bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating the coding capacity of rotaviruses using a newly developed reverse genetics system
Authors: Lee Ola , Min Lee Hui , Maria Pinto Rute , Digard Paul , Gaunt Eleanor
Published: July 2020

Bovine rotavirus (RV) infection causes severe diarrhoea in young dairy calves and has a significant economic impact on livestock production as a result of high morbidity and mortality caused. Development of technologies to engineer infectious RV using an entirely plasmid-based reverse genetics (RG) system has proven challenging. A breakthrough was made when Kanaiand co-authors (PNAS, 2017)developed a plasmid-only-based RG system for the simian RV strain SA11.We are currently developing an analogous RG system for the bovine RF RV strain. Having parallel systems for different RV strains will help to validate phenotypic changes induced by site-directed mutagenesis (SDM) within the RV genome.

The coding capacity of the 11-segmented dsRNA RV genome has been largely unexplored. Using bioinformatic analyses, we have identified four segments with up to five putative alternative initiation codons which are in moderate or strong Kozak context. Furthermore, some occur in segments for which the canonical start codon occurs within 15 nucleotides of the start of the segment, further suggesting the possibility of alternative translation start sites to generate coding diversity. We are now applying our RG systems to investigate RV coding capacity using TnT transcription assays, radiolabelling and SDM.
Safe water for all: A nature-based approach for cyanotoxin elimination from potable water
Authors: Soldatou Sylvia , Jaykumar Anjali , H.A.S.N Abeysiri , M. Manage Pathmalal , Mašek Ondřej , A. Lawton Linda , Edwards Christine
Published: July 2020

Cyanobacterial blooms are a serious threat to public health and water quality due to the production of cyanotoxins as a result of nutrient pollution from industry, agriculture, domestic waste as well as global warming. The microcystins (MCs) are the most abundant cyanotoxins consisting of >200 analogues causing both acute and chronic toxicity, sometimes resulting in death. In Asian countries, such as Sri Lanka, reports of kidney disease are constantly increasing. Although no direct link between metal and pesticide contamination in water and kidney disease has been found, high concentration of cyanobacteria cells in drinking water wells implies that the nephrotoxic effects of cyanotoxins might play a key factor in the reports of Chronic Kidney Disease of unknown aetiology (CKDu) in Sri Lanka. Therefore, we propose a nature-based approach for water treatment which will study the hypotheses that cyanotoxins can cause CKDu. Sri Lankan bacterial isolates (Alcaligens sp., Roseateles sp., Bacillus sp., and Micrococcus sp.) known to degrade microcystins, were used to form biofilm on biochar from Sri Lankan crop residues, such as coconut shells. The immobilisation of the microbes was assessed via a high-throughput colourimetric assay, followed by monitoring the biodegradation rate of microcystins when added to the immobilised cultures. Biodegradation products were analysed and identified through molecular networking and quantified via LC-MS/MS. Ultimately, this project will provide safe water in line with UN Sustainable Development Goal 6.1 as well contributing in sustainable goals 7 (Affordable and Clean Energy), 11 (Sustainable Cities and Communities) and 12 (Responsible Production and Consumption).
How the colonic environment influences Enterohaemorrhagic E. coli outer membrane vesicle production, and the interaction between outer membrane vesicles with human host cells
Authors: Yara Daniel , Stentz Regis , Wileman Tom , Schuller Stephanie
Published: July 2020

Enterohaemorrhagic E. coli (EHEC) may instigate bloody diarrhoea and haemolytic uraemic syndrome (HUS) due to Shiga toxin (Stx) production. Stx has been detected within outer membrane vesicles (OMVs), which are membrane-derived nanosized proteoliposomes. During colonisation, EHEC encounters many environmental surroundings such as the presence of bile salts and carbon dioxide (CO2). Here, the influence of different intestinal cues on EHEC OMV production was studied. OMV yield was quantified by densitometric analysis of outer membrane proteins F/C and A, following OMV protein separation by SDS-PAGE. Compared to cultures in Luria broth, higher OMV yields were attained following culture in human cell growth medium and simulated colonic environmental medium, with further increases in the presence of bile salts. Interestingly, lower yields were attained in the presence of T84 cells and CO2. The interaction between OMVs and different human cells was also examined by fluorescence microscopy. Here, OMVs incubated with cells showed internalisation by semi confluent but not fully confluent T84 cell monolayers. OMVs were internalised into the lysosomes in confluent Vero and Caco-2 cells, with Stx being transported to the Golgi and then the Endoplasmic reticulum. OMVs were detected within polarised Caco-2 cells, with no impact on the transepithelial electrical resistance by 24 hours. These results suggest that the colonic environmental factors influences OMV production in vivo. Additionally, results highlight the discrepancies which arise when using different cells lines to examine the intestine. Nevertheless, coupled with Stx, OMVs may serve as tools of EHEC which are involved in HUS development.
Incidence of malaria parasites in human immuno-deficiency virus clients attending General Hospital Awo-Omamma, Imo State Nigeria
Authors: Njoku-Obi Treasure , Nwofor Chioma , Ohalete Chinyere , Osuoha Chinyere
Published: July 2020

