bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct cryo-EM Structure of α-synuclein Filaments derived by Tau
Authors: Hojjatian Alimohammad , Dasari Anvesh K. R. , Sengupta Urmi , Taylor Dianne , Daneshparvar Nadia , Yeganeh Fatemeh Abbasi , Dillard Lucas , Michael Brian , Griffin Robert G. , Borgnia Mario , Kayed Rakez , Taylor Kenneth A. , Lim Kwang Hun
Published: January 2021

Recent structural studies of ex vivo amyloid filaments extracted from human patients demonstrated that the ex vivo filaments associated with different disease phenotypes adopt diverse molecular conformations distinct from those in vitro amyloid filaments. A very recent cryo-EM structural study also revealed that ex vivo α-synuclein filaments extracted from multiple system atrophy (MSA) patients adopt quite distinct molecular structures from those of in vitro α-synuclein filaments, suggesting the presence of co-factors for α-synuclein aggregation in vivo. Here, we report structural characterizations of α-synuclein filaments derived by a potential co-factor, tau, using cryo-EM and solid-state NMR. Our cryo-EM structure of the tau-promoted α-synuclein filament at 4.0 Å resolution is somewhat similar to one of the polymorphs of in vitro α-synuclein filaments. However, the N- and C-terminal regions of the tau-promoted α-synuclein filament have different molecular conformations. Our structural studies highlight the conformational plasticity of α-synuclein filaments, requiring additional structural investigation of not only more ex vivo α-synuclein filaments, but also in vitro α-synuclein filaments formed in the presence of diverse co-factors to better understand molecular basis of diverse molecular conformations of α-synuclein filaments.
A Nanoceutical Agent for Chemoprevention of Bilirubin Encephalopathy
Authors: Adhikari Aniruddha , Bhutani Vinod K , Mondal Susmita , Das Monojit , Darbar Soumendra , Ghosh Ria , Polley Nabarun , Das Anjan Kumar , Bhattacharya Siddhartha Sankar , Pal Debasish , Mallick Asim Kumar , Pal Samir Kumar
Published: January 2021

Background

Targeted degradation of bilirubinin vivomay enable safer and more effective approach to manage incipient bilirubin encephalopathy consequent to severe neonatal hyperbilirubinemia (SNH). This report builds on the use of a spinel structured mixed-valence transition metal oxide (trimanganese tetroxide) nanoparticle duly functionalized with biocompatible ligand citrate (C-Mn3O4NP) having the ability to degrade bilirubin without photo-activation.

Method

The efficiency of C-Mn3O4NP inin vivodegradation of serum bilirubin and amelioration of severe bilirubin encephalopathy and associated neurobehavioral changes was evaluated in C57BL/6j animal model of SNH.

Results

Oral single dose (0.25 mg kg-1body weight) of the NPs efficiently reduced serum bilirubin levels (both conjugated and unconjugated) in study mice. It prevents bilirubin-induced neurotoxicity with reduction of SNH as observed by neurobehavioral and movement studies of SNH-mice. Pharmacokinetic data suggests intestinal reabsorption of the NPs and explain sustainable action. Biodistribution, pharmacokinetics, and biocompatibility of the NPs were tested during sub-chronic exposure.

Conclusion

Thus, we report preliminary studies that explore an affordable chemoprevention mechanism to acutely prevent or minimize bilirubin neurotoxicity in newborn infants.

IMPACT STATEMENT

Despite several attempts, no pharmaco-therapeutics are available for the treatment of severe neonatal hyperbilirubinemia (SNH) and associated neurotoxicity.

Our newly developed nanodrug, citrate functionalized Mn3O4nanoparticles (C-Mn3O4NPs), can efficiently ameliorate SNH and associated neurotoxicity as investigated in preclinical rodent model.

Chemoprevention effect of the nanodrug is found to be safe and sustainable.

If successfully translated into clinical trials, C-Mn3O4NPs could become the first drug to treat SNH.
Identification of Discriminative Gene-level and Protein-level Features Associated with Gain-of-Function and Loss-of-Function Mutations
Authors: Bayrak Cigdem S. , Jain Aayushee , Stein David , Chaudhary Kumardeep , Nadkarni Girish N. , Van Vleck Tielman , Puel Anne , Boisson-Dupuis Stephanie , Okada Satoshi , Stenson Peter D. , Cooper David N. , Schlessinger Avner , Itan Yuval
Published: January 2021

Identifying whether a given genetic mutation results in a gene product with increased (gain-of-function; GOF) or diminished (loss-of-function; LOF) activity is an important step toward understanding disease mechanisms as they may result in markedly different clinical phenotypes. Here, we generated the first extensive database of all currently known germline GOF and LOF pathogenic mutations by employing natural language processing (NLP) on the available abstracts in theHuman Gene Mutation Database. We then investigated various gene- and protein-level features of GOF and LOF mutations by applying machine learning and statistical analyses to identify discriminative features. We found that GOF mutations were enriched in essential genes, autosomal dominant inheritance, protein binding and interaction domains, whereas LOF mutations were enriched in singleton genes, protein-truncating variants, and protein core regions. We developed a user-friendly web-based interface that enables the extraction of selected subsets from the GOF/LOF database by a comprehensive set of annotated features, and downloading up-to-date versions (https://itanlab.shinyapps.io/goflof/). These results could ultimately improve our understanding of how mutations affect gene/protein function thereby guiding future treatment options.
Structured illumination microscopy artifacts caused by illumination scattering
Authors: Mo Yanquan , Feng Fan , Mao Heng , Fan Junchao , Chen Liangyi
Published: January 2021

