bluuebunny/crossref_metadata_2025 huggingface dataset:
Severe COVID-19 infection is associated with increased antibody-mediated platelet apoptosis
Authors: Althaus Karina , Marini Irene , Zlamal Jan , Pelzl Lisann , Häberle Helene , Mehrländer Martin , Hammer Stefanie , Schulze Harald , Bitzer Michael , Malek Nisar , Rath Dominik , Bösmüller Hans , Nieswandt Bernard , Gawaz Meinrad , Bakchoul Tamam , Rosenberger Peter
Published: September 2020

The pathophysiology of COVID-19 associated thrombosis seems to be multifactorial, involving interplay between cellular and plasmatic elements of the hemostasis. We hypothesized that COVID-19 is accompanied by platelet apoptosis with subsequent alteration of the coagulation system. We investigated depolarization of mitochondrial inner transmembrane potential (ΔΨm), cytosolic calcium (Ca2+) concentration, and phosphatidylserine (PS) externalization by flow cytometry. Platelets from intensive care unit (ICU) COVID-19 patients (n=21) showed higher ΔΨm depolarization, cytosolic Ca2+concentration and PS externalization, compared to healthy controls (n=18) and COVID-19 non-ICU patients (n=4). Moreover significant higher cytosolic Ca2+concentration and PS was observed compared to septic ICU control group (ICU control). In ICU control group (n=5; ICU non-COVID-19) cytosolic Ca2+concentration and PS externalization was comparable to healthy control, with an increase ΔΨm depolarization. Sera from ICU COVID-19 13 patients induced significant increase in apoptosis markers (ΔΨm depolarization, cytosolic Ca2+concentration and PS externalization). compared to healthy volunteer and septic ICU control. Interestingly, immunoglobulin G (IgG) fractions from COVID-19 patients induced an Fc gamma receptor IIA dependent platelet apoptosis (ΔΨm depolarization, cytosolic Ca2+concentration and PS externalization). Enhanced PS externalization in platelets from ICU COVID-19 patients was associated with increased sequential organ failure assessment (SOFA) score (r=0.5635) and DDimer (r=0.4473). Most importantly, patients with thrombosis had significantly higher PS externalization compared to those without. The strong correlations between apoptosis markers and increased D-Dimer levels as well as the incidence of thrombosis may indicate that antibody-mediated platelet apoptosis potentially contributes to sustained increased thromboembolic risk in ICU COVID-19 patients.

Key points

Severe COVID-19 is associated with increased antibody-mediated platelet apoptosis.

Platelet apoptosis in severe COVID-19 is correlated with D-Dimer and higher incidence of thromboembolisms.
Household Secondary Attack Rate in Gandhinagar district of Gujarat state from Western India
Authors: Shah Komal , Desai Nupur , Saxena Deepak , Mavalankar Dileep , Mishra Umang , Patel G C
Published: September 2020

Objectives: Current retrospective study aims to evaluate household Secondary Attack Rate (SAR) of COVID-19 in Gandhinagar (rural) district of Gujarat, India. Methods: Line-listing of 486 laboratory-confirmed patients, tested between 28th March to 2nd July was collected, out of them 80 (15% of overall sample) cases were randomly selected. Demographic, clinical and household details of cases were collected through telephonic interview. During interview 28 more patients were identified from the same household and were added accordingly. So, study included 74 unrelated cluster of households with 74 primary cases and 386 close contacts. Results: SAR in household contacts of COVID-19 in Gandhinagar was 8.8%. Out of 108, 8 patients expired (7.4%), where higher mortality was observed in primary cases (9.5%) as compared to secondary cases (3%). Occupational analysis showed that majority of the secondary cases (88%) were not working and hence had higher contact time with patient. No out-of-pocket expenditure occurred in 94% of the patients, in remaining 6% average expenditure of 1,49,633INR (2027 USD) was recorded. Conclusions: Key observations from the study are 1) SAR of 8.8% is relatively low and hence home isolation of the cases can be continued 2) Primary case is more susceptible to fatal outcome as compared to secondary cases 3) Government has covered huge population of the COVID-19 patients under cost protection. However, more robust studies with larger datasets are needed to further validate the findings.
High prevalence of deep venous thrombosis in non-severe COVID-19 patients hospitalized for a neurovascular disease
Authors: Rouyer Olivier , Pierre-Paul Irène Nora , Balde Amadou Talibe , Jupiter Damaris , Bindila Daniela , Geny Bernard , Wolff Valérie
Published: September 2020

Introduction

Severe SARS-CoV-2 infection, responsible for COVID-19, is accompanied by venous thromboembolic events particularly in intensive care unit. In non-severe COVID-19 patients affected by neurovascular diseases, the prevalence of deep venous thrombosis (DVT) is unknown. The aim of or study was to report data obtained after systematic Doppler ultrasound scanning (DUS) of lower limbs in such patients.

Methods

Between March 20 and May 2, 2020, consecutive patients with neurovascular diseases with non-severe COVID-19 were investigated with a systematic bedside DUS.

