bluuebunny/crossref_metadata_2025 huggingface dataset:
Brief Bubble and Intermittent Surface Oxygenation Is a Simple and Effective Alternative for Membrane Oxygenation During Hypothermic Machine Perfusion in Kidneys
Authors: Darius Tom , Vergauwen Martial , Mueller Matteo , Aydin Selda , Dutkowski Philipp , Gianello Pierre , Mourad Michel
Published: July 2020

Background.

The aim of this feasibility study was to determine an alternative oxygenation technique (easy, cheap, and compatible with air transport) for membrane oxygenation during hypothermic machine perfusion (HMP) to improve early graft function in a porcine ischemia-reperfusion autotransplant model.

Methods.

The left kidney of a ±40- kg pig was exposed to 30 minutes of warm ischemia before 22 hours of preservation and autotransplantation. In the experimental group, oxygenation of the perfusate during HMP was obtained by direct bubble and 30-minute surface oxygenation at start and 1-hour end ischemic (n = 4) and outcome measures compared with historical HMP without active oxygenation (n = 6), 22-hour continuous oxygenated HMP (HMPO2) (n = 8), and 2-hour HMPO2 + 20-hour HMP (n = 6) using membrane oxygenation in both historical oxygenated control groups.

Results.

Brief bubble and 30-minute surface oxygenation of the perfusate effectively maintained supraphysiological Po
2 levels during the first 2 hours of HMP with improved flow dynamics. Although the metabolic profile of the perfusate (ie, flavin mononucleotide) and tissue (ie, glutamate, ATP) after brief O2 uploading at the start of HMP seemed to be slightly better with the use of a membrane oxygenator compared with bubble and interrupted surface oxygenation, both techniques yielded similar, superior early graft function when compared with HMP without active oxygenation.

Conclusions.

The data presented in this feasibility study support the conclusion that brief bubble and intermittent surface oxygenation could be an alternative oxygenation technique during HMP to achieve an improved kidney graft function compared with HMP without active oxygenation and similar functional outcome when compared with membrane HMPO2.
Syntactic and semantic processing of passive BEI sentences in Mandarin Chinese: evidence from event-related potentials
Authors: Zeng Tao , Li Yuxi , Wu Mingjun
Published: July 2020

Scalp-recorded event-related potentials (ERPs) appear to be sensitive to sentence processing, especially in some particular aspects. ERP studies on inflectional Indo-European languages report that N400 (negativity around 400 ms), typically elicited by semantic anomalies, is absent when a sentence involves both syntactic and semantic violations. It has been considered that syntactic structure building takes precedence over semantic parsing, and lexical-semantic processing can be blocked by syntactic category incongruence. An ERP experiment was conducted to examine whether such syntactic primacy also exists equally in sentence comprehension in Mandarin Chinese, using the long passive sentences of bei constructions (bei is a preposition preceding a predicate verb and expressing a passive meaning) with either semantic or syntactic violations, combined violations of both, or no violations. Results showed that a broad negativity appeared in both purely semantic and combined violations in the time window of 300–500 ms, which implies that lexical-semantic parsing is not blocked by syntactic structure failure. Instead, it is of great significance to the comprehension of long passive sentences in Mandarin Chinese (see Video, Supplemental Digital Content1, http://links.lww.com/WNR/A592, which introduces the article).
Cardiometabolic medicine – the US perspective on a new subspecialty
Authors: Reiter-Brennan Cara , Cainzos-Achirica Miguel , Soroosh Garshasb , Saxon David R. , Blaha Michael J. , Eckel Robert H.
Published: July 2020

The high prevalence of cardiovascular disease and worldwide diabetes epidemic has created an ever-increasing burden on the healthcare system. This calls for the creation of a new medicine subspecialty: cardiometabolic medicine. Using information from review articles listed on PubMed and professional society guidelines, the authors advocate for a cardiometabolic medicine specialization training program. The curriculum would integrate relevant knowledge and skills of cardiology and endocrinology as well as content of other disciplines essential to the optimal care of cardiometabolic patients, such as epidemiology, biostatistics, behavioral science and psychology. Cardiometabolic medicine should be seen as an opportunity for life-long learning, with core concepts introduced in medical school and continuing through CME courses for practicing physicians. To improve care for complex patients with multiple co-morbidities, a paradigm shift must occur, transforming siloed education, and treatment and training to interdisciplinary and collaborative work.
Inference in road ecology research: what we know versus what we think we know
Authors: Teixeira Fernanda Z. , Rytwinski Trina , Fahrig Lenore
Published: July 2020

Roads and traffic impacts on wildlife populations are well documented. Three major mechanisms can cause them: reduced connectivity, increased mortality and reduced habitat quality. Researchers commonly recommend mitigation based on the mechanism they deem responsible. We reviewed the 2012–2016 literature to evaluate authors' inferences, to determine whether they explicitly acknowledge all possible mechanisms that are consistent with their results. We found 327 negative responses of wildlife to roads, from 307 studies. While most (84%) of these responses were consistent with multiple mechanisms, 60% of authors invoked a single mechanism. This indicates that many authors are over-confident in their inferences, and that the literature does not allow estimation of the relative importance of the mechanisms. We found preferences in authors' discussion of mechanisms. When all three mechanisms were consistent with the response measured, authors were 2.4 and 2.9 times as likely to infer reduced habitat quality compared to reduced connectivity or increased mortality, respectively. When both reduced connectivity and increased mortality were consistent with the response measured, authors were 5.2 times as likely to infer reduced connectivity compared to increased mortality. Given these results, road ecologists and managers are likely over-recommending mitigation for improving habitat quality and connectivity, and under-recommending measures to reduce road-kill.
A novel antiviral formulation inhibits a range of enveloped viruses
Authors: Fletcher Nicola F. , Meredith Luke W. , Tidswell Emma L. , Bryden Steven R. , Gonçalves-Carneiro Daniel , Chaudhry Yasmin , Shannon-Lowe Claire , Folan Michael A. , Lefteri Daniella A. , Pingen Marieke , Bailey Dalan , McKimmie Clive S. , Baird Alan W.
Published: July 2020