Despite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artifacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index (RI) from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artifacts caused by scattering in thick samples.
Deciphering how naturally occurring sequence features impact the phase behaviors of disordered prion-like domains
Authors: Bremer Anne , Farag Mina , Borcherds Wade M. , Peran Ivan , Martin Erik W. , Pappu Rohit V. , Mittag Tanja
Published: January 2021

Phase separation of intrinsically disordered prion-like low-complexity domains (PLCDs) derived from RNA-binding proteins enable the formation of biomolecular condensates in cells. PLCDs have distinct amino acid compositions, and here we decipher the physicochemical impact of conserved compositional biases on the driving forces for phase separation. We find that tyrosine residues make for stronger drivers of phase separation than phenylalanine. Depending on their sequence contexts, arginine residues enhance or weaken phase separation, whereas lysine residues weaken cohesive interactions within PLCDs. Increased net charge per residue (NCPR) weakens the driving forces for phase separation of PLCDs and this effect can be modeled quantitatively. The effects of NCPR also weaken known correlations between the dimensions of single chains in dilute solution and the driving forces for phase separation. We build on experimental data to develop a coarse-grained model for accurate simulations of phase separation that yield novel insights regarding PLCD phase behavior.
POT1 Stability and Binding Measured by Fluorescence Thermal Shift Assays
Authors: DeLeeuw Lynn W. , Monsen Robert C. , Petrauskas Vytautas , Gray Robert D. , Baranauskiene Lina , Matulis Daumantas , Trent John O. , Chaires Jonathan B.
Published: January 2021

The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 – DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.
Viral competence data improves rodent reservoir predictions for American orthohantaviruses
Authors: Mull Nathaniel , Carlson Colin J. , Forbes Kristian M. , Becker Daniel J.
Published: January 2021

Identifying reservoir host species is crucial for understanding the risk of pathogen spillover from wildlife to people. Orthohantaviruses are zoonotic pathogens primarily carried by rodents that cause the diseases hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS) in humans. Given their diversity and abundance, many orthohantaviruses are expected to be undiscovered, and several host relationships remain unclear, particularly in the Americas. Despite the increasing use of predictive models for understanding zoonotic reservoirs, explicit comparisons between different evidence types for demonstrating host associations, and relevance to model performance in applied settings, have not been previously made. Using multiple machine learning methods, we identified phylogenetic patterns in and predicted unidentified reservoir hosts of New World orthohantaviruses based on evidence of infection (RT-PCR data) and competence (live virus isolation data). Infection data were driven by phylogeny, unlike competence data, and boosted regression tree (BRT) models using competence data displayed higher accuracy and a narrower list of predicted reservoirs than those using infection data. Eight species were identified by both BRT models as likely orthohantavirus hosts, with a total of 98 species identified by our infection models and 14 species identified by our competence models. Hosts predicted by competence models are concentrated in the northeastern United States (particularlyMyodes gapperiandReithrodontomys megalotis) and northern South America (several members of tribe Oryzomyini) and should be key targets for empirical monitoring. More broadly, these results demonstrate the value of infection competence data for predictive models of zoonotic pathogen hosts, which can be applied across a range of settings and host-pathogen systems.

Author Summary

Human diseases with wildlife origins constitute a significant risk for human health. Orthohantaviruses are viruses found primarily in rodents that cause disease with high rates of mortality and other complications in humans. An important step in disease prevention is to identify which rodent species carry and transmit orthohantaviruses. By incorporating species relatedness and evidence of different levels of host capacity to be infected and transmit virus, we used predictive modeling to determine unidentified rodent hosts of orthohantaviruses. Models using host competence data outperformed models using host infection data, highlighting the importance of stronger data in model optimization. Our results highlighted roughly a dozen key target species to be monitored that are concentrated in two geographic regions—northeastern United States and northern South America. More broadly, the approaches used in this study can be applied to a variety of other host-pathogen systems that threaten public health.
The histologic phenotype of lung cancers may be driven by transcriptomic features rather than genomic characteristics
Authors: Tang Ming , Abbas Hussein A , Negrao Marcelo Vailati , Ramineni Maheshwari , Hu Xin , Fujimoto Junya , Reuben Alexdrandre , Varghese Susan , Zhang Jianhua , Li Jun , Chow Chi-Wan , Mao Xizeng , Song Xingzhi , Lee Won-chul , Wu Jia , Little Latasha , Gumbs Curtis , Behrens Carmen , Moran Cesar , Weissferdt Annikka , Lee J.Jack , Sepesi Boris , Swisher Stephen , Heymach John V. , Wistuba Ignacio I. , Futreal P. Andrew , Kalhor Neda , Zhang Jianjun
Published: January 2021

