result of a successful B-EF relationships.
Multinomial Convolutions for Joint Modeling of Sequence Motifs and Enhancer Activities
Authors: Park Minjun , Singh Salvi , Canozo Francisco Jose Grisanti , Samee Md. Abul Hassan
Published: July 2020

Massively parallel reporter assays (MPRAs) have enabled the study of transcriptional regulatory mechanisms at an unprecedented scale and with high quantitative resolution. However, this realm lacks models that can discover sequence-specific signals de novo from the data and integrate them in a mechanistic way. We present MuSeAM (Multinomial CNNs for Sequence Activity Modeling), a convolutional neural network that overcomes this gap. MuSeAM utilizes multinomial convolutions that directly model sequence-specific motifs of protein-DNA binding. We demonstrate that MuSeAM fits MPRA data with high accuracy and generalizes over other tasks such as predicting chromatin accessibility and prioritizing potentially functional variants.
TOR coordinates with transcriptional and chromatin machinery to regulate thermotolerance and thermomemory
Authors: Sharma Mohan , Jamsheer K Muhammed , Shukla Brihaspati Narayan , Sharma Manvi , Awasthi Prakhar , Mahtha Sanjeet Kumar , Yadav Gitanjali , Laxmi Ashverya
Published: July 2020

Global warming exhibits profound effects on plant fitness and productivity. To withstand stress, plants sacrifice their growth and activate protective stress responses for ensuring survival. However, the switch between growth and stress is largely elusive. In the past decade, emerging role of Target of Rapamycin (TOR) has been studied linking energy and stress signaling. Here, we have identified an important role of Glc-TOR signaling in plant adaptation to heat stress (HS). Glc-TOR via the E2Fa signaling module regulates the transcription of heat shock factor genes through direct recruitment of E2Fa onto their promoter regions. Glc also epigenetically governs the transcription of core HS signaling genes in a TOR-dependent manner. TOR acts in concert with p300/CREB HISTONE ACETYLTRANSFERASE1 (HAC1) and dictates the epigenetic landscape of HS loci to regulate thermotolerance. Arabidopsis plants defective inTORandHAC1exhibited reduced thermotolerance with a decrease in expression of core HS signaling genes. In addition, TOR also promotes accumulation of histone H3K4me3 marks at the promoters of thermomemory-related genes and therefore, governs thermomemory. Collectively, our findings thus reveal a mechanistic framework in which Glc-TOR signaling through different modules determines the integration of stress and energy signaling to regulate thermotolerance and thermomemory.
Early Postnatal Tobacco Smoke Exposure Aggravates Experimental Autoimmune Encephalomyelitis in Adult Rats
Authors: Wang Zhaowei , Wang Liping , Zhong Fangfang , Wu Chenglong , Hou Sheng-Tao
Published: July 2020

Although substantial evidence supports smoking as a risk factor for the development of multiple sclerosis (MS) in adulthood, it remains controversial as to whether early-life exposure to environmental tobacco smoke (ETS) increases the risk of MS later in life. Here, using experimental autoimmune encephalomyelitis (EAE) as an animal model for MS, we show that exposing neonatal rats during the 1stweek (ETS1-EAE), but not the 2ndweek (ETS2-EAE) and the 3rdweek (ETS3-EAE) after birth, increased the severity of EAE in adulthood in comparison to pups exposed to filtered compressed air (AIR-EAE). The EST1-EAE rats showed a worse neurological deficit score and a significant increase in CD4+cell infiltration, demyelination, and axonal injury in the spinal cord compared to AIR-EAE, ETS2-EAE, and ETS3-EAE groups. Flow cytometry analysis showed that the ETS1 group had decreased numbers of regulatory T (Treg) cells and increased effector T (Teff) cells in the brain and spinal cord. The expressions of Treg upstream regulator Foxp3 and downstream cytokines such as IL-10 were also altered accordingly. Together, these findings demonstrate that neonatal ETS exposure suppresses Treg functions and aggravates the severity of EAE, confirming early-life exposure to EST as a potential risk factor for multiple sclerosis in adulthood.
Regulation of specific cell clusters in TCR-T cells responding to differential expression of tumor PD-L1
Authors: Ding Renpeng , Liu Shang , Chen Huanyi , Kang Bin , Drmanac Radoje , Gu Ying , Dong Xuan , Gao Qianqian
Published: July 2020