Some free fatty acids derived from milk and vegetable oils are known to have potent antiviral and antibacterial properties. However, therapeutic applications of short- to medium-chain fatty acids are limited by physical characteristics such as immiscibility in aqueous solutions. We evaluated a novel proprietary formulation based on an emulsion of short-chain caprylic acid, ViroSAL, for its ability to inhibit a range of viral infections in vitro and in vivo. In vitro, ViroSAL inhibited the enveloped viruses Epstein–Barr, measles, herpes simplex, Zika and orf parapoxvirus, together with Ebola, Lassa, vesicular stomatitis and severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) pseudoviruses, in a concentration- and time-dependent manner. Evaluation of the components of ViroSAL revealed that caprylic acid was the main antiviral component; however, the ViroSAL formulation significantly inhibited viral entry compared with caprylic acid alone. In vivo, ViroSAL significantly inhibited Zika and Semliki Forest virus replication in mice following the inoculation of these viruses into mosquito bite sites. In agreement with studies investigating other free fatty acids, ViroSAL had no effect on norovirus, a non-enveloped virus, indicating that its mechanism of action may be surfactant disruption of the viral envelope. We have identified a novel antiviral formulation that is of great interest for the prevention and/or treatment of a broad range of enveloped viruses, particularly those of the skin and mucosal surfaces.
Streptomyces from traditional medicine: sources of new innovations in antibiotic discovery
Authors: Quinn Gerry A. , Banat Aiya M. , Abdelhameed Alyaa M. , Banat Ibrahim M.
Published: July 2020

Given the increased reporting of multi-resistant bacteria and the shortage of newly approved medicines, researchers have been looking towards extreme and unusual environments as a new source of antibiotics.

Streptomyces

currently provides many of the world’s clinical antibiotics, so it comes as no surprise that these bacteria have recently been isolated from traditional medicine. Given the wide array of traditional medicines, it is hoped that these discoveries can provide the much sought after core structure diversity that will be required of a new generation of antibiotics. This review discusses the contribution of

Streptomyces

to antibiotics and the potential of newly discovered species in traditional medicine. We also explore how knowledge of traditional medicines can aid current initiatives in sourcing new and chemically diverse antibiotics.
Preliminary optimisation of simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse- transcription loop-mediated isothermal amplification (RT-LAMP)
Authors: Howson Emma L. A. , Kidd Stephen P. , Sawyer Jason , Cassar Claire , Cross David , Lewis Tom , Hockey Jess , Rivers Samantha , Cawthraw Saira , Banyard Ashley , Andreou Michael , Morant Nick , Clark Duncan , Walsh Charlotte , Laxman Shailen , Houghton Rebecca , Slater-Jefferies Joanne , Costello Paula , Brown Ian , Cortes Nicholas , Godfrey Keith M. , Fowler Veronica L.
Published: July 2020

We describe the optimization of a simplified sample preparation method which permits rapid and direct detection of SARS-CoV-2 RNA within saliva using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). Treatment of saliva samples prior to RT-LAMP by dilution 1:1 in Mucolyse™, followed by dilution (within the range of 1:5 to 1:40) in 10% (w/v) Chelex© 100 Resin and a 98°C heat step for 2 minutes enabled detection of SARS-CoV-2 RNA in all positive saliva samples tested, with no amplification detected in pooled negative saliva. The time to positivity for which SARS- CoV-2 RNA was detected in these positive saliva samples was proportional to the real-time reverse- transcriptase PCR cycle threshold (CT), with SARS-CoV-2 RNA detected in as little as 05:43 (CT 21.08), 07:59 (CT 24.47) and 08:35 (CT 25.27) minutes, respectively. The highest CT where direct RT-LAMP detected SARS-CoV-2 RNA was 31.39 corresponding to a 1:40 dilution of a positive saliva sample with a starting CT of 25.27. When RT-LAMP was performed on pools of SARS-CoV-2 negative saliva samples spiked with whole inactivated SARS-CoV-2 virus, RNA was detected at dilutions spanning 1:5 to 1:160 representing CT’s spanning 22.49-26.43. Here we describe a simple but critical rapid sample preparation method which can be used up front of RT-LAMP to permit direct detection of SARS-CoV- 2 within saliva samples. Saliva is a sample which can be collected non-invasively without the use of highly skilled staff and critically can be obtained from both health care and home settings. Critically, this approach overcomes both the requirement and validation of different swabs and the global bottleneck observed in obtaining RNA extraction robots and reagents to enable molecular testing by PCR. Such testing opens the possibility of public health approaches for effective intervention to control the COVID-19 pandemic through regular SARS-CoV-2 testing at a population scale, combined with isolation and contact tracing for positive cases.
Detecting Emerging COVID-19 Community Outbreaks at High Spatiotemporal Resolution — New York City, June–July 2020
Authors: Greene Sharon K. , Peterson Eric R. , Balan Dominique , Jones Lucretia , Culp Gretchen M. , Fine Annie D. , Kulldorff Martin
Published: July 2020

