bluuebunny/crossref_metadata_2025 huggingface dataset:
Between Geography and Demography: Key Interdependencies and Exit Mechanisms for Covid-19
Authors: Scala Antonio , Flori Andrea , Spelta Alessandro , Brugnoli Emanuele , Cinelli Matteo , Quattrociocchi Walter , Pammolli Fabio
Published: April 2020

We develop a minimal compartmental model to analyze policies on mobility restriction in Italy during the Covid-19 outbreak. Our findings show that a premature lockdown barely shifts the epidemic in time: moreover, beyond a critical value of the lockdown strength, an epidemic that seems to be quelled fully recovers after lifting the restrictions. We investigate the effects on lockdown scenarios and exit strategies by introducing heterogeneities in the model. In particular, we consider Italian regions as separate administrative entities in which social interactions through different age classes occur. We find that, due to the sparsity of the mobility matrix, epidemics develop independently in different regions once the outbreak starts. Moreover, after the epidemics ha started, the influence of contacts with other regions becomes soon irrelevant. Sparsity might be responsible for the observed delays among different regions. Analogous arguments apply to the world/countries scenario. We also find that disregarding the structure of social contacts could lead to severe underestimation of the post-lockdown effects. Nevertheless, age class based strategies can help to mitigate rebound effects with milder strategies. Finally, we point out that these results can be generalized beyond this particular model by providing a description of the effects of key parameters on non-medical epidemic mitigation strategies.
Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level
Authors: Leary Shay , Gaudieri Silvana , Parker Matthew D. , Chopra Abha , James Ian , Pakala Suman , Alves Eric , John Mina , Lindsey Benjamin B. , Keeley Alexander J , Rowland-Jones Sarah L. , Swanson Maurice S. , Ostrov David A. , Bubenik Jodi L. , Das Suman , Sidney John , Sette Alessandro ,   COVID-19 Genomics UK (COG-UK) consortium, de Silva Thushan I. , Phillips Elizabeth , Mallal Simon
Published: April 2020

Background

Genetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the host’s anti-viral immune response, in turn affecting the frequency of variants over-time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally.

Methods

Deep sequencing data of SARS-CoV-2 from public databases and from clinical samples were analyzed to identify and map genetic variants and sub-genomic RNA transcripts across the genome.

Results

Sequence analysis suggests that the three adjacent nucleotide changes that result in the K203/R204 variant have arisen by homologous recombination from the core sequence (CS) of the leader transcription-regulating sequence (TRS) rather than by stepwise mutation. The resulting sequence changes generate a novel sub-genomic RNA transcript for the C-terminal dimerization domain of nucleocapsid. Deep sequencing data from 981 clinical samples confirmed the presence of the novel TRS-CS-dimerization domain RNA in individuals with the K203/R204 variant. Quantification of sub-genomic RNA indicates that viruses with the K203/R204 variant may also have increased expression of sub-genomic RNA from other open reading frames.

Conclusions

The finding that homologous recombination from the TRS may have occurred since the introduction of SARS-CoV-2 in humans resulting in both coding changes and novel sub-genomic RNA transcripts suggests this as a mechanism for diversification and adaptation within its new host.
Environmental enrichment alleviates the deleterious effects of stress in experimental autoimmune encephalomyelitis
Authors: Fournier Antoine Philippe , Baudron Erwan , Wagnon Isabelle , Aubert Philippe , Vivien Denis , Neunlist Michel , Bardou Isabelle , Docagne Fabian
Published: April 2020

Clinical observations support the hypothesis that stressful events increase relapse occurrence in multiple sclerosis patients, while stress-reduction strategies can modulate this effect. However, a direct cause-effect relationship between stress level and relapse cannot be firmly established from these data. The purpose of this work was to address whether modulation of stress could interfere with symptom relapse in an animal model of multiple sclerosis with relapsing-remitting course. We report that repeated acute stress induced a twofold increase in relapse incidence in experimental autoimmune encephalomyelitis. On the other hand, environmental enrichment reduced relapse incidence and severity, and reversed the effects of repeated acute stress. These data provide the platform for further studies on the biological processes that link stress and multiple sclerosis relapses in a suitable animal model.
Competition for glutamate between NMDA and AMPA receptors prevents runaway synaptic dynamics
Authors: Guo Qingchen
Published: April 2020

Homeostatic plasticity is an important guarantee for proper neural function. However, long term potentiation (LTP) was thought of as positive feedback in Hebbian plasticity. In this condition, synapse after potentiation is prone to be further potentiated. This can cause runaway dynamics of synapse and affect the stability of neural network. In order to prevent runaway synaptic dynamics, negative feedback is needed. Upon induction of LTP, the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors was increased in the postsynaptic density (PSD). Due to the competition for glutamate between AMPA receptors and N-Methyl-D-aspartic acid (NMDA) receptors, the number of opened NMDA receptor channels will reduce. Since the induction of LTP is NMDA receptors dependent, reduction of the number of activated NMDA receptors will increase the threshold of LTP induction. So the LTP of synapse itself can form a negative feedback to LTP induction. To test this hypothesis, a synaptic model with NMDA receptors and AMPA receptors coexisted was developed. When the number of AMPA receptors was increased in the PSD, the number of opened NMDA receptors was reduced though the same number of glutamate was released from presynaptic terminal. This will increase the threshold of further LTP induction and stability of synapse and neural network.
Nanovibrational stimulation of mesenchymal stem cells induces therapeutic reactive oxygen species and inflammation for 3D bone tissue engineering
Authors: Orapiriyakul Wich , Tsimbouri Penelope M. , Childs Peter G. , Campsie Paul , Wells Julia , Fernandez-Yague Marc , Burgess Karl , Tanner K. Elizabeth , Tassieri Manlio , Meek R.M. Dominic , Vassalli Massimo , Biggs Manus JP , Salmerón-Sánchez Manuel , Oreffo Richard O.C. , Reid Stuart , Dalby Matthew J
Published: April 2020

