bluuebunny/crossref_metadata_2025 huggingface dataset:
Rehabilitation in Survivors of COVID-19 (RE2SCUE): a nonrandomized, controlled, and open protocol
Authors: Campos Maria Cristine , Nery Tatyana , de Bem Alves Ana Cristina , Speck Ana Elisa , Rocha Vieira Danielle Soares , Ceola Schneider Ione Jayce , Pereira Matos Maria Paula , Arcêncio Livia , Aguiar Aderbal Silva
Published: September 2021

Objective

This study aimed to evaluate the effects of physical rehabilitation for adults with sequelae after COVID-19.

Methods

This clinical, nonrandomized, controlled, and open study will examine 82 participants who have met the inclusion criteria and who will be divided into treatment and control groups according to participant preference. The intervention group will receive face-to-face care; the control group will receive remote educational guidance for 8 weeks, with pre-post evaluations. The primary outcomes are dyspnea, fatigue, and exercise capacity; the secondary outcomes are lung function, heart rate variability, handgrip strength, knee extensor strength and electrical activity, physical activity, functional limitation, cognitive function, depression and anxiety, and biochemical measures of hypoxia, inflammation, oxidative stress, blood glucose, and lactate blood tests. The survey will follow theStandard Protocol Items for Randomized Trialsguidelines, and the results will be reported according to theConsolidated Standards of Reporting Trialsguidelines. Effects will be assessed based on the intent-to-treat data collected. Analysis of covariance will be used for the initial and final evaluations, with a significance level of 5%.

Results and Conclusions

The results will show the effectiveness of rehabilitation in adults with post-COVID-19 sequelae.

Impact

Fatigue, dyspnea, cough, and muscle and joint pain are common sequelae of post-COVID-19 syndrome. Physical rehabilitation is one modality for treating these sequelae. This protocol can provide a treatment model for patients with post-COVID-19 sequelae.
SARS-CoV2 wild type and mutant specific humoral and T cell immunity is superior after vaccination than after natural infection
Authors: Richardson Jennifer R. , Götz Ralph , Mayr Vanessa , Lohse Martin J. , Holthoff Hans-Peter , Ungerer Martin
Published: September 2021

Objective

We investigated blood samples from fully SARS-CoV2-vaccinated subjects and from previously positive tested patients up to one year after infection with SARS-CoV2, and compared short- and long-term T cell and antibody responses, with a special focus on the recently emerged delta variant (B.1.617.2).

Methods and Results

In 23 vaccinated subjects, we documented high anti-SARS-CoV2 spike protein receptor binding domain (RBD) antibody titers. Average virus neutralization by antibodies, assessed as inhibition of ACE2 binding to RBD, was 2.2-fold reduced for delta mutant vs. wild type (wt) RBD. The mean specific antibody titers were lower one year after natural infection than after vaccination; ACE2 binding to delta mutant vs. wt RBD was 1.65-fold reduced. In an additional group, omicron RBD binding was reduced compared to delta.

Specific CD4+ T cell responses were measured after stimulation with peptides pools from wt, alpha, beta, gamma, or delta variant SARS-CoV2 spike proteins by flow cytometric intracellular cytokine staining. There was no significant difference in cytokine production of IFN-γ, TNF-α, or IL-2 between vaccinated subjects. T cell responses to wt or mutant SARS-CoV2 spike were significantly weaker after natural occurring infections compared to those in vaccinated individuals.

Conclusion

Antibody neutralisation of the delta mutant was reduced compared to wt, as assessed in a novel inhibition assay with a finger prick blood drop. Strong CD4 T cell responses were present against wt and mutant SARS-CoV2 variants, including the delta (B.1.617.2) strain, in fully vaccinated individuals, whereas they were partly weaker 1 year after natural infection. Hence, immune responses after vaccination are stronger compared to those after naturally occurring infection, pointing out the need of the vaccine to overcome the pandemic.
INTESTINAL GLUCONEOGENESIS IS DOWNREGULATED IN PAEDIATRIC PATIENTS WITH COELIAC DISEASE
Authors: Karlson Olof , Arnell Henrik , Gudjonsdottir Audur H. , Agardh Daniel , Naluai Åsa Torinsson
Published: September 2021

Objective

Untreated coeliac disease (CD) patients have increased levels of blood glutamine and a lower duodenal expression of glutaminase (GLS). Intestinal gluconeogenesis (IGN) is a process through which glutamine is turned into glucose in the small intestine, for which GLS is crucial. Animal studies suggest impaired IGN may have long-term effects on metabolic control and be associated with development of type 2 diabetes and non-alcoholic fatty liver disease (NAFLD). The aim of this study was to thoroughly investigate IGN at the gene expression level in children with untreated coeliac disease.

Design

Quantitative polymerase chain reaction (qPCR) was used to quantify expression of 11 target genes related to IGN using the delta-delta Ct method with three reference genes (GUSB, IPO8 and YWHAZ) in duodenal biopsies collected from 84 children with untreated coeliac disease and 58 disease controls.

Results

Significantly lower expression of nine target genes involved in IGN was seen in duodenal biopsies from CD patients compared with controls: FBP1, G6PC, GLS, GPT1, PCK1, PPARGC1A, SLC2A2, SLC5A1, and SLC6A19. No significant differences in expression were seen for G6PC3 and GOT1.

Conclusion

Children with untreated coeliac disease have lower expression of genes important for IGN. Further studies are warranted to disentangle whether this is a consequence of intestinal inflammation or due to an impaired metabolic pathway shared with other chronic metabolic diseases. Impaired IGN could be a mechanism behind the increased risk of NAFLD seen in CD patients.