Histology plays an essential role in therapeutic decision-making for lung cancer patients. However, the molecular determinants of lung cancer histology are largely unknown. We conducted whole-exome sequencing(WES) and microarray profiling on 19 micro-dissected tumor regions of different histologic subtypes from 9 patients with lung cancers of mixed histology. A median of 68.9% of point mutations and 83% of copy number aberrations were shared between different histologic components within the same tumors. Furthermore, different histologic components within the tumors demonstrated similar subclonal architecture. On the other hand, transcriptomic profiling revealed shared pathways between the same histologic subtypes from different patients, which was supported by the analyses of the transcriptomic data from 141 cell lines and 343 lung cancers of different histologic subtypes. These data suggest that histology of lung cancers may be determined at the transcriptomic level rather than the genomic level.
Testing the efficacy of hyperspectral (AVIRIS-NG), multispectral (Sentinel-2) and radar (Sentinel-1) remote sensing images to detect native and invasive non-native trees
Authors: Arasumani M , Singh Aditya , Bunyan Milind , Robin V.V.
Published: January 2021

Invasive alien species (IAS) threaten tropical grasslands and native biodiversity and impact ecosystem service delivery, ecosystem function, and associated human livelihoods. Tropical grasslands have been dramatically and disproportionately lost to invasion by trees. The invasion continues to move rapidly into the remaining fragmented grasslands impacting various native grassland-dependent species and water streamflow in tropical montane habitats. The Shola Sky Islands of the Western Ghats host a mosaic of native grasslands and forests; of which the grasslands have been lost to exotic tree invasion (Acacias, Eucalyptus and Pines) since the 1950s. The invasion intensities, however, differ between these species whereinAcacia mearnsiiandPinus patulaare highly invasive in contrast toEucalyptus globulus. These disparities necessitate distinguishing these species for effective grassland restoration. Further, these invasive alien trees are highly intermixed with native species, thus requiring high discrimination abilities to native species apart from the non-native species.

Here we assess the accuracy of various satellite and airborne remote sensing sensors and machine learning classification algorithms to identify the spatial extent of native habitats and invasive trees. Specifically, we test Sentinel-1 SAR and Sentinel-2 multispectral data and assess high spatial and spectral resolution AVIRIS-NG imagery identifying invasive species across this landscape. Sensor combinations thus include hyperspectral, multispectral and radar data and present tradeoffs in associated costs and ease of procurement. Classification methods tested include Support Vector Machine (SVM), Classification and Regression Trees (CART) and Random Forest (RF) algorithms implemented on the Google Earth Engine platform. Results indicate that AVIRIS-NG data in combination with SVM recover the highest classification skill (Overall −98%, Kappa-0.98); while CART and RF yielded < 90% accuracy. Fused Sentinel-1 and Sentinel-2 produce 91% accuracy, while Sentinel-2 alone yielded 91% accuracy with RF and SVM classification; but only with higher coverage of ground control points. AVIRIS-NG imagery was able to accurately (97%) demarcate the Acacia invasion front while Sentinel-1 and Sentinel-2 data failed. Our results suggest that Sentinel-2 images could be useful for detecting the native and non-native forests with more ground truth points, but hyperspectral data (AVIRIS-NG) permits distinguishing, native and non-native tree species and recent invasions with high precision using limited ground truth points. We suspect that large areas will have to be mapped and assessed in the coming years by conservation managers, NGOs to plan restoration, or to assess the success of restoration activities, and several data procurement and analysis steps may have to be simplified.
A conserved HSF:miR169:NF-YA loop involved in tomato and Arabidopsis heat stress tolerance
Authors: Rao Sombir , Jha Sarita , Bansal Chandni , Gupta Apoorva , Sorin Celine , Crespi Martin , Mathur Saloni
Published: January 2021

Regulatory feedbacks are at the basis of different stress and developmental networks in plants. Here, we report that tomato and Arabidopsis plants improve their heat stress tolerance through Heat stress transcription factor (HSF)-mediated transcriptional regulation ofMIR169and post-transcriptional regulation ofNF-YAtranscription factors. We show that HSFs recognize tomato and ArabidopsisMIR169promoters using yeast-one-hybrid/ChIP-qPCR. Silencing tomato HSFs using virus-induced-gene-silencing (VIGS) reduceSly-MIR169levels and enhanceSly-NF-YA9/A10target expression. Further, tomato transgenic plants overexpressingSly-MIR169andSly-NF-YA9/A10-VIGSknock-down tomato plants as well as Arabidopsis plants overexpressingAt-MIR169dandAt-nf-ya2mutants showed a link with increased heat tolerance. In contrast, Arabidopsis plants overexpressingAt-NF-YA2,or those expressing a non-cleavableAt-NF-YA2form (miR169-resistantAt-NF-YA2) as well as plants inhibited for At-miRNA169d regulation (miR169d mimic plants) were more sensitive to heat stress, highlightingNF-YAas negative regulator of heat tolerance. Furthermore, post-transcriptional cleavage ofNF-YAby elevated miR169 levels result in alleviating the repression of heat stress effectors HSFA7a/b in tomato and Arabidopsis revealing a retroactive control of HSFs by the miR169:NF-YA node. Hence, a regulatory feedback loop involving HSFs, miR169s and NF-YAs plays a critical role in the regulation of heat stress response in tomato and Arabidopsis plants.
COVID-19 Pandemic and Behavioural Response to Self-Medication Practice in Western Uganda
Authors: Dare Samuel S. , Eze Ejike Daniel , Isaac Echoru , Usman Ibe Michael , Ssempijja Fred , Bukenya Edmund Eriya , Ssebuufu Robinson
Published: January 2021