PD-L1 signaling is important in regulating T cell function and keeping balance of tumor microenvironment, but its role in modifying TCR-T cell cytotoxicity remains unknown. MART-1-specific TCR-T cells (TCR-TMART-1) were stimulated by MEL-526 tumor cells expressing different proportions of PD-L1 and used to perform cytotoxicity assays and single-cell RNA sequencing. Percentage changes of different specific cell clusters were analyzed. The percentage of cluster HLA-DR+CD38+CD8+was upregulated after antigen stimulation and tumor PD-L1 modified TCR-T cell function through downregulating the percentages of clusters HLA-DR+CD28+CD8+and HLA-DR+CD38+CD8+which were higher in TCR-TMART-1than in Tnull.
MSK-mediated phosphorylation of Histone 3 Ser28 couples MAPK signaling with early gene induction and cardiac hypertrophy
Authors: Robinson Emma L. , Drawnel Faye M , Mehdi Saher , Archer Caroline R. , Liu Wei , Okkenhaug Hanneke , Alkass Kanar , Aronsen Jan Magnus , Nagaraju Chandan K , Sjaastad Ivar , Sipido Karin R , Bergmann Olaf , Arthur J. Simon C. , Wang Xin , Roderick H. Llewelyn
Published: July 2020

Heart failure is a leading cause of death that develops subsequent to deleterious hypertrophic cardiac remodelling. MAPK pathways play a key role in coordinating the induction of gene expression during hypertrophy. Induction of the immediate early gene (IEG) response is a necessary and early event in this process. How MAPK and IEG expression are coupled during cardiac hypertrophy is not yet resolved. Here, in vitro, in rodent models and in human samples, we demonstrate that MAPK-stimulated IEG induction depends on the Mitogen and Stress activated protein Kinase (MSK) and its phosphorylation of histone H3 at serine 28 (pH3S28). pH3S28 in IEG promoters in turn recruits Brg1, a BAF60 ATP-dependent chromatin remodelling complex component, initiating gene expression. Without MSK activity and IEG induction, the hypertrophic response is suppressed. These studies provide new mechanistic insights and highlight the role of signalling to the epigenome in gene expression regulation during cardiac hypertrophy.

Brief summary one sentence

MSK1/2 phosphorylation of Histone 3 Serine 28 couples MAPK signalling with chromatin remodelling and immediate early gene expression to induce pro-hypertrophic cardiac transcriptional responses.
Further evidence that CP-AMPARs are critically involved in synaptic tag and capture at hippocampal CA1 synapses
Authors: Park Pojeong , Kang Heather , Georgiou John , Zhuo Min , Kaang Bong-Kiun , Collingridge Graham L.
Published: July 2020

The synaptic tag and capture (STC) hypothesis provides an important theoretical basis for understanding the synaptic basis of associative learning. We recently provided pharmacological evidence that calcium-permeable AMPA receptors (CP-AMPARs) are a crucial component of this process. Here we have investigated two predictions that arise on the basis of CP-AMPARs serving as a trigger of the STC effect. Firstly, we compared the effects of the order in which we delivered a strong theta burst stimulation (TBS) protocol (75 pulses) and a weak TBS protocol (15 pulses) to two independent inputs. We only observed a significant STC effect when the strong preceded the weak TBS. Second, we found that pausing stimulation following either the sTBS or the wTBS for ∼20 min largely eliminates the STC effect. These observations are exactly as predicted for a process that is triggered by the synaptic insertion of CP-AMPARs and provide a framework for establishing the underlying molecular mechanism.
Sustained anti-obesity effects of life-style change and anti-inflammatory interventions after conditional inactivation of the activin receptor ALK7
Authors: Srivastava Raj Kamal , Lee Ee-Soo , Sim Eunice , Sheng New Chih , Ibáñez Carlos F.
Published: July 2020

Life-style change and anti-inflammatory interventions have only transient effects in obesity. It is not clear how benefits obtained by these treatments can be maintained longer term, specially during sustained high caloric intake. Constitutive ablation of the activin receptor ALK7 in adipose tissue enhances catecholamine signaling and lipolysis in adipocytes, and protects mice from diet-induced obesity. Here, we investigated the consequences of conditional ALK7 ablation in adipocytes of adult mice with pre-existing obesity. Although ALK7 deletion had little effect on its own, it synergized strongly with a transient switch to low-fat diet (life-style change) or anti-inflammatory treatment (Na-salicylate), resulting in enhanced lipolysis, increased energy expenditure, and reduced adipose tissue mass and body weight gain, even under sustained high caloric intake. By themselves, diet-switch and salicylate had only a temporary effect on weight gain. Mechanistically, combination of ALK7 ablation with either treatment strongly enhanced the levels of β3-AR, the main adrenergic receptor for catecholamine stimulation of lipolysis, and C/EBPα, an upstream regulator of β3-AR expression. These results suggest that inhibition of ALK7 can be combined with simple interventions to produce longer-lasting benefits in obesity.
Light environment influences mating behaviours during the early stages of divergence in tropical butterflies
Authors: Hausmann Alexander E. , Kuo Chi-Yun , Freire Marília , Rueda-M Nicol , Linares Mauricio , Pardo-Diaz Carolina , Salazar Camilo , Merrill Richard M.
Published: July 2020