SIGNIFICANCE OF THIS STUDY

What is already known about this subject?

Genome-wide association studies have shown an association between coeliac disease (CD) and glutaminase (GLS).

Intestinal gluconeogenesis (IGN) is a process with a recently described important function in energy homeostasis and metabolic disease. GLS is critical for IGN by enabling it to use glutamine, its main substrate.

CD patients are at an increased risk of non-alcoholic fatty liver disease (NAFLD) as adults.

What are the new findings?

Nine genes involved in IGN are downregulated at the gene expression level in the small intestine of children with untreated CD, suggesting impairment of IGN.

How might it impact on clinical practice in the foreseeable future?

Impaired IGN might be a mechanism behind the increased risk of NAFLD seen in CD patients as adults.

Early diagnosis and treatment of CD may restore IGN and prevent CD patients from NAFLD later in adulthood.
Fundamental limits on inferring epidemic resurgence in real time using effective reproduction numbers
Authors: Parag Kris V. , Donnelly Christl A.
Published: September 2021

We find that epidemic resurgence, defined as an upswing in the effective reproduction number (R) of the contagion from subcritical to supercritical values, is fundamentally difficult to detect in real time. Inherent latencies in pathogen transmission, coupled with smaller and intrinsically noisier case incidence across periods of subcritical spread, mean that resurgence cannot be reliably detected without significant delays of the order of the generation time of the disease, even when case reporting is perfect. In contrast, epidemic suppression (where R falls from supercritical to subcritical values) may be ascertained 5–10 times faster due to the naturally larger incidence at which control actions are generally applied. We prove that these innate limits on detecting resurgence only worsen when spatial or demographic heterogeneities are incorporated. Consequently, we argue that resurgence is more effectively handled proactively, potentially at the expense of false alarms. Timely responses to recrudescent infections or emerging variants of concern are more likely to be possible when policy is informed by a greater quality and diversity of surveillance data than by further optimisation of the statistical models used to process routine outbreak data.

Author summary

The timely detection of epidemic resurgence (i.e., upcoming waves of infected cases) is crucial for informing public health policy, providing valuable signals for implementing interventions and identifying emerging pathogenic variants or important population-level behavioural shifts. Increases in epidemic transmissibility, parametrised by the time-varying reproduction number, R, commonly signify resurgence. While many studies have improved computational methods for inferring R from case data, to enhance real-time resurgence detection, few have examined what limits, if any, fundamentally restrict our ability to perform this inference. We apply optimal Bayesian detection algorithms and sensitivity tests and discover that resurgent (upward) R-changes are intrinsically more difficult to detect than equivalent downward changes indicating control. This asymmetry derives from the often lower and stochastically noisier case numbers that associate with resurgence, and induces detection delays on the order of the disease generation time. We prove these delays only worsen if spatial or demographic differences in transmissibility are modelled. As these fundamental limits exist even if case data are perfect, we conclude that designing integrated surveillance systems that fuse potentially timelier data sources (e.g., wastewater) may be more important than improving R-estimation methodology and deduce that there may be merit (subject to false alarm costs) in conservative resurgence response initiatives.
Calibration of Two Validated SARS-CoV-2 Pseudovirus Neutralization Assays for COVID-19 Vaccine Evaluation
Authors: Huang Yunda , Borisov Oleg , Kee Jia Jin , Carpp Lindsay N. , Wrin Terri , Cai Suqin , Sarzotti-Kelsoe Marcella , McDanal Charlene , Eaton Amanda , Pajon Rolando , Hural John , Posavad Christine M. , Gill Katherine , Karuna Shelly , Corey Lawrence , McElrath M. Juliana , Gilbert Peter B. , Petropoulos Christos J. , Montefiori David C.
Published: September 2021

Vaccine-induced neutralizing antibodies (nAbs) are key biomarkers considered to be associated with vaccine efficacy. In United States Government-sponsored phase 3 efficacy trials of COVID-19 vaccines, nAbs are measured by two different validated pseudovirus-based SARS-CoV-2 neutralization assays, with each trial using one of the two assays. Here we describe and compare the nAb titers obtained in the two assays. We observe that one assay consistently yielded higher nAb titers than the other when both assays were performed on the World Health Organization’s anti-SARS-CoV-2 immunoglobulin International Standard, COVID-19 convalescent sera, and mRNA-1273 vaccinee sera. To overcome the challenge this difference in readout poses in comparing/combining data from the two assays, we evaluate three calibration approaches and show that readouts from the two assays can be calibrated to a common scale. These results may aid decision-making based on data from these assays for the evaluation and licensure of new or adapted COVID-19 vaccines.
Machine Learning to Predict 10-year Cardiovascular Mortality from the Electrocardiogram: Analysis of the Third National Health and Nutrition Examination Survey (NHANES III)
Authors: Kim Chang H. , Al-Kindi Sadeer , Tarabichi Yasir , Gohel Suril , Vyas Riddhi , Srinivasan Shankar
Published: September 2021

Background

The value of the electrocardiogram (ECG) for predicting long-term cardiovascular outcomes is not well defined. Machine learning methods are well suited for analysis of highly correlated data such as that from the ECG.