Results

Thirteen patients were enrolled including 10 acute ischemic strokes, one transient ischemic attack, one cerebral venous thrombosis and one haemorrhagic stroke. At admission the median National Institute of Health Stroke Scale (NIHSS) was of 6 (IQR, 0–20). We found a prevalence of 38.5% of asymptomatic calves’ DVT (n = 5) during the first week after admission despite thromboprophylaxis. Among them, one patient had a symptomatic pulmonary embolism. Two patients died during hospitalization but the outcome was favourable in the others with a discharge median NIHSS of 1 (IQR, 0–11).

Discussion/Conclusion

Despite thromboprophylaxis, systematic bedside DUS showed a high prevalence of 38.5% of DVT in non-severe COVID-19 patients with neurovascular diseases. Therefore, we suggest that this non-invasive investigation should be performed in all patients of this category.
Investigating the causal nature of the relationship of subcortical brain volume with smoking and alcohol use
Authors: Logtenberg Emma , Overbeek Martin F , Pasman Joëlle A , Abdellaoui Abdel , Luijten Maartje , van Holst Ruth J , Vink Jacqueline M , Denys Damiaan , Medland Sarah E , Verweij Karin JH , Treur Jorien L
Published: September 2020

Background

Structural variation in subcortical brain regions has been linked to substance use, including the most prevalent substances nicotine and alcohol. It may be that pre-existing differences in subcortical brain volume affect smoking and alcohol use, but there is also evidence that smoking and alcohol use can lead to structural changes. We assess the causal nature of this complex relationship with bi-directional Mendelian randomization (MR).

Methods

MR uses genetic variants predictive of a certain trait (‘exposure’) as instrumental variables to test causal effects on a certain outcome. Due to random assortment at meiosis, genetic variants shouldn’t be associated with confounders, allowing less biased causal inference. We employed summary-level data of the largest available genome-wide association studies of subcortical brain region volumes (nucleus accumbens, amygdala, caudate nucleus, hippocampus, pallidum, putamen, and thalamus; n = 50,290) and smoking and alcohol use (smoking initiation, n = 848,460; cigarettes per day, n = 216,590; smoking cessation, n = 378,249; alcohol drinks per week, n = 630,154; alcohol dependence, n = 46,568). The main analysis, inverse-variance weighted regression, was verified by a wide range of sensitivity methods.

Results

There was strong evidence that alcohol dependence decreased amygdala and hippocampal volume and that smoking more cigarettes per day decreased hippocampal volume. From subcortical brain volumes to substance use, there was no or weak evidence for causal effects.

Conclusions

Our findings suggest that heavy alcohol use and smoking can causally reduce subcortical brain volume. This adds to accumulating evidence that alcohol and smoking affect the brain, and most likely mental health, warranting more recognition in public health efforts.
The role of school reopening in the spread of COVID-19
Authors: Beesley Richard
Published: September 2020

Many countries chose to close schools as part of their response to the SARS-CoV2 coronavirus (COVID-19) pandemic. Whilst nations are gradually reopening schools, and many politicians advise that schools remain safe and the risks of increases in the spread of COVID-19 are low, little evidence has been presented to confirm those statements.

A review of the numbers of new confirmed COVID-19 cases by country suggests that the reopening of schools is likely to be a driver in the increase of the number of new cases. This is likely exacerbated by accompanying changes and easing of restrictions. However, with the exception of China, notable for its robust test, track, trace, and isolate processes, no other countries that had significant numbers of COVID-19 cases have successfully reopened schools without an increase in cases as a consequence.

Whilst reopening of schools following an initial peak and decrease in COVID-19 infections is desirable for a range of reasons, doing so without adequate controls and protections may lead to an exacerbation of spread within the school environment, which could then lead to increased community spread of disease.
Autoimmune and Inflammatory Mechanisms in Cervical Dystonia
Authors: Kilic-Berkmen Gamze , Scorr Laura , Dinasarapu Ashok R. , McKay Lucas , Rosen Ami , Bagchi Pritha , Hanfelt John , McKeon Andrew , Jinnah H. A.
Published: September 2020

There are many causes for cervical dystonia (CD), although most cases are idiopathic and a cause cannot be identified. The observation that 10-15% of cases have an affected family member has pointed to genetic causes, but known genes account for only a small fraction of all cases. The current manuscript describes a series of studies focusing on potential autoimmune or inflammatory mechanisms in CD. First, a case-control survey for 32 autoimmune diseases in 271 subjects with CD confirmed prior anecdotal observations that CD is associated with thyroid disease, which often results from autoimmune mechanisms. Second, unbiased proteomic methods involving a total of 20 subjects with CD, with or without associated thyroid disease, pointed towards a series of overlapping mechanisms relating to the immune system. Third, a multiplex immunoassay focusing on 37 markers associated with neuroinflammation applied to a total of 20 subjects with CD with or without thyroid disease and 20 controls pointed to abnormalities in several specific measures of the immune system. Finally, a broad screening test for neuronal antibodies in a total of 58 subjects with CD did not disclose any specific antibodies. Altogether, the association of CD with thyroid disease and blood-based immune measures point to abnormalities in cell-mediated immunity that may play a pathogenic role for a subgroup of subjects with CD.
Feasibility of Establishing a Return-To-Work Protocol Based on COVID-19 Antibodies Testing
Authors: Okungbowa-Ikponmwosa Jennifer , Mu Yijia , Job Gerard
Published: September 2020

Introduction

Prior to the diagnosis of the first SARS-CoV2 patient in Florida, the Miami Dade Fire Rescue developed and implemented its return-to-work protocol based on guidelines from the CDC and Florida Fire Chiefs Association. As of February 17, 2020, all asymptomatic employees exposed to PCR-confirmed positive SARS-CoV2 individuals would be excluded from work for 14 days and report absence of symptoms to a delegated supervisor every 24 hours. We postulated that if COVID-19 transmission rate continues at the current rate in the absence of systemic vaccination strategy for SARS-CoV2, then a safer and more efficient return-to-work policy is needed for exposed first responders who are identified as low-risk for disease transmission.

