bluuebunny/crossref_metadata_2025 huggingface dataset:
Benefits and Risks of Chloroquine and Hydroxychloroquine in The Treatment of Viral Diseases: A Meta-Analysis of Placebo Randomized Controlled Trials
Authors: Wang Jing , Yu Li , Li Kefeng
Published: April 2020

Background and Objective

Recently, in the scramble to find drugs to treat COVID-19, chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) have rapidly gained the public’s attention. In this study, we conducted a meta-analysis of randomized clinical trials (RCTs) to evaluate the efficacy and safety of CQ and HCQ in the treatment of viral diseases.

Methods

We searched PubMed, EMBASE, Cochrane Central, Web of Science, Clinical Trials Registries, CNKI, Wanfang Data, CQVIP, and Preprint Servers through April 4, 2020, for randomized controlled trials (RCTs) that examined the efficacy and safety of CQ and HCQ against viral infection. We analyzed pooled data on the overall efficacy, the relative risks over the placebo, and the prevalence of adverse events. Trial sequential analysis (TSA) was also performed to evaluate the random errors in the meta-analysis. Potential moderators of drug-placebo efficacy differences were analyzed by meta-regression.

Results

The analysis included 11 RCTs with 2613 adult patients. Both the plasma viral load (standard mean difference: 0.29, 95% CI: −1.19 - 1.76, P = 0.70) and the improvement of clinical symptoms (odds ratio: 2.36, 95% CI: 0.81 - 6.92, P = 0.11) were not different between the intervention and placebo arm. There was significant heterogeneity for the efficacy assessment, which was primarily explained by the mean patients’ age and the sample size. Compared to the placebo, CQ and HCQ had increased risk of mild adverse events (risk ratio: 1.51, 95% CI: 1.35 - 1.70, P < 0.05, TSA adjusted 95% CI: 1.31 - 2.19), which were statistically significant in nervous, integumentary, and gastrointestinal systems. The most common adverse events were observed in the nervous system, with the pooled prevalence of 31.4 % (95% CI: 10.5% - 56.7%).

Conclusions

Insufficient data were available to support the antiviral efficacy of CQ and HCQ due to the high heterogeneity caused by patients’ age. Mild side effects are expected for the current antiviral dose regimens of CQ and HCQ. Treatment outcomes may be enhanced by better-selected patients based on age and well-controlled adverse events.

This meta-analysis was registered on OSF (ID: https://osf.io/386aw)
Parkinson’s disease-related motor and non-motor symptoms are not more prevalent in the Lancaster Amish
Authors: Goldenberg Michael D.F. , Huang Xuemei , Chen Honglei , Kong Lan , Postolache Teodor T. , Stiller John W. , Ryan Katherine A. , Pavlovich Mary , Pollin Toni I. , Shuldiner Alan R. , Mailman Richard B. , Mitchell Braxton D.
Published: April 2020

Abstract

Introduction

Previous studies have suggested that the Amish may experience a relatively high prevalence of Parkinson’s disease (PD) and/or parkinsonian-motor signs.

Methods

We assessed the frequency of PD-related motor and no-motor symptoms in a large sample from the Amish Community in Lancaster County, Pennsylvania age ≥ 18 y.

Results

Of 430 participants ≥ 60 years, five (1.2%) reported a PD diagnosis, a prevalence similar to estimates in the general older adult populations. Of those without a PD diagnosis, 10.5% reported ≥ 1 and 1.2% ≥ 4 motor symptoms for the nine-item PD screening questionnaire. We also used questionnaires to assess non-motor symptoms. Constipation was reported in 0.7%, and daytime sleepiness in 8.1% of the participants. These frequencies are similar to, or lower than, corresponding frequencies reported in the US National Health and Nutrition Examination Surveys.

Discussion

These data neither support a markedly higher PD prevalence in the Lancaster Amish, nor do they show that non-motor symptoms occur with prevalence different that the general US population. It is possible that the Lancaster Amish differ from other US Amish populations in genetics or environmental exposures, or that there were methodological differences between this study and prior ones.
Efficacy and Safety of Antibiotic Agents in Children with COVID-19: A Rapid Review
Authors: Wang Jianjian , Tang Yuyi , Ma Yanfang , Zhou Qi , Li Weiguo , Baskota Muna , Yang Yinmei , Wang Xingmei , Li Qingyuan , Luo Xufei , Fukuoka Toshio , Ahn Hyeong Sik , Lee Myeong Soo , Luo Zhengxiu , Liu Enmei , Chen Yao-long
Published: April 2020

Background

The aim of this review was to evaluate the efficacy and safety of antibiotic agents in children with COVID-19, as well as to introduce the present situation of antibiotics use and bacterial coinfections in COVID-19 patients.

Methods

We searched Cochrane library, Medline, Embase, Web of Science, CBM, Wanfang Data and CNKI from their inception to March 31, 2020. In addition, we searched related studies on COVID-19 published before March 31, 2020 through Google Scholar. We evaluated the risk of bias of included studies, and synthesized the results using a qualitative synthesis.