Species divergence is facilitated when traits under divergent selection also act as mating cues. Fluctuations in sensory conditions can alter signal perception independently of adaptation to contrasting sensory environments, but how this fine scale variation affects behavioural isolation has received less attention, especially in terrestrial organisms. The warning patterns ofHeliconiusbutterflies are under selection for aposematism and act as mating cues. Using computer vision, we extracted behavioural data from 1481 hours of video footage for 387 individuals. We show that the putative hybrid speciesH. heurippaand its close relativeH. timareta linaresidiffer in their response to divergent warning patterns, and that these differences are strengthened with increased local illuminance. Trials with live individuals reveal low-level assortative mating that are sufficiently explained by differences in visual attraction. Finally, results from hybrid butterflies are consistent with linkage between a major warning pattern gene and the corresponding behaviour, though the differences in behaviour we observe are unlikely to cause rapid reproductive isolation as predicted under a model of hybrid trait speciation. Overall, our results highlight that the role of ecological mating cues for behavioural isolation may depend on the immediate sensory conditions during which they are displayed to conspecifics.
The PopN gate-keeper complex acts on the ATPase PscN to regulate the T3SS secretion switch from early to middle substrates inPseudomonas aeruginosa
Authors: Ngo Tuan-Dung , Perdu Caroline , Jneid Bakhos , Ragno Michel , Ducassou Julia Novion , Kraut Alexandra , Couté Yohann , Stopford Charles , Attree Ina , Rietsch Arne , Faudry Eric
Published: July 2020

Pseudomonas aeruginosais an opportunistic bacterium of which the main virulence factor is the Type III Secretion System. The ATPase of this machinery, PscN (SctN), is thought to be localized at the base of the secretion apparatus and to participate in the recognition, chaperone dissociation and unfolding of exported T3SS proteins. In this work, a protein-protein interaction ELISA revealed the interaction of PscN with a wide range of exported T3SS proteins including the needle, translocator, gate-keeper and effector. These interactions were further confirmed by Microscale Thermophoresis that also indicated a preferential interaction of PscN with secreted proteins or protein-chaperone complex rather than with chaperones alone, in line with the release of the chaperones in the bacterial cytoplasm after the dissociation from their exported proteins. Moreover, we suggest a new role of the gate-keeper complex and the ATPase in the regulation of early substrates recognition by the T3SS. This finding sheds a new light on the mechanism of secretion switching from early to middle substrates inP. aeruginosa.

Highlights

T3SS substrates are secreted sequentially but information on the switches are missing

Interaction of the T3SS ATPase with secreted proteins were investigated by different approaches

Microscale Thermophoresis revealed a lower affinity for chaperones alone compared to complexes

The Gate-keeper complex binds to the ATPase and increases its affinity for the needle complex

A new role of the Gate-keeper complex is proposed, directly acting on the T3SS ATPase
Discerning cellular response using statistical discrimination of fluorescence images of membrane receptors
Authors: Munaweera Rangika , O’Neill William D. , Hu Ying S.
Published: July 2020

We demonstrate a statistical modeling technique to recognize T cell responses to different external environmental conditions using membrane distributions of T cell receptors. We transformed fluorescence images of T cell receptors from each T cell into estimated model parameters of a partial differential equation. The model parameters enabled the construction of an accurate classification model using linear discrimination techniques. We further demonstrated that the technique successfully differentiated immobilized T cells on non-activating and activating surfaces. Compared to machine learning techniques, our statistical technique relies upon robust image-derived statistics and achieves effective classification with a limited sample size and a minimal computational footprint. The technique provides an effective strategy to quantitatively characterize the global distribution of membrane receptors under various physiological and pathological conditions.
Dynamic signatures of lipid droplets as new markers to quantify cellular metabolic changes
Authors: Zhang Chi , Boppart Stephen A.
Published: July 2020