Methods

Using demographic, clinical, and 12-lead ECG data from the Third National Health and Nutrition Examination Survey (NHANES III), machine learning models were trained to predict 10-year cardiovascular mortality in ambulatory U.S. adults. Predictive performance of each model was assessed using area under receiver operating characteristic curve (AUROC), area under precision-recall curve (AUPRC), sensitivity, and specificity. These were compared to the 2013 American College of Cardiology/American Heart Association Pooled Cohort Equations (PCE).

Results

7,067 study participants (mean age: 59.2 ± 13.4 years, female: 52.5%, white: 73.9%, black: 23.3%) were included. At 10 years of follow up, 338 (4.8%) had died from cardiac causes. Compared to the PCE (AUROC: 0.668, AUPRC: 0.125, sensitivity: 0.492, specificity: 0.859), machine learning models only required demographic and ECG data to achieve comparable performance: logistic regression (AUROC: 0.754, AUPRC: 0.141, sensitivity: 0.747, specificity: 0.759), neural network (AUROC: 0.764, AUPRC: 0.149, sensitivity: 0.722, specificity: 0.787), and ensemble model (AUROC: 0.695, AUPRC: 0.166, sensitivity: 0.468, specificity: 0.912). Additional clinical data did not improve the predictive performance of machine learning models. In variable importance analysis, important ECG features clustered in inferior and lateral leads.

Conclusions

Machine learning can be applied to demographic and ECG data to predict 10-year cardiovascular mortality in ambulatory adults, with potentially important implications for primary prevention.
Urinary metabolic biomarkers of diet quality in European children are associated with metabolic health
Authors: Stratakis Nikolaos , Siskos Alexandros P. , Papadopoulou Eleni , Nguyen Anh N. , Zhao Yinqi , Margetaki Katerina , Lau Chung-Ho E. , Coen Muireann , Maitre Lea , Fernández-Barrés Silvia , Agier Lydiane , Andrusaityte Sandra , Basagaña Xavier , Brantsaeter Anne Lise , Casas Maribel , Fossati Serena , Grazuleviciene Regina , Heude Barbara , McEachan Rosemary R C , Meltzer Helle Margrete , Millett Christopher , Rauber Fernanda , Robinson Oliver , Roumeliotaki Theano , Borràs Eva , Sabidó Eduard , Urquiza Jose , Vafeiadi Marina , Vineis Paolo , Voortman Trudy , Wright John , Conti David V. , Vrijheid Martine , Keun Hector C. , Chatzi Leda
Published: September 2021

Urinary metabolic profiling is a promising powerful tool to reflect dietary intake and can help understand metabolic alterations in response to diet quality. Here, we used1H-NMR spectroscopy in a multi-country study in European children (1147 children from 6 different cohorts) and identified a common panel of 4 urinary metabolites (hippurate,N-methylnicotinic acid, urea and sucrose) that was predictive of Mediterranean diet adherence (KIDMED) and ultra-processed food (UPF) consumption and also had higher capacity in discriminating children’s diet quality than that of established sociodemographic determinants. Further, we showed that the identified metabolite panel also reflected the associations of these diet quality indicators with C-peptide, a stable and accurate marker of insulin resistance and future risk of metabolic disease. This methodology enables objective assessment of dietary patterns in European child populations, complementary to traditional questionary methods, and can be used in future studies to evaluate diet quality. Moreover, this knowledge can provide mechanistic evidence of common biological pathways that characterize healthy and unhealthy dietary patterns, and diet-related molecular alterations that could associate to metabolic disease.
A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia
Authors: Sánchez Cecilia A. , Li Hongying , Phelps Kendra L. , Zambrana-Torrelio Carlos , Wang Lin-Fa , Olival Kevin J. , Daszak Peter
Published: September 2021

Emerging diseases caused by coronaviruses of likely bat origin (e.g. SARS, MERS, SADS and COVID-19) have disrupted global health and economies for two decades.

Evidence suggests that some bat SARS-related coronaviruses (SARSr-CoVs) could infect people directly, and that their spillover is more frequent than previously recognized. Each zoonotic spillover of a novel virus represents an opportunity for evolutionary adaptation and further spread; therefore, quantifying the extent of this “hidden” spillover may help target prevention programs. We derive biologically realistic range distributions for known bat SARSr-CoV hosts and quantify their overlap with human populations. We then use probabilistic risk assessment and data on human-bat contact, human SARSr-CoV seroprevalence, and antibody duration to estimate that ∼400,000 people (median: ∼50,000) are infected with SARSr-CoVs annually in South and Southeast Asia. These data on the geography and scale of spillover can be used to target surveillance and prevention programs for potential future bat-CoV emergence.
Antibody responses to BNT162b2 mRNA vaccine: infection-naïve individuals with abdominal obesity warrant attention
Authors: Malavazos Alexis Elias , Basilico Sara , Iacobellis Gianluca , Milani Valentina , Cardani Rosanna , Boniardi Federico , Dubini Carola , Prandoni Ilaria , Capitanio Gloria , Renna Laura Valentina , Boveri Sara , Carrara Matteo , Spuria Giovanni , Cuppone Teresa , D’acquisto Aurelia , Carpinelli Luca , Sacchi Marta , Morricone Lelio , Secchi Francesco , Costa Elena , Menicanti Lorenzo , Nisoli Enzo , Carruba Michele , Ambrogi Federico , Corsi Romanelli Massimiliano Marco
Published: September 2021

Objective

The excess of visceral adipose tissue might hinder and delay the immune response. How people with abdominal obesity will respond to mRNA vaccines against SARS-CoV-2 is yet to be established. We evaluated SARS-CoV-2-specific antibody responses after the first and second dose of the BNT162b2 mRNA vaccine comparing the response of individuals affected by abdominal obesity (AO) to those without, discerning between individuals with or without prior infection.