Results

Six studies met our inclusion criteria. Five studies on SARS showed an overall risk of death of 7.2% to 20.0%. One study of SARS patients who used macrolides, quinolones or beta lactamases showed that the mean duration of hospital stay was 14.2, 13.8 and 16.2 days, respectively, and their average duration of fever was 14.3, 14.0 and 16.2 days, respectively. One cohort study on MERS indicated that macrolide therapy was not associated with a significant reduction in 90-day mortality (adjusted odds ratio [OR] 0.84, 95% confidence interval [CI] 0.47-1.51, P = 0.56) and improvement in MERS-CoV RNA clearance (adjusted hazard ratio [HR] 0.88, 95% CI 0.47, -1.64], P = 0.68). According to the findings of 33 studies, the proportion of antibiotics use ranged from 19.4% to 100.0% in children and 13.2% to 100.0% in adults, despite the lack of etiological evidence. The most commonly used antibiotics in adults were quinolones, cephalosporins and macrolides and in children meropenem and linezolid.

Conclusions

The benefits of antibiotic agents for adults with SARS or MERS were questionable in the absence of bacterial coinfections. There is no evidence to support the use of antibiotic agents for children with COVID-19 in the absence of bacterial coinfection.
Auditory Profile-based Hearing-aid Fitting: A Proof-Of-Concept Study
Authors: Sanchez-Lopez Raul , Fereczkowski Michal , Santurette Sébastien , Dau Torsten , Neher Tobias
Published: April 2020

Objective

The clinical characterization of hearing deficits for hearing-aid fitting purposes is typically based on the pure-tone audiogram only. In a previous study, a group of hearing-impaired listeners were tested using a comprehensive test battery designed to tap into different aspects of hearing. A data-driven analysis of the data yielded four clinically relevant patient subpopulations or “auditory profiles”. In the current study, profile-based hearing-aid settings were proposed and evaluated to explore their potential for providing more targeted hearing-aid treatment.

Design

Four candidate hearing-aid settings were implemented and evaluated by a subset of the participants tested previously. The evaluation consisted of multi-comparison preference ratings carried out in realistic sound scenarios.

Results

Listeners belonging to the different auditory profiles showed different patterns of preference for the tested hearing-aid settings that were largely consistent with the expectations.

Conclusion

The results of this proof-of-concept study support further investigations into stratified, profile-based hearing-aid fitting with wearable hearing aids.
Open Development and Clinical Validation Of Multiple 3D-Printed Sample-Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck
Authors: Callahan Cody J , Lee Rose , Zulauf Katelyn E. , Tamburello Lauren , Smith Kenneth P. , Previtera Joe , Cheng Annie , Green Alex , Azim Ahmed Abdul , Yano Amanda , Doraiswami Nancy , Kirby James E. , Arnaout Ramy A.
Published: April 2020

The SARS-CoV-2 pandemic has caused a severe international shortage of the nasopharyngeal swabs that are required for collection of optimal specimens, creating a critical bottleneck in the way of high-sensitivity virological testing for COVID-19. To address this crisis, we designed and executed an innovative, radically cooperative, rapid-response translational-research program that brought together healthcare workers, manufacturers, and scientists to emergently develop and clinically validate new swabs for immediate mass production by 3D printing. We performed a rigorous multi-step preclinical evaluation on 160 swab designs and 48 materials from 24 companies, laboratories, and individuals, and shared results and other feedback via a public data repository (http://github.com/rarnaout/Covidswab/). We validated four prototypes through an institutional review board (IRB)-approved clinical trial that involved 276 outpatient volunteers who presented to our hospital’s drive-through testing center with symptoms suspicious for COVID-19. Each participant was swabbed with a reference swab (the control) and a prototype, and SARS-CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) results were compared. All prototypes displayed excellent concordance with the control (κ=0.85-0.89). Cycle-threshold (Ct) values were not significantly different between each prototype and the control, supporting the new swabs’ non-inferiority (Mann-Whitney U [MWU] p>0.05). Study staff preferred one of the prototypes over the others and the control swab overall. The total time elapsed between identification of the problem and validation of the first prototype was 22 days. Contact information for ordering can be found at http://printedswabs.org. Our experience holds lessons for the rapid development, validation, and deployment of new technology for this pandemic and beyond.
Optimal Allocation of COVID-19 Test Kits Among Accredited Testing Centers in the Philippines
Authors: Buhat Christian Alvin H. , Duero Jessa Camille C. , Felix Edd Francis O. , Rabajante Jomar F. , Mamplata Jonathan B.
Published: April 2020

Testing is crucial for early detection, isolation, and treatment of coronavirus disease (COVID-19)-infected individuals. However, in resource-constrained countries such as the Philippines, test kits have limited availability. As of 12 April 2020, there are 11 testing centers in the country that have been accredited by the Department of Health (DOH) to conduct testing. In this paper, we determine the optimal percentage allocation of COVID-19 test kits among accredited testing centers in the Philippines that gives an equitable chance to all infected individuals to be tested. Heterogeneity in testing accessibility, population density of municipalities, and the capacity of testing facilities are included in the model. Our results showed that the range of optimal allocation per testing center are: Research Institute for Tropical Medicine (4.17% −6.34%), San Lazaro Hospital (14.65% −24.03%), University of the Philippines-National Institutes of Health (16.25% −44.80%), Lung Center of the Philippines (15.8% −26.40%), Baguio General Hospital Medical Center (0.58% −0.76%), The Medical City, Pasig City (5.96% −25.51%), St. Luke’s Medical Center, Quezon City (1.09% −6.70%), Bicol Public Health Laboratory (0.06% −0.08%), Western Visayas Medical Center (0.71% −4.52%), Vicente Sotto Memorial Medical Center (1.02% −2.61%), and Southern Philippines Medical Center (≈0.01%). If there will be changes in the number of testing centers, our model can still be used to modify the test kit allocation. Our results can serve as a guide to the authorities in distributing the COVID-19 test kits. These can also be used to determine the capacity of testing centers and the effects of increasing its number. The model can also be used for proposing additional number and location of new testing centers.
Model calibration, nowcasting, and operational prediction of the COVID-19 pandemic
Authors: Annan J. D. , Hargreaves J. C.
Published: April 2020