The metabolic properties of live cells are very susceptible to intra- or extra-cellular perturbations, making their measurements challenging tasks. We show that the dynamics of lipid droplets (LDs) carry information to measure the lipid metabolism of live cells. Coherent anti-Stokes Raman scattering microscopy was used to statistically quantify LD dynamics in living cells in a label-free manner. We introduce dynamic signatures of cells derived from the LD displacement, speed, travel length, and directionality, which allows for the detection of cellular changes induced by stimuli such as fluorescent labeling, temperature change, starvation, and chemical treatment. Histogram fittings of the dynamic signatures using lognormal distribution functions provide quantification of changes in cellular metabolic states. The LD dynamics also enable separation of subpopulations of LDs correlated with different functions. We demonstrate that LD dynamics are new markers to quantify the metabolic changes in live cells.
Mapping the Functional Landscape of the Receptor Binding Domain of T7 Bacteriophage by Deep Mutational Scanning
Authors: Huss Phil , Meger Anthony , Leander Megan , Nishikawa Kyle , Raman Srivatsan
Published: July 2020

The interaction between a bacteriophage and its host is mediated by the phage’s receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, the molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP using a novel phage genome engineering method called ORACLE (OptimizedRecombination,Accumulation andLibraryExpression). ORACLE is a high-throughput, locus-specific, sequence-programmable method to create a large, unbiased library of phage variants at a targeted gene locus. Using ORACLE, we generated all single amino acid substitutions at every site (1660 variants) of the tip domain to quantify the functional role of all variants on multiple bacterial hosts. This rich dataset allowed us to cross compare functional profiles of each host to precisely identify regions of functional importance, many which were previously unknown. Host-specific substitution patterns displayed differences in site specificity and physicochemical properties of mutations indicating exquisite adaptation to individual hosts. Comparison of enriched variants across hosts also revealed a tradeoff between activity and host range. We discovered gain-of-function variants effective against resistant hosts and host-constricting variants that selectively eliminated certain hosts. We demonstrate therapeutic utility against uropathogenicE. coliby engineering a highly active T7 variants to avert emergence of spontaneous resistance of the pathogen. Our approach presents a generalized framework for systematic and comprehensive characterization of sequence-function relationships in phages on an unprecedented scale.
The surface of lipid droplets constitutes a barrier for endoplasmic reticulum residential integral membrane spanning proteins
Authors: Khaddaj Rasha , Mari Muriel , Cottier Stéphanie , Reggiori Fulvio , Schneiter Roger
Published: July 2020

Lipid droplets (LDs) are globular subcellular structures that mainly serve to store energy in form of neutral lipids, particularly triacylglycerols and steryl esters. LDs are closely associated with the membrane of the endoplasmic reticulum (ER), and are limited by a monolayer membrane of phospholipids harboring a specific set of proteins. Most of these proteins associate with LDs through either an amphipathic helix or a membrane-embedded hairpin motif. Here we address the question whether integral membrane spanning proteins could localize to the surface of LDs. To test this, we fused perilipin 3 (PLIN3), a mammalian LD-targeted protein, to ER resident proteins, such as Wbp1 (a N-glycosyl transferase complex subunit), Sec61 (a translocon subunit), and Pmt1 (a protein O-mannosyltransferase). The resulting fusion proteins localize to the periphery of LDs in both yeast and mammalian cells. This peripheral LD localization of the fusion proteins, however, is due to redistribution of the ER around LDs, as revealed by bimolecular fluorescence complementation between ER- and LD-localized partners in cells coexpressing the membrane-anchored perilipin. A LD-tethering function of PLIN3-containing membrane proteins was confirmed by fusing PLIN3 to the cytoplasmic domain of OM14, an outer mitochondrial membrane protein. Expression of OM14-PLIN3 resulted in close apposition of mitochondria and LDs. Taken together, these data indicate that the LD surface constitutes a barrier for ER-localized integral membrane spanning proteins.
Mind reading of the proteins: Deep-learning to forecast molecular dynamics
Authors: Gupta Chitrak , Cava John Kevin , Sarkar Daipayan , Wilson Eric , Vant John , Murray Steven , Singharoy Abhishek , Karmaker Shubhra Kanti
Published: July 2020

Molecular dynamics (MD) simulations have emerged to become the back-bone of today’s computational biophysics. Simulation tools such as, NAMD, AMBER and GROMACS have accumulated more than 100,000 users. Despite this remarkable success, now also bolstered by compatibility with graphics processor units (GPUs) and exascale computers, even the most scalable simulations cannot access biologically relevant timescales - the number of numerical integration steps necessary for solving differential equations in a million-to-billion-dimensional space is computationally in-tractable. Recent advancements in Deep Learning has made it such that patterns can be found in high dimensional data. In addition, Deep Learning have also been used for simulating physical dynamics. Here, we utilize LSTMs in order to predict future molecular dynamics from current and previous timesteps, and examine how this physics-guided learning can benefit researchers in computational biophysics. In particular, we test fully connected Feed-forward Neural Networks, Recurrent Neural Networks with LSTM / GRU memory cells with TensorFlow and PyTorch frame-works trained on data from NAMD simulations to predict conformational transitions on two different biological systems. We find that non-equilibrium MD is easier to train and performance improves under the assumption that each atom is independent of all other atoms in the system. Our study represents a case study for high-dimensional data that switches stochastically between fast and slow regimes. Applications of resolving these sets will allow real-world applications in the interpretation of data from Atomic Force Microscopy experiments.
Fast cortical dynamics encode tactile grating orientation during active touch
Authors: Harrell Evan R. , Renard Anthony , Bathellier Brice
Published: July 2020