Objectives

We sought to establish a safe and shortened return-to-work protocol to maintain our workforce. We evaluated the utility of serological antibody testing in predicting negative seroconversion of first responders at 7 days post low-risk exposure to confirmed COVID-19 individuals.

Methods

All exposed, asymptomatic employees underwent serology testing for SARS-CoV2 one week after the initial exposure. Participants who were serologically negative had follow-up RT-PCR within 24 hours and serology testing 14 days after the initial serological test.

Results

Overall, of the 71 firefighters who have had documented exposures to SARS-CoV2 positive individuals in the fire rescue agency, 41 of 71 had initially negative serology studies. Of the 41 patients with negative serology studies, 20 voluntarily underwent confirmatory PCR testing within one day after serology testing and all 20 participants were negative. Subsequently, out of the 20 participants who underwent serology and PCR testing, 10 participants followed up and underwent repeat serology testing 14 days after exposure and all 10 participants had negative repeat serology tests. The other ten who chose not to retest remained asymptomatic 14 days after exposure.

Conclusions

Although serology testing has limitations, it correlated with negative prediction of disease in low-risk participants with exposures in this study. Serology testing may offer a feasible, alternative return-to-work strategy for fire agencies.
Immunological characteristics govern the changing severity of COVID-19 during the transition to endemicity
Authors: Lavine Jennie S , Bjornstad Ottar N , Antia Rustom
Published: September 2020

1

As prospects for eradicating CoV-2 dwindle, we are faced with the question of how the severity of CoV-2 disease may change in the years ahead. Will CoV-2 continue to be a pathogenic scourge that, like smallpox or measles, can be tamed only by ongoing vaccination, or will it join the ranks of mild endemic human coronaviruses (HCoVs)? Our analysis of immunological and epidemiological data on HCoVs shows that infection-blocking immunity wanes rapidly, but disease-reducing immunity is long-lived. We estimate the relevant parameters and incorporate them into a new epidemiological model framework which separates these different components of immunity. Our model recapitulates both the current severity of CoV-2 and the relatively benign nature of HCoVs; suggesting that once the endemic phase is reached, CoV-2 may be no more virulent than the common cold. The benign outcome at the endemic phase is contingent on the virus causing primary infections in children. We predict a very different outcome were a CoV like MERS (that causes severe disease in children) to become endemic. These results force us to re-evaluate control measures that rely on identifying and isolating symptomatic infections, and reconsider ideas regarding herd immunity and the use of immune individuals as shields to protect vulnerable groups.
Forecasting the outbreak of COVID-19 in Lebanon
Authors: Deeb Omar El , Jalloul Maya
Published: September 2020

This note explores the spread of the Coronavirus disease 2019 (COVID-19) in Lebanon using available data until August 25th, 2020 and forecasts the number of infections until the end of September using four diffierent scenarios for mitigation measures reflected in the reproductive number Rt. Mitigation measures in Lebanon date back to early March soon after the first confirmed cases, and have been gradually lifted as of May. Thereafter, the country has witnessed a slow yet steady increase in the number of cases that has been significantly exacerbated after the explosion at Beirut harbor on August 4. Furthermore, we estimate the daily active cases in need of intensive care compared to the available number of beds and we assess accordingly that this capacity will be exhausted within a short span of time, unless severe measures are imposed.
Switched and unswitched memory B cells detected during SARS-CoV-2 convalescence correlate with limited symptom duration
Authors: Newell Krista L. , Clemmer Deanna C. , Cox Justin B. , Kayode Yetunde I. , Zoccoli-Rodriguez Victoria , Taylor Harry E. , Endy Timothy P. , Wilmore Joel R. , Winslow Gary M.
Published: September 2020

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the pandemic human respiratory illness COVID-19, is a global health emergency. While severe acute disease has been linked to an expansion of antibody-secreting plasmablasts, we sought to identify B cell responses that correlated with positive clinical outcomes in convalescent patients. We characterized the peripheral blood B cell immunophenotype and plasma antibody responses in 40 recovered non-hospitalized COVID-19 subjects that were enrolled as donors in a convalescent plasma treatment study. We observed a significant negative correlation between the frequency of peripheral blood memory B cells and the duration of symptoms for convalescent subjects. Memory B cell subsets in convalescent subjects were composed of classical CD24+class-switched memory B cells, but also activated CD24-negative and natural unswitched CD27+IgD+IgM+subsets. Memory B cell frequency was significantly correlated with both IgG1 and IgM responses to the SARS-CoV-2 spike protein receptor binding domain (RBD).