We present a simple operational nowcasting/forecasting scheme based on a joint state/parameter estimate of the COVID-19 epidemic at national or regional scale, performed by assimilating the time series of reported daily death numbers into a simple SEIR model. This system generates estimates of the current reproductive rate, Rt, together with predictions of future daily deaths and clearly outperforms a number of alternative forecasting systems that have been presented recently. Our current (14th April 2020) estimates for Rt are, respectively, UK 0.49 (0.0 – 1.02), Spain 0.55 (0.33 – 0.77), Italy 0.90 (0.74 – 1.06) and France 0.67 (0.40 – 0.94) (mean and 95% credible intervals). Thus, we believe that the epidemics have been successfully suppressed in each of these countries, with high probability. Our approach is trivial to set up for any region and generates results in a few minutes on a laptop. We believe it would be straightforward to set up equivalent frameworks using more complex and realistic models, and hope that some experts in the field of epidemiological modelling will consider investigating this approach further.
Redox imbalance and oxidative DNA damage during isoniazid treatment: A clinical and translational pharmacokinetic study
Authors: Zentner Isaac , Back Hyun-moon , Kagan Leonid , Subbian Selvakumar , Nagajyothi Jyothi , Srivastava Shashikant , Pasipanodya Jotam , Gumbo Tawanda , Bisson Gregory P. , Vinnard Christopher
Published: April 2020

Background

The potential for hepatotoxicity during isoniazid-based tuberculosis (TB) treatment presents a major challenge for TB control programs worldwide. We sought to determine whether pharmacokinetic exposures of isoniazid and its metabolites were related to cellular oxidation/reduction status and downstream markers of oxidative DNA damage.

Methods

We performed intensive pharmacokinetic sampling among isoniazid-treated patients to determine the relative plasma exposures of isoniazid, acetylisoniazid, hydrazine, and acetylhydrazine. Physiologically-based pharmacokinetic modeling was used to estimate liver tissue exposures during a 24-hour dosing interval for each compound. We experimentally treated HepG2 cells with isoniazid and metabolites at equimolar concentrations corresponding to these exposures for 7, 14, and 28 day periods, and performed assays related to redox imbalance and oxidative DNA damage at each timepoint. We related a urine marker of oxidative DNA damage to serum isoniazid pharmacokinetic exposures and pharmacogenetics in a clinical study.

Results

Among isoniazid-treated patients, serum concentrations of hydrazine and isoniazid concentrations were highly correlated. At equimolar concentrations that approximated hepatic tissue exposures during a 24-hour dosing interval, hydrazine demonstrated the highest levels of redox imbalance, mitochondrial injury, and oxidative DNA damage over a 28-day treatment period. In a clinical validation study of isoniazid-treated TB patients, peak isoniazid serum concentrations were positively associated with a urine biomarker of oxidative DNA damage.

Conclusions

Isoniazid and its metabolites share the potential for oxidative cellular damage, with the greatest effects observed for hydrazine. Future studies should investigate the clinical consequences of oxidative stress with regards to clinical episodes of drug induced liver injury during isoniazid treatment.
Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis
Authors: Gao Yelei , Liu Rui , Zhou Qi , Wang Xingmei , Huang Liping , Shi Qianling , Wang Zijun , Lu Shuya , Li Weiguo , Ma Yanfang , Luo Xufei , Fukuoka Toshio , Ahn Hyeong Sik , Lee Myeong Soo , Luo Zhengxiu , Liu Enmei , Chen Yaolong , Shu Chang , Tian Daiying
Published: April 2020

Background

As COVID-19 has become a global pandemic, early prevention and control of the epidemic is extremely important. Telemedicine, which includes medical advice given over telephone, Internet, mobile phone applications or other similar ways, may be an efficient way to reduce transmission and pressure on medical institutions.

Methods

We searched MEDLINE, Web of science, Embase, Cochrane, CBM, CNKI and Wanfang databases for literature on the use of telemedicine for COVID-19, SARS and MERS. from their inception to March 31st, 2020. We included studies about the content of the consultation (such as symptoms, therapy and prevention, policy, public service), screening of suspected cases, the provision of advice given to those people who may have symptoms or contact history. We conducted meta-analyses on the main outcomes of the studies.

Results

A total of 2041 articles were identified after removing duplicates. After reading the full texts, we finally included nine studies. People were most concerned about symptoms (64.2%), epidemic situation and public problems (14.5%), and psychological problems (10.3%) during COVID-19 epidemic. During the SARS epidemic, the proportions of people asking for consultation for symptoms, prevention and therapy, and psychological problems were 35.0%, 22.0%, and 23.0%, respectively. Two studies demonstrated that telemedicine can be used to screen the suspected patients and give advice. One study emphasized the limited possibilities to follow up people calling hotlines and difficulties in identifying all suspect cases.