Touch-based object recognition relies on perception of compositional tactile features like roughness, shape, and surface orientation. However, besides roughness, it remains unclear how these different tactile features are encoded to guide perception. Here, we establish a barrel cortex-dependent perceptual task in which mice discriminate tactile gratings based on orientation using only their whiskers. Multi-electrode recordings in barrel cortex reveal weak orientation tuning in average firing rates during grating exploration despite high levels of cortical activity. Just before decision, orientation information extracted from fast cortical dynamics more closely resembles concurrent psychophysical measurements than single neuron orientation tuning curves. This temporal code conveys both stimulus and choice-related information, suggesting that fast cortical dynamics during exploration of a tactile object both reflect the physical stimulus and impact the upcoming perceptual decision of the animal.
Wavefront-sensorless adaptive optics with a laser-free spinning disk confocal microscope
Authors: Hussain Syed Asad , Kubo Toshiki , Hall Nicholas , Gala Dalia , Hampson Karen , Parton Richard , Phillips Mick A. , Wincott Matthew , Fujita Katsumasa , Davis Ilan , Dobbie Ian , Booth Martin J.
Published: July 2020

Adaptive optics is being applied widely to a range of microscopies in order to improve imaging quality in the presence of specimen-induced aberrations. We present here the first implementation of wavefront-sensorless adaptive optics for a laser-free, aperture correlation, spinning disk microscope. This widefield method provides confocal-like optical sectioning through use of a patterned disk in the illumination and detection paths. Like other high-resolution microscopes, its operation is compromised by aberrations due to refractive index mismatch and variations within the specimen. Correction of such aberrations shows improved signal level, contrast and resolution.
Co-circulation of multiple influenza A variants in swine harboring genes from seasonal human and swine influenza viruses
Authors: Ryt-Hansen Pia , Krog Jesper Schak , Østergaard Breum Solvej , Hjulsager Charlotte Kristiane , Pedersen Anders Gorm , Trebbien Ramona , Larsen Lars Erik
Published: July 2020

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018.

In total, 3800 submissions were received with a steady increase in swIAV positive submissions, reaching 56% in 2018. Ten different swIAV subtypes were detected. Full genome sequences were obtained from 129 swIAV positive samples. Altogether, 17 different circulating genotypes were identified including novel reassortants and subtypes harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx viruses.

The results provide essential data for the control of swIAV in pigs and for early detection of novel swIAV strains with zoonotic potential.
Lesion Quantification Toolkit: A MATLAB software tool for estimating grey matter damage and white matter disconnections in patients with focal brain lesions
Authors: Griffis Joseph C. , Metcalf Nicholas V. , Corbetta Maurizio , Shulman Gordon L.
Published: July 2020

Lesion studies are an important tool for cognitive neuroscientists and neurologists. However, while brain lesion studies have traditionally aimed to localize neurological symptoms to specific anatomical loci, a growing body of evidence indicates that neurological diseases such as stroke are best conceptualized as brain network disorders. While researchers in the fields of neuroscience and neurology are therefore increasingly interested in quantifying the effects of focal brain lesions on the white matter connections that form the brain’s structural connectome, few dedicated tools exist to facilitate this endeavor. Here, we present the Lesion Quantification Toolkit, a publicly available MATLAB software package for quantifying the structural impacts of focal brain lesions. The Lesion Quantification Toolkit uses atlas-based approaches to estimate parcel-level grey matter lesion loads and multiple measures of white matter disconnection severity that include tract-level disconnection measures, voxel-wise disconnection maps, and parcel-wise disconnection matrices. The toolkit also estimates lesion-induced increases in the lengths of the shortest structural paths between parcel pairs, which provide information about changes in higher-order structural network topology. We describe in detail each of the different measures produced by the toolkit, discuss their applications and considerations relevant to their use, and perform example analyses using real behavioral data collected from sub-acute stroke patients. We show that analyses performed using the different measures produced by the toolkit produce results that are highly consistent with results that have been reported in the prior literature, and we demonstrate the consistency of results obtained from analyses conducted using the different disconnection measures produced by the toolkit. We anticipate that the Lesion Quantification Toolkit will empower researchers to address research questions that would be difficult or impossible to address using traditional lesion analyses alone, and ultimately, lead to advances in our understanding of how white matter disconnections contribute to the cognitive, behavioral, and physiological consequences of focal brain lesions.
Drug Screening with Zebrafish Visual Behavior Identifies Carvedilol as a Potential Treatment for Retinitis Pigmentosa
Authors: Ganzen Logan , Ko MeeJung , Zhang Mengrui , Xie Rui , Chen Yongkai , Zhang Liyun , James Rebecca , Mumm Jeff , van Rijn Richard , Zhong Wenxuan , Pang Chi Pui , Zhang Mingzhi , Tsujikawa Motokazu , Leung Yuk Fai
Published: July 2020