The incidence of malaria parasite in Human Immuno-deficiency Virus clients attending Awo-omamma General Hospital, Owerri Imo state Nigeria was studied. A total of 200 blood samples were collected; 150 samples were collected from sero-positive HIV clients while 50 samples were collected from sero-negative HIV clients which served as control samples. Out of this 200 clients 85(42.5%) were males while 65(32.5%) were females. The blood samples were analyzed using Malaria Rapid Test Kit for the presence of Plasmodium falciparum, using standard medical laboratory procedure. The result revealed an overall prevalence of 43 (28.7%) for HIV positive participants that tested positive to malaria parasite, 15 (17.6%) were male while 28 (43.1%) were female. Analysis based on age revealed that the highest prevalence was among those within the age group 30-39 years having 20 (10%) while those with the least prevalence were observed among those within the age group 20-29 years having 32 (16%). Analysis of malaria parasite based on CD4+ cell count among HIV clients revealed that 51(34%) had CD4+ cell count above 200cell/μl while 23 (15.3%) had CD4+cell count below 200cell\μl. This study has shown that there is a low prevalence of malaria parasite (Plasmodium falciparum) among HIV/AIDs clients with high CD4+ attending HIV clinic in Awo-omamma General Hospital, Imo state. It is recommended that more efforts be made to eradicate malaria completely as this will go a long way in reducing the rate of mortality among HIV clients.
Differences in acid-base regulation of haploid and diploid life-cycle stages of Coccolithus braarudii and their consequences for the sensitivity towards ocean acidification
Authors: Kottmeier Dorothee , Chrachri Abdesslam , Langer Gerald , Wheeler Glen , Brownlee Colin
Published: July 2020

Coccolithophores are calcifying microalgae that carry characteristic calcite platelets (coccoliths) on their surfaces. Most coccolithophore species exhibit diploid and haploid life cycle stages, each adjusted to different environmental conditions. The diploid life cycle stage of the coccolithophore C. braarudii is heavily calcifying with calcification rates that exceed the rates of photosynthesis. Haploid life-cycle stages are often weakly calcifying, generating significantly less H+ from the intracellular calcification reaction. We show how these different cellular “H+ burdens” require substantially different physiological molecular strategies to regulate intracellular pH under changing environmental conditions. Voltage-gated H+ channels (Hv) have been shown to play a role in the release of H+ in the diploid life cycle previously (Taylor et al. 2011). Combining scanning electron microscopy, electrophysiology, gene expression approaches and physiological measurements, we here show a direct link between the function of proton channels and coccolith formation of the diploid but not the haploid life-cycle stage. Our data also indicate how the different mechanisms for acid-base regulation of the diploid and haploid life-cycle stages may result in different sensitivities towards ocean acidification.
A horizontally gene transferred copper resistance locus enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in host cells
Authors: Spencer Daniella , Kaur Inderpreet , Purves Jo , Andrew Peter , Planet Paul , Geoghegan Joan , Waldron Kevin , Morrissey Julie
Published: July 2020

The spread of community acquired, methicillin resistant Staphylococcus aureus (CA-MRSA) is an increasing problem seen outside the healthcare setting. One such strain, CA-MRSA USA300, is epidemic in the United States. USA300 shows a heightened resistance to the innate immune system, in particular to macrophage engulfment. Two horizontally acquired genes, encoding an efflux pump (CopX) and lipoprotein (CopL), were discovered in 2 different lineages of USA300, representing CA-MRSA epidemics in North and South America. Removal of either of these genes resulted in elevated copper concentrations in the cytoplasm of S. aureus, implying a function in copper hyper-resistance. While copper is an essential part of metabolic machinery, it is toxic at high concentrations and is utilised by macrophages to kill bacteria in the phagosome. Supporting this, USA300 with functional copXL genes showed increased survival in macrophages compared to their copXL negative counterparts. Although the role of CopX as an efflux pump explains the rise in intracellular copper concentration upon its mutation, the role of the CopL lipoprotein is still unknown. Therefore, to better understand the function of CopL and how it might influence S. aureus host interaction, transcriptomic analysis is underway to identify downstream targets. This has the potential to uncover an exciting mechanism linking metal resistance to host virulence.
Replication kinetics of a CHIKV Asian strain with 76 aa duplication in the nsP3 HVD, in comparison to the wild-type Asian and ECSA strains
Authors: Abdullah Nurshariza , Wai Tham Hong , Abdullah Nafees , RMT Balasubramaniam Vinod , Sam I-Ching , Syed Hassan Sharifah
Published: July 2020