Conclusions

Telemedicine services should focus on the issues that the public is most concerned about, such as then symptoms, prevention and treatment of the disease, and provide reasonable advice to patients with symptoms or people with epidemic history.
Association of inflammatory markers with the severity of COVID-19
Authors: Zeng Furong , Guo Ying , Yin Mingzhu , Chen Xiang , Deng Guangtong
Published: April 2020

Background

The ongoing worldwide epidemic of Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2), has posed a huge threat to global public health. However, with regard to the effects of inflammatory markers on the severity of COVID-19, studies have reported associations that vary in strength and direction.

Aims

In the meta-analysis, we aimed to provide an overview of the association of inflammatory markers with severity of COVID-19.

Methods

The following databases were searched: PubMed, Embase, Cochrane Library, Wanfang database and CNKI (China National Knowledge Infrastructure) database until March 20, 2020. Weighted mean difference (WMD) and 95% confidence intervals (CIs) were pooled using random or fixed-effects models.

Results

A total of 16 studies were included in our analysis comprising of 3962 patients with COVID-19. Random-effects results demonstrated that patients with COVID-19 in non-severe group had lower levels for CRP (WMD = -41.78 mg/l, 95% CI = [-52.43, - 31.13], P < 0.001), PCT (WMD = -0.13 ng/ml, 95% CI = [-0.20, -0.05], P < 0.001), IL- 6 (WMD = -21.32 ng/l, 95% CI = [-28.34, -14.31], P < 0.001), ESR (WMD = - 8.40 mm/h, 95% CI = [-14.32, -2.48], P = 0.005), SAA (WMD = -43.35 μg/ml, 95% CI = [-80.85, -5.85], P = 0.020) and serum ferritin (WMD = -398.80 mg/l, 95% CI = [- 625.89, -171.71], P < 0.001), compared with those in severe group. Moreover, survivors had lower level for IL-6 than non-survivors with COVID-19 (WMD = -4.80 ng/ml, 95% CI = [-5.87, -3.73], P < 0.001). These results were consistent through sensitivity analysis and publication bias assessment.

Conclusions

The meta-analysis highlights the association of inflammatory markers with the severity of COVID-19. Measurement of inflammatory markers might help clinicians to monitor and evaluate the severity and prognosis of COVID-19.
Nature of transmission of Covid19 in India
Authors: Roy Anushree , Kar Sayan
Published: April 2020

We examine available data on the number of individuals infected by the Covid-19 virus, across several different states in India, over the period January 30, 2020 to April 10, 2020. It is found that the growth of the number of infected individuals N(t) can be modeled across different states with a simple linear function N(t) = γ + αt beyond the date when reasonable number of individuals were tested (and when a countrywide lockdown was imposed). The slope α is different for different states. Following recent work by Notari (arxiv:2003.12417), we then consider the dependency of the α for different states on the average maximum and minimum temperatures, the average relative humidity and the population density in each state. It turns out that like other countries, the parameter α, which determines the rate of rise of the number of infected individuals, seems to have a weak correlation with the average maximum temperature of the state. In contrast, any significant variation of α with humidity or minimum temperature seems absent with almost no meaningful correlation. Expectedly, α increases (slightly) with increase in the population density of the states; however, the degree of correlation here too is negligible. These results seem to barely suggest that a natural cause like a hot summer (larger maximum temperatures) may contribute towards reducing the transmission of the virus, though the role of minimum temperature, humidity and population density remains somewhat obscure from the inferences which may be drawn from presently available data.
Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution
Authors: Zehner Jennifer , Røyne Anja , Wentzel Alexander , Sikorski Pawel
Published: April 2020

Concrete is the second most consumed product by humans, after water. However, the production of cement, which is used as a binding material in concrete, causes more than 5% of anthropogenic CO2emissions and has therefore a significant contribution to climate change and global warming. Due to increasing environmental awareness and international climate goals, there is a need for emission-reduced materials, that can replace conventional concrete in certain applications. One path to produce a solid, concrete-like construction material is microbial-induced calcium carbonate precipitation (MICP). As a calcium source in MICP, crushed limestone, which mainly consists out of CaCO3, can be dissolved with acids, for example lactic acid. The pH evolution during crystallization and dissolution processes provides important information about kinetics of the reactions. However, previous research on MICP has mainly been focused on macro-scale pH evolution and on characterization of the finished material. To get a better understanding of MICP it is important to be able to follow also local pH changes in a sample. In this work we present a new method to study processes of MICP at micro-scalein situand in real time. We present two different methods to monitor the pH changes during the precipitation process of CaCO3. In the first method, the average pHs of small sample volumes are measured in real time, and pH changes are subsequently correlated with processes in the sample by comparing to optical microscope results. The second method is introduced to follow local pH changes at a grain scale insituand in real time. Furthermore, local pH changes during the dissolution of CaCO3crystals are monitored. We demonstrate that these two methods are powerful tools to investigate pH changes for both MICP precipitation and CaCO3dissolution for knowledge-based improvement of MICP-based material properties.