There is a pressing clinical need to develop cell-based bone therapies due to a lack of viable, autologous bone grafts and a growing demand for bone grafts in musculoskeletal surgery. Such therapies can be tissue engineered and cellular, such as osteoblasts combined with a material scaffold. Because mesenchymal stem cells (MSCs) are both available and fast growing compared to mature osteoblasts, therapies that utilise these progenitor cells are particularly promising. We have developed a nanovibrational bioreactor that can convert MSCs into bone-forming osteoblasts in 2D and 3D but the mechanisms involved in this osteoinduction process remain unclear. Here, to elucidate this mechanism, we use increasing vibrational amplitude, from 30 nm (N30) to 90 nm (N90) amplitudes at 1000 Hz, and assess MSC metabolite, gene and protein changes. These approaches reveal that dose-dependent changes occur in MSCs’ responses to increased vibrational amplitude, particularly in adhesion and mechanosensitive ion channel expression, and that energetic metabolic pathways are activated, leading to low-level reactive oxygen species (ROS) production and to low-level inflammation, as well as to ROS- and inflammation-balancing pathways. These events are analogous to those that occur in the natural bone-healing processes. We have also developed a tissue engineered MSC-laden scaffold designed using cells’ mechanical memory, driven by the stronger N90 stimulation. These new mechanistic insights and cell-scaffold design are underpinned by a process that is free of inductive chemicals.
Multiobjective Optimization Identifies Cancer-Selective Combination Therapies
Authors: Pulkkinen Otto I. , Gautam Prson , Mustonen Ville , Aittokallio Tero
Published: April 2020

Combinatorial therapies are required to treat patients with advanced cancers that have become resistant to monotherapies through rewiring of redundant pathways. Due to a massive number of potential drug combinations, there is a need for systematic approaches to identify safe and effective combinations for each patient, using cost-effective methods. Here, we developed an exact multiobjective optimization method for identifying pairwise or higher-order combinations that show maximal cancer-selectivity. The prioritization of patient-specific combinations is based on Pareto-optimization in the search space spanned by the therapeutic and nonselective effects of combinations. We demonstrate the performance of the method in the context of BRAF-V600E melanoma treatment, where the optimal solutions predicted a number of co-inhibition partners for vemurafenib, a selective BRAF-V600E inhibitor, approved for advanced melanoma. We experimentally validated many of the predictions in BRAF-V600E melanoma cell line, and the results suggest that one can improve selective inhibition of BRAF-V600E melanoma cells by combinatorial targeting of MAPK/ERK and other compensatory pathways using pairwise and third-order drug combinations. Our mechanism-agnostic optimization method is widely applicable to various cancer types, and it takes as input only measurements of a subset of pairwise drug combinations, without requiring target information or genomic profiles. Such data-driven approaches may become useful for functional precision oncology applications that go beyond the cancer genetic dependency paradigm to optimize cancer-selective combinatorial treatments.
Traumatic Joint Injury Induces Acute Catabolic Bone Turnover Concurrent with Articular Cartilage Damage in a Rat Model of Post-Traumatic Osteoarthritis
Authors: Maerz Tristan , Newton Michael D. , Fleischer Mackenzie , Hartner Samantha E. , Gawronski Karissa , Junginger Lucas , Baker Kevin C.
Published: April 2020

Objective

Assess acute alterations in bone turnover, microstructure, and histomorphometry following noninvasive anterior cruciate ligament rupture (ACLR).

Methods

Twelve female Lewis rats were randomized to receive noninvasive ACLR or Sham loading (n=6/group). In vivoμCT was performed at 3, 7, 10, and 14 days post-injury to quantify compartment-dependent subchondral (SCB) and epiphyseal trabecular bone remodeling. Near-infrared (NIR) molecular imaging was used to measurein vivobone anabolism (800 CW BoneTag) and catabolism (Cat K 680 FAST). Metaphyseal bone remodeling and articular cartilage morphology was quantified usingex vivoμCT and contrast-enhanced µCT, respectively. Calcein-based dynamic histomorphometry was used to quantify bone formation. OARSI scoring was used to assess joint degeneration, and osteoclast number was quantified on TRAP stained-sections.

Results

ACLR induced acute catabolic bone remodeling in subchondral, epiphyseal, and metaphyseal compartments. Thinning of medial femoral condyle (MFC) SCB was observed as early as 7 days post-injury, while lateral femoral condyles (LFC) exhibited SCB gains. Trabecular thinning was observed in MFC epiphyseal bone, with minimal changes to LFC. NIR imaging demonstrated immediate and sustained reduction of bone anabolism (∼15-20%), and a ∼32% increase in bone catabolism at 14 days, compared to contralateral limbs. These findings were corroborated by reduced bone formation rate and increased osteoclast numbers, observed histologically. ACLR-injured femora had significantly elevated OARSI score, cartilage thickness, and cartilage surface deviation.