Introduction: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus which causes fever, rash and polyarthralgia. CHIKV has expanded its circulating regions to the Indian Ocean islands, Europe, Americas and Southeast Asia. Two CHIKV lineages, the ASIAN and ECSA are circulating in Malaysia. In 2009, a CHIKV strain with a 76 amino acid (aa) duplication in its nsP3 hypervariable domain (HVD), identified as CHIKvASIAN09MUM-Dup+ was isolated from a patient co-infected with DENV-2. Indels and duplication have been found in many other alphaviruses, and suggested to play a role in the survivality of the viruses.

Objectives: We aim to compare and relate the replication kinetics and virulency in-vitro of CHIKvASIAN09MUM-Dup+ with the wild-type Asian and ECSA strains.

Methods & Results: Genotypic analysis was conducted on three CHIKV strains in Malaysia, the CHIKvASIAN06UM-Dup-, CHIKvECSA08UM-Dup- and CHIKvASIAN09MUM-Dup+. We found that CHIKvASIAN09MUM-Dup+ has significant low replication rates in Vero, C6/36 and Rhabdosarcoma cells as compared to the wild-type strains. The highest titers were reached by CHIKvASIAN09MUM-Dup+ in all cells are 6.5 to 6.75 log10 TCID50/mL, which is 100 fold lower compared to the wild-type strains.

Conclusion: The significantly low replication rate of Dup+ strain in all the cells, maybe suggestive to be due to co-infection and co-existence with DENV, where the aa duplication may play a role in overcoming competitive suppression. This preliminary finding agrees with reported events, where alphaviruses use insertion, deletion and duplication of amino acid in nsP3 HVD as strategies to influence replication in host, viral virulency, pathogenesis and survivality for evolution adaptation.
Investigating the mechanism of the Tup1-Cyc8 (Ssn6) Co-Repressor complex in the yeast Saccharomyces cerevisiae
Authors: Lee Brenda
Published: July 2020

The Tup1-Cyc8 (Ssn6) complex is a powerful epigenetic repressor of genes in the yeast Saccharomyces cerevisiae. The highly conserved complex brings about a repressive chromatin structure at regulatory regions of its target genes or prevents the recruitment of factors needed for activation of transcription. A gap in the current understanding is whether each of the subunits contribute differently to repression. The FLO family of genes are repressed by the Tup1-Cyc8 complex, these genes encode the proteins required for flocculation, a stress response in yeast where the cells aggregate, or form flocs, to protect cells within the floc. Interestingly, each mutant strain has a distinct flocculant phenotype. The tup1Δ strain displays large, dense flocs compared to smaller, more dispersed flocs associated with the cyc8Δ strain. RT-qPCR showed that FLO1 is highly de-repressed in the tup1Δ strain whereas it is de-repressed to a significantly lower level in the cyc8Δ strain. Using the Anchor Away (AA) technique, which allows for a nuclear protein to be conditionally sequestered to the cytoplasm, I am investigating differences in the sequence of events at the FLO1 promoter when Tup1p or when Cyc8p is removed from the nucleus. Six hours after Cyc8p is removed from the nucleus transcription of FLO1 almost reaches the maximum transcription seen in the cyc8Δstrain. However, six hours after removing Tup1p the level of transcription of FLO1 is still over ten times lower than the maximum transcription in tup1Δ. This difference indicates that each of the subunits have independent functions within the complex.
Investigating the functional relationship between streptokinase variants from Group A Streptococcus, and associated M-like proteins
Authors: Cherrington Sophie , Maqbool Azhar , Philippou Helen , Thelwell Craig
Published: July 2020

Background: Streptokinase (SK) from Group A streptococcus (GAS) activates human plasminogen to generate plasmin, which degrades fibrin clots tofacilitate bacterial dissemination. Sequence variants of SK from diverse GAS strains form distinct evolutionary clusters.Unlike cluster 1 SK, cluster 2 variants have very little activity in solution and depend on co-factors (e.g. fibrin(ogen)).Cluster 2 SK variants also appear to correlate with cell-surface M-like proteins: SK2a with M1 (fibrinogen-binding) and SK2b with PAM (plasminogen-binding).