Methods

IgG neutralizing antibodies against the Trimeric complex (IgG-TrimericS) were measured at four time points: at baseline, at day 21 after vaccine dose-1, at one month and three months after dose-2. Nucleocapsid antibodies were assessed to detect prior SARS-CoV-2 infection. Waist circumference was measured to determine abdominal obesity.

Results

Between the first and third month after vaccine dose-2, the drop in IgG-TrimericS levels was more remarkable in individuals with AO compared to those without AO (2.44 fold [95%CI: 2.22-2.63] vs 1.82 fold [95%CI: 1.69-1.92], respectively, p<0.001). Multiple linear regression confirmed this result even when adjusting for possible confounders (p<0.001).

Conclusions

Our findings highlight the need to extend the duration of serological monitoring of antibody levels in infection-naive individuals with abdominal obesity, a higher-risk population category in terms of possible weaker antibody response.
Variants inALDH1A2reveal an anti-inflammatory role for retinoic acid and a new class of disease-modifying drugs in osteoarthritis
Authors: Zhu Linyi , Kamalathevan Pragash , Koneva Lada , Zarebska Jadwiga Miotla , Chanalaris Anastasios , Ismail Heba , Wiberg Akira , Ng Michael , Muhammed Hayat , Watt Fiona E. ,   The Oxford Hand Surgical Team, Sansom Stephen , Furniss Dominic , Gardiner Matthew D. , Vincent Tonia L.
Published: September 2021

Over 40% of individuals will develop osteoarthritis (OA) during their lifetime, yet there are currently no licensed disease modifying treatments for this disabling condition. Common polymorphic variants inALDH1A2, that encodes the key enzyme in the synthesis of all-trans retinoic acid (atRA), have been associated with severe hand OA. In this study, we sought to elucidate the biological significance of this association. We first confirmed thatALDH1A2risk variants were associated with hand OA in UK Biobank. Articular cartilage was acquired from 33 consenting individuals with hand OA at the time of routine hand OA surgery. They were stratified by genotype and RNA sequencing performed. A reciprocal relationship betweenALDH1A2mRNA and inflammatory genes was observed. Articular cartilage injury up-regulates similar inflammatory genes by a process that we have previously termed mechanoflammation, and which we believe is a primary driver of OA. Cartilage injury was also associated with a concomitant drop in atRA-dependent genes, indicative of cellular atRA levels, and both responses to injury were reversed using talarozole, a retinoic acid metabolism blocking agent (RAMBA). Suppression of mechanoflammation by talarozole was mediated by a peroxisome proliferator activated receptor (PPAR)-γ dependent mechanism. Talarozole, delivered by minipump, was able to suppress mechano-inflammatory genes in articular cartilagein vivo6h after mouse knee joint destabilization, and reduced cartilage degradation and osteophyte formation after 4 weeks. These data show that boosting atRA suppresses mechanoflammation in the articular cartilagein vitroandin vivo, and identifies RAMBAs as potential disease modifying drugs in OA.

One Sentence Summary

Analysis of hand OA cartilage stratified byALDH1A2polymorphic variants reveals a targetable, anti-inflammatory role for retinoic acid in OA.
Structure-activity relationships of B.1.617 and other SARS-CoV-2 spike variants
Authors: Yang Tzu-Jing , Yu Pei-Yu , Chang Yuan-Chih , Chang Ning-En , Tsai Yu-Xi , Liang Kang-Hao , Draczkowski Piotr , Lin Bertina , Wang Yong-Sheng , Chien Yu-Chun , Khoo Kay-Hooi , Wu Han-Chung , Hsu Shang-Te Danny
Published: September 2021

The surge of COVID-19 infection cases is spurred by emerging SARS-CoV-2 variants such as B.1.617. Here we report 38 cryo-EM structures, corresponding to the spike protein of the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Kappa (B.1.617.1) variants in different functional states with and without its receptor, ACE2. Mutations on the N-terminal domain not only alter the conformation of the highly antigenic supersite of the Delta variant, but also remodel the glycan shield by deleting or adding N-glycans of the Delta and Gamma variants, respectively. Substantially enhanced ACE2 binding was observed for all variants, whose mutations on the receptor binding domain modulate the electrostatics of the binding interfaces. Despite their abilities to escape host immunity, all variants can be potently neutralized by three unique antibodies.
A screen for mutants deficient in coronatine-mediated suppression of root immunity identifies Arabidopsis SDA1 as a novel integrator of immunity and phytohormone signaling
Authors: Song Yi , Zhang Xue-Cheng , Qiu Yichun , Briggs Annika , Millet Yves , Bartenstein Diana , Mankiw Catherine , Cerulli Mary L. , Bush Jenifer , Adams Keith L. , Diener Andrew C. , Ausubel Frederick M. , Haney Cara H.
Published: September 2021