New York City’s Health Department developed a SARS-CoV-2 percent test positivity cluster detection system using census tract resolution and the SaTScan prospective space-time scan statistic. One cluster led to identifying a gathering with inadequate social distancing where viral transmission likely occurred, and another cluster prompted targeted community testing and outreach.
Evaluation of diversity levels of the integrase gene sequences coming from HIV-1 virus, supporting the lack of target specificity of ivermectinversusthe integrase-importin complex in SARS-CoV-2 infection
Authors: Félix Pierre Teodósio
Published: July 2020

Therapies with new drugs have been appearing in tests worldwide as potential inhibitors of sars-cov-2 virus replication. Recently, one of these drugs, Ivermectin, was reported as an inhibitor of the nuclear import of HIV-1 proteinsin vitro, soon becoming the target of an international prospecting work (not yet published), with patients tested for COVID-19. However, understanding the evolutionary aspects of the biological components involved in the complex drug-nuclear import helps in understanding how these relationships exist in the deactivation of viral infections. Thus, 153 sequences of the HIV-1 integrase gene were analyzed for their genetic structure and molecular diversity and the presence of two distinct groups for the Gene and not only one, was detected; As well as different degrees of structuring for each of these groups. These results support the interpretation of the lack of conservation of the HIV-1 gene and that the number of existing polymorphisms, only for this structure of the complex, implies the non-efficiency of a drug at population levels. Thus, the molecular diversity found in HIV-1 can be extrapolated to other viruses, such as Including, SARS-CoV-2 and the functionality of the drug, interacting with the integrase-importin complex, can be further decreased.
High Community SARS-CoV-2 Antibody Seroprevalence in a Ski Resort Community, Blaine County, Idaho, US. Preliminary Results
Authors: McLaughlin Colleen C. , Doll Margaret K. , Morrison Kathryn T. , McLaughlin William L. , O’Connor Terry , Sholukh Anton M. , Bossard Emily L. , Phasouk Khamsone , Ford Emily S. , Diem Kurt , Klock Alexis M. , Jerome Keith R. , Corey Lawrence
Published: July 2020

Community-level seroprevalence surveys are needed to determine the proportion of the population with previous SARS-CoV-2 infection, a necessary component of COVID-19 disease surveillance. In May, 2020, we conducted a cross-sectional seroprevalence study of IgG antibodies for nucleocapsid of SARS-CoV-2 among the residents of Blaine County, Idaho, a ski resort community with high COVID-19 attack rates in late March and Early April (2.9% for ages 18 and older). Participants were selected from volunteers who registered via a secure web link, using prestratification weighting to the population distribution by age and gender within each ZIP Code. Participants completed a survey reporting their demographics and symptoms; 88% of volunteers who were invited to participate completed data collection survey and had 10 ml of blood drawn. Serology was completed via the Abbott Architect SARS-CoV-2 IgG immunoassay. Primary analyses estimated seroprevalence and 95% credible intervals (CI) using a hierarchical Bayesian framework to account for diagnostic uncertainty. Stratified models were run by age, sex, ZIP Code, ethnicity, employment status, and a priori participant-reported COVID-19 status. Sensitivity analyses to estimate seroprevalence included base models with post-stratification for ethnicity, age, and sex, with or without adjustment for multi-participant households. IgG antibodies to the virus that causes COVID-19 were found among 22.7% (95% CI: 20.1%, 25.5%) of residents of Blaine County. Higher levels of antibodies were found among residents of the City of Ketchum 34.8% (95% CI 29.3%, 40.5%), compared to Hailey 16.8% (95%CI 13.7%, 20.3%) and Sun Valley 19.4% (95% 11.8%, 28.4%). People who self-identified as not believing they had COVID-19 had the lowest prevalence 4.8% (95% CI 2.3%, 8.2%). The range of seroprevalence after correction for potential selection bias was 21.9% to 24.2%. This study suggests more than 80% of SARS-CoV-2 infections were not reported. Although Blaine County had high levels of SARS-CoV-2 infection, the community is not yet near the herd immunity threshold.
“Sleepless in Lockdown”: unpacking differences in sleep loss during the coronavirus pandemic in the UK
Authors: Falkingham Jane , Evandrou Maria , Qin Min , Vlachantoni Athina
Published: July 2020

Background

Covid-19 has been shown to be having a disproportionate impact on the health of individuals from different ethnic groups and those employed in certain occupations, whilst the indirect impacts of Covid-19, including the closure of schools and business and the move to home working, fall disproportionately on the young and on women. These factors may in turn impact upon sleep health. Research on sleep deprivation during the pandemic crisis to date has been limited. The present study aimed to explore the levels and social determinants of self-reported sleep loss among the general population during the Covid-19 pandemic in the UK, with a particular focus on ethnic and gender disparities.