Conclusion

ACL rupture induces immediate and sustained reduction of bone anabolism and overactivation of bone catabolism, with mild-to-moderate articular cartilage damage at 14 days post-injury.
Discovery of pharmaceutically-targetable pathways and prediction of survivorship for pneumonia and sepsis patients from the view point of ensemble gene noise
Authors: de Jong Tristan , Guryev Victor , Moshkin Yury M.
Published: April 2020

Finding novel biomarkers for human pathologies and predicting clinical outcomes for patients is rather challenging. This stems from the heterogenous response of individuals to disease which is also reflected in the inter-individual variability of gene expression responses. This in turn obscures differential gene expression analysis (DGE). In the midst of the COVID-19 pandemic, we wondered whether an alternative to DGE approaches could be applied to dissect the molecular nature of a host-response to infection exemplified here by an analysis of H1N1 influenza, community/hospital acquired pneumonia (CAP) and sepsis. To this end, we turned to the analysis of ensemble gene noise. Ensemble gene noise, as we defined it here, represents a variance within an individual for a collection of genes encoding for either members of known biological pathways or subunits of annotated protein complexes. From the law of total variance, ensemble gene noise depends on the stoichiometry of the ensemble genes’ expression and on their average noise (variance). Thus, rather than focusing on specific genes, ensemble gene noise allows for the holistic identification and interpretation of gene expression disbalance on the level of gene networks and systems. Comparing H1N1, CAP and sepsis patients we spotted common disturbances in a number of pathways/protein complexes relevant to the sepsis pathology which lead to an increase in the ensemble gene noise. Among others, these include mitochondrial respiratory chain complex I and peroxisomes which could be readily targeted for adjuvant treatment by methylene blue and 4-phenylbutyrate respectively. Finally, we showed that ensemble gene noise could be successfully applied for the prediction of clinical outcome, namely mortality, of CAP and sepsis patients. Thus, we conclude that ensemble gene noise represents a promising approach for the investigation of molecular mechanisms of a pathology through a prism of alterations in coherent expression of gene circuits.
Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice
Authors: Holmes Zachary C. , Silverman Justin D. , Dressman Holly K. , Wei Zhengzheng , Dallow Eric P. , Armstrong Sarah C. , Seed Patrick C. , Rawls John F. , David Lawrence A.
Published: April 2020

Pediatric obesity remains a public health burden and continues to increase in prevalence. The gut microbiota plays a causal role in obesity and is a promising therapeutic target. Specifically, the microbial production of short-chain fatty acids (SCFA) from the fermentation of otherwise indigestible dietary carbohydrates may protect against pediatric obesity and metabolic syndrome. Still, it has not been demonstrated that therapies involving microbiota-targeting carbohydrates, known as prebiotics, will enhance gut bacterial SCFA production in children and adolescents with obesity (age 10-18). Here, we used an in vitro system to examine the SCFA production by fecal microbiota from 17 children with obesity when exposed to five different commercially available over-the-counter (OTC) prebiotic supplements. We found microbiota from all 17 patients actively metabolized most prebiotics. Still, supplements varied in their acidogenic potential. Significant inter-donor variation also existed in SCFA production, which 16S rRNA sequencing supported as being associated with differences in the host microbiota composition. Last, we found that neither fecal SCFA concentration, microbiota SCFA production capacity, nor markers of obesity positively correlated with one another. Together, these in vitro findings suggest the hypothesis that OTC prebiotic supplements may be unequal in their ability to stimulate SCFA production in children and adolescents with obesity, and that the most acidogenic prebiotic may differ across individuals.

IMPORTANCE

Pediatric obesity remains a major public health problem in the US, where 17% of children and adolescents are obese, and rates of pediatric ‘severe obesity’ are increasing. Children and adolescents with obesity face higher health risks, and non-invasive therapies for pediatric obesity often have limited success. The human gut microbiome has been implicated in adult obesity, and microbiota-directed therapies can aid weight loss in adults with obesity. However, less is known about the microbiome in pediatric obesity, and microbiota-directed therapies are understudied in children and adolescents. Our research has two important findings: 1) dietary prebiotics (fiber) cause the microbiota from adolescents with obesity to produce more SCFA, and 2) the effectiveness of each prebiotic is donor-dependent. Together, these findings suggest that prebiotic supplements could help children and adolescents with obesity, but that these therapies may not be one-size-fits-all.
Scutellaria baicalensisextract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like proteasein vitro
Authors: Liu Hongbo , Ye Fei , Sun Qi , Liang Hao , Li Chunmei , Lu Roujian , Huang Baoying , Tan Wenjie , Lai Luhua
Published: April 2020