Retinitis Pigmentosa (RP) is an incurable inherited retinal degeneration affecting approximately 1 in 4,000 individuals globally. The goal of this work was to identify drugs that can help patients suffering from the disease. To accomplish this, we screened drugs on a zebrafish RP model. This model expresses a truncated humanrhodopsintransgene (Tg(rho:Hsa.RH1_Q344X)) causing significant rod degeneration by 7 days post-fertilization (dpf). Consequently, the larvae displayed a deficit in visual motor response (VMR) under scotopic condition. The diminished VMR was leveraged to screen an ENZO SCREEN-WELL® REDOX library since oxidative stress is postulated to play a role in RP progression. Our screening identified a beta-blocker, carvedilol, that ameliorated the deficient VMR of the RP larvae and increased their rod number. Carvedilol can act directly on rods as it affected the adrenergic pathway in a rod-like human Y79 cell line. Since carvedilol is an FDA-approved drug, our findings suggest that carvedilol can potentially be repurposed to treat RP patients.

Summary Statement

This paper presents the utilization of zebrafish visual behavior, a novel paradigm to screen and identify drugs to treat retinitis pigmentosa, an incurable retinal-degenerative disease.
Crystal structure reveals the full Ras:Raf interface and advances mechanistic understanding of Raf activation
Authors: Cookis Trinity , Mattos Carla
Published: July 2020

The interaction between Ras and Raf-kinase through the Ras-binding (RBD) and cysteine-rich domains (CRD) of Raf is essential for signaling through the mitogen-activated protein kinase (MAPK) pathway, yet the molecular mechanism leading to Raf activation has remained elusive. We present the 2.8 Å crystal structure of the HRas/CRaf-RBD_CRD complex showing the Ras/Raf interface as a continuous surface on Ras. In the Ras dimer, with helices roughly perpendicular to the membrane, the CRD is located between the two Ras protomers and far from the membrane, where its dynamic nature in the Ras binding pocket is expected to accommodate BRaf and CRaf heterodimers. Our structure and its analysis by MD simulations, combined with work in the literature, result in a molecular model in which Ras binding is involved in the release of Raf autoinhibition while the Ras/Raf complex dimerizes to promote a platform for signal amplification, with Raf-CRD poised to have direct and allosteric effects on both the Ras active site and the dimerization interface.
Paracoccidioides HSP90 can be found in the cell surface and is a target for antibodies with therapeutic potential
Authors: Moura Ágata Nogueira D’Áurea , de Oliveira Diane Sthefany Lima , Paredes Verenice , Rocha Letícia Barboza , Casadevall Arturo , Albuquerque Patrícia , Felipe Maria Sueli Soares , Piazza Roxane Maria Fontes , Nicola André Moraes
Published: July 2020

Paracoccidioidomycosis (PCM) is one of the most frequent systemic mycoses in Latin America. It affects mainly male rural workers in impoverished regions, and the therapy can last up to two years or use drugs that are very toxic. Given the need for novel safe and effective approaches to treat PCM, we have been developing monoclonal antibodies (mAbs) that could be used not only to block specific fungal targets, but also modulate the host’s antifungal immunity. In this work we show the generation of and promising results with a mAb against HSP90, a molecular chaperone that is an important virulence factor in fungi. Using recombinantParacoccidioides lutzii(Pb01) andP. brasiliensis(Pb18) HSP90 proteins produced inE. coli, we immunized mice and generated polyclonal antibodies and an IgG1 hybridoma mAb. The proteins were very immunogenic and both the polyclonal serum and mAb were used in immunofluorescence experiments, which showed binding of antibodies to the yeast cell surface. The mAb successfully opsonizedP. lutziiandP. brasiliensiscells in co-incubations with J774.16 macrophage-like cells. Our results suggest that this mAb could serve as the basis for new immunotherapy regimens for PCM.