Background

Self-medication has become is a serious public health problem globally posing great risks, especially with the increasing number of cases of COVID-19 disease in Uganda. This is may be partly because of the absence of a recognized treatment for the disease, however, the prevalence and nature differ from country to country which may influence human behavioural responses.

Aim

This study aimed to investigated the beharioural response of the community towards self- medication practices during this COVID-19 pandemic and lockdown.

Methods

A cross sectional household and online survey was conducted during the months of June-to- August. The study was conducted among adult between age 18 above in communities of western Uganda who consented to participate in the study. Study participants were selected using a convenience sampling technique and sampling was done by sending a structured online questionnaire via Google forms and a printed copies questionnaire made available to other participants that did not use the online questionnaire

Results

The percentage of respondents that know about self-medication is (97%) and those that practice self-medication are approximately (88%). 97% of respondents have heard about self-medication either through health workers, media, family members, friends and/or school while 3% said they have not heard about self-medication. The percentage of respondents who practiced self- medication during COVID-19 pandemic is 57% while those that did not is 43%. There is statistically difference in the number of those that practice self-medication and those that do not p < 0.005 at 95% confidence interval. Also there was a statistically significant decrease in the number of respondents that practice self-medication during COVID-19 pandemic lockdown compare to the practice before the pandemic lockdown p < 0.05 at 95% confidence interval.

Conclusion

Our investigation showed adequate knowledge of self-medication and high level of self- medication practice with a decrease in self-medication practices during the COVID-19 pandemic lockdown compared to the practice before the lockdown.
Can Catastrophe Theory explain expansion and contagious of Covid-19?
Authors: Leonel Caetano Marco Antonio
Published: January 2021

Since SARS-Cov-2 started spreading in China and turned into a pandemic disease called Covid-19, many articles about prediction with mathematical model have appeared in the literature. In addition to models in specialized journals, a significant amount of software was made available, presenting with dashboards spreading of the pandemic for each new. These models are solved by computer simulation of traditional exponential models as a representation of the growth of cases and deaths. Some more accurate models are based on existing variations of SIR model (Susceptible, Infected and Recovered). A third class of study is developed in spatial or probabilistic models as a way of forecasting the effect of Covid-19 around the world. Data on the number of positive cases in all countries, show that SARS-Cov-2 shows great resistance even after strategies of lockdown or social distancing. The purpose of this article is to show how the bifurcation theory, known as Catastrophe Theory, can help to understand why Covid-19 expansion rates change so much and even with low values for a longtime trigger contagion quickly and abruptly.

The Catastrophe Theory was conceived by the mathematician René Thom in the 60s with wide applications in works in the 70s. The outbreak of spruce budworm in Canada revealed a very interesting opportunity to test Catastrophe Theory whose explanation for the phenomenon was widely debated in the academic world. Inspired by the same mathematical approach to this phenomenon in Canada in the 1970s, we applied the Catastrophe Theory in the current Covid-19 pandemic. We observed that sudden outbreaks occur when the carrying capacity and the rate of expansion of the virus reach a region of bifurcation on the cusp surface. With actual Covid-19 data obtained from WHO, we fitted the dynamic model using the particle swarm technique and compared the results in the bifurcation plan with the Covid-19 outbreaks in different regions of the world. It is possible in many cases to observe the trajectory of the parameters between limit points in the bistable region and the consequent explosion of cases observed for each country assessed.
Knowledge, attitude and practice toward COVID-19 among healthcare workers in public health facilities, Eastern Ethiopia
Authors: Farah Alinoor Mohamed , Nour Tahir Yousuf , Obsiye Muse , Adan Mowlid Aqil , Ali Omar Moeline , Hussein Muktar Arab , Budul Abdullahi Bedel , Omer Muktar , Getnet Fentabil
Published: January 2021

On 13 March 2020, Ethiopia reported the first confirmed case of COVID-19 in Addis Ababa. COVID-19 is likely to overwhelm an already fragile health-care delivery system and reduce the availability of services for endemic health concerns such as malaria and diarrheal diseases.