IgM+memory, but not switched memory, directly correlated with virus-specific antibody responses, and remained stable over time. Our findings suggest that the frequency of memory B cells is a critical indicator of disease resolution, and that IgM+memory B cells play an important role in SARS-CoV-2 immunity.
Public Preferences for Government Response Policies on Outbreak Control
Authors: Ozdemir Semra , Tan Si Ning Germaine , Chaudhry Isha , Maholtra Chetna , Finkelstein Eric Andrew
Published: September 2020

Objectives

To assess the extent to which public support for outbreak containment policies varies with respect to the severity of an infectious disease outbreak.

Methods

A web-enabled survey was administered to 1,017 residents of Singapore during the COVID-19 pandemic, and was quota-sampled based on age, gender and ethnicity. A fractional-factorial design was used to create hypothetical outbreak vignettes characterised by morbidity and fatality rates, and local and global spread of an infectious disease. Each respondent was asked to indicate which response policies (among 5 policies restricting local movement and 4 border control policies) they would support in 5 randomly-assigned vignettes. Binomial logistic regressions were used to predict the probabilities of support as a function of outbreak attributes, personal characteristics and perceived policy effectiveness.

Results

Likelihood of support varied across government response policies; however, was generally higher for border control policies compared to internal policies. The fatality rate was the most important factor for internal policies while the degree of global spread was the most important for border control policies. In general, individuals who were less healthy, had higher income and were older were more likely to support these policies. Perceived effectiveness of a policy was a consistent and positive predictor of public support.

Conclusions

Our findings suggest that campaigns to promote public support should be designed specifically to each policy and tailored to different segments of the population. They should also be adapted based on the evolving conditions of the outbreak in order to receive continued public support.
Long, thin transmission chains of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) may go undetected for several weeks at low to moderate reproductive numbers: Implications for containment and elimination strategy
Authors: Killeen Gerry F.
Published: September 2020

Especially at low to moderate reproductive numbers, the generally mild, non-specific symptomology of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) allows long, thin transmission chains to go undetected by passive surveillance over several weeks. This phenomenon has important implications: (1) Surveillance becomes less sensitive and reliable as an indicator of freedom from infection at the low reproductive numbers required to achieve elimination end points, passive surveillance systems may need to document an absence of new cases for at least a month to establish certainty of elimination. (2) Reproductive numbers should be kept as low as possible throughout such follow up periods without confirmed cases, to ensure such long, thin, undetected transmission chains all collapse before restrictions are eased and reproduction numbers are allowed to rebound. (3) While contact tracing systems may be highly effective when applied to large clusters in foci of elevated transmission where wide, rapidly expanding transmission chains are detected within two viral generations, large fractions of community transmission occurring through thinner, more extended transmission chains at lower reproductive numbers are often be too long to trace retrospectively and will be underrepresented in surveillance data. (4) Wherever surveillance systems are weak and/or younger age groups with lower rates of overt symptoms dominate transmission, containment effectiveness of contact tracing and isolation may be more severely limited, even at the higher reproduction numbers associated with larger outbreaks. While, contact tracing and isolation will remain vital for at least partially containing larger outbreaks, containment and elimination of SARS-CoV-2 will have to rely primarily upon the more burdensome and presumptive population-wide prevention measures that have proven so effective thus far against community transmission. Furthermore, these will have to be sustained at a much more stringent level and for longer periods after the last detected case than was necessary for SARS-CoV-1.
Estimating COVID-19 hospital demand using a non-parametric model: a case study in Galicia (Spain)
Authors: López-Cheda Ana , Jácome María-Amalia , Cao Ricardo , De Salazar Pablo M
Published: September 2020

Understanding the demand for hospital beds for COVID-19 patients is key for decision-making and planning mitigation strategies, as overwhelming healthcare systems has critical consequences for disease mortality. However, accurately mapping the time-to-event of hospital outcomes, such as the length-of-stay in the ICU, requires understanding patient trajectories while adjusting for covariates and observation bias, such as incomplete data. Standard methods, like the Kaplan-Meier estimator, require prior assumptions that are untenable given current knowledge. Using real-time surveillance data from the first weeks of the COVID-19 epidemic in Galicia (Spain), we aimed to model the time-to-event and event probabilities of patients hospitalized, without parametric priors and adjusting for individual covariates. We applied a nonparametric Mixture Cure Model and compared its performance in estimating hospital ward/ICU lengths-of-stay to the performances of commonly used methods to estimate survival. We showed that the proposed model outperformed standard approaches, providing more accurate ICU and hospital ward length-of-stay estimates. Finally, we applied our model estimates to simulate COVID-19 hospital demand using a Monte Carlo algorithm. We provided evidence that adjusting for sex, generally overlooked in prediction models, together with age is key for accurately forecasting ICU occupancy, as well as discharge or death outcomes.
CARE OF PERIPHERAL INTRAVENOUS CATHETERS IN THREE HOSPITALS IN SPAIN: MAPPING CLINICAL OUTCOMES AND IMPLEMENTATION OF CLINICAL PRACTICE GUIDELINES
Authors: Blanco-Mavillard Ian , Parra-García Gaizka , Fernández-Fernández Ismael , Rodríguez-Calero Miguel Ángel , Personat-Labrador Celia , Castro-Sánchez Enrique
Published: September 2020

Background

Peripheral intravenous catheters (PIVCs) are the most widely used invasive devices worldwide. Up to 42% of PIVCs are prematurely removed during intravenous therapy due to failure. To date, there have been few systematic attempts in European hospitals to measure adherence to recommendations to mitigate PIVC failures.