Methods: Plasminogen activation by recombinant SKs (rSK2a, rSK2b) was investigated by chromogenic assay; nickel-coated microtiter plates were used to immobilise recombinant M proteins (rPAM and rM1) via a C–terminal His tag to mimic cell surface plasmin generation.

Results: Plasminogen activation by rSK2b is stimulated ∼18-fold by rPAM in solution; when rPAM is immobilised stimulation exceeds 100-fold. Fibrin is the most potent stimulator of rSK2a activity (7-fold increase) compared to fibrinogen (4-fold); when rM1 was included, either in solution or immobilised, there was no further stimulation of rSK2a activity with fibrinogen.

Discussion: Stimulation ofSK2b activity by plasminogen bound to immobilised PAM suggests an important role for cell-surface plasmin generation. SK2a activity appears to be independent of M1, targeting fibrin directly. SK variants are commonly associated with distinct disease manifestations with SK2b commonly expressed by invasive skin-tropic strains of GAS and SK2a by nasopharynx-tropic strains. An improved understanding of the molecular mechanism of action by GAS SK variants may help to identify potential novel therapeutic targets for the treatment of invasive GAS diseases.
Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon
Authors: Pascoe Ben , Kosek Margaret , Sheppard Samuel
Published: July 2020

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n=62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs. Preprint: https://www.medrxiv.org/content/10.1101/2020.04.26.20075689v1
Strategies for glycan acquisition by Bacteroidetes in the soil: The carbohydrate enzymology of Chitinophaga pinensis
Authors: Lu Zijia , Inman Annie , Ergenlioglu Irem , Rämgård Carl , Sara McKee Lauren
Published: July 2020

The secretion of extracellular enzymes by soil microbes is rate-limiting in the global recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant bacterial phylum, just like in human and animal intestines. The enzymology of Bacteroidetes in the dynamic and competitive soil environment is under-explored compared to their cousins from the human and ruminant gut ecosystems. We are exploring carbohydrate binding and deconstruction by Chitinophaga pinensis. This species was isolated from the leaf litter of a pine forest, and our ongoing microbiological, biochemical, and proteomic analyses show that C. pinensis has a marked metabolic preference for carbohydrates (glycans) of microbial, rather than plant, origin. The species has a repertoire of enzymes that degrade components of the fungal cell wall, and we are characterising several important enzyme activities, including some with unusual substrate specificity.

Several features of the C. pinensis “cazome” make it note-worthy. In particular, there is a significantly reduced reliance on the Polysaccharide Utilisation Loci that define glycan acquisition in most well-studied gut symbiont Bacteroidetes. Instead, C. pinensis produces some large multi-modular enzymes that convey multiple complementary carbohydrate-binding and -degrading functions, and which are often secreted via the phylum-specific Type IX Secretion System.

This presentation will highlight our latest enzyme characterisation data, discussed in the context of the environmental functions of soil bacteria, as well as the use of enzymes for industrial biotechnology.
Identification of potential key genetic factors in the long-term success of Shigella as pathogens
Authors: Bennett Rebecca , Bengtsson Rebecca , Baker Kate
Published: July 2020

Bacterial of the genus Shigella are a major contributor to the global diarrhoea burden causing 100,000 deaths per annum globally. Further to this, increasing antibiotic resistance in Shigella and the lack of a licenced vaccine has led WHO to recognise Shigella as a priority organism for the development of new antibiotics. Understanding what drives the long-term persistence and success of this pathogen will thus aid the global management of shigellosis and may identify targets relevant to other enteric bacteria. To identify key genetic drivers of Shigella evolution over the past 100 years, we have used the historical Murray collection; comprising several hundred pre-antibiotic era (1917 – 1954) Enterobacteriaceae from diverse geographical locations. We employed genome-wide association studies to sequences from over 100 Shigella isolates from the Murray collection alongsidemore modern (i.e. 1950s – 2018) isolates to identify genetic factors (SNPs and genes) significantly associated with time as a continuous variable. GWAS hits (e.g. a putative resistance protein) then underwent variation, functional and phenotypic analysis to examine the plausibility of their role in shaping Shigella populations and as potential targets for managing this pathogen.
Luminore CopperTouch™ surface coating effectively inactivates SARS-CoV-2, Ebola, and Marburg viruses in vitro
Authors: Mantlo Emily K. , Paessler Slobodan , Seregin Alexey , Mitchell Alfred
Published: July 2020