Methods

Newly available national representative survey data from Understanding Society COVID- 19 Study collected during April 2020 were analysed. These data were linked to Wave 9 of Understanding Society conducted in 2018/19, providing information about the respondents prior to the outbreak of the pandemic. Cross-sectional analysis provided prevalence estimates, whilst analysis of the linked longitudinal data provided incidence estimates. The analytical sample included 15,360 respondents aged 16 and above; among these, 12,206 reported no problem of sleep loss before the epidemic.

Results

Prevalence and incidence rates of perceived sleep loss were 24.7% and 20.2% respectively. Women (at the level of 31.8% and 27.0%) and individuals from Black, Asian, and minority ethnic (BAME) communities (at the level of 32.0% and 24.6%) were more vulnerable to sleep deprivation due to the pandemic. Multivariate regression analysis shows that being female, the presence of young children in the household, perceived financial difficulties and being a Covid-19-related key worker were all predictive of sleep loss. Once these covariates were controlled for the bivariate relationship between ethnicity and sleep loss was reversed, reflecting the complex interaction between the coronavirus epidemic and ethnicity.

Conclusions

The pandemic has widened the disparity of sleep deprivation across different groups, with women with young children, key workers and people of BAME heritage all experiencing difficulty in sleeping, which in turn may negatively affect mental and physical health and well-being.
Recurrent SARS-CoV-2 RNA positivity after COVID-19: A systematic review and meta-analysis
Authors: Azam Mahalul , Sulistiana Rina , Ratnawati Martha , Fibriana Arulita Ika , Bahrudin Udin , Aljunid Syed Mohamed
Published: July 2020

Background

Previous studies reported recurrent SARS-CoV-2 RNA positivity in individuals who had recovered from COVID-19 infections. However, little is known regarding the systematic review of recurrent SARS-CoV-2 RNA positivity. The current study conducted a systematic review and meta-analysis, aimed to estimate the incidence of recurrent SARS-CoV-2 RNA positivity after recovery from COVID-19 and to determine the factors associated with recurrent positivity.

Methods

We searched the PubMed, MedRxiv, BioRxiv, the Cochrane Library, ClinicalTrials.gov, and the World Health Organization International Clinical Trials Registry for studies published to June 12, 2020. Studies were reviewed to determine the risk of bias. A random-effects model was used to pool results. Heterogeneity was assessed using I2.

Results

Fourteen studies of 2,568 individuals were included. The incidence of recurrent SARS-CoV-2 positivity was 14.81% (95% confidence interval [CI]: 11.44–18.19%). The pooled estimate of the interval from disease onset to recurrence was 35.44 days (95% CI: 32.65–38.24 days), and from the last negative to recurrent positive result was 9.76 days (95% CI: 7.31–12.22 days). Patients with younger age (mean difference [MD]=-2.27, 95% CI: -2.95 to -1.80) and a longer initial illness (MD=8.24 days; 95% CI: 7.54 – 8.95; I2=98.9%) were more likely to experience recurrent SARS-CoV-2 positivity, while patients with diabetes (RR=0.52; 95% CI: 0.30-0.90; I2=53%), severe disease (RR=0.54; 95% CI: 0.35-0.84; I2=70%), and a low lymphocyte count (RR=0.58; 95% CI: 0.39 – 0.86; I2=48%) were less likely to experience recurrent SARS-CoV-2 positivity.

Conclusions

The incidence of recurrent SARS-CoV-2 positivity was 14.81%. The estimated interval from disease onset to repeat positivity was 35.44 days, and the estimated interval from the last negative result to recurrent positive result duration was 9.76 days.
Bioaersols in orthopedic surgical procedures and implications for clinical practice in the times of COVID-19 pandemic: a protocol for systematic review and meta-analysis
Authors: Sharma Siddhartha , John Rakesh , Neradi Deepak , Patel Sandeep , Dhillon Mandeep Singh
Published: July 2020

Background

Orthopedic surgical procedures involve a number of aerosol generating procedures; these include electrocautery, power instruments for bone cutting, burring and drilling, and tools for wound lavage. This assumes a great significance in the context of the current COVD-19 pandemic, as there are chances of aerosol-borne disease transmission in orthopedic surgical procedures. Hence, this systematic review and meta-analysis will be undertaken to assimilate and analyse the available evidence on bioaerosols in orthopedic surgical procedures and their significance with respect to SARS-CoV-2 virus transmission.

Objectives

To determine the characteristics (amount and/or density, size, infectivity, and spread etc.) of bioaerosols found in orthopaedic operating rooms (ORs) and to determine the characteristics of aerosols generated by different orthopaedic power tools and devices.

Methods

A systematic review and meta-analysis will be conducted. The PRISMA guidelines will be strictly followed. The primary search will be conducted on the PubMed, EMBASE, Scopus, Cochrane Library, medRxiv, bioRxix and Lancet preprint databases, using a well-defined search strategy. Any original research study (including cohort, case-control, case series, cadaveric studies and studies, animal models, laboratory based experimental studies) looking at aerosol generation in orthopedic surgical procedures, or aerosol generation by orthopaedic power tools and devices will included. Outcome measures will include characteristics (amount and/or density, size, infectivity, and spread etc.) of bioaerosols found in orthopaedic operating rooms (ORs) and those generated by various orthopaedics power tools and devices. Metanalysis using the random-effects model will be conducted to determined pooled estimates of the outcome variables. Heterogeneity will be assessed by the I2 test. Risk of bias will be assessed by the Risk of Bias in Studies estimating Prevalence of Exposure to Occupational risk factors (RoB-SPEO) tool. The overall strength of evidence will be assessed by the GRADE approach.
‘Stray Appetites’: A Socio-Ecological Analysis of Free-Ranging Dogs Living Alongside Human Communities in Bangalore, India
Authors: Bhalla Shireen Jagriti , Kemmers Roy , Vasques Ana , Vanak Abi Tamim
Published: July 2020