Aim

To analyse the clinical outcomes from clinical practice guideline recommendations for PIVC care on different hospital types and environments.

Methods

We conducted an observational study in three hospitals in Spain from December 2017 to April 2018. The adherence to recommendations was monitored via visual inspection in situ evaluations of all PIVCs inserted in adults admitted. Context and clinical characteristics were collected by an evaluation tool, analysing data descriptively.

Results

646 PIVCs inserted in 624 patients were monitored, which only 52.7% knew about their PIVC. Regarding PIVC insertion, 3.4% (22/646) patients had at least 2 PIVCs simultaneously. The majority of PIVCs were 20G (319/646; 49.4%) and were secured with transparent polyurethane dressing (605/646; 93.7%). Most PIVCs (357/646; 55.3%) had a free insertion site during the visual inspection at first sight. We identified 342/646 (53%) transparent dressings in optimal conditions (clean, dry, and intact dressing). PIVC dressings in medical wards were much more likely to be in intact conditions than those in surgical wards (234/399, 58.7% vs. 108/247, 43.7%). We identified 55/646 (8.5%) PIVCs without infusion in the last 24 hours and 58/646 (9.0%) PIVCs without infusion for more than 24 hours. Regarding PIVC failure, 74 (11.5%) adverse events were identified, all of them reflecting clinical manifestation of phlebitis.

Conclusions

Our findings indicate that the clinical outcome indicators from CPG for PIVC care were moderate, highlighting differences between hospital environments and types. Also, we observed that nearly 50% of patients did not know what a PIVC is.
Large Mammals Have More Powerful Antibacterial Defenses Than Expected from Their Metabolic Rates
Authors: Downs Cynthia J. , Schoenle Laura A. , Goolsby Eric W. , Oakey Samantha J. , Ball Ray , Jiang Rays H.Y. , Klasing Kirk C. , Martin Lynn B.
Published: September 2020

Terrestrial mammals span 7 orders of magnitude in body size, ranging from the < 2 g pygmy shrew (Suncus etruscus) to the > 3900 kg African elephant (Loxodonta africana). Although body size has profound effects on the behavior, physiology, ecology, and evolution of animals, how investment in immune defenses changes with body size is unknown. Here, we develop a novel 12-point dilution-curve approach to describe and compare antibacterial capacity against 3 bacterial species among >160 terrestrial species of mammals. We show that antibacterial activity in serum across mammals exhibits isometry, but the serum of large mammals is less hospitable to bacteria than would be predicted by their metabolic rates. Specifically, hypometric metabolic rates would predict that a large species should have disproportionately lower antibacterial capacity than small species, but body size is unrelated to killing capacity across species. Scaling of antibacterial immune defenses provides novel perspectives on the ecology of host-pathogen interactions, and on their co-evolutionary dynamics. These results have direct implications for effectively modeling the evolution of immune defenses and identifying potential reservoir hosts of zoonotic pathogens.
Fibrinogen anchors for micropatterning of active proteins and subcellular receptor relocalisation
Authors: Watson Joseph L. , Aich Samya , Salvia Benjamí Oller , Drabek Andrew A. , Blacklow Stephen C. , Chin Jason , Derivery Emmanuel
Published: September 2020

Protein micropatterning allows proteins to be precisely deposited onto a substrate of choice, and is now routinely used in cell biology and in vitro reconstitution. However, a drawback of current technology is that micropatterning efficiency can be variable between proteins, and that proteins may lose activity on the micropatterns. Here, we describe a general method to enable micropatterning of virtually any protein at high specificity and homogeneity while maintaining its activity. Our method is based on an anchor that micropatterns well, Fibrinogen, which we functionalized to bind to common purification tags. This enhances micropatterning on various substrates, facilitates multiplexed micropatterning, and dramatically improves the on-pattern activity of fragile proteins like molecular motors. Furthermore, it enhances the micropatterning of hard to micropattern cells. Last, this method enables subcellular micropatterning, whereby complex micropatterns simultaneously control cell shape and the distribution of transmembrane receptors within that cell. Altogether, these results open new avenues for cell biology.
Mutagenic mechanisms of cancer-associated DNA polymerase ε alleles
Authors: Herzog Mareike , Alonso-Perez Elisa , Salguero Israel , Warringer Jonas , Adams David J. , Jackson Stephen P. , Puddu Fabio
Published: September 2020

A single amino acid residue change in the exonuclease domain of human DNA polymerase ε, P286R, is associated with the development of colorectal cancers, and has been shown to impart a mutagenic phenotype. Perhaps unexpectedly, the corresponding Pol ε allele in the yeastSaccharomyces cerevisiae(pol2-P301R), was found to drive greater mutagenesis than exonuclease-deficient Pol ε (pol2-4), a phenotype sometimes termedultra-mutagenesis. By studying the impact on mutation frequency, type, replication-strand bias, and sequence context, we show thatultra-mutagenesis is commonly observed in cells carrying a range of cancer-associated Pol ε exonuclease domain alleles. Similarities between mutations generated by these alleles and those generated inpol2-4cells indicate a shared mechanism of mutagenesis that yields a mutation pattern similar to cancer Signature 14. Comparison ofPOL2 ultra-mutator withpol2-M644G, a mutant in the polymerase domain decreasing Pol ε fidelity, revealed unexpected analogies in the sequence context and strand bias of mutations. Analysis of mutational patterns unique to exonuclease domain mutant cells suggests that backtracking of the polymerase, when the mismatched primer end cannot be accommodated in the proofreading domain, results in the observed increase in insertions and T>A mutations in specific sequence contexts.
Ratio of hydrophobic-hydrophilic and positive-negative residues at lipid-water-interface influences surface expression and channel-gating of TRPV1
Authors: Saha Somdatta , Das Rashmita , Divyanshi Divyanshi , Tiwari Nikhil , Tiwari Ankit , Dalai Ritesh , Kumar Abhishek , Goswami Chandan
Published: September 2020