We investigated the ability of Luminore CopperTouch™ copper and copper-nickel surfaces to inactivate filoviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For this purpose, we compared viral titers in Vero cells from viral droplets exposed to copper surfaces for 30 min. The copper and copper–nickel surfaces inactivated 99.9% of the viral titer of both Ebola and Marburg viruses. The copper surfaces also inactivated 99% of SARS-CoV-2 titers in 2 hours to close to the limit of detection. These data add Ebolavirus, Marburgvirus, and SARS-CoV-2 (COVID-19) to the list of pathogens that can be inactivated by exposure to copper ions, validating Luminore CopperTouch™ technology (currently the only Environmental Protection Agency-registered cold spray antimicrobial surface technology) as an efficacious, cost-friendly tool to improve infection control in hospitals, long-term care facilities, schools, hotels, buses, trains, airports, and other highly trafficked areas.
Predicting outcomes of cross-sex hormone therapy in gender dysphoria based on pre-therapy resting-state brain connectivity
Authors: Moody Teena D , Feusner Jamie D , Reggente Nicco , Vanhoecke Jonathan , Holmberg Mats , Manzouri Amirhossein , Khorashad Behzad Sorouri , Savic Ivanka
Published: July 2020

Individuals with gender dysphoria experience serious distress due to incongruence between their gender identity and birth-assigned sex. Sociological, cultural, interpersonal, and biological factors are likely contributory, and for some individuals medical treatment such as cross-hormone therapy and gender affirming surgery can be helpful. Cross-hormone therapy can be effective for reducing body incongruence, but responses vary, and there is no reliable way to predict therapeutic outcomes. We used clinical and MRI data before cross-sex hormone therapy as features to train a machine learning model to predict individuals’ post-therapy body congruence (the degree to which photos of their bodies match their self-identities). Twenty-five trans women and trans men with gender dysphoria participated. The model significantly predicted post-therapy body congruence, with the highest predictive features coming from the fronto-parietal and cingulo-opercular networks. This study provides evidence that hormone therapy efficacy can be predicted from information collected before therapy and that patterns of functional brain connectivity may provide insights into body-brain effects of hormones, affecting one’s sense of body congruence. Results could help identify the need for personalized therapies in individuals predicted to have low body-self congruence after standard therapy.
Low-Dose Whole-Lung Radiation for COVID-19 Pneumonia
Authors: Hess Clayton B. , Buchwald Zachary S. , Stokes William , Nasti Tahseen H. , Switchenko Jeffrey M. , Weinberg Brent D. , Rouphael Nadine , Steinberg James P. , Godette Karen D. , Murphy David , Ahmed Rafi , Curran Walter J. , Khan Mohammad K.
Published: July 2020

Background

Safety of whole-lung low-dose radiation therapy (LD-RT) for COVID-19 pneumonia has been established in two phase I trials. By focally dampening pulmonary cytokine hyperactivation, LD-RT may improve outcomes in hospitalized and oxygen-dependent COVID-19 patients.

Methods

Patients with COVID-19 pneumonia were treated with 1.5 Gy whole-lung LD-RT, followed for 28 days or at least until hospital discharge, and compared to an age- and comorbidity-matched control cohort. COVID-19-positive patients eligible for this protocol were hospitalized, had radiographic consolidations, and required supplemental oxygen. Efficacy endpoints were time to clinical recovery, radiographic improvement, and serologic responses.

Results

Ten patients received whole-lung LD-RT between April 24 and May 24, 2020 and were compared to ten matched control patients, of whom six received COVID-directed therapy. Median time to clinical recovery was 12 days for the control cohort vs 3 days for LD-RT (HR 2.9, p=0.05). Median time to hospital discharge (20 and 12 days, p=0.19), and intubation rates (40% and 10%, p=0.12) were shorter for the LD-RT cohort. The LD-RT cohort had faster radiographic improvement (p=0.03), even among patients with high COVID burden. Serologic recovery in specific hematologic, cardiac, hepatic, clotting, and inflammatory markers occurred more rapidly following LD-RT than among matched controls.

Conclusions

Strong efficacy signals, including a 3-fold risk reduction in time to clinical improvement, were observed following LD-RT compared to matched patients receiving COVID-directed therapy for COVID-19 pneumonia. Given the global availability of radiation accelerators, ongoing international efforts to investigate the optimal role of LD-RT in COVID-19 pneumonia are justified.