Across the developing world, humans and free-ranging domestic dogs share common spaces. The relationship between these dogs and humans can range from one of dependence, to apathy, to conflict. Given the high number of humans attacked by dogs every year in India, and the lack of an effective population control strategy, we seek to provide insights into the conflict and propose alternative population management options based on reducing the carrying capacity of the environment. We used a mixed methods approach to understand both ecological and sociological underpinnings of free-ranging dog-human relationships in Bangalore, India. We conducted a photographic capture-recapture survey of free-ranging dogs to estimate population size and linked it to the availability of potential food sources. We also conducted a qualitative survey to assess attitudes of residents towards the dog population. We found that dog population varied from 192 to 1888 per square kilometre across a gradient of housing densities. The density of houses, bakeries and garbage piles were significant predictors of dog population size. Crucially, as low as 10 to 18.3% of houses supported the large population of dogs, highlighting the need for residents to act responsibly towards the dogs. Further, we found that garbage, although significant, is a secondary food source to household-maintained dogs. Since on the whole, respondents expressed the desire for a reduction in dog population, we suggest decreasing the carrying capacity of the environment by targeting these three food sources.
A deep learning framework for high-throughput mechanism-driven phenotype compound screening
Authors: Pham Thai-Hoang , Qiu Yue , Zeng Jucheng , Xie Lei , Zhang Ping
Published: July 2020

Target-based high-throughput compound screening dominates conventional one-drug-one-gene drug discovery process. However, the readout from the chemical modulation of a single protein is poorly correlated with phenotypic response of organism, leading to high failure rate in drug development. Chemical-induced gene expression profile provides an attractive solution to phenotype-based screening. However, the use of such data is currently limited by their sparseness, unreliability, and relatively low throughput. Several methods have been proposed to impute missing values for gene expression datasets. However, few existing methods can performde novochemical compound screening. In this study, we propose a mechanism-driven neural network-based method named DeepCE (Deep Chemical Expression) which utilizes graph convolutional neural network to learn chemical representation and multi-head attention mechanism to model chemical substructure-gene and gene-gene feature associations. In addition, we propose a novel data augmentation method which extracts useful information from unreliable experiments in L1000 dataset. The experimental results show that DeepCE achieves the superior performances not only inde novochemical setting but also in traditional imputation setting compared to state-of-the-art baselines for the prediction of chemical-induced gene expression. We further verify the effectiveness of gene expression profiles generated from DeepCE by comparing them with gene expression profiles in L1000 dataset for downstream classification tasks including drug-target and disease predictions. To demonstrate the value of DeepCE, we apply it to patient-specific drug repurposing of COVID-19 for the first time, and generate novel lead compounds consistent with clinical evidences. Thus, DeepCE provides a potentially powerful framework for robust predictive modeling by utilizing noisy omics data as well as screening novel chemicals for the modulation of systemic response to disease.
Structural models of mitochondrial uncoupling proteins obtained in DPC micelles are not physiologically relevant for their uncoupling activity
Authors: Piel Mathilde S. , Masscheleyn Sandrine , Bouillaud Frédéric , Moncoq Karine , Miroux Bruno
Published: July 2020

Uncoupling protein 1 (UCP1) is found in the inner mitochondrial membrane of brown adipocyte. In the presence of long-chain fatty acids (LCFA), UCP1 increases the proton conductance, which, in turn, increases fatty acid oxidation and energy release as heat. Several atomic models of UCP1 and UCP2 have been obtained by NMR in dodecylphosphocholine (DPC), a detergent known to inactivate UCP1. Based on NMR titration experiment on UCP1 with LCFA, it has been proposed that K56 and K269 are crucial for LCFA binding and UCP1 activation. Given the numerous controversies on the use of DPC for structure-function analyses of membrane proteins, we revisited those UCP1 mutants in a more physiological context by expressing them in the mitochondria ofS. cerevisiae. Mitochondrial respiration, assayed on permeabilized spheroplasts, enables the determination of UCP1 activation and inhibition. The K56S, K269S and K56S/K269S mutants did not display any default in activation, which shows that the NMR experiments in DPC detergent are not relevant to understand UCP1 function.
Leaf and flower consumption modulate the drinking behavior in a folivorous-frugivorous arboreal mammal
Authors: Chaves Óscar M. , Fortes Vanessa B. , Hass Gabriela P. , Azevedo Renata B. , Stoner Kathryn E. , Bicca-Marques Júlio César
Published: July 2020