During evolution, TRPV1 has lost, retained or selected certain residues at Lipid-Water-Interface (LWI) and formed specific patterns there. The ratio of “hydrophobic-hydrophilic” and “positive-negative charged” residues at the inner LWI remains conserved throughout vertebrate evolution and play important role in regulating TRPV1 trafficking, localization and functions. Arg575 is an important residue as Arg575Asp mutant has reduced Capsaicin-sensitivity, surface expression, colocalization with lipid-raft markers, cell area, and increased cell lethality. This lethality is due to the disruption of the ratio between positive-negative charges there. Such lethality can be rescued by either using TRPV1-specfic inhibitor 5’-IRTX or by restoring the positive-negative charge ratio at that position, i.e. by introducing Asp576Arg mutation in Arg575Asp backbone. We propose that Arg575Asp mutant confers TRPV1 in a “constitutive-open-like” condition. These findings have broader implication in understanding the molecular basis of thermo-gating and channel-gating and the microenvironments involved in such process that goes erratic in different diseases.
Monoclonal Antibodies Capable of Binding SARS-CoV-2 Spike Protein Receptor Binding Motif Specifically Prevent GM-CSF Induction
Authors: Qiang Xiaoling , Zhu Shu , Li Jianhua , Wang Ping , Tracey Kevin J. , Wang Haichao
Published: September 2020

A severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) has recently caused a pandemic COVID-19 disease that infected more than 25.6 million and killed 852,000 people worldwide. Like the SARS-CoV, SARS-CoV-2 also employs a receptor-binding motif (RBM) of its envelope spike protein for binding the host angiotensin-converting enzyme 2 (ACE2) to gain viral entry. Currently, extensive efforts are being made to produce vaccines against a surface fragment of a SARS-CoV-2, such as the spike protein, in order to boost protective antibody responses. It was previously unknown how spike protein-targeting antibodies would affect innate inflammatory responses to SARS-CoV-2 infections. Here we generated a highly purified recombinant protein corresponding to the RBM of SARS-CoV-2, and used it to screen for cross-reactive monoclonal antibodies (mAbs). We found two RBM-binding mAbs that competitively inhibited its interaction with human ACE2, and specifically blocked the RBM-induced GM-CSF secretion in both human monocyte and murine macrophage cultures. Our findings have suggested a possible strategy to prevent SARS-CoV-2-elicited “cytokine storm”, and provided a potentially useful criteria for future assessment of innate immune-modulating properties of various SARS-CoV-2 vaccines.

One Sentence Summary

RBM-binding Antibodies Inhibit GM-CSF Induction.
Chemical validation ofMycobacterium tuberculosisphosphopantetheine adenylyltransferase using fragment linking and CRISPR interference
Authors: El Bakali Jamal , Blaszczyk Michal , Evans Joanna C. , Boland Jennifer A. , McCarthy William J. , Dias Marcio V. B. , Coyne Anthony G. , Mizrahi Valerie , Blundell Tom L. , Abell Chris , Spry Christina
Published: September 2020

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused byMycobacterium tuberculosis (Mtb). Seeking to identify the first inhibitors ofMtbphosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of theMtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a KD< 20 μM and on-target anti-Mtbactivity, as demonstrated using CRISPR interference. This study represents a big step toward validatingMtbPPAT as a potential drug target and designing aMtbPPAT-targeting anti-TB drug.

Abstract Figure
The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis
Authors: Stagsted Lotte Victoria Winther , O’Leary Eoghan Thomas , Hansen Thomas Birkballe
Published: September 2020

Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs, however the principles of biogenesis are currently not fully understood. To elucidate features important for circRNA production, we performed global analyses of RNA-binding proteins associating with the flanking introns of circRNAs, and we identified two factors, SFPQ and NONO, to be highly enriched with circRNAs. Using transient knockdown of both proteins in two human cell lines followed by total RNAseq, we found a subclass of circRNAs with distal invertedAluelements and long introns to be highly deregulated upon SFPQ knockdown. In addition, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing prevalent for long introns causing in some cases premature transcription termination and polyadenylation. While SFPQ depletion has an overall negative effect on circRNA production, premature termination is not the main causative explanation. Instead, data suggests that aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we observe a conserved impact of missplicing in the immediate upstream region to drive circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governingAlu-independent circRNA production.
Intensity coded octopaminergic modulation of aversive crawling behavior inDrosophila melanogasterlarvae
Authors: Bilz Florian , Gilles Madeleine-Marie , Schatton Adriana , Pflüger Hans-Joachim , Schubert Marco
Published: September 2020