Clinical Trial Registration

NCT04366791.
Identification of Vulnerable Populations and Areas at Higher Risk of COVID-19 Related Mortality in the U.S.
Authors: Correa-Agudelo Esteban , Mersha Tesfaye B. , Hernández Andrés , Branscum Adam J. , MacKinnon Neil J. , Cuadros Diego F.
Published: July 2020

Background

The role of health-related disparities including sociodemographic, environmental, and critical care capacity in the COVID-19 pandemic are poorly understood. In the present study, we characterized vulnerable populations located in areas at higher risk of COVID-19 related mortality and low critical healthcare capacity in the U.S.

Methods

Using Bayesian multilevel analysis and small area disease risk mapping, we assessed the spatial variation of COVID-19 related mortality risk for the U.S. in relation with healthcare disparities including race, ethnicity, poverty, air quality, and critical healthcare capacity.

Results

Overall, highly populated, regional air hub areas, and minorities had an increased risk of COVID-19 related mortality. We found that with an increase of only 1 ug/m3 in long term PM2.5 exposure, the COVID-19 mortality rate increased by 13%. Counties with major air hubs had 18% increase in COVID-19 related death compared to counties with no airport connectivity. Sixty-eight percent of the counties with high COVID-19 related mortality risk were also counties with lower critical care capacity than national average. These counties were primary located at the North- and South-Eastern regions of the country.

Conclusion

The existing disparity in health and environmental risk factors that exacerbate the COVID-19 related mortality, along with the regional healthcare capacity, determine the vulnerability of populations to COVID-19 related mortality. The results from this study can be used to guide the development of strategies for the identification and targeting preventive strategies in vulnerable populations with a higher proportion of minority groups living in areas with poor air quality and low healthcare capacity.

KEY POINTS

Question

What are the sociodemographic and environmental drivers of the heterogeneous distribution of the COVID-19 related mortality in the U.S., and what are the vulnerable areas at higher risk of COVID-19 related mortality and low critical healthcare capacity?

Findings

Higher proportions of African American and Latino populations, as well as high levels of air pollution and airport connectivity were linked to higher risk of COVID-19 related mortality. Over 68% of the counties with high COVID-19 related mortality risk were also counties with lower critical care capacity than national average.

Meaning

In a time-limited response, the identification and targeting prevention efforts should focus in vulnerable populations located in high risk areas in which sociodemographic and environmental factors are exacerbating the burden of COVID-19 related deaths.
Multitask Learning over Shared Subspaces
Authors: Menghi Nicholas , Kacar Kemal , Penny Will
Published: July 2020

This paper uses constructs from machine learning to define pairs of learning tasks that either shared or did not share a common subspace. Human subjects then learnt these tasks using a feedback-based approach. We found, as hypothesised, that subject performance was significantly higher on the second task if it shared the same subspace as the first. Additionally, accuracy was positively correlated over subjects learning same-subspace tasks, and negatively correlated for those learning different-subspace tasks. These results were compared to the behaviour of a Neural Network model trained using sequential Bayesian learning. Human performance was found to be consistent with a minimal capacity variant of this model. Networks with an increased representational capacity, and networks without Bayesian learning, did not show these transfer effects. We propose that the concept of shared subspaces provides a useful framework for the experimental study of human multitask and transfer learning.

Author summary

How does knowledge gained from previous experience affect learning of new tasks ? This question of “Transfer Learning” has been addressed by teachers, psychologists, and more recently by researchers in the fields of neural networks and machine learning. Leveraging constructs from machine learning, we designed pairs of learning tasks that either shared or did not share a common subspace. We compared the dynamics of transfer learning in humans with those of a multitask neural network model, finding that human performance was consistent with a minimal capacity variant of the model. Learning was boosted in the second task if the same subspace was shared between tasks. Additionally, accuracy between tasks was positively correlated but only when they shared the same subspace. Our results highlight the roles of subspaces, showing how they could act as a learning boost if shared, and be detrimental if not.
Long-term live imaging of epithelial organoids and corresponding multiscale analysis reveal high heterogeneity and identify core regulatory principles
Authors: Hof Lotta , Moreth Till , Koch Michael , Liebisch Tim , Kurtz Marina , Tarnick Julia , Lissek Susanna M. , Verstegen Monique M.A. , van der Laan Luc J.W. , Huch Meritxell , Matthäus Franziska , Stelzer Ernst H.K. , Pampaloni Francesco
Published: July 2020

Organoids are morphologically heterogeneous three-dimensional cell culture systems. To understand the cell organisation principles of their morphogenesis, we imaged hundreds of pancreas and liver organoids in parallel using light sheet and bright field microscopy for up to seven days. We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation and degeneration, and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright field macroscale analyses of entire cultures. Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying core regulatory principles of organoid morphogenesis.