Despite the importance of the root immune system in the interaction with rhizosphere microbes, the majority of genetic screens for immunity regulators have been performed in leaves. A previous screen identified 27 hsm (hormone-mediated suppression of MAMP-triggered immunity) mutants that are impaired in jasmonic acid (JA)-mediated suppression of pattern-triggered immunity (PTI) in roots. Here we characterized 16 of the hsm mutants that retain JA sensitivity and are potential negative regulators of root immunity. We found that the majority of hsm mutants show enhanced resistance to Fusarium, a root fungal pathogen; however, only a subset are more resistant to a foliar pathogen. Surprisingly, 12 of 16 hsm mutants are also impaired in abscisic acid (ABA)-mediated suppression of PTI, suggesting a largely shared pathway between JA- and ABA-mediated immune suppression in roots. Although all hsm mutants are insensitive to JA-mediated suppression of root immunity, hsm4 shows hypersensitivity to JA-mediated root growth inhibition and JA-induced gene expression. Consistently, hsm4 is more resistant to leaf pathogens, suggesting that HSM4 is a negative regulator of both root and leaf immunity. Hsm4 was mapped to a mutation in a conserved ARM-repeat protein homologous to yeast SDA1, which has been reported to regulate 60S ribosome biogenesis. As translational reprogramming is a critical layer of immune regulation, this work suggests that AtSDA1 is a novel negative translational regulator of immunity. Additionally, a comprehensive characterization of all 16 hsm mutants provides a genetic toolkit to identify novel mechanisms that regulate root immunity.
Distinct roles of glutamine metabolism in benign and malignant cartilage tumors with IDH mutations
Authors: Zhang Hongyuan , Puviindran Vijitha , Nadesan Puviindran , Ding Xiruo , Shen Leyao , Tang Yuning J. , Tsushima Hidetoshi , Yahara Yasuhito , Ban Ga I , Zhang Guo-Fang , Karner Courtney M. , Alman Benjamin
Published: September 2021

Enchondromas and chondrosarcomas are common cartilage neoplasms that are either benign or malignant respectively. The majority of these tumors harbor mutations in either IDH1 or IDH2. Glutamine metabolism has been implicated as a critical regulator of tumors with IDH mutations. Chondrocytes and chondrosarcomas with mutations in the IDH1 or IDH2 genes showed enhanced glutamine utilization in downstream metabolism. Using genetic and pharmacological approaches, we demonstrated that glutaminase-mediated glutamine metabolism played distinct roles in enchondromas and chondrosarcomas with IDH1 or IDH2 mutations. Deletion of glutaminase in chondrocytes with Idh1 mutation increased the number and size of enchondroma-like lesions. Pharmacological inhibition of glutaminase in chondrosarcoma xenografts reduced overall tumor burden. Glutamine affected cell differentiation and viability in these tumors differently through different downstream metabolites. During murine enchondroma-like lesion development, glutamine-derived α-ketoglutarate promoted hypertrophic chondrocyte differentiation and regulated chondrocyte proliferation. In human chondrosarcoma, glutamine-derived non-essential amino acids played an important role in preventing cell apoptosis. This study reveals that glutamine metabolism can play distinct roles in benign and malignant cartilage tumors sharing the same genetic mutations. Inhibiting GLS may provide a therapeutic approach to suppress chondrosarcoma tumor growth.
Thermoregulatory morphodynamics of honeybee clusters
Authors: Peters Jacob M. , Peleg Orit , Mahadevan L.
Published: September 2021

During reproductive swarming, honeybees form clusters of more than 10,000 bees that hang from structures in the environment (e.g., tree branches) and are exposed to diurnal variations in ambient temperature for up to one week during the search for a new nesting site. Swarm clusters collectively modulate their morphology in response to these variations (i.e., expanding/contracting in response to heating/cooling) to maintain their internal temperature within a tolerable range and to avoid exhausting their honey stores prematurely. To understand the spatiotemporal aspects of thermoregulatory morphing, we measured the change in size and shape of swarm clusters over time and the internal temperature profiles in response to dynamic temperature ramp perturbations. We found that swarm clusters can achieve a twofold increase/decrease their volume/density when heated from 15°C to 30°C, but they do not reach an equilibrium size or shape when held at 30°C for 5 hours, long after the core temperature of the cluster has stabilized. Furthermore, the changes in cluster shape and size are hysteretic, contracting in response to cooling faster than expanding in response to heating. Although the contact diameter of the cluster increased continuously when the swarm is heated, the change in length of the swarm (base to tip) over time is non-monotonic. Consequently, the aspect ratio of the swarm fluctuated continuously even when held at a constant temperature. Taken together, our results quantify the hysteretic and anisotropic morphological responses of swarm clusters to ambient temperature variations while suggesting that both mechanical constraints and heat transfer govern the thermoregulatory morphing dynamics of swarm clusters.
Glucose controls co-translation of structurally related mRNAs via the mTOR and eIF2 pathways in human pancreatic beta cells
Authors: Bulfoni Manuel , Bouyioukos Costas , Zakaria Albatoul , Nigon Fabienne , Rapone Roberta , Maestro Laurence Del , Ait-Si-Ali Slimane , Scharfmann Raphaël , Cosson Bertrand
Published: September 2021

Pancreatic beta cell response to glucose is critical for the maintenance of normoglycemia. A strong transcriptional response was classically described in rodent models but, interestingly, not in human cells. In this study, we exposed human pancreatic beta cells to an increased concentration of glucose and analysed at a global level the mRNAs steady state levels and their translationalability. Polysome profiling analysis showed an early acute increase in protein synthesis and a specific translation regulation of more than 400 mRNAs, independently of their transcriptional regulation. We clustered the co-regulated mRNAs according to their behaviour in translation in response to glucose and discovered common structural and sequence mRNA features. Among them mTOR- and eIF2-sensitive elements have a predominant role to increase mostly the translation of mRNAs encoding for proteins of the translational machinery. Furthermore, we show that mTOR and eIF2α pathways are independently regulated in response to glucose, participating to a translational reshaping to adapt beta cell metabolism. The early acute increase in the translation machinery components prepare the beta cell for further protein demand due to glucose-mediated metabolism changes.