COVID-19 has become a global pandemic that threatens millions of people worldwide. There is an urgent call for developing effective drugs against the virus (SARS-CoV-2) causing this disease. The main protease of SARS-CoV-2, 3C-like protease (3CLpro), is highly conserved across coronaviruses and is essential for the maturation process of viral polyprotein. Scutellariae radix (Huangqin in Chinese), the root ofScutellaria baicalensishas been widely used in traditional Chinese medicine to treat viral infection related symptoms. The extracts ofS. baicalensishave exhibited broad spectrum antiviral activities. We studied the anti-SARS-CoV-2 activity ofS. baicalensisand its ingredient compounds. We found that the ethanol extract ofS. baicalensisinhibits SARS-CoV-2 3CLproactivityin vitroand the replication of SARS-CoV-2 in Vero cells with an EC50of 0.74 μg/ml. Among the major components ofS. baicalensis, baicalein strongly inhibits SARS-CoV-2 3CLproactivity with an IC50of 0.39 μM. We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLproactivity at microM concentration. Our study demonstrates that the extract ofS. baicalensishas effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLproinhibitors.
Positive selection of ORF3a and ORF8 genes drives the evolution of SARS-CoV-2 during the 2020 COVID-19 pandemic
Authors: Velazquez-Salinas Lauro , Zarate Selene , Eberl Samantha , Gladue Douglas P. , Novella Isabel , Borca Manuel V.
Published: April 2020

In this study, we analyzed full-length SARS-CoV-2 genomes from multiple countries to determine early trends in the evolutionary dynamics of the novel COVID-19 pandemic. Results indicated SARS-CoV-2 evolved early into at least three phylogenetic groups, characterized by positive selection at specific residues of the accessory proteins OFR3a and ORF8a. We also report evidence of epistatic interactions among sites in the genome that may be important in the generation of variants adapted to humans. These observations might impact not only public health, but also suggest more studies are needed to understand the genetic mechanisms that may affect the development of therapeutic and preventive tools, like antivirals and vaccines.
Analysis of Ten Microsecond simulation data of SARS-CoV-2 dimeric main protease
Authors: Parves Md. Rimon , Riza Yasir Mohamed , Mahmud Shafi , Islam Rajib , Ahmed Sinthyia , Evy Bibi Ashiana , Hasanuzzaman Md. , Halim Mohammad A
Published: April 2020

The authors have withdrawn this manuscript because of a violation of research ethics. Unknown to the first author, the corresponding author - the main designer of the project - did not obtain consent for the use of a data-set. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author”
The SARS-CoV-2 receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement
Authors: Quinlan Brian D. , Mou Huihui , Zhang Lizhou , Guo Yan , He Wenhui , Ojha Amrita , Parcells Mark S. , Luo Guangxiang , Li Wenhui , Zhong Guocai , Choe Hyeryun , Farzan Michael
Published: April 2020

The SARS-coronavirus 2 (SARS-CoV-2) spike (S) protein mediates entry of SARS-CoV-2 into cells expressing the angiotensin-converting enzyme 2 (ACE2). The S protein engages ACE2 through its receptor-binding domain (RBD), an independently folded 197-amino acid fragment of the 1273-amino acid S-protein protomer. Antibodies to the RBD domain of SARS-CoV (SARS-CoV-1), a closely related coronavirus which emerged in 2002-2003, have been shown to potently neutralize SARS-CoV-1 S-protein-mediated entry, and the presence of anti-RBD antibodies correlates with neutralization in SARS-CoV-2 convalescent sera. Here we show that immunization with the SARS-CoV-2 RBD elicits a robust neutralizing antibody response in rodents, comparable to 100 µg/ml of ACE2-Ig, a potent SARS-CoV-2 entry inhibitor. Importantly, anti-sera from immunized animals did not mediate antibody-dependent enhancement (ADE) of S-protein-mediated entry under conditions in which Zika virus ADE was readily observed. These data suggest that an RBD-based vaccine for SARS-CoV-2 could be safe and effective.
Magnetic Bead-Quantum Dot (MB-Qdot) CRISPR Assay for Instrument-Free Viral DNA Detection
Authors: Bao Mengdi , Jensen Erik , Chang Yu , Korensky Grant , Du Ke
Published: April 2020

We have developed a novel detection system which couples CRISPR-Cas recognition of target sequences, Cas mediated nucleic acid probe cleavage, and quantum dots as highly sensitive reporter molecules for instrument-free detection of viral nucleic acid targets. After target recognition and Cas mediated cleavage of biotinylated ssDNA probe molecules, the probe molecules are bound to magnetic particles. A complimentary ssDNA oligonucleotide quantum dot conjugate is then added, which only hybridizes to un-cleaved probes on the magnetic beads. After separation of hybridized from unhybridized quantum dot conjugates by magnetic sequestration, the signal is measured fluorometrically to provide a signal proportional to the cleaved probes and therefore the amount of target nucleic acid. To demonstrate the power of this assay, a 250 bp DNA target sequence matching a portion of the African swine fever virus (ASFV) genome is used and a detection limit of ~0.5 nM is achieved without target amplification using a simple portable ultraviolet flashlight. The positive samples are readily confirmed by visual inspection, completely avoiding the need for complicated devices and instruments. This work establishes the feasibility of a simple, instrument free assay for rapid nucleic acid screening in both hospitals and point-of-care settings.
Clinical features and management of severe COVID-19: A retrospective study in Wuxi, Jiangsu Province, China
Authors: Jiang Xiufeng , Tao Jianxin , Wu Hui , Wang Yixin , Zhao Wei , Zhou Min , Huang Jiehui , You Qian , Hua Meng , Zhu Feng , Zhang Xiaoqing , Qian Meifang , Qiu Yuanwang
Published: April 2020

Objective

We aimed to investigate clinical features and management of 55 COVID-19 patients in Wuxi, especially severe COVID-19.

Methods

Epidemiological, demographic, clinical, laboratory, imaging, treatment, and outcome data of patients were collected. Follow-up lasted until April 6, 2020.