Graphical Abstract

Created withBioRender.com.
KHz-rate volumetric voltage imaging of the whole zebrafish heart
Authors: Sacconi L. , Silvestri L. , Rodríguez E.C. , Armstrong G.A.B. , Pavone F.S. , Shrier A. , Bub G.
Published: July 2020

Fast volumetric imaging is essential for understanding the function of excitable tissues such as those found in the brain and heart. Measuring cardiac voltage transients in tissue volumes with spatial and temporal resolutions needed to give insight to cardiac function has so far been impossible. We introduce a new imaging modality based on simultaneous illumination of multiple planes in the tissue and parallel detection with multiple cameras, avoiding compromises inherent in any scanning approach. The system enables imaging of voltage transients in-situ, allowing us, for the first time, to map voltage activity in the whole heart volume at KHz rates. The unprecedented spatio-temporal resolution of our method enabled the observation of novel dynamics of electrical propagation through the zebrafish atrioventricular canal.
Tobacco, but not nicotine and flavor-less electronic cigarettes, induces ACE2 and immune dysregulation
Authors: Lee Abby C. , Chakladar Jaideep , Li Wei Tse , Chen Chengyu , Chang Eric Y. , Wang-Rodriguez Jessica , Ongkeko Weg M.
Published: July 2020

COVID-19, caused by the virus SARS-CoV-2, has infected millions worldwide. This pandemic overlaps with the ongoing epidemics of cigarette smoking and electronic cigarette (e-cig) vaping, with over 1 billion smokers and vapers worldwide. However, there is scarce data relating COVID-19 risks and outcome with cigarette or e-cig use. In this study, we mined 3 independent RNA expression datasets from smokers and vapers to understand the potential relationship between vaping/smoking and the dysregulation of key genes and pathways related to COVID-19. We found that smoking, but not vaping, upregulates ACE2, the cellular receptor that SARS-CoV-2 requires for infection. Both smoking and use of nicotine and flavor-containing e-cig led to upregulations of pro-inflammatory cytokine production and expression of genes related to inflammasomes. Vaping flavor-less and nicotine-less e-cig, however, did not lead to significant cytokine dysregulation and inflammasome activation. Release of inflammasome products, such as IL-1B, and cytokine storms are hallmarks of COVID-19 infection, especially in severe cases. Therefore, our findings demonstrated that smoking or vaping, specifically use of flavored or nicotine-containing e-cigs, may critically exacerbate COVID-19-related inflammation or increase susceptibility to the disease. Further scientific and public health investigations should be undertaken to address these concerning links between COVID-19 and e-cig/smoking.
A multifunctional type IA DNA/RNA topoisomerase with RNA hydrolysis and rRNA processing activities fromMycobacterium smegmatisandMycobacterium tuberculosis
Authors: Rani Phoolwanti , Kalladi Shashwath Malli , Bansia Harsh , Rao Sandhya , Jha Rajiv Kumar , Jain Paras , Bhaduri Tisha , Nagaraja Valakunja
Published: July 2020

Topoisomerases maintain topological homeostasis of bacterial chromosomes by catalysing changes in DNA linking number. The resolution of RNA entanglements occurring in the cell would also require catalytic action of topoisomerases. We describe RNA topoisomerase and hydrolysis activities in DNA topoisomerase I (topo I) from mycobacteria. The interaction of topo I with mRNA, tRNA and rRNA suggested its role in some aspect of RNA metabolism; the enzyme participates in rRNA maturation via its RNA hydrolysis activity. Accumulation of rRNA precursors in a topo I knockdown strain and the rescue of rRNA processing deficiency in RNaseE knockdown cells by topo I expression, indicated the enzyme’s back-up support to RNases involved in rRNA processing. We demonstrate that the active site tyrosine of the enzyme mediates catalytic reactions with both DNA/RNA substrates, and RNA topoisomerase activity can follow two reaction paths in contrast to its DNA topoisomerase activity. Mutation in the canonical proton relay pathway impacts DNA topoisomerase activity while retaining activity on RNA substrates. The mycobacterial topo I thus exemplifies the resourcefulness and parsimony of biological catalysis in harnessing the limited chemical repertoire at its disposal to find common solutions to mechanistically-related challenges of phosphodiester breakage/exchange reactions in DNA and RNA that are essential for cell survival.
tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast
Authors: Tavares Joana F , Davis Nick K. , Poim Ana , Reis Andreia , Kellner Stefanie , Sousa Inês , Soares Ana R. , Moura Gabriela M R , Dedon Peter C , Santos Manuel A S
Published: July 2020