AUTHOR SUMMARY

Adaptation and response to glucose of pancreatic beta cells is critical for the maintenance of normoglycemia. Its deregulation is associated to Diabetic Mellitus (DM), a significant public health concern worldwide with an increased incidence of morbidity and mortality. Despite extensive research in rodent models, gene expression regulation in response to glucose remains largely unexplored in human cells. In our work, we have tackled this question by exposing human EndoC-BH1 cells to high glucose concentration. Using polysome profiling, the gold standard technique to analyse cellular translation activity, we observed a global protein synthesis increase, independent from transcription activity. Among the specific differentially translated mRNAs, we found transcripts coding for ribosomal proteins, allowing the cell machinery to be engaged in a metabolic response to glucose. Therefore, the regulation in response to glucose occurs mainly at the translational level in human cells, and not at the transcriptional level as described in the classically used rodent models.

Furthermore, by comparing the features of the differentially translated mRNAs, and classifying them according to their translational response, we show that the early response to glucose occurs through the coupling of mRNA structure and sequence features impacting translation and regulation of specific signalling pathways. Collectively, our results support a new paradigm of gene expression regulation on the translation level in human beta cells.
USP5 enhances SGTA mediated protein quality control
Authors: Hill Jake , Nyathi Yvonne
Published: September 2021

Mislocalised membrane proteins (MLPs) present a risk to the cell due to exposed hydrophobic amino acids which cause MLPs to aggregate. Previous studies identified SGTA as a key component of the machinery that regulates the quality control of MLPs. Overexpression of SGTA promotes deubiqutination of MLPs resulting in their accumulation in cytosolic inclusions, suggesting SGTA acts in collaboration with deubiquitinating enzymes (DUBs) to exert these effects. However, the DUBs that play a role in this process have not been identified. In this study we have identified the ubiquitin specific peptidase 5 (USP5) as a DUB important in regulating the quality control of MLPs. We show that USP5 is in complex with SGTA, and this association is increased in the presence of an MLP. Overexpression of SGTA results in an increase in steady-state levels of MLPs suggesting a delay in proteasomal degradation of substrates. However, our results show that this effect is strongly dependent on the presence of USP5. We find that in the absence of USP5, the ability of SGTA to increase the steady state levels of MLPs is compromised. Moreover, knockdown of USP5 results in a reduction in the steady state levels of MLPs, while overexpression of USP5 increases the steady state levels. Our findings suggest that the interaction of SGTA with USP5 enables specific MLPs to escape proteasomal degradation allowing selective modulation of MLP quality control. These findings progress our understanding of aggregate formation, a hallmark in a range of neurodegenerative diseases and type II diabetes, as well as physiological processes of aggregate clearance.
Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector
Authors: Grüschow Sabine , Adamson Catherine S. , White Malcolm F.
Published: September 2021

Type III CRISPR systems detect invading RNA, resulting in the activation of the enzymatic Cas10 subunit. The Cas10 cyclase domain generates cyclic oligoadenylate (cOA) second messenger molecules, activating a variety of effector nucleases that degrade nucleic acids to provide immunity. The prophage-encoded Vibrio metoecus type III-B (VmeCmr) locus is uncharacterised, lacks the HD nuclease domain in Cas10 and encodes a NucC DNA nuclease effector that is also found associated with Cyclic-oligonucleotide-based anti-phage signalling systems (CBASS). Here we demonstrate that VmeCmr is activated by target RNA binding, generating cyclic-triadenylate (cA3) to stimulate a robust NucC-mediated DNase activity. The specificity of VmeCmr is probed, revealing the importance of specific nucleotide positions in segment 1 of the RNA duplex and the protospacer flanking sequence (PFS). We harness this programmable system to demonstrate the potential for a highly specific and sensitive assay for detection of the SARS-CoV-2 virus RNA with a limit of detection (LoD) of 2 fM using a commercial plate reader without any extrinsic amplification step. The sensitivity is highly dependent on the guide RNA used, suggesting that target RNA secondary structure plays an important role that may also be relevant in vivo.
A non-bactericidal cathelicidin provides prophylactic efficacy against bacterial infection by driving phagocyte influx
Authors: Yang Yang , Wu Jing , Li Qiao , Mu Lixian , Hui Li , Li Min , Xu Wei , Yang Hailong , Wei Lin
Published: September 2021