Results

All 55 patients included 47 (85.5%) non-severe patients and 8 (14.5%) severe patients. Common comorbidities were hypertension and diabetes. Common symptoms were fever, cough and sputum. Lymphopenia was a common laboratory finding, and ground-glass opacity was a common chest CT feature. All patients received antiviral therapy of α-interferon inhalation and lopinavir-ritonavir tablets. Common complications included acute liver injury and respiratory failure. All patients were discharged. No death was occurred and no medical staff got infected. Patients with severe COVID-19 showed significantly older age, decreased lymphocytes, increased C reactive protein, and higher frequency of bilateral lung infiltration compared to non-severe patients. Significantly more treatments including antibiotic therapy and mechanical ventilation, longer hospitalization stay and higher cost were shown on severe patients.

Conclusions

Our study suggested that patients with severe COVID-19 may be more likely to have an older age, present with lymphopenia and bilateral lung infiltration, receive multiple treatments and stay longer in hospital.
COVID-19 lockdowns cause global air pollution declines with implications for public health risk
Authors: Venter Zander S. , Aunan Kristin , Chowdhury Sourangsu , Lelieveld Jos
Published: April 2020

The lockdown response to COVID-19 has caused an unprecedented reduction in global economic activity. We test the hypothesis that this has reduced tropospheric and ground-level air pollution concentrations using satellite data and a network of >10,000 air quality stations. After accounting for the effects of meteorological variability, we find remarkable declines in ground-level nitrogen dioxide (NO2: −29 % with 95% confidence interval −44% to −13%), ozone (O3: −11%; −20% to −2%) and fine particulate matter (PM2.5: −9%; −28% to 10%) during the first two weeks of lockdown (n = 27 countries). These results are largely mirrored by satellite measures of the troposphere although long-distance transport of PM2.5 resulted in more heterogeneous changes relative to NO2. Pollutant anomalies were related to short-term health outcomes using empirical exposure-response functions. We estimate that there was a net total of 7400 (340 to 14600) premature deaths and 6600 (4900 to 7900) pediatric asthma cases avoided during two weeks post-lockdown. In China and India alone, the PM2.5-related avoided premature mortality was 1400 (1100 to 1700) and 5300 (1000 to 11700), respectively. Assuming that the lockdown-induced deviations in pollutant concentrations are maintained for the duration of 2020, we estimate 0.78 (0.09 to 1.5) million premature deaths and 1.6 (0.8 to 2) million pediatric asthma cases could be avoided globally. While the state of global lockdown is not sustainable, these findings illustrate the potential health benefits gained from reducing “business as usual” air pollutant emissions from economic activities. Explore trends here: www.covid-19-pollution.zsv.co.za

Significance statement

The global response to the COVID-19 pandemic has resulted in unprecedented reductions in economic activity. We find that lockdown events have reduced air pollution levels by approximately 20% across 27 countries. The reduced air pollution levels come with a substantial health co-benefit in terms of avoided premature deaths and pediatric asthma cases that accompanied the COVID-19 containment measures.
COVID-19: Recovering estimates of the infected fatality rate during an ongoing pandemic through partial data
Authors: Villa Matteo , Myers James F. , Turkheimer Federico
Published: April 2020

In an ongoing epidemic, the case fatality rate is not a reliable estimate of a disease’s severity. This is particularly so when a large share of asymptomatic or pauci-symptomatic patients escape testing, or when overwhelmed healthcare systems are forced to limit testing further to severe cases only. By leveraging data on COVID-19, we propose a novel way to estimate a disease’s infected fatality rate, the true lethality of the disease, in the presence of sparse and partial information. We show that this is feasible when the disease has turned into a pandemic and data comes from a large number of countries, or regions within countries, as long as testing strategies vary sufficiently. For Italy, our method estimates an IFR of 1.1% (95% CI: 0.2% – 2.1%), which is strongly in line with other methods. At the global level, our method estimates an IFR of 1.6% (95% CI: 1.1% – 2.1%). This method also allows us to show that the IFR varies according to each country’s age structure and healthcare capacity.
‘Keeping the kids at home’ can limit the persistence of contagious pathogens in social animals
Authors: Marescot L. , Franz M. , Benhaiem S. , Hofer H. , East M.L. , Kramer-Schadt S.
Published: April 2020

In social species where offspring are reared together in communal burrows or similar structures, young animals typically do not engage in between-group contact during their development – a behavioural trait we call ‘offspring with restricted between-group contact’ (ORC). The impact of this trait on the persistence of contagious pathogens that generate lifelong immunity in their hosts is currently unclear. We hypothesize that in populations with ORC, the formation, in groups, of a ‘protective barrier’ of only recovered adults, prevents the transmission of this type of pathogens to the new susceptible hosts (i.e. young animals), thereby increasing the probability of epidemic fade-out. We implement a spatially implicit individual-based Susceptible-Infected-Recovered (SIR) model for a large range of host and pathogen traits and show that the epidemic fade-out probability is consistently higher in populations with ORC, especially when disease spread is fast (high basic reproduction number R0). We also show that ORC can counteract the cost of group-living in terms of disease risk to a greater extent than variation in other traits. We discuss our findings in relation to herd immunity and outline how they could be used to implement efficient management measures such as vaccinations.
Proteomic analysis of necroptotic extracellular vesicles
Authors: Shlomovitz Inbar , Yanovich-Arad Gali , Erlich Ziv , Edry-Botzer Liat , Zargarian Sefi , Cohen Hadar , Ofir-Birin Yifat , Regev-Rudzki Neta , Gerlic Motti
Published: April 2020