Abstract/Summary

Protein synthesis rate and accuracy are essential forbona fideprotein synthesis and proteome homeostasis (proteostasis), however the mRNA translation elongation factors that prevent protein mistranslation, misfolding and aggregation are poorly understood. To address this question, we evaluated the role of 70 yeast tRNA modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated and mistranslated proteins. We show that the mitochondrial tRNA-modifying enzyme Slm3 thiolates the cytoplasmic tRNAs at position 34 and that decreased levels of mcm5s2U34inSLM3mutants are compensated by increasing mcm5U34, ncm5U34and ncm5Um34levels. In the tRNA gene knockout strains, stress response proteins are overrepresented in protein aggregates and their genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications. Increased rates of amino acid misincorporation were detected in the yeastELP1, SLM3andTRM9gene knockout mutants at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34tRNA modifications safeguard the proteome from translational errors, misfolding and cellular proteotoxic stress.
Single-cell analysis reveals the function of lung progenitor cells in COVID-19 patients
Authors: Zhao Zixian , Zhao Yu , Zhou Yueqing , Wang Xiaofan , Zhang Ting , Zuo Wei
Published: July 2020

The high mortality of severe 2019 novel coronavirus disease (COVID-19) cases is mainly caused by acute respiratory distress syndrome (ARDS), which is characterized by increased permeability of the alveolar epithelial barriers, pulmonary edema and consequently inflammatory tissue damage. Some but not all patients showed full functional recovery after the devastating lung damage, and so far there is little knowledge about the lung repair process1. Here by analyzing the bronchoalveolar lavage fluid (BALF) of COVID-19 patients through single cell RNA-sequencing (scRNA-Seq), we found that in severe (or critical) cases, there is remarkable expansion of TM4SF1+ and KRT5+ lung progenitor cells. The two distinct populations of progenitor cells could play crucial roles in alveolar cell regeneration and epithelial barrier re-establishment, respectively. In order to understand the function of KRT5+ progenitors in vivo, we transplanted a single KRT5+ cell-derived cell population into damaged mouse lung. Time-course single-cell transcriptomic analysis showed that the transplanted KRT5+ progenitors could long-term engrafted into host lung and differentiate into HOPX+ OCLN+ alveolar barrier cell which restored the epithelial barrier and efficiently prevented inflammatory cell infiltration. Similar barrier cells were also identified in some COVID-19 patients with massive leukocyte infiltration. Altogether this work uncovered the mechanism that how various lung progenitor cells work in concert to prevent and replenish alveoli loss post severe SARS-CoV-2 infection.
Complex plant metabolomes guide fitness-relevant foraging decisions of a specialist herbivore
Authors: Machado Ricardo A. R. , Theepan Vanitha , Robert Christelle A.M. , Züst Tobias , Hu Lingfei , Su Qi , Schimmel Bernardus C. J. , Erb Matthias
Published: July 2020

Plants produce complex mixtures of primary and secondary metabolites. Herbivores use these metabolites as behavioral cues to increase their fitness. However, how herbivores integrate different metabolite classes into fitness-relevant foraging decisionsin plantais poorly understood. We developed a molecular manipulative approach to modulate the availability of sugars and benzoxazinoid secondary metabolites as foraging cues for a specialist maize herbivore, the western corn rootworm. By disrupting sugar perception in the western corn rootworm and benzoxazinoid production in maize, we show that sugars and benzoxazinoids act as distinct and dynamically integrated mediators of short-distance host finding and acceptance. While sugars improve the capacity of rootworm larvae to find a host plant and to distinguish post-embryonic from less nutritious embryonic roots, benzoxazinoids are specifically required for the latter. Host acceptance in the form of root damage is increased by benzoxazinoids and sugars in an additive manner. This pattern is driven by increasing damage to post-embryonic roots in the presence of benzoxazinoids and sugars. Benzoxazinoid- and sugar-mediated foraging directly improves western corn rootworm growth and survival. Interestingly, western corn rootworm larvae retain a substantial fraction of their capacity to feed and survive on maize plants even when both classes of chemical cues are almost completely absent. This study unravels fine-grained differentiation and integration of primary and secondary metabolites into herbivore foraging and documents how the capacity to compensate for the lack of important chemical cues enables a specialist herbivore to survive within unpredictable metabolic landscapes.
Cigarette Smoke and Nicotine-Containing E-cigarette Vapor Downregulate Lung WWOX Expression Which is Associated with Increased Severity of Murine ARDS
Authors: Zeng Zhenguo , Chen Weiguo , Moshensky Alexander , Khan