The roles of bactericidal cathelicidins against bacterial infection have been extensively studied. However, the anti-bacterial property and mechanism of action of non-bactericidal cathelicidins are rarely known. Herein, a novel naturally occurring cathelicidin (PopuCATH) from tree frog (Polypedates puerensis) didn’t show any direct anti-bacterial activity in vitro. Intriguingly, intraperitoneal injection of PopuCATH before bacterial inoculation significantly reduced the bacterial load in tree frogs and mice, and reduced the inflammatory response induced by bacterial inoculation in mice. PopuCATH pretreatment also increased the survival rates of septic mice induced by a lethal dose of bacterial inoculation or cecal ligation and puncture (CLP). Intraperitoneal injection of PopuCATH significantly drove the leukocyte influx in both frogs and mice. In mice, PopuCATH rapidly drove neutrophil, monocyte/macrophage influx in mouse abdominal cavity and peripheral blood with a negligible impact on T and B lymphocytes, and neutrophils, monocytes/macrophages, but not T and B lymphocytes, were required for the preventive efficacy of PopuCATH. PopuCATH did not directly act as chemoattractant for phagocytes, but PopuCATH obviously drove phagocyte migration when it was cultured with macrophages. PopuCATH significantly elicited chemokine/cytokine production in macrophages through activating p38/ERK mitogen-activated protein kinases (MAPKs) and NF-κB p65. PopuCATH markedly enhanced neutrophil phagocytosis via promoting the release of neutrophil extracellular traps (NETs). Additionally, PopuCATH showed low side effects both in vitro and in vivo. Collectively, PopuCATH acts as a host-based immune defense regulator that provides prophylactic efficacy against bacterial infection without direct antimicrobial effects. Our findings reveal a non-bactericidal cathelicidin which possesses unique anti-bacterial action, and highlight the potential of PopuCATH to prevent bacterial infection.
TRIM25 inhibits Influenza A infection by destabilising its mRNA and is redundant for the RIG-I pathway
Authors: Choudhury Nila Roy , Heikel Gregory , Trus Ivan , Dos Santos Pinto Rute Maria , Trubitsyna Maryia , Gaunt Eleanor , Digard Paul , Michlewski Gracjan
Published: September 2021

The E3 ubiquitin ligase TRIM25 is a key factor in the innate immune response to RNA viruses. TRIM25 has been shown to play a role in the retinoic-acid-inducible gene-1 (RIG-I) pathway, which triggers expression of type 1 interferons upon viral infection. We and others have recently shown that TRIM25 is an RNA-binding protein, however not much is known about the RNA-binding roles of TRIM25 in the innate immune response to RNA viruses. Here, we demonstrate that influenza Avirus (IAV A/PR/8/34_NS1(R38K41A)) infection is inhibited by TRIM25. Surprisingly, host RNA-binding deficient mutant TRIM25ΔRBD and TRIM25ΔRING, which lack E3 ubiquitin ligase activity rescued IAV inhibition in TRIM25 knock-out cells. Furthermore, we show that in human cultured cells activation of the RIG-I/interferon type 1 pathway mediated by an IAV-derived 5’-triphosphate RNA does not require TRIM25 activity. Additionally, knocking out TRIM25 does not affect the activity of the IAV polymerase. We present new evidence that TRIM25 restricts IAV by directly binding to and destabilising its mRNAs. Finally, we show that direct tethering of TRIM25 to RNA is sufficient to downregulate the targeted RNA. In summary, our results uncover a novel mechanism that TRIM25 uses to inhibit IAV infection and regulate RNA metabolism.
Systemic and local immune response to intraocular AAV vector administration in non-human primates
Authors: Ail Divya , Ren Duohao , Brazhnikova Elena , Nouvel-Jaillard Céline , Bertin Stephane , Fisson Sylvain , Dalkara Deniz
Published: September 2021

The positive clinical outcomes in adeno-associated virus (AAV)-mediated retinal gene therapy have often been attributed to the low immunogenicity of AAVs along with the immune-privilege of the eye. However, several recent preclinical studies and clinical trials have shown potential for inflammatory responses to AAV mediated gene therapy. Our current understanding of the factors contributing to intraocular inflammation such as the existence of serum antibodies against AAVs prior to injection and their contribution to increases in antibody levels post-injection is incomplete. The parameters that regulate the generation of new antibodies in response to the AAV capsid or transgene post-injection after intraocular administration are also insufficiently described. In this study we carried out a retrospective analysis of the pre-existing serum antibodies in correlation with changes in antibody levels after intraocular injections of AAV in non-human primates (NHPs). We analyzed NHP serums for the presence of both Binding Antibodies (BABs), as well as a subset of these called Neutralizing Antibodies (NABs) that impede AAV transduction upon binding. We observed significantly higher pre-existing serum BABs against AAV8 compared to other serotypes. We observed a dose-dependent increase in both BABs and NABs in the serums collected post-injection, irrespective of the serotype or the mode of injection. Lastly, we were able to demonstrate a co-relation between the serum BAB levels with clinical grading of inflammation and levels of transgene expression.
Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq
Authors: Dewachter Liselot , Liu Xue , Dénéréaz Julien , de Bakker Vincent , Costa Charlotte , Baldry Mara , Sirard Jean-Claude , Veening Jan-Willem
Published: September 2021