Graphical TOC Entry
Optimizing RT-PCR detection of SARS-CoV-2 for developing countries using pool testing
Authors: Farfan Mauricio J. , Torres Juan P. , O’Ryan Miguel , Olivares Mauricio , Gallardo Pablo , Salas Carolina
Published: April 2020

The global shortage of reagents and kits for nucleic acid extraction and molecular detection of SARS-CoV-2, requires new cost-effective strategies for the diagnosis of suspected COVID-19 cases, especially in countries that need to increase detection capacity. Pooled nucleic acid testing has been extensively used as a cost-effective strategy for HIV, HepB, HepC and influenza. Also, protocols dispensing of RNA extraction appears as an attractive option for detection of SARS-CoV-2. In this study, pooling nasopharyngeal samples with both automated and manual extraction proved reliable, and thus a potential efficient alternative for the diagnosis of suspected COVID-19 in developing countries.
A region of Drosophila SLBP distinct from the histone pre-mRNA binding and processing domains is essential for deposition of histone mRNA in the oocyte
Authors: Potter-Birriel Jennifer , Gonsalvez Graydon B. , Marzluff William F.
Published: April 2020

DuringDrosophilaoogenesis, large amounts of histone mRNA and proteins are deposited in the developing oocyte. These are sufficient for the first 14 embryonic cell cycles and provide the developing embryo with sufficient histone proteins until the zygotic histone genes are activated. The maternally deposited histone mRNA is synthesized in stage 10b of oogenesis after completion of endoreduplication of the nurse cells. Histone mRNAs are the only cellular mRNAs that are not polyadenylated, ending instead in a conserved stemloop instead of a polyA tail. The Stem-loop binding protein (SLBP) binds the 3’ end of histone mRNA and is essential for both the biosynthesis and translation of histone mRNA. We report that a 10 aa region in SLBP, which is not required for processing in vitro, is essential for transcription of histone mRNA in the stage 10b oocyte. In stage 10b the Histone Locus Bodies (HLBs) produce histone mRNAs in the absence of phosphorylation of Mxc, normally required for histone gene expression in S-phase cells. Mutants expressing this SLBP develop normally, produce small amounts of polyadenylated histone mRNA throughout development, but little histone mRNA in stage 10b resulting in death of the embryos in the first hr of development.
Omics-Based Interaction Framework – a systems model to reveal molecular drivers of synergy
Authors: García Jezreel Pantaleón , Kulkarni Vikram V. , Reese Tanner C. , Wali Shradha , Wase Saima J. , Zhang Jiexin , Singh Ratnakar , Caetano Mauricio S. , Moghaddam Seyed Javad , Johnson Faye M. , Wang Jing , Wang Yongxing , Evans Scott E.
Published: April 2020

Bioactive molecule library screening strategies may empirically identify effective combination therapies. However, without a systems theory to interrogate synergistic responses, the molecular mechanisms underlying favorable drug-drug interactions remain unclear, precluding rational design of combination therapies. Here, we introduce Omics-Based Interaction Framework (OBIF) to reveal molecular drivers of synergy through integration of statistical and biological interactions in supra-additive biological responses. OBIF performs full factorial analysis of feature expression data from single vs. dual factor exposures to identify molecular clusters that reveal synergy-mediating pathways, functions and regulators. As a practical demonstration, OBIF analyzed a therapeutic dyad of immunostimulatory small molecules that induces synergistic protection against influenza A pneumonia. OBIF analysis of transcriptomic and proteomic data identified biologically relevant, unanticipated cooperation between RelA and cJun that we subsequently confirmed to be required for the synergistic antiviral protection. To demonstrate generalizability, OBIF was applied to data from a diverse array of Omics platforms and experimental conditions, successfully identifying the molecular clusters driving their synergistic responses. Hence, OBIF is a phenotype-driven systems model that supports multiplatform exploration of synergy mechanisms.
Evolutionary divergence of potential drought adaptations between two subspecies of an annual plant: Do some constraints need to be broken?
Authors: Burnette Timothy E. , Eckhart Vincent M.
Published: April 2020

Premise

Whether mechanisms of drought adaptation tend to evolve together, evolve independently, and/or evolve constrained by genetic architecture is incompletely resolved, particularly for water-relations traits besides gas exchange. We addressed this question in two subspecies ofClarkia xantiana(Onagraceae), California winter annuals that diverged approximately 65,000 years ago and that are adapted, partly by differences in flowering time, to native ranges that differ in precipitation.

Methods

In these subspecies and in F5recombinant inbred lines (RILs) from a cross between them we scored drought-adaptation traits related to phenology (times to seed germination and to flowering) and tissue water relations (measures of succulence; pressure-volume curve parameters), in common environments.

Results

Subspecies differed distinctly. The one native to more arid environments had some trait values associated with drought adaptation (e.g., early flowering and high succulence) but had higher osmotic potential at full turgor and lost turgor at higher water potential, indicating poorer tolerance of dehydration. Traits that differed between subspecies exhibited substantial genetic variation, with broad-sense heritability from 0.09 (stem succulence) to 0.43 (time to flowering). The genetic correlation structure suggests facilitated evolution of some trait combinations that might enhance drought adaptation (e.g., high succulence plus low turgor loss point), but the subspecies exhibit some trait combinations that do not follow genetic correlations.