Author summary

Paracoccidioidomycosis (PCM) is a severe disease caused by fungi, common in Latin America. It is treatable, but some of the drugs that are available are very toxic or not very effective, and the treatment can take as long as two years to clear the infection. To address the need for improved therapeutic alternatives, we have been developing drug candidates based on antibody technologies againstParacoccidioides brasiliensisandP. lutzii, which cause PCM. In this work, we produced monoclonal antibodies (mAbs) that bind to the fungal protein HSP90, which is essential for fungal cells to survive. One mAb, 4D11, recognized the HSP90 target on the surface of fungal cells. These antibody-covered cells were ingested more efficiently by immune cells called macrophages, suggesting they could improve the host resistance to infection byParacoccidioides. Future improvements on these antibodies could thus lead to more effective and safer PCM treatments.
Variation in relaxation of non-photochemical quenching in a soybean nested association mapping panel as a potential source for breeding improved photosynthesis
Authors: Burgess Steven J. , de Becker Elsa , Cullum Stephanie , Causon Isla , Floristeanu Iulia , Chan Kher Xing , Moore Caitlin E. , Diers Brian W. , Long Stephen P.
Published: July 2020

Improving the efficiency of crop photosynthesis has the potential to increase yields. Genetic manipulation showed photosynthesis can be improved in Tobacco by speeding up relaxation of photoprotective mechanisms, known as non-photochemical quenching (NPQ), during high to low light transitions. However, it is unclear if natural variation in NPQ relaxation can be exploited in crop breeding programs. To address this issue, we measured NPQ relaxation in the 41 parents of a soybean NAM population in field experiments in Illinois during 2018 and 2019. There was significant variation in amount and rate of fast, energy dependent quenching (qE) between genotypes. However, strong environmental effects led to a lack of correlation between values measured over the two growing season, and low broad-sense heritability estimates (< 0.3). These data suggest that either improvements in screening techniques, or transgenic manipulation, will be required to unlock the potential for improving the efficiency of NPQ relaxation in soybean.

Table of Abbreviations
Early Clinical Factors Predicting the Development of Critical Disease in Japanese Patients with COVID-19: A Single-Center Retrospective, Observational Study
Authors: Higuchi Takatoshi , Nishida Tsutomu , Iwahashi Hiromi , Morimura Osamu , Otani Yasushi , Okauchi Yukiyoshi , Yokoe Masaru , Suzuki Norihiro , Inada Masami , Abe Kinya
Published: July 2020

Background

Insufficient evidence of factors predicting the COVID-19 progression from mild to moderate to critical has been established. We retrospectively evaluated risk factors for critical progression in Japanese COVID-19 patients.

Method

Seventy-four laboratory-confirmed COVID-19 patients were hospitalized in our hospital between February 20, 2020, and June 10, 2020. We excluded asymptomatic, non-Japanese, and child patients. We divided patients into the stable group (SG) and the progression group (PG) (patients requiring mechanical ventilation). We compared the clinical factors in both groups. We established the cutoff values (COVs) for significantly different factors via receiver operating characteristic (ROC) curve analysis and evaluated risk factors by univariate regression.

Results

We enrolled 57 COVID-19 patients (median age 52 years, 56.1% male). The median progression time from symptom onset was eight days. Seven patients developed critical disease (PG: 12.2%), two (3.5%) of whom died; 50 had stable disease. Univariate logistic analysis identified elevated lactate dehydrogenase (LDH) (COV: 309 U/l), decreased estimated glomerular filtration rate (eGFR) (COV: 68 ml/min), lymphocytopenia (COV: 980/μl), and statin use as significantly associated with disease progression. However, in Cox proportional hazards analysis, lymphocytopenia at symptom onset was not significant.

Conclusions

We identified three candidate risk factors for adult Japanese patients with mild to moderate COVID-19: statin use, elevated LDH level, and decreased eGFR.
Model stability of COVID-19 mortality prediction with biomarkers
Authors: Huang Chenyan , Long Xi , Zhan Zhuozhao , van den Heuvel Edwin
Published: July 2020