Cross sectional study was conducted on heath care workers in three public health facilities in Somali region to assess knowledge, attitude and practice towards COVID-19. T-test and ANOVA were used to analyze the relationship between the dependent, and independent variables. Spearman’s correlation was used to assess the relationship between mean knowledge and attitude scores.

A vast majority of the participants were male (n = 293, 67.5%), with a mean age of 27.6 (SD: 5.3) years. The mean knowledge score was 13.7 (SD: 2.6) and the mean attitude score 10.5 (SD: 4.1). Only 45.2 % (n = 196) of the participants had a good attitude toward COVID-19. There was a negative correlation between knowledge scores, attitude scores (r=-0.295, P<0.001) and practice (r=-0.298, P<0.001).

The overall level of knowledge was good. However, the attitude and practice were relatively low. We recommend strategies for enhancing the capacity of healthcare workers to develop positive attitude and practice.
Real-World Clinical Performance of the Abbott Panbio with Nasopharyngeal, Throat and Saliva Swabs Among Symptomatic Individuals with COVID-19
Authors: Stokes William , Berenger Byron M. , Portnoy Danielle , Scott Brittney , Szelewicki Jonas , Singh Takshveer , Venner Allison A. , Turnbull LeeAnn , Pabbaraju Kanti , Shokoples Sandy , Wong Anita A. , Gill Kara , Guttridge Tracy , Proctor Dustin , Hu Jia , Tipples Graham
Published: January 2021

BACKGROUND

Point of Care Testing (POCT) SARS-CoV-2 antigen tests, such as the Abbott Panbio, have great potential to help combat the COVID-19 pandemic. The Panbio is Health Canada approved for the detection of SARS-CoV-2 in symptomatic individuals within the first 7 days of COVID-19 symptom onset(s).

METHODS

Symptomatic adults recently diagnosed with COVID-19 in the community were recruited into the study. Paired nasopharyngeal (NP), throat, and saliva swabs were collected, with one paired swab tested immediately with the Panbio, and the other transported in universal transport media and tested using reverse-transcriptase polymerase chain reaction (RT-PCR). Positive percent agreement (PPA) was calculated. Subsequently, individuals within 7 days of symptom onset who presented to community assessment centres for SARS-CoV-2 testing had Panbio testing completed and paired with RT-PCR results from parallel NP or throat swabs.

RESULTS

145 individuals were included in the study. Collection of throat and saliva was stopped early due to poor performance (throat PPA 57.7%, n=61, and saliva PPA 2.6%, n=41). NP swab PPA was 87.7% [n=145, 95% confidence interval 81.0% - 92.7%]. There were 1,641 symptomatic individuals tested by Panbio in community assessment centres, with 268/1641 (16.3%) positive for SARS-CoV-2. There were 37 false negatives, corresponding to a PPA of 86.2% [81.5% - 90.1%].

CONCLUSIONS

The Panbio test reliably detects most cases of SARS-CoV-2 from adults in the POCT community setting presenting within 7 days of symptom onset using nasopharyngeal swabs. Throat and saliva swabs are not reliable specimens for the Panbio.
Diagnostic performance and clinical implications of rapid SARS-CoV-2 antigen testing in Mexico using real-world nationwide COVID-19 registry data
Authors: Bello-Chavolla Omar Yaxmehen , Antonio-Villa Neftali Eduardo , Fernández-Chirino Luisa , Guerra Enrique C. , Fermín-Martínez Carlos A. , Márquez-Salinas Alejandro , Vargas-Vázquez Arsenio , Bahena-López Jessica Paola
Published: January 2021

BACKGROUND

SARS-CoV-2 testing capacity is important to monitor epidemic dynamics and as a mitigation strategy. Given difficulties of large-scale quantitative reverse transcription polymerase chain reaction (qRT-PCR) implementation, rapid antigen tests (Rapid Ag-T) have been proposed as alternatives in settings like Mexico. Here, we evaluated diagnostic performance of Rapid Ag-T for SARS-CoV-2 infection and its associated clinical implications compared to qRT-PCR testing in Mexico.

METHODS

We analyzed data from the COVID-19 registry of the Mexican General Directorate of Epidemiology up to April 30th, 2021 (n=6,632,938) and cases with both qRT-PCR and Rapid Ag-T (n=216,388). We evaluated diagnostic performance using accuracy measures and assessed time-dependent changes in the Area Under the Receiver Operating Characteristic curve (AUROC). We also explored test discordances as predictors of hospitalization, intubation, severe COVID-19 and mortality.

RESULTS

Rapid Ag-T is primarily used in Mexico City. Rapid Ag-T have low sensitivity 37.6% (95%CI 36.6-38.7), high specificity 95.5% (95%CI 95.1-95.8) and acceptable positive 86.1% (95%CI 85.0-86.6) and negative predictive values 67.2% (95%CI 66.2-69.2). Rapid Ag-T has optimal diagnostic performance up to days 3 after symptom onset, and its performance is modified by testing location, comorbidity, and age. qRT-PCR (-) / Rapid Ag-T (+) cases had higher risk of adverse COVID-19 outcomes (HR 1.54 95% CI 1.41-1.68) and were older, qRT-PCR (+)/ Rapid Ag-T(-) cases had slightly higher risk or adverse outcomes and ≥7 days from symptom onset (HR 1.53 95% CI 1.48-1.59). Cases detected with rapid Ag-T were younger, without comorbidities, and milder COVID-19 course.