Necroptosis is a regulated and inflammatory form of cell death. We, and others, have previously reported that necroptotic cells release extracellular vesicles (EVs). We have found that necroptotic EVs are loaded with proteins, including the phosphorylated form of the key necroptosis-executing factor, mixed lineage kinase domain-like kinase (MLKL). However, neither the exact protein composition, nor the impact, of necroptotic EVs have been delineated. To characterize their content, EVs from necroptotic and untreated U937 cells were isolated and analyzed by mass spectrometry-based proteomics. A total of 3337 proteins were identified, sharing a high degree of similarity with exosome proteome databases, and clearly distinguishing necroptotic and control EVs. A total of 352 proteins were significantly upregulated in the necroptotic EVs. Among these were MLKL and caspase-8, as validated by immunoblot. Components of the ESCRTIII machinery and inflammatory signaling were also upregulated in the necroptotic EVs, as well as currently unreported components of vesicle formation and transport, and necroptotic signaling pathways. Moreover, we found that necroptotic EVs can be phagocytosed by macrophages to modulate cytokine and chemokine secretion. Finally, we uncovered that necroptotic EVs contain tumor neoantigens, and are enriched with components of antigen processing and presentation. In summary, our study reveals a new layer of regulation during the early stage of necroptosis, mediated by the secretion of specific EVs that influences the microenvironment and may instigate innate and adaptive immune responses. This study sheds light on new potential players in necroptotic signaling and its related EVs, and uncovers the functional tasks accomplished by the cargo of these necroptotic EVs.
PALP: An imaging method for detecting and quantifying polyunsaturated phospholipids via peroxidation
Authors: Zou Yilong , Graham Emily T. , Huang Yuwei , Salmon Wendy , Yu Li , Schreiber Stuart L.
Published: April 2020

Polyunsaturated phospholipids are essential for multiple cellular functions; however, their uncontrolled peroxidation leads to ferroptosis. Here we describephotochemicalactivation of membranelipidperoxidation (PALP), which uses localized laser pulses to induce lipid peroxidation photochemically. While PALP bypasses enzymatic requirements for lipid peroxidation, the resulting BODIPY-C11-based signal is largely correlated with local polyunsaturated phospholipid concentration on membranes. This technique enables non-invasive reporting of lipid unsaturation levels and sensitivity to ferroptosis in live cells.
miR-34c-3p regulates PKA activity independent of cAMP via ablation of PRKAR2B inTheileria annulata-infected leukocytes
Authors: Haidar Malak , Tajeri Shahin , Momeux Laurence , Mourier Tobias , Ben-Rached Fathia , Mfarrej Sara , Rchiad Zineb , Pain Arnab , Langsley Gordon
Published: April 2020

MicroRNAs (miRNAs) are small non-coding RNAs that can play critical roles in regulating various cellular processes including during many parasitic infections. Here, we report a regulatory role for miR-34c-3p in cAMP-independent regulation of PKA activity inTheileria annulatainfection of bovine leukocytes. We identifiedprkar2b(cAMP-dependent protein kinase A type II-beta regulatory subunit), as a novel miR-34c-3p target gene and demonstrated how infection-induced up-regulation of miR-34c-3p in leukocytes repressed PRKAR2B expression to increase PKA activity and promote the virulent disseminating tumour phenotype ofT. annulata-transformed macrophages. Finally, we demonstrate that miR-34c-3p regulation ofprkar2bexpression is generalizable, by confirming thatPlasmodium falciparuminfection of red blood cells also raises intracellular levels of miR-34c-3p and show that this negatively regulates hostprkar2bexpression so increasing PKA activity. Infection-induced increase in miR-34c-3p levels, therefore, represents a novel cAMP-independent way of regulating host cell PKA activity in infections byTheileriaandPlasmodiumparasites.

Abstract Importance

TheileriaandPlasmodiuminfections of leukocytes and erythrocytes; respectively, lead to an increase in host cell miR-34c-3p levels and we identifiedprkar2b(cAMP-dependent protein kinase A type II-beta regulatory subunit), as a specific miR-34c-3p target gene. We demonstrate how infection-induced up-regulation of miR-34c-3p repressed PRKAR2B expression to increase PKA activity independent of fluxes in cAMP. Thus, in two different host-parasite combinations infection-induced increase in miR-34c-3p represents a novel epigenetic way of increasing in host PKA activity that contributes to the pathology of disease.
Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing inSetaria viridis
Authors: Weiss Trevor , Wang Chunfang , Kang Xiaojun , Zhao Hui , Gamo Maria Elena , Starker Colby G. , Crisp Peter A. , Zhou Peng , Springer Nathan M. , Voytas Daniel F. , Zhang Feng
Published: April 2020