Coronavirus disease 2019 (COVID-19) is an unprecedented and fast evolving pandemic, which has caused a large number of critically ill patients and deaths globally. It is an acute public health crisis leading to overloaded critical care capacity. Timely prediction of the clinical outcome (death/survival) of hospital-admitted COVID-19 patients can provide early warnings to clinicians, allowing improved allocation of medical resources. In a recently published paper, an interpretable machine learning model was presented to predict the mortality of COVID-19 patients with blood biomarkers, where the model was trained and tested on relatively small data sets. However, the model or performance stability was not explored and assessed. By re-analyzing the data, we reveal that the reported mortality prediction performance was likely over-optimistic and its uncertainty was underestimated or overlooked, with a large variability in predicting deaths.
Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England
Authors: Wells Philippa M. , Doores Katie J. , Couvreur Simon , Nunez Rocio Martinez , Seow Jeffrey , Graham Carl , Acors Sam , Kouphou Neophytos , Neil Stuart J.D. , Tedder Richard S. , Matos Pedro M. , Poulton Kate , Lista Maria Jose , Dickenson Ruth E. , Sertkaya Helin , Maguire Thomas J.A. , Scourfield Edward J. , Bowyer Ruth C. E. , Hart Deborah , O’Bryne Aoife , Steel Kathyrn J.A. , Hemmings Oliver , Rosadas Carolina , McClure Myra O. , Capedevilla-pujol Joan , Wolf Jonathan , Ourselin Sebastien , Brown Matthew A. , Malim Michael H. , Spector Tim , Steves Claire J.
Published: July 2020

Background

Understanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms.

Methods

We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million.

Findings

We demonstrated a seroprevalence of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive.

Interpretation

Seroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response.

Funding

NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC
Back to school: use of Dried Blood Spot for the detection of SARS-CoV-2-specific immunoglobulin G (IgG) among schoolchildren in Milan, Italy
Authors: Amendola Antonella , Bianchi Silvia , Gori Maria , Barcellini Lucia , Colzani Daniela , Canuti Marta , Giacomet Vania , Fabiano Valentina , Folgori Laura , Zuccotti Gian Vincenzo , Tanzi Elisabetta
Published: July 2020

Serological surveillance is necessary to the reestablishment of school activities in safe conditions and to avoid school-related outbreaks. In this study, DBS (Dried Blood Spots) have proven to be a simple, rapid and reliable sample collection tool for detecting antibodies against SARS-CoV-2 by ELISA test compared to matched serum samples from venous sampling (R2=0.9553; Pearson’s coefficient=0.98; Cohen’s unweighted k=0.93; overall agreement=96.2%). This approach may facilitate sample collection from schoolchildren for serological surveys useful to an adequate risk-assessment.
Analysis: The potential health and economic impact of dexamethasone treatment for patients with COVID-19
Authors: Águas Ricardo , Mahdi Adam , Shretta Rima , Horby Peter , Landray Martin , White Lisa ,   the CoMo Consortium
Published: July 2020

Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.
Persistent fatigue following SARS-CoV-2 infection is common and independent of severity of initial infection
Authors: Townsend Liam , Dyer Adam H. , Jones Karen , Dunne Jean , Kiersey Rachel , Gaffney Fiona , O’Connor Laura , Mooney Aoife , Leavy Deirdre , Ridge Katie , King Catherine , Cox Fionnuala , O’Brien Kate , Dowds Joanne , Sugrue Jamie A , Hopkins David , Byrne Patricia , Kingston Tara , Cheallaigh Cliona Ni , Nadarajan Parthiban , McLaughlin Anne Marie , Bourke Nollaig M , Bergin Colm , O’Farrelly Cliona , Bannan Ciaran , Conlon Niall
Published: July 2020

Fatigue is a common symptom in those presenting with symptomatic COVID-19 infection. However, it is unknown if COVID-19 results in persistent fatigue in those recovered from acute infection. We examined the prevalence of fatigue in individuals recovered from the acute phase of COVID-19 illness using the Chalder Fatigue Score (CFQ-11). We further examined potential predictors of fatigue following COVID-19 infection, evaluating indicators of COVID-19 severity, markers of peripheral immune activation and circulating pro-inflammatory cytokines. Of 128 participants (49.5 ± 15 years; 54% female), more than half reported persistent fatigue (52.3%; 45/128) at 10 weeks (median) after initial COVID-19 symptoms. There was no association between COVID-19 severity (need for inpatient admission, supplemental oxygen or critical care) and fatigue following COVID-19. Additionally, there was no association between routine laboratory markers of inflammation and cell turnover (leukocyte, neutrophil or lymphocyte counts, neutrophil-to-lymphocyte ratio, lactate dehydrogenase, C-reactive protein) or pro-inflammatory molecules (IL-6 or sCD25) and fatigue post COVID-19. Female gender and those with a pre-existing diagnosis of depression/anxiety were over-represented in those with fatigue. Our findings demonstrate a significant burden of post-viral fatigue in individuals with previous SARS-CoV-2 infection after the acute phase of COVID-19 illness. This study highlights the importance of assessing those recovering from COVID-19 for symptoms of severe fatigue, irrespective of severity of initial illness, and may identify a group worthy of further study and early intervention.