Conclusions

As lineages diverged in their potential to escape drought by early flowering, other traits diverged as well. Genetic architecture might facilitate some correlated evolutionary responses to drought, but particular trait combinations also can evolve despite apparent genetic constraints.
Neuronal Subcompartment Classification and Merge Error Correction
Authors: Li Hanyu , Januszewski Michał , Jain Viren , Li Peter H.
Published: April 2020

Recent advances in 3d electron microscopy are yielding ever larger reconstructions of brain tissue, encompassing thousands of individual neurons interconnected by millions of synapses. Interpreting reconstructions at this scale demands advances in the automated analysis of neuronal morphologies, for example by identifying morphological and functional subcompartments within neurons. We present a method that for the first time uses full 3d input (voxels) to automatically classify reconstructed neuron fragments as axon, dendrite, or somal subcompartments. Based on 3d convolutional neural networks, this method achieves a mean f1-score of 0.972, exceeding the previous state of the art of 0.955. The resulting predictions can support multiple analysis and proofreading applications. In particular, we leverage finely localized subcompartment predictions for automated detection and correction of merge errors in the volume reconstruction, successfully detecting 90.6% of inter-class merge errors with a false positive rate of only 2.7%.
Expression of aMalasseziacodon optimized mCherry fluorescent protein in a bicistronic vector
Authors: Goh Joleen P.Z. , Ianiri Giuseppe , Heitman Joseph , Dawson Thomas L.
Published: April 2020

The use of fluorescent proteins allows a multitude of approaches from live imaging and fixed cells to labelling of whole organisms, making it a foundation of diverse experiments. Tagging a protein of interest or specific cell type allows visualization and studies of cell localization, cellular dynamics, physiology, and structural characteristics. In specific instances fluorescent fusion proteins may not be properly functional as a result of structural changes that hinder protein function, or when overexpressed may be cytotoxic and disrupt normal biological processes. In our study, we describe application of a bicistronic vector incorporating a Picornavirus 2A peptide sequence between a NAT antibiotic selection marker and mCherry. This allows expression of multiple genes from a single open reading frame and production of discrete protein products through a cleavage event within the 2A peptide. We demonstrate integration of this bicistronic vector into a modelMalasseziaspecies, the haploid strainM. furfurCBS 14141, with both active selection, high fluorescence, and proven proteolytic cleavage. Potential applications of this technology can include protein functional studies,Malasseziacellular localization, and co-expression of genes required for targeted mutagenesis.
Comparative RNA-Seq Analyses ofDrosophilaPlasmatocytes Reveal Gene Specific Signatures In Response To Clean Injury And Septic Injury
Authors: Ramond Elodie , Dudzic Jan Paul , Lemaitre Bruno
Published: April 2020

Drosophila melanogaster’s blood cells (hemocytes) play essential roles in wound healing and are involved in clearing microbial infections. Here, we report the transcriptional changes of larval plasmatocytes after clean injury or infection with the Gram-negative bacteriumEscherichia colior the Gram-positive bacteriumStaphylococcus aureuscompared to hemocytes recovered from unchallenged larvae via RNA-Sequencing. This study reveals 676 differentially expressed genes (DEGs) in hemocytes from clean injury samples compared to unchallenged samples, and 235 and 184 DEGs inE. coliandS. aureussamples respectively compared to clean injury samples. The clean injury samples showed enriched DEGs for immunity, clotting, cytoskeleton, cell migration, hemocyte differentiation, and indicated a metabolic reprogramming to aerobic glycolysis, a well-defined metabolic adaptation observed in mammalian macrophages. Microbial infections trigger significant transcription of immune genes, with significant differences between theE. coliandS. aureussamples suggesting that hemocytes have the ability to engage various programs upon infection. Collectively, our data bring new insights onDrosophilahemocyte function and open the route to post-genomic functional analysis of the cellular immune response.
SARS-CoV-2 is transmitted via contact and via the air between ferrets
Authors: Richard Mathilde , Kok Adinda , de Meulder Dennis , Bestebroer Theo M. , Lamers Mart M. , Okba Nisreen M.A. , van Vlissingen Martje Fentener , Rockx Barry , Haagmans Bart L. , Koopmans Marion P.G. , Fouchier Ron A.M. , Herfst Sander
Published: April 2020

SARS-CoV-2, a coronavirus that newly emerged in China in late 20191,2and spread rapidly worldwide, caused the first witnessed pandemic sparked by a coronavirus. As the pandemic progresses, information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets. Intranasal inoculation of donor ferrets resulted in a productive upper respiratory tract infection and long-term shedding, up to 11 to 19 days post-inoculation. SARS-CoV-2 transmitted to four out of four direct contact ferrets between 1 and 3 days after exposure and via the air to three out of four independent indirect recipient ferrets between 3 and 7 days after exposure. The pattern of virus shedding in the direct contact and indirect recipient ferrets was similar to that of the inoculated ferrets and infectious virus was isolated from all positive animals, showing that ferrets were productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings3.
Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry
Authors: Steigenberger Barbara , van den Toorn Henk W.P. , Bijl Emiel , Greisch Jean-François , Räther Oliver , Lubeck Markus , Pieters Roland J. , Heck Albert J.R. , Scheltema Richard A.
Published: April 2020