CONCLUSIONS

Rapid Ag-T could be used as an alternative to qRT-PCR for large scale SARS-CoV-2 testing in Mexico. Interpretation of Rapid Ag-T results should be done with caution to minimize the risk associated with false negative results.
Production and assessment of monoclonal antibodies against the SpyCas9 protein ofStreptococcus pyogenes
Authors: Park Mi-Jin , Park Jongjin , Park Slki , Choe Sunghwa
Published: January 2021

The biotechnological applications of the programmable DNA-cleaving enzymes known as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) continue to expand from agricultural trait development to therapeutic gene therapies. The Cas9 CRISPR system isolated fromStreptococcus pyogenes(SpyCas9) is classified as class II, which is popular due to high efficiency and robustness. Antibodies that specifically detect SpyCas9 could expand the applicability of this enzyme. Here, we report on the development of monoclonal antibodies against SpyCas9. Four hybridoma cells were selected for their expression of anti-SpyCas9. Hybridoma supernatant contained reactive and highly specific antibodies to SpyCas9. Anti-SpyCas9 antibody was purified and was non-selective against six other bacterial Cas9 proteins. SpyCas9 protein could be detected in HEK293T cells in decreasing amounts over a 48 hour period, indicating the antibody could be used to detect residual levels of SpyCas9 remaining following cell treatment with a CRISPR/SpyCas9 system. The anti-SpyCas9 antibody may help researchers facilitate Cas9 for further study for the use of techniques such as enzyme-linked immunosorbent assays (ELISAs), western blot, immunoprecipitation, and immunohistochemical staining.
A metagenomic-based study of two sites from the Barbadian reef system
Authors: Simpson S , Bettauer V , Ramachandran A , Kramer S , Mahon S , Medina M , Valles Y , Dumeaux V , Valles H , Walsh D , Hallett MT
Published: January 2021

We study the microbiome of sea water collected from two locations of the Barbadian coral reefs. The two sites differ in several environmental and ecological variables including their endogenous benthic community in addition to their proximity to urban development and runoffs from inland watersheds. The composition of the microbial community was estimated using whole genome DNA shotgun sequencing. Although both sites exhibit a similar degree of richness, the less urbanized site (Maycocks reef at Hangman’s Bay) is strongly concentrated with phototrophs. In comparison, the more urbanized location (Bellairs Research Institute) is enriched for copiotrophs, macroalgal symbionts and marine-related disease-bearing organisms from taxa scattered across the tree of life. Overall, our samples and associated measurements of chemical and environmental qualities of the water are in line with previous marine microbiome profiles of warm ocean surface waters. This suggests our approach captures salient information regarding the state of each coral reef site and sets the stage for larger longitudinal studies of coral reef dynamics in Barbados.
Graph Signal Processing on protein residue networks helps in studying its biophysical properties
Authors: Srivastava Divyanshu , Bagler Ganesh , Kumar Vibhor
Published: January 2021

Understanding the physical and chemical properties of proteins is vital, and many efforts have been made to study the emergent properties of the macro-molecules as a combination of long chains of amino acids. Here, we present a graph signal processing based approach to model the biophysical property of proteins. For each protein inter-residue proximity-based network is used as basis graph and the respective amino acid properties are used as node-signals. Signals on nodes are decomposed on network’s Laplacian eigenbasis using graph Fourier transformations. We found that the intensity in low-frequency components of graph signals of residue features could be used to model few biophysical properties of proteins. Specifically, using our approach, we could model protein folding-rate, globularity and fraction of alpha-helices and beta-sheets. Our approach also allows amalgamation of different types of chemical and graph theoretic properties of residue to be used together in a multi-variable regression model to predict biophysical properties.
Spike protein disulfide disruption as a potential treatment for SARS-CoV-2
Authors: Grishin Andrey M. , Dolgova Nataliya V. , Harms Shelby , Pickering Ingrid J. , George Graham N. , Falzarano Darryl , Cygler Miroslaw
Published: January 2021