In recent years,Setaria viridishas been developed as a model plant to better understand the C4 photosynthetic pathway in major crops. With the increasing availability of genomic resources forS. viridisresearch, highly efficient genome editing technologies are needed to create genetic variation resources for functional genomics. Here, we developed a protoplast assay to rapidly optimize the multiplexed CRISPR/Cas9 system inS. viridis.Targeted mutagenesis efficiency was further improved by an average of 1.4-fold with the exonuclease,Trex2.Distinctive mutation profiles were found in the Cas9_Trex2 samples with 94% of deletions larger than 10bp, and less than 1% of mutations being insertions. Further analyses indicated that 52.2% of deletions induced by Cas9_Trex2, as opposed to 3.5% by Cas9 alone, were repaired through microhomology-mediated end joining (MMEJ) rather than the canonical NHEJ DNA repair pathway. Combined with the robust agrobacterium-mediated transformation method with more than 90% efficiency, the multiplex CRISPR/Cas9_Trex2 system was demonstrated to induce targeted mutations in two tightly linked genes,svDrm1aandsvDrm1b,at the frequency ranging from 73% to 100% in T0 plants. These mutations were transmitted to at least 60% of the transgene-free T1 plants with 33% of them containing bi-allelic or homozygous mutations in both genes. This highly efficient multiplex CRISPR/Cas9_Trex2 system makes it possible to create a large mutant resource forS. viridisin a rapid and high throughput manner, and has the potential to be widely applicable in achieving more predictable MMEJ-mediated mutations in many plant species.
Blueprint for a Pop-up SARS-CoV-2 Testing Lab
Authors:   Innovative Genomics Institute SARS-CoV-2 Testing Consortium, Hockemeyer Dirk , Urnov Fyodor , Green Ralph , Doudna Jennifer A.
Published: April 2020

The appearance and spread of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) led to the official declaration of a global pandemic, with states in the US implementing shelter-in-place orders at an unprecedented scale. SARS-CoV-2 has a robust person-to-person transmission rate and an asymptomatic period of two weeks or more, leading to widespread infection that has overwhelmed healthcare infrastructures around the globe. Effective public health measures require extensive, accurate, and rapid testing to determine infection rates. Here we describe the strategy we used to establish a CLIA-licensed clinical laboratory to perform a validated Laboratory-Developed Test (LDT) for SARS-CoV-2 in Berkeley, California and the surrounding Bay Area community. Our procedures for implementing the technical, regulatory, and data management workstreams necessary for clinical sample processing provide a roadmap to aid others in setting up similar testing centers.

Note on Nomenclature

in accordance with established virology and infectious disease nomenclature, throughout this document we use “SARS-CoV-2” to refer to the viral agent causing infection and “COVID-19” to refer to the human infectious disease caused by that viral agent.
A phenotype-specific framework for identifying the eye abnormalities causative nonsynonymous-variants
Authors: Liu Han-Kui , Dang Xiao , Guan Li-Ping , Tian Chang-Geng , Zhang Sheng-Hai , Ye Chen , Tellier Laurent Christian Asker M. , Chen Fang , Yang Huan-Ming , Sun Hao-Xiang , Wu Ji-Hong , Zhang Jian-Guo
Published: April 2020

The most important role of variant pathogenicity predictors is to identify the disease-phenotype causative variant in studying monogenic diseases. In the last decade, machine-learning based predictors exhibited a relatively accurate performance for distinguishing the pathogenic variants and contributed a significant role for all disease-spectrums. Yet, few predictors can investigate the phenotypic significance of variants. Here we presented a phenotype-specific framework aimed to directly point out the phenotypic significance of predicted candidates, and showed its advancing performance in eye abnormalities. By training on eye-abnormalities causative variants, our method presented 96.2% accuracy, 96.1% precision, 93.4% recall for pathogenicity identification. Inconsistent with the modeling performance, identifying the single phenotype-causative variant from various sequencing variants is challenging for all predictors. Underlying the phenotype-oriented, our method significantly promoted the precision and reduced the cost for identifying the single causative variant from thousands of candidates. These advances highlight the significance of the phenotype-specific training method for studying disease.
Generalized gametic relationships for flexible analyses of parent-of-origin effects
Authors: Reinsch N. , Mayer M. , Blunk I.
Published: April 2020

Genomic imprinting causes alleles to influence the phenotype in a parent-of-origin-specific manner. In attempts to determine the effects of imprinted loci, gametic relationship matrices have widely been used in pedigree-based parent-of-origin analyses of population data. One drawback of this is the size of these matrices because they represent each individual by two gametic effects. Significantly fewer equations are needed if a previously published reduced imprinting model is used that relates observations from progeny without its own offspring to the transmitting abilities of their parents. This can be accomplished using a numerator relationship matrix, with only a single row and column per parent and ancestors. However, the reduced model is not applicable when the parents have records. To better handle the curse of dimensionality, we propose a combination of average gametic effects (transmitting abilities) for individuals without their own records and single gametic effects for others. The generalized gametic relationship matrix is the covariance of this mixture of genetic effects that allows for a significant reduction in the number of equations in gametic models depending on the trait, depth of pedigree, and population structure. It can also render the reduced model much more flexible by including observations from parents. Rules for setting-up its inverse from a pedigree are derived and implemented on an open-source program. The application of the same principles to phased marker data leads to a genomic version of the generalized gametic relationships. The implementation of generalized gametic models to the ASReml package is illustrated through worked examples.
Universal patterns of matter and energy fluxes in land and ocean ecosystems
Authors: Nefiodov A. V.
Published: April 2020