Water is vital for the survival of any species because of its key role in most physiological processes. However, little is known about the non-food-related water sources exploited by arboreal mammals, the seasonality of their drinking behavior and its potential drivers (including diet composition, temperature, and rainfall). We investigated this subject in 14 wild groups of brown howler monkeys (Alouatta guariba clamitans) inhabiting small, medium, and large Atlantic Forest fragments in southern Brazil. We found a wide variation in the mean rate of drinking among groups (range=0-16 records/day). Streams (44% of 1,258 records) and treeholes (26%) were the major types of water sources, followed by bromeliads in the canopy (16%), pools (11%), and rivers (3%). The type of source influenced whether howlers used a hand to access the water or not. Drinking tended to be evenly distributed throughout the year, except for a slightly lower number of records in the spring than in the other seasons, but it was unevenly distributed during the day. It increased in the afternoon in all groups, particularly during temperature peaks around 15:00 and 17:00. We found via generalized linear mixed modelling that the daily frequency of drinking was mainly influenced by flower (negatively) and leaf (positively) consumption, whereas fruit consumption, fragment size, rainfall, and mean ambient temperature played negligible roles. The influence of leaf consumption is compatible with the ‘metabolite detoxification hypothesis,’ which states that the processing of this fibrous food requires the ingestion of larger volumes of water to help in the detoxification/excretion of its metabolites. In sum, we found that irrespective of habitat size and climatic conditions, brown howlers seem to seek a positive water balance by complementing preformed and metabolic water with drinking water, even when it is associated with a high predation risk in terrestrial sources.
A human disease model of SARS-CoV-2-induced lung injury and immune responses with a microengineered organ chip
Authors: Zhang Min , Wang Peng , Luo Ronghua , Wang Yaqing , Li Zhongyu , Guo Yaqiong , Yao Yulin , Li Minghua , Tao Tingting , Chen Wenwen , Han Jianbao , Liu Haitao , Cui Kangli , zhang Xu , Zheng Yongtang , Qin Jianhua
Published: July 2020

Coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that seriously endangers human health. There is an urgent need to build physiological relevant human models for deep understanding the complex organ-level disease processes and facilitating effective therapeutics for COVID-19. Here, we first report the use of microengineered alveolus chip to create a human disease model of lung injury and immune responses induced by native SARS-CoV-2 at organ-level. This biomimetic system is able to reconstitute the key features of human alveolar-capillary barrier by co-culture of alveolar epithelial and microvascular endothelial cells under microfluidic flow. The epithelial cells on chip showed higher susceptibility to SARS-CoV-2 infection than endothelial cells identified by viral spike protein expression. Transcriptional analysis showed distinct responses of two cell types to SARS-CoV-2 infection, including activated type I interferon (IFN-I) signaling pathway in epithelium and activated JAK-STAT signaling pathway in endothelium. Notably, in the presence of circulating immune cells, a series of alveolar pathological changes were observed, including the detachment of endothelial cells, recruitment of immune cells, and increased production of inflammatory cytokines (IL-6, IL-8, IL-1β and TNF-α). These new findings revealed a crucial role of immune cells in mediating lung injury and exacerbated inflammation. Treatment with antiviral compound remdesivir could suppress viral copy and alleviate the disruption of alveolar barrier integrity induced by viral infection. This bioengineered human organ chip system can closely mirror human-relevant lung pathogenesis and immune responses to SARS-CoV-2 infection, not possible by otherin vitromodels, which provides a promising and alternative platform for COVID-19 research and preclinical trials.
Neurometabolite Mapping Highlights Elevated Myo-inositol Profiles within the Developing Brain in Down Syndrome
Authors: Patkee Prachi A. , Baburamani Ana A. , Long Katherine R. , Dimitrova Ralica , Ciarrusta Judit , Allsop Joanna , Hughes Emer , Kangas Johanna , McAlonan Grainne , Rutherford Mary A.
Published: July 2020

The neurodevelopmental phenotype in Down Syndrome (DS), or Trisomy 21, is variable including a wide spectrum of cognitive impairment and a high risk of early-onset Alzheimer’s disease (AD). A key metabolite of interest within the brain in DS is Myo-inositol (Myo-ins). The NA+/Myo-ins co-transporter, is located on human chromosome 21 and is overexpressed in DS. In adults with DS, elevated brain Myo-ins has previously been associated with cognitive impairment and proposed as a risk marker for progression to AD. However, it is unknown if brain Myo-ins is increased earlier in development.

The aim of this study was to assess Myo-ins and key brain metabolites [N-acetylaspartate (NAA), Choline (Cho) and Creatine(Cr)] in the developing brain in DS and aged-matched controls. To achieve this we used mass spectrometry in early (10-20 weeks post conception)ex vivofetal brain tissue samples from DS (n=14) and control (n=30) cases; andin vivomagnetic resonance spectroscopy (MRS) in neonates with DS (n=18) and aged matched controls (n= 25) scanned just after birth (36-45 weeks postmenstrual age.

We observed elevated Myo-ins in theex vivofetal cortical brain tissue in DS compared with controls. Relative to reference metabolites Cho and Cr, we also detected elevated ratios of Myo-ins and NAAin vivoin the basal ganglia and thalami, in neonates with DS, when compared to age-matched typically developing controls. Thus, a higher level of brain Myo-ins was evident as early as 10 weeks post conception and was measurablein vivofrom 36 weeks post-menstrual age. Future work will determine if this early difference in metabolites is linked to cognitive outcomes in childhood or has utility as a potential treatment biomarker for early intervention.
Axon guidance at the midline – a live imaging perspective
Authors: Dumoulin Alexandre , Zuñiga Nikole R. , Stoeckli Esther T.
Published: July 2020

During neural circuit formation, axons navigate several choice points to reach their final target. At each one of these intermediate targets, growth cones need to switch responsiveness from attraction to repulsion in order to move on. Molecular mechanisms that allow for the precise timing of surface expression of a new set of receptors that support the switch in responsiveness are difficult to studyin vivo. Mostly, mechanisms are inferred from the observation of snapshots of many different growth cones analyzed in different preparations of tissue harvested at distinct time points. However, to really understand the behavior of growth cones at choice points, a single growth cone should be followed arriving at and leaving the intermediate target.