The coronaviral pandemic is exerting a tremendously detrimental impact on global health, quality of life and the world economy, emphasizing the need for effective medications for current and future coronaviral outbreaks as a complementary approach to vaccines. The Spike protein, responsible for cell receptor binding and viral internalization, possesses multiple disulfide bonds raising the possibility that disulfide-reducing agents might disrupt Spike function, prevent viral entry and serve as effective drugs against SARS-CoV-2. Here we show the first experimental evidence that reagents capable of reducing disulfide bonds can inhibit viral infection in cell-based assays. Molecular dynamics simulations of the Spike receptor-binding domain (RBD) predict increased domain flexibility when the four disulfide bonds of the domain are reduced. This flexibility is particularly prominent for the surface loop, comprised of residues 456-490, which interacts with the Spike cell receptor ACE2. Consistent with this finding, the addition of exogenous disulfide bond reducing agents affects the RBD secondary structure, lowers its melting temperature from 52 to 36-39°C and decreases its binding affinity to ACE2 by two orders of magnitude at 37°C. Finally, the reducing agents dithiothreitol (DTT) and tris(2-carboxyethyl)phosphine (TCEP) inhibit viral replication at high µM – low mM levels with a negligible effect on cell viability at these concentrations. The antiviral effect of monothiol-based reductants N-Acetyl-L-cysteine (NAC) and reduced glutathione (GSH) was not observed due to decreases in cell viability. Our research demonstrates the clear potential for medications that disrupt Spike disulfides as broad-spectrum anticoronaviral agents and as a first-line defense against current and future outbreaks.
Synonymous Mutation Generator: a web tool for designing RNAi-resistant sequences
Authors: Ong Joseph Y.
Published: January 2021

RNA interference (RNAi) is a useful technique for knocking down a protein of interest, allowing for the study of the function of a gene product. However, RNAi techniques are prone to off-target effects, such as non-specific knockdown of genes besides the protein of interest. An important control and companion to RNAi knockdown experiments is the rescue experiment, wherein gene function is restored by expression of an RNAi-resistant construct of the protein of interest. Generating an RNAi-resistant construct of the protein of interest involves generating silent mutations within the coding sequence of the protein so that the resulting amino acid product is the same, but the protein mRNA is no longer a target for the RNAi. Here, Synonymous Mutation Generator, a Python-based web tool that takes an input DNA coding sequence and outputs a synonymous DNA coding sequence that is RNAi-resistant, is described. This web tool should be a useful resource for researchers cloning RNAi-resistant constructs. Synonymous Mutation Generator is easy to use and can be found atjong2.pythonanywhere.com, and the source code is available on GitHub.
SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection
Authors: Havervall Sebastian , Falk August Jernbom , Klingström Jonas , Ng Henry , Greilert-Norin Nina , Gabrielsson Lena , Salomonsson Ann-Christin , Isaksson Eva , Rudberg Ann-Sofie , Hellström Cecilia , Andersson Eni , Olofsson Jennie , Skoglund Lovisa , Yousef Jamil , Pin Elisa , Christ Wanda , Olausson Mikaela , Hedhammar My , Tegel Hanna , Mangsbo Sara , Phillipson Mia , Månberg Anna , Hober Sophia , Nilsson Peter , Thålin Charlotte
Published: January 2021

Current SARS-CoV-2 serological assays generate discrepant results, and the longitudinal characteristics of antibodies targeting various antigens after asymptomatic to mild COVID-19 are yet to be established. This longitudinal cohort study including 1965 healthcare workers, of which 381 participants exhibited antibodies against the SARS-CoV-2 spike antigen at study inclusion, reveal that these antibodies remain detectable in most participants, 96%, at least four months post infection, despite having had no or mild symptoms. Virus neutralization capacity was confirmed by microneutralization assay in 91% of study participants at least four months post infection. Contrary to antibodies targeting the spike protein, antibodies against the nucleocapsid protein were only detected in 80% of previously anti-nucleocapsid IgG positive healthcare workers. Both anti-spike and anti-nucleocapsid IgG levels were significantly higher in previously hospitalized COVID-19 patients four months post infection than in healthcare workers four months post infection (p=2*10−23 and 2*10−13 respectively). Although the magnitude of humoral response was associated with disease severity, our findings support a durable and functional humoral response after SARS-CoV-2 infection even after no or mild symptoms. We further demonstrate differences in antibody kinetics depending on the antigen, arguing against the use of the nucleocapsid protein as target antigen in population-based SARS-CoV-2 serological surveys.
What is the value of community oximetry monitoring in people with SARS-CoV-2? – A prospective, open-label clinical study
Authors: Wilcock Jane , Grafton-Clarke Ciaran , Coulson Tessa
Published: January 2021

Background

In people with COVID-19, hypoxia at the time of admission is known to be related to mortality. Monitoring of oxygen saturations (SpO2) is therefore an increasingly common part of community-based care, with the aim of improving the identification of adults who are deteriorating. We set out to investigate whether rigid SpO2 triggers, or absolute change in SpO2, is more indicative of deterioration in COVID-19.

Methods

A prospective, uncontrolled, open-label study in a large UK general practice was conducted between May and November 2020. Participants recorded twice daily oximetry and symptom diary for 14 days after test-confirmed COVID-19. Primary outcomes were the proportion of people whose SpO2 dropped to ≤ 94% and ≤ 92%, the average maximum reduction in SpO2, and admission to hospital. We also investigated the relationship between MRC Dyspnoea scale, modified Roth score, and SpO2 through correlation analyses.