Ion mobility separates molecules in the gas-phase on their physico-chemical properties, providing information about their size as collisional cross-sections. The timsTOF Pro combines trapped ion mobility with a quadrupole, collision cell and a time-of-flight mass analyzer, to probe ions at high speeds with on-the-fly fragmentation. Here, we show that on this platform ion mobility is beneficial for cross-linking mass spectrometry (XL-MS). Cross-linking reagents covalently link amino acids in close proximity, resulting in peptide pairs after proteolytic digestion. These cross-linked peptides are typically present at low abundance in the background of normal peptides, which can partially be resolved by using enrichable cross-linking reagents. Even with a very efficient enrichable cross-linking reagent, like PhoX, the analysis of cross-linked peptides is still hampered by the co-enrichment of peptides connected to a partially hydrolyzed reagent – termed mono-linked peptides. For experiments aiming to uncover protein-protein interactions these are unwanted byproducts. Here, we demonstrate that gas-phase separation by ion mobility enables the separation of mono-linked peptides from cross-linked peptide pairs. A clear partition between these two classes is observed at a CCS of 500 Å2and a monoisotopic mass of 2 kDa, which can be used for targeted precursor selection. A total of 50 - 70% of the mono-linked peptides are prevented from sequencing, allowing the analysis to focus on sequencing the relevant cross-linked peptide pairs. In applications to both simple proteins and protein mixtures and a complete highly complex lysate this approach provides a substantial increase in detected cross-linked peptides.
The evaluation of miR-874 antagomiR and miR-146a toxicity in cardiomyocytes
Authors: Guo Linlin , Zhang Yue , Chen Zhiwei , Dou Wenjing , Wu Jiamei , Xu Heli , Tan Hongyou , Wang Xiyan
Published: April 2020

More and more studies have shown that microRNAs (miRNAs) play key roles in the treatment of heart failure. Studies have shown that miR-874 (miR-874) inhibitors can reduce H2O2-induced cardiomyocyte necrosis and may have a therapeutic effect on heart failure in terms of cardiomyocyte necrosis. Therefore, the purpose of this experiment is to study the other effects of miR-874 and miR-146a on the key pathways in cardiomyocytes and cardiac fibroblasts. In this study, the roles of miR-874 antagomiR and miR-146a in cardiomyocytes and cardiac fibroblasts were analyzed. we investigated the level of miR-874 expression in H9C2 cardiomyocytes after miR-874 antagomiR transfection and found that the miR-874 expression in the H9C2 cells transfected with miR-874 antagomiR group was significantly lower than that in the control group. The results showed that miR-874 was successfully knocked down by the transfection of miR-874 antagomiR. Our results demonstrated that miR-874 inhibition has no effect on the activity of Caspase-3/7 in cardiomyocytes. miR-874 antagomiR has no effect on the proliferation of cardiac fibroblasts, whereas it can inhibit the activity of caspase-8 in cardiac fibroblasts. In addition, the potential effect of miR-874 antagomiR on cardiac remodeling associated genes were examined. miR-874 antagomiR had no effect on SERCA2a mRNA level in H9C2 cells. In addition, miR-874 antagomiR were able to down-regulate the mRNA level of MMP9 and had no effect on MMP2 mRNA levels in H9C2 cells. Finally, The concentration of Ca2+was measured using Fluo-4 NW Calcium Assay Kits following transfection of miRNAs or negative control in primary cardiomyocytes. miR-874 antagomiR was found to have no effect on Ca2+concentration in cardiomyocytes. the concentration of Ca2+in the cardiomyocytes transfected with miR-146a mimics was significantly lower than the mimic negative control group. In summary, miR-874 antagomiR and miR-146a may have a therapeutic effect on heart failure, but may also have side effects on heart failure treatment. Therefore, miR-874 antagomiR should be further studied to provide a basis for the development of drugs for heart failure.
Elucidation and refinement of synthetic receptor mechanisms
Authors: Edelstein Hailey I. , Donahue Patrick S. , Muldoon Joseph J. , Kang Anthony K. , Dolberg Taylor B. , Battaglia Lauren M. , Allchin Everett R. , Hong Mihe , Leonard Joshua N.
Published: April 2020

Synthetic receptors are powerful tools for engineering mammalian cell-based devices. These biosensors enable cell-based therapies to perform complex tasks such as regulating therapeutic gene expression in response to sensing physiological cues. Although multiple synthetic receptor systems now exist, many aspects of receptor performance are poorly understood. In general, it would be useful to understand how receptor design choices influence performance characteristics. In this study, we examined the modular extracellular sensor architecture (MESA) and systematically evaluated previously unexamined design choices, yielding substantially improved receptors. A key finding that might extend to other receptor systems is that the choice of transmembrane domain (TMD) is important for generating high-performing receptors. To provide mechanistic insights, we adopted and employed a Förster resonance energy transfer (FRET)-based assay to elucidate how TMDs affect receptor complex formation and connected these observations to functional performance. To build further insight into these phenomena, we developed a library of new MESA receptors that sense an expanded set of ligands. Based upon these explorations, we conclude that TMDs affect signaling primarily by modulating intracellular domain geometry. Finally, to guide the design of future receptors, we propose general principles for linking design choices to biophysical mechanisms and performance characteristics.
Immune modulation to improve survival of respiratory virus infections in mice
Authors: Wali Shradha , Flores Jose R. , Jaramillo Ana Maria , Goldblatt David L. , Pantaleón García Jezreel , Tuvim Michael J. , Dickey Burton F. , Evans Scott E.
Published: April 2020