Here, we describe a spinal cord preparation that allows for live imaging of individual axons during navigation in their intact environment. The possibility to observe single growth cones navigating their intermediate target allows for measuring growth speed, changes in morphology, or aberrant behavior. Moreover, observation of the intermediate target – the floor plate – revealed its active participation and interaction with commissural axons during midline crossing.

Summary statement

Live tracking of single growth cones is more informative about axonal behavior during navigation than inference of behavior from the analyses of snapshots of different growth cones.
Three-dimensional beating dynamics ofChlamydomonasflagella
Authors: Mojiri Soheil , Isbaner Sebastian , Mühle Steffen , Jang Hongje , Bae Albert Johann , Gregor Ingo , Gholami Azam , Enderlein Jörg
Published: July 2020

Axonemes are the basic structure of motile cilia and flagella, and the investigation of how they function and move requires rapid three-dimensional imaging. We built a multi-plane phase-contrast microscope for imaging the three-dimensional motion of unlabeled flagella of the model organismChlamydomonas reinhardtiiwith sub-μm spatial and 4 ms temporal resolution. This allows us to observe not only bending but also the three-dimensional torsional dynamics of these small structures. We observe that flagella swim counter-clockwise close to a surface, with negatively-valued torsion at their basal and positively-valued torsion at their distal tips. To explain the torsional dynamics and signature, we suggest the existence of an intrinsic negative twist at the basal end that is untwisted by active positive-twist-inducing dynein motor proteins. Moreover, dyneins walking towards the basal induce an opposite twist at the distal tip. Bending of the whole axoneme structure then translates this twist into an observable torsion. This interconnection between chiral structure, twist, curvature, and torsion is fundamental for understanding flagellar mechanics.
Light-powered reactivation of flagella and contraction of microtubules network: towards building an artificial cell
Authors: Ahmad Raheel , Kleineberg Christin , Nasirimarekani Vahid , Su Yu-Jung , Pozveh Samira Goli , Bae Albert , Sundmacher Kai , Bodenschatz Eberhard , Guido Isabella , Vidakovic-Koch Tanja , Gholami Azam
Published: July 2020

Artificial systems capable of self-sustained movement with self-sufficient energy are of high interest with respect to the development of many challenging applications including medical treatments but also technical applications. The bottom-up assembly of such systems in the context of synthetic biology is still a challenging task. In this work, we demonstrate the biocompatibility and efficiency of an artificial light-driven energy module and a motility functional unit by integrating light-switchable photosynthetic vesicles with demembranated flagella that provide ATP for dynein molecular motors upon illumination. The flagellar propulsion is coupled to the beating frequency and dynamic ATP synthesis in response to illumination allows us to control beating frequency of flagella in a light-dependent manner. In addition, we verified the functionality of light-powered synthetic vesicles inin vitromotility assays by encapsulating microtubules assembled with force-generating kinesin-1 motors and the energy module to investigate the dynamics of a contractile filamentous network in cell-like compartments by optical stimulation. Integration of this photosynthetic system with various biological building blocks such as cytoskeletal filaments and molecular motors may contribute to the bottom-up synthesis of artificial cells that are able to undergo motor-driven morphological deformations and exhibit directional motion in a light-controllable fashion.

Graphical TOC Entry
Fluorescence Correlation and Cross-Correlation Spectroscopy Unveil Cytoplasmic mRNP Composition and Dynamics
Authors: Mateu-Regué Àngels , Christiansen Jan , Hellriegel Christian , Nielsen Finn Cilius
Published: July 2020

Understanding the mRNA life cycle requires analysis of the dynamic macromolecular composition and stoichiometry of mRNPs. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are appealing technologies to study mRNP complexes because they readily provide information about the molecular composition, stoichiometry, heterogeneity and dynamics of the particles. We developed FCS protocols for analysis of live cells and cellular lysates, and demonstrate the feasibility of analysing common cytoplasmic mRNPs composed of core factor YBX1, IMPs (or IGF2BPs) and their interactions with other RNA binding proteins such as PABPC1, ELAVL2 (HuB), STAU1 and FMRP. FCCS corroborated previously reported RNA dependent interactions between the factors and provided an estimate of the relative overlap between the factors in the mRNPs. In this way FCS and FCCS provide a new and useful approach for the quantitative and dynamic analysis of mRNP macromolecular complexes that may complement current biochemical approaches.
Sex-specific speed-accuracy tradeoffs shape neural processing of acoustic signals in a grasshopper
Authors: Clemens Jan , Ronacher Bernhard , Reichert Michael S.
Published: July 2020