In work [1], the fundamental relationships for the fluxes of matter and energy in terrestrial ecosystems were obtained. Taking into account the universal characteristics of biota, these relationships permitted an estimate to be made of the vertical thickness of the live biomass layer for autotrophs and heterotrophs. The distribution of consumption of biota production as dependent on the body size of heterotrophs was also investigated. For large animals (vertebrates), the energy consumption in sustainable ecosystems was estimated to be of the order of one percent of primary production. In this comment, it is shown that the results of work [1] also hold true for ocean ecosystems and thus are universal for life as a whole. This is of paramount importance for human life on Earth.
Presence of polyadenylated 3’ tail in RNA ofPepper mild mottle virusallows the Oligo(dT)18in Priming cDNA Synthesis of its genomic RNA template
Authors: Kumari Nidhi , Sharma Vivek , Choudhary Sneha , Sharma P.N.
Published: April 2020

The PCR amplification of majority of the ssRNA of both genomic and non-genomic mRNA is accomplished by RT-PCR. The mRNA is subjected to cDNA synthesis using reverse transcriptase and either Oligo(dT)18, or random or gene specific reverse primers based priming strategies. The choice of primer largely depends on the nature of 3 prime terminus of mRNA and length of cDNA synthesized. In general, oligo(dT)18 is the preferred choice for mRNAs having poly(A) tail at 3 prime terminus. In general, tobamoviruses lack any poly(A) tail at their 3 prime untranslated region (UTR) which forms a tRNA like structure and upstream pseudoknot domain except tow viruses viz., Hibiscus latent Fort Pierce virus (HLFPV) and Hibiscus latent Singapore virus (HLSV) which accommodate internal poly(A) sequences of 46 and 87 nucleotides long, respectively in their 3 prime UTR. However, determination of full nucleotide sequence of Pepper mild mottle virus (PMMoV) using an oligo(dT)18 primed cDNA as template indicated the libertinism of oligo(dT)18 in priming cDNA synthesis of RNA template which are known to lack poly(A) tail. at the end or internally at its 3 prime end. Moreover, coat protein (CP) gene of PMMoV and bean common mosaic virus (BCMV) (Potyvirus with a poly(A) tract at its 3 prime end) was amplified using cDNA primed with random primer as well as oligo(dT)18 was successfully amplified but with significant variation in the intensity of the amplification band in case of PMMoV but not in BCMV. This clearly indicated the presence of PMMoV mRNA with polyadenylated 3 prime tail in total RNA isolated from PMMoV infected capsicum leaves with abundance of non-polyadenylated PMMoV genomic RNA (gRNA). Hence, we hypothesize that the generation of polyadenylated RNA population during the infection cycle of PMMoV in pepper may be possible reason for libertinism of oligo(dT)18 in priming cDNA synthesis of RNA template isolated from PMMoV infected leaves followed by amplification of entire PMMoV genome through RT-PCR. This is first study indicating the presence of polyadenylated or polyadenylated rich regions in PMMoV gRNA acquired during the infection cycle in pepper.
Subpopulations of stressedY. pseudotuberculosispreferentially survive doxycycline treatment within host tissues
Authors: Raneses Jasmine Ramirez , Ellison Alysha L. , Liu Bessie , Davis Kimberly M.
Published: April 2020

Severe systemic bacterial infections result in colonization of deep tissues, which can be very difficult to eliminate with antibiotics. It remains unclear if this is because antibiotics are not reaching inhibitory concentrations within tissues, if subsets of bacteria are less susceptible to antibiotics, or if both contribute to limited treatment efficacy. To determine the concentration of doxycycline (Dox) present within deep tissues following treatment, we generated a fluorescent transcriptional reporter derived from thetetoperon to specifically detect intracellular tetracycline exposure at the single bacterial cell level. Dox exposure was detected in the spleen 2 hours after intraperitoneal injection, and by 4 hours post-injection, this treatment resulted in a significant decrease in viableYersinia pseudotuberculosisin the spleen. Nitric oxide-stressed bacteria preferentially survived treatment, suggesting stress was sufficient to alter Dox susceptibility. Many bacteria (~10%) survived a single dose of Dox, and the antibiotic accumulated at the periphery of microcolonies to growth inhibitory concentrations until 48 hours post-treatment. After this timepoint, antibiotic concentrations decreased and bacterial growth resumed. Dox-treated mice eventually succumbed to the infection, albeit with significantly prolonged survival relative to untreated mice. These results indicate that Dox delivery by intraperitoneal injection results in rapid diffusion of inhibitory concentrations of antibiotic into the spleen, but stressed cells preferentially survive drug treatment, and bacterial growth resumes once drug concentrations decrease. This fluorescent reporter strategy for antibiotic detection could easily be modified to detect the concentration of additional antimicrobial compounds within host tissues following drug administration.

Importance

Bacterial infections are very difficult to treat when bacteria spread into the bloodstream and begin to replicate within deep tissues, such as the spleen. Subsets of bacteria can survive antibiotic treatment, but it remains unclear if this survival is because of limited drug diffusion into tissues, or if something has changed within the bacteria, promoting survival of some bacterial cells. Here, we have developed a fluorescent reporter to detect doxycycline (Dox) diffusion into host tissues, and show that Dox impacts the bacterial population within hours of administration, and inhibits bacterial growth for 48 hours. However, bacterial growth resumes when antibiotic concentrations decrease. Subsets of bacteria, stressed by the host response to infection, survive Dox treatment at a higher rate. These results provide critical information about the dynamics that occur within deep tissues following antibiotic administration, and suggests subsets of bacteria are predisposed to survive inhibitory concentrations of antibiotic before exposure.