Results

52 participants were recruited, following which 41 participants completed the study. The average age was 45.9 years with 63.4% identifying as female. The mean maximum reduction in SpO2 was 2.8%. The average time to maximum reduction in SpO2 was 6.4 days. Nine participants (22.0%) had a reduction in SpO2 to ≤94%. Three of these had a reduction in SpO2 to ≤92%, for which all three were admitted to hospital. Modified Roth score and SpO2 were weakly positively correlated (.31). MRC dyspnoea scale score and SpO2 were moderately negatively correlated (-.53).

Conclusions

A reduction in SpO2 to ≤92% was found to be highly predictive for admission to hospital. Modified Roth score or MRC dyspnoea scale scores should not be used as proxy measures for oximetry. This study contributes to the ongoing narrative around community-based oximetry and provides insight and recommendations for those currently engaging in or planning to roll out similar schemes.

Strengths and limitations of this study

This study is pragmatically designed to answer an important clinical question in primary care.

This study focused on previously published values of SpO2 for triggering escalation of care and therefore provides answers based on current clinical practice.

11 of the 52 patients who were recruited into the study did not return their oximeter or oximetry diary at the end of the study period.

We did not validate the accuracy or reliability of the oximetry / symptom diaries, as these were self-completed by the participants themselves.

Other than admission to hospital and mortality within the study period, no other clinical outcomes have been recorded.

Funding statement

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

Competing interests

Jane Wilcock has no competing interests to declare.

Ciaran Grafton-Clarke has no competing interests to declare.

Tessa Coulson has no competing interests to declare.
Dynamic persistence of intracellular bacterial communities of uropathogenicEscherichia coliin a human bladder-chip model of urinary tract infections
Authors: Sharma Kunal , Dhar Neeraj , Thacker Vivek V. , Simonet Thomas M. , Signorino-Gelo François , Knott Graham , McKinney John D.
Published: January 2021

UropathogenicEscherichia coli(UPEC) proliferate within superficial bladder umbrella cells to form intracellular bacterial communities (IBCs) during early stages of urinary tract infections. However, the dynamic responses of IBCs to host stresses and antibiotic therapy are difficult to assessin situ. We develop a human bladder-chip model wherein umbrella cells and bladder microvascular endothelial cells are co-cultured under flow in urine and nutritive media respectively, and bladder filling and voiding mimicked mechanically by application and release of linear strain. Using time-lapse microscopy, we show that rapid recruitment of neutrophils from the vascular channel to sites of infection leads to swarm and neutrophil extracellular trap formation but does not prevent IBC formation. Subsequently, we tracked bacterial growth dynamics in individual IBCs through two cycles of antibiotic administration interspersed with recovery periods which revealed that the elimination of bacteria within IBCs by the antibiotic was delayed, and in some instances, did not occur at all. During the recovery period, rapid proliferation in a significant fraction of IBCs reseeded new foci of infection through bacterial shedding and host cell exfoliation. These insights reinforce a dynamic role for IBCs as harbours of bacterial persistence, with significant consequences for non-compliance with antibiotic regimens.
Mapping the mechanical microenvironment in the ovary
Authors: Hopkins Thomas I. R. , Bemmer Victoria L. , Franks Stephen , Dunlop Carina , Hardy Kate , Dunlop Iain E.
Published: January 2021

Follicle development in the human ovary must be tightly regulated to ensure cyclical release of oocytes (ovulation), and disruption of this process is a common cause of infertility. Recent ex vivo studies suggest that follicle growth may be mechanically regulated, however the actual mechanical properties of the follicle microenvironment have remained unknown. Here we map and quantify the mechanical microenvironment in mouse ovaries using colloidal probe atomic force microscope (AFM) indentation, finding an overall mean Young’s Modulus 3.3 ± 2.5 kPa. Spatially, stiffness is low at the ovarian edge and centre, which are dominated by extra-follicular ECM, and highest in an intermediate zone dominated by large follicles. This suggests that large follicles should be considered as mechanically dominant structures in the ovary, in contrast to previous expectations. Our results provide a new, physiologically accurate framework for investigating how mechanics impacts follicle development and will underpin future tissue engineering of the ovary.
Elucidating biosynthetic pathway of piperine using comparative transcriptome analysis of leaves, root and spike inPiper longumL
Authors: Dantu Prem Kumar , Prasad Mrinalini , Ranjan Rajiv
Published: January 2021

Piper longum(Pipli; Piperaceae) is an important spice valued for its pungent alkaloids, especially piperine. Albeit, its importance, the mechanism of piperine biosynthesis is still poorly understood. The Next Generation Sequencing (NGS) forP. longumleaves, root and spikes was performed using Illumina platform, which generated 16901456, 54993496 and 22900035, respectively of high quality reads. Inde novoassemblyP. longum173381 numbers of transcripts were analyzed. Analysis of transcriptome data from leaf, root and spike showed gene families that were involved in the biosynthetic pathway of piperine and other secondary metabolites. To validate differential expression of the identified genes, 27 genes were randomly selected to confirm the expression level by quantitative real time PCR (qRT-PCR) based on the up regulation and down regulation of differentially expressed genes obtained through comparative transcriptome analysis of leaves and spike ofP. longum. With the help of UniProt database the function of all characterized genes was generated.