Activation and modulation of sensory-guided behaviors by biogenic amines assure appropriate adaptations to changes in an insect’s environment. Given its genetic tool kitDrosophila melanogasterrepresents an excellent model organism to study larger networks of neurons by optophysiological methods. Here, we studied stationary crawling movements of 3rdinstar larvae and revealed how the octopaminergic VUM neuron system reacts during crawling behavior and tactile stimulations. We conducted calcium imaging experiments on dissections of the isolated nervous system (missing all sensory input) and found spontaneous rhythmic wave pattern of neuronal activity in VUM neuron clusters over the range of thoracic and abdominal neuromeres in the VNC. In contrast,in vivopreparations (semi-intact animals, receiving sensory input) did not reveal such spontaneous rhythmic pattern. However, tactile stimulations activated different clusters of the VUM neuron system simultaneously in these preparations. The activation intensity of VUM neurons in the VNC was correlated with the location and degree of body wall stimulation. While VUM neuron cluster near the respective location of body wall stimulation were less activated more distant cluster showed stronger activation. Repeated gentle touch stimulations led to decreased response intensities, repeated harsh stimulations resulted in increasing intensities over trials. Optophysiological signals correlated highly with crawling behavior in freely moving larvae stimulated similarly. We conclude that the octopaminergic system is strongly coupled to the neuronal pattern generator of crawling movements and that it is simultaneously activated by physical stimulation, rather intensity than sequential coded. We hope that our work raises the interest in whole biogenic network activity and shows that octopamine release does not only underlie “the more the better” principle but instead has a more complex function in control and modulation of insect’s locomotion.
Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization
Authors: Brovkina Margarita V. , Duffié Rachel , Burtis Abbigayl E. C. , Clowney E. Josephine
Published: September 2020

In the fruit flyDrosophila melanogaster, male-specific splicing and translation of the Fruitless transcription factor (FruM) alters the presence, anatomy, and/or connectivity of >60 types of central brain neurons that interconnect to generate male-typical behaviors. While the indispensable function of FruMin sex-specific behavior has been understood for decades, the molecular mechanisms underlying its activity remain unknown. Here, we take a genome-wide, brain-wide approach to identifying regulatory elements whose activity depends on the presence of FruM. We identify 436 high-confidence genomic regions differentially accessible in malefruitlessneurons, validate candidate regions as bona-fide, differentially regulated enhancers, and describe the particular cell types in which these enhancers are active. We find that individual enhancers are not activated universally but are dedicated to specificfru+cell types. Aside fromfruitself, genes are not dedicated to or common across thefrucircuit; rather, FruMappears to masculinize each cell type differently, by tweaking expression of the same effector genes used in other circuits. Finally, we find FruMmotifs enriched among regulatory elements that are open in the female but closed in the male. Together, these results suggest that FruMacts cell-type-specifically to decommission regulatory elements in malefruitlessneurons.
Development of Resistance to 4’-Ethynyl-2-Fluoro-2’-Deoxyadenosine (EFdA) by WT and Nucleoside Reverse Transcriptase Inhibitor Resistant Human Immunodeficiency Virus Type 1
Authors: Cilento Maria E. , Michailidis Eleftherios , Ilina Tatiana V. , Nagy Eva , Mitsuya Hiroaki , Parniak Michael A. , Tedbury Philip R. , Sarafianos Stefan G.
Published: September 2020

4’-ethynyl-2-fluoro-2’-deoxyadenosine (EFdA, MK-8591, islatravir) is a nucleoside reverse transcriptase translocation inhibitor (NRTTI) with exceptional potency against WT and drug-resistant HIV strains. However, HIV resistance to EFdA is not well characterized. We therefore developed resistance to EFdA by serial passages using progressively increasing concentrations of EFdA. The starting virus was either WT or clinically relevant NRTI-resistant viruses K65R, M184V, and D67N/K70R/T215F/K219Q). In all cases, the selected mutations included M184V. Additional mutations in the RT connection domain (R358K and E399K) and one mutation in the RNase H domain (A502V) were noted. Site-specific mutagenesis validated the role for M184V as the primary determinant for resistance to EFdA; none of the connection domain mutations contributed significantly to phenotypic resistance to EFdA. A novel EFdA resistance mutation was also observed in the background of M184V. The A114S/M184V combination of mutations imparted higher resistance to EFdA (~24-fold) than M184V (−8-fold) or A114S (~2-fold) alone. Virus fitness data suggested that A114S affects HIV fitness by itself and in the presence of M184V. This is consistent with biochemical experiments that showed decreases in the enzymatic efficiency (kcat/Km) of WT RTvs.A114S (2.1-fold) and A114S/M184V/502V (6.5-fold), whereas there was no significant effect of A502V on RT or virus fitness. The observed EFdA resistance of M184V by itself and in combination with A114S combined with the strong publishedin vitroandin vivodata, confirm that EFdA is an excellent candidate as a potential HIV therapeutic.
A conserved choreography of mRNAs at centrosomes reveals a localization mechanism involving active polysome transport
Authors: Safieddine Adham , Coleno Emeline , Traboulsi Abdel-Meneem , Kwon Oh Sung , Lionneton Frederic , Georget Virginie , Robert Marie-Cécile , Gostan Thierry , Lecellier Charles , Salloum Soha , Chouaib Racha , Pichon Xavier , Le Hir Hervé , Zibara Kazem , Peter Marion , Bertrand Edouard
Published: September 2020