Viral pneumonia remains a global health threat requiring novel treatment strategies, as strikingly exemplified in the SARS-CoV-2 pandemic of 2019-2020. We have reported that mice treated with a combination of inhaled Toll-like receptor (TLR) 2/6 and TLR 9 agonists (Pam2-ODN) to stimulate innate immunity are broadly protected against respiratory pathogens, but the mechanisms underlying this protection remain incompletely elucidated. Here, we show in a lethal paramyxovirus model that Pam2-ODN-enhanced survival is associated with robust virus inactivation by reactive oxygen species (ROS), which occurs prior to internalization by lung epithelial cells. However, we also found that mortality in sham-treated mice temporally corresponded with CD8+T cell-enriched lung inflammation that peaks on days 11-12 after viral challenge, when the viral burden has waned to a scarcely detectable level. Pam2-ODN treatment blocked this injurious inflammation by reducing the viral burden, and alternatively, depleting CD8+T cells 8 days after viral challenge also decreased mortality. These findings reveal opportunities for targeted immunomodulation to protect susceptible individuals against the morbidity and mortality of respiratory viral infections.
CRISPR-Cas9 cytidine and adenosine base editing of splice-sites mediates highly-efficient disruption of proteins in primary cells
Authors: Kluesner Mitchell G. , Lahr Walker S. , Lonetree Cara-Lin , Smeester Branden A. , Claudio-Vázquez Patricia N. , Pitzen Samuel P. , Vignes Madison J. , Lee Samantha C. , Bingea Samuel P. , Andrews Aneesha A. , Webber Beau R. , Moriarity Branden S.
Published: April 2020

Base editors allow for precise nucleotide editing without the need for genotoxic double-stranded breaks. Prior work has used base editors to knockout genes by introducing premature stop codons or by disrupting conserved splice-sites, but no direct comparison exists between these methods. Additionally, while base editor mediated disruption of splice sites has been used to shift the functional isoform pool, its utility for gene knockout requires further validation. To address these needs, we developed the program SpliceR (z.umn.edu/spliceR) to design cytidine-deaminase base editor (CBE) and adenosine-deaminase base editor (ABE) splice-site targeting guides. We compared the splice-site targeting and premature stop codon introduction in a knockout screen against the TCR-CD3 immune synapse in primary human T-cells. Our data suggests that 1) the CBE, BE4 is more reliable than the ABE, ABE7.10 for splice-site targeting knockout and 2) for both CBEs and ABEs, splice-donor targeting is the most reliable approach for base editing induced knockout.
Nucleotide excision repair hotspots and coldspots of UV-induced DNA damage in the human genome
Authors: Jiang Yuchao , Li Wentao , Lindsey-Boltz Laura A , Yang Yuchen , Li Yun , Sancar Aziz
Published: April 2020

We recently developed high-throughput sequencing approaches, eXcision Repair sequencing (XR-seq) and Damage-seq, to generate genome-wide mapping of DNA excision repair and damage formation, respectively, with single-nucleotide resolution. Here, we used time-course XR-seq data to profile UV-induced excision repair dynamics, paired with Damage-seq data to quantify the overall induced DNA damage. We identified genome-wide repair hotspots exhibiting high-level nucleotide excision repair immediately after UV irradiation. We show that such repair hotspots do not result from hypersensitivity to DNA damage, and are thus not damage hotspots. We find that the earliest repair occurs preferentially in promoters and enhancers from open-chromatin regions. The repair hotspots are also significantly enriched for frequently interacting regions and super-enhancers, both of which are themselves hotspots for local chromatin interactions. Further interrogation of chromatin organization to include DNA replication timing allows us to conclude that early-repair hotspots are enriched for early-replication domains. Collectively, we report genome-wide early-repair hotspots of UV-induced damage, in association with chromatin states and epigenetic compartmentalization of the human genome.
Detecting Genes Associated with Pathogenicity and Antimicrobial Resistance in Three New Zealand Waterways
Authors: Davis Meredith T. , Midwinter Anne C. , Death Russell G. , Cosgrove Richard , Winkworth Richard C.
Published: April 2020

Background

More than 100 zoonoses may be transmitted via water, among them enteric diseases are leading causes of human mortality. Traditional monitoring for zoonoses relies on culturing of indicator species, but environmental DNA (eDNA) provides an alternative, allowing direct testing for genetic loci associated with pathogenicity and/or antimicrobial resistance in zoonotic bacteria.

Objectives

To evaluate whether genes associated with Shiga toxin producingEscherichia coli(STEC) and antimicrobial resistance can be monitored in waterways using culture-free sampling of eDNA combined with PCR-based testing.

Methods

Water and sediment samples were collected from two sites on each of three rivers in Canterbury, New Zealand; sample sites were situated above and below reaches bordered by intensive dairy farming. Samples from each site were tested for genes typically associated withEscherichia coli, STEC serogroups O26 and O157, human pathogenic strains of STEC, and resistance to a broad range of antibiotics.

Results

Both culturing and genetic testing confirmed the presence ofE. coliin all samples. In contrast, presence of genes associated with STEC and antibiotic resistance varied by season and substrate. The O157 serogroup was identified at more than twice as many sites as O26, with the latter more common in autumn samples. In autumn, genes associated with pathogenic STEC were detected in one Ashley and both Rangitata River samples but were present in all spring samples, except one Ashley and one Selwyn River collection. The antibiotic resistance gene was only identified in spring, predominantly at sites downstream of intensive dairying.

Discussion

While our sample is small this study indicates that genetic testing of eDNA can be a useful tool for monitoring the presence and persistence of zoonoses in waterways. How the presence of these genetic elements is related to that of pathogenic STEC and incidence of disease in humans now needs to be examined.