Speed-accuracy tradeoffs – being fast at the risk of being wrong – are fundamental to many decisions and natural selection is expected to resolve these tradeoffs according to the costs and benefits of behavior. We here test the prediction that females and males should integrate information from courtship signals differently because they experience different payoffs along the speed-accuracy continuum. We fitted a neural model of decision making (a drift-diffusion model of integration to threshold) to behavioral data from the grasshopperChorthippus biguttulusto determine the parameters of temporal integration of acoustic directional information used by male grasshoppers to locate receptive females. The model revealed that males had a low threshold for initiating a turning response, yet a large integration time constant enabled them to continue to gather information when cues were weak. This contrasts with parameters estimated for females of the same species when evaluating potential mates, in which response thresholds were much higher and behavior was strongly influenced by unattractive stimuli. Our results reveal differences in neural integration consistent with the sex-specific costs of mate search: Males often face competition and need to be fast, while females often pay high error costs and need to be deliberate.
Ether lipid and sphingolipid expression patterns are G-protein coupled estrogen receptor 1-dependently altered in breast cancer cells
Authors: Hahnefeld Lisa , Gruber Lisa , Schömel Nina , Fischer Caroline , Mattjus Peter , Gurke Robert , Beretta Martina , Ferreirós Nerea , Geisslinger Gerd , Wegner Marthe-Susanna
Published: July 2020

Identifying co-expression of lipid species is challenging, but indispensable to identify novel therapeutic targets for breast cancer treatment. Lipid metabolism is often dysregulated in cancer cells, and changes in lipid metabolism affect cellular processes such as proliferation, autophagy, and tumor development. In addition to mRNA analysis of sphingolipid metabolizing enzymes, we performed liquid chromatography time-of-flight mass spectrometry analysis in three breast cancer cell lines. These breast cancer cell lines differ in estrogen receptor and G-protein coupled estrogen receptor 1 status. Our data show that sphingolipids and non-sphingolipids are strongly increased in SKBr3 cells. SKBr3 cells are estrogen receptor negative and G-protein coupled estrogen receptor 1 positive. Treatment with G15, a G-protein coupled estrogen receptor 1 antagonist, abolishes the effect of increased sphingolipid and non-sphingolipid levels in SKBr3 cells. In particular, ether lipids are expressed at much higher levels in cancer compared to normal cells and are strongly increased in SKBr3 cells. Our analysis reveals that this is accompanied by increased sphingolipid levels such as ceramide, sphingadiene-ceramide and sphingomyelin. This shows the importance of focusing on more than one lipid class when investigating molecular mechanisms in breast cancer cells. Our analysis allows unbiased screening for different lipid classes leading to identification of co-expression patterns of lipids in the context of breast cancer. Co-expression of different lipid classes could influence tumorigenic potential of breast cancer cells. Identification of co-regulated lipid species is important to achieve improved breast cancer treatment outcome.

Highlights

LC-HRMS analysis allows identification of co-expression between lipid classes

Putative co-expression of sphingolipid and non-sphingolipid classes

Ether lipids are strongly upregulated in SKBr3 cells (ER negative, GPER1 positive)
S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit
Authors: Nguyen-Contant Phuong , Embong A. Karim , Kanagaiah Preshetha , Chaves Francisco A. , Yang Hongmei , Branche Angela R. , Topham David J. , Sangster Mark Y.
Published: July 2020

The high susceptibility of humans to SARS-CoV-2 infection, the cause of COVID-19, reflects the novelty of the virus and limited preexisting B cell immunity. IgG against the SARS-CoV-2 spike (S) protein, which carries the novel receptor binding domain (RBD), is absent or at low levels in unexposed individuals. To better understand the B cell response to SARS-CoV-2 infection, we asked whether virus-reactive memory B cells (MBCs) were present in unexposed subjects and whether MBC generation accompanied virus-specific IgG production in infected subjects. We analyzed sera and PBMCs from non-SARS-CoV-2-exposed healthy donors and COVID-19 convalescent subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD and S2 subunit, and nucleocapsid [N]) and non-SARS-CoV-2 proteins were related to measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Most unexposed subjects had anti-S2 IgG and a minority had anti-N IgG, but IgG MBCs with these specificities were not detected, perhaps reflecting low frequencies. Convalescent subjects had high levels of IgG against the RBD, S2, and N, together with large populations of RBD- and S2-reactive IgG MBCs. Notably, IgG titers against the S protein of the human coronavirus OC43 in convalescent subjects were higher than in unexposed subjects and correlated strongly with anti-S2 titers. Our findings indicate cross-reactive B cell responses against the S2 subunit that might enhance broad coronavirus protection. Importantly, our demonstration of MBC induction by SARS-CoV-2 infection suggests that a durable form of B cell immunity is maintained even if circulating antibody levels wane.

IMPORTANCE

Recent rapid worldwide spread of SARS-CoV-2 has established a pandemic of potentially serious disease in the highly susceptible human population. Key questions are whether humans have preexisting immune memory that provides some protection against SARS-CoV-2 and whether SARS-CoV-2 infection generates lasting immune protection against reinfection. Our analysis focused on pre- and post-infection IgG and IgG memory B cells (MBCs) reactive to SARS-CoV-2 proteins. Most importantly, we demonstrate that infection generates both IgG and IgG MBCs against the novel receptor binding domain and the conserved S2 subunit of the SARS-CoV-2 spike protein. Thus, even if antibody levels wane, long-lived MBCs remain to mediate rapid antibody production. Our study also suggests that SARS-CoV-2 infection strengthens preexisting broad coronavirus protection through S2-reactive antibody and MBC formation.