Local translation allows for a spatial control of gene expression. Here, we used high-throughput smFISH to screen centrosomal protein-coding genes, and we describe 8 human mRNAs accumulating at centrosomes. These mRNAs localize at different stages during cell cycle with a remarkable choreography, indicating a finely regulated translational program at centrosomes. Interestingly, drug treatments and reporter analyses revealed a common translation-dependent localization mechanism requiring the nascent protein. Using ASPM and NUMA1 as models, single mRNA and polysome imaging revealed active movements of endogenous polysomes towards the centrosome at the onset of mitosis, when these mRNAs start localizing. ASPM polysomes associate with microtubules and localize by either motor-driven transport or microtubule pulling. Remarkably, theDrosophilaorthologs of the human centrosomal mRNAs also localize to centrosomes and also require translation. These data identify a conserved family of centrosomal mRNAs that localize by active polysomes transport mediated by nascent proteins.
Mitochondrial, cell cycle control and neuritogenesis alterations in an iPSC-based neurodevelopmental model for schizophrenia
Authors: Zuccoli Giuliana S. , Nascimento Juliana M. , Codo Ana Campos , Moraes-Vieira Pedro M. , Rehen Stevens K. , Martins-de-Souza Daniel
Published: September 2020

Schizophrenia is a severe psychiatric disorder of neurodevelopmental origin that affects around 1% of the world’s population. Proteomic studies and other approaches have provided evidence of compromised cellular processes in the disorder, including mitochondrial function. Most of the studies so far have been conducted on postmortem brain tissue from patients and do not allow the evaluation of the neurodevelopmental aspect of the disorder. To circumvent that, we studied the mitochondrial and nuclear proteomes of neural stem cells (NSCs) and neurons derived from induced pluripotent stem cells (iPSCs) from schizophrenia patients versus healthy controls. Our results revealed differentially regulated proteins in pathways related to mitochondrial function, oxidative phosphorylation, cell cycle control, DNA repair, and neuritogenesis. Moreover, metabolic analysis of NSCs revealed alterations in mitochondrial function in schizophrenia-derived cells. Hence, this study shows that changes in important cellular processes are present during neurodevelopment and could be involved with the establishment of schizophrenia, as well as the phenotypic traits observed in adult patients.
Cholinergic neuromodulation of inhibitory interneurons facilitates functional integration in whole-brain models
Authors: Coronel-Oliveros Carlos , Cofré Rodrigo , Orio Patricio
Published: September 2020

Segregation and integration are two fundamental principles of brain structural and functional organization. Neuroimaging studies have shown that the brain transits between different functionally segregated and integrated states, and neuromodulatory systems have been proposed as key to facilitate these transitions. Although computational models have reproduced the effect of neuromodulation at the whole-brain level, the role of local inhibitory circuits and their cholinergic modulation has not been studied. In this article, we consider a Jansen & Rit whole-brain model in a network interconnected using a human connectome, and study the influence of the cholinergic and noradrenergic neuromodulatory systems on the segregation/integration balance. In our model, a newly introduced local inhibitory feedback enables the integration of whole-brain activity, and its modulation interacts with the other neuromodulatory influences to facilitate the transit between different functional states. Moreover, the new proposed model is able to reproduce an inverted-U relationship between noradrenergic modulation and network integration. Our work proposes a new possible mechanism behind segregation and integration in the brain.
Non-permissive human conventional CD1c+dendritic cells enabletrans-infection of human primary renal tubular epithelial cells and protect BK polyomavirus from neutralization
Authors: Sikorski Mathieu , Coulon Flora , Peltier Cécile , Braudeau Cécile , Garcia Alexandra , Giraud Matthieu , Renaudin Karine , Kandel-Aznar Christine , Nedellec Steven , Hulin Philipe , Branchereau Julien , Véziers Joëlle , Gaboriaud Pauline , Touzé Antoine , Burlaud-Gaillard Julien , Josien Régis , McIlroy Dorian , Bressollette-Bodin Céline , Halary Franck
Published: September 2020

The BK polyomavirus (BKPyV) is a ubiquitous human virus that persists in the renourinary epithelium. Immunosuppression can lead to BKPyV reactivation in the first year post-transplantation in kidney (KTR) and hematopoietic stem cell transplant recipients. In KTR, persistent DNAemia has been correlated to the occurrence of polyomavirus-associated nephropathy (PVAN) that can lead to graft loss if not properly controlled. Based on recent observations that conventional dendritic cells (cDC) specifically infiltrate PVAN lesions, we hypothesized that those cells could play a role in BKPyV infection. We first demonstrated that monocyte-derived DC (MDDC), anin vitromodel for mDC, captured BKPyV particles through an unconventional GRAF-1 endocytic pathway. Neither BKPyV particles nor BKPyV-infected cells were shown to activate MDDC. Endocytosed virions were efficiently transmitted to permissive cells and shown to be protected from the antibody-mediated neutralization. Finally, we demonstrated that freshly isolated CD1c+mDC from the blood and kidney parenchyma behaved similarly to MDDC thus extending our results to cells of clinical relevance. This study sheds light on a potential unprecedented CD1c+mDC involvement in the BKPyV infection as a promoter of viral spreading.