Antibiotic resistance in the important opportunistic human pathogen Streptococcus pneumoniae is on the rise. This is particularly problematic in the case of the β-lactam antibiotic amoxicillin, which is the first-line therapy. It is therefore crucial to uncover targets that would kill or resensitize amoxicillin-resistant pneumococci. To do so, we developed a genome-wide, single-cell based, gene silencing screen using CRISPR interference called sCRilecs-seq (subsets of CRISPR interference libraries extracted by fluorescence activated cell sorting coupled to next generation sequencing). Since amoxicillin affects growth and division, sCRilecs-seq was used to identify targets that are responsible for maintaining proper cell size. Our screen revealed that downregulation of the mevalonate pathway leads to extensive cell elongation. Further investigation into this phenotype indicates that it is caused by insufficient transport of cell wall precursors across the cell membrane due to a limitation in the production of undecaprenyl phosphate (Und-P), the lipid carrier responsible for this process. The data suggest that whereas peptidoglycan synthesis continues even with reduced Und-P levels, cell constriction is specifically halted. We successfully exploited this knowledge to create a combination treatment strategy where the FDA-approved drug clomiphene, an inhibitor of Und-P synthesis, is paired up with amoxicillin. Our results show that clomiphene potentiates the antimicrobial activity of amoxicillin and that combination therapy resensitizes amoxicillin-resistant S. pneumoniae. These findings could provide a starting point to develop a solution for the increasing amount of hard-to-treat amoxicillin-resistant pneumococcal infections.
Elicitation of potent SARS-CoV-2 neutralizing antibody responses through immunization using a versatile adenovirus-inspired multimerization platform
Authors: Chevillard C , Amen A , Besson S , Hannani D , Bally I , Dettling V , Gout E , Moreau CJ , Buisson M , Gallet S , Fenel D , Vassal-Stermann E , Schoehn G , Poignard P , Dagher MC , Fender P
Published: September 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown that vaccine preparedness is critical to anticipate a fast response to emergent pathogens with high infectivity. To rapidly reach herd immunity, an affordable, easy to store and versatile vaccine platform is thus desirable. We previously designed a non-infectious adenovirus-inspired nanoparticle (ADDomer), and in the present work, we efficiently decorated this original vaccine platform with glycosylated receptor binding domain (RBD) of SARS-CoV-2. Cryo-Electron Microscopy structure revealed that up to 60 copies of this antigenic domain were bound on a single ADDomer particle with the symmetrical arrangements of a dodecahedron. Mouse immunization with the RBD decorated particles showed as early as the first immunization a significant anti-coronavirus humoral response, which was boosted after a second immunization. Neutralization assays with spike pseudo-typed-virus demonstrated the elicitation of strong neutralization titers. Remarkably, the existence of pre-existing immunity against adenoviral-derived particles enhanced the humoral response against SARS-CoV-2. This plug and play vaccine platform revisits the way of using adenovirus to combat emergent pathogens while potentially taking advantage of the adenovirus pre-immunity.
Decoding the olfactory map: targeted transcriptomics link olfactory sensory neurons to glomeruli
Authors: Zhu Kevin W. , Burton Shawn D. , Nagai Maira H. , Silverman Justin D. , de March Claire A. , Wachowiak Matt , Matsunami Hiroaki
Published: September 2021

Sensory processing in vertebrate olfactory systems is organized across olfactory bulb glomeruli, wherein axons of peripheral sensory neurons expressing the same olfactory receptor co-terminate to transmit receptor-specific activity to central neurons. Understanding how receptors map to glomeruli is therefore critical to understanding olfaction. High-throughput spatial transcriptomics is a rapidly advancing field, but low-abundance olfactory receptor expression within glomeruli has previously precluded high-throughput mapping of receptors to glomeruli. Here we combined spatial sectioning along the anteroposterior, dorsoventral, and mediolateral axes with target capture enrichment sequencing to overcome low-abundance target expression. This strategy allowed us to spatially map 86% of olfactory receptors across the olfactory bulb and uncover a relationship between OR sequence and glomerular position.

ONE SENTENCE SUMMARY

Targeted enrichment of olfactory receptor mRNA in olfactory bulb sections determines spatial positions for murine glomeruli.
Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods
Authors: Giritlioglu Nazli Irmak , Kucuk Gizem Koprululu
Published: September 2021

COVID-19 is a viral disease that has been a threat to the whole world since 2019. Although effective vaccines against the disease have been developed, there are still points to be clarified about the mechanism of SARS-CoV-2, which is the causative agent of COVID-19. In this study, we determined the binding energies and the bond types of complexes formed by open (6VYB) and closed (6VXX) forms of the Spike protein of SARS-CoV-2 and wild and mutant forms of IFITM1, IFITM2, and IFITM3 proteins using the molecular docking approach. First, all missense SNPs were found in the NCBI Single Nucleotide Polymorphism database (dbSNP) for IFITM1, IFITM2, and IFITM3 and analyzed with SIFT, PROVEAN, PolyPhen-2, SNAP2, Mutation Assessor, and PANTHER cSNP web-based tools to determine their pathogenicity. When at least four of these analysis tools showed that the SNP had a pathogenic effect on the protein product, this SNP was saved for further analysis. Delta delta G (DDG) and protein stability analysis for amino acid changes were performed in the web-based tools I-Mutant, MUpro, and SAAFEC-SEQ. The structural effect of amino acid change on the protein product was made using the HOPE web-based tool. HawkDock server was used for molecular docking and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis and binding energies of all complexes were calculated. BIOVIA Discovery Studio program was utilized to visualize the complexes. Hydrogen bonds, salt bridges, and non-bonded contacts between Spike and IFITM protein chains in the complexes were detected with the PDBsum web-based tool. The best binding energy among the 6VYB-IFITM wild protein complexes belong to 6VYB-IFITM1 (-46.16 kcal/mol). Likewise, among the 6VXX-IFITM wild protein complexes, the most negative binding energy belongs to 6VXX-IFITM1 (-52.42 kcal/mol). An interesting result found in the study is the presence of hydrogen bonds between the cytoplasmic domain of the IFITM1 wild protein and the S2 domain of 6VYB. Among the Spike-IFITM mutant protein complexes, the best binding energy belongs to the 6VXX-IFITM2 N63S complex (-50.77 kcal/mol) and the worst binding energy belongs to the 6VXX-IFITM3 S50T complex (4.86 kcal/mol).

The study suggests that IFITM1 protein may act as a receptor for SARS-CoV-2 Spike protein. Assays must be advanced from in silico to in vitro for the determination of the receptor-ligand interactions between IFITM proteins and SARS-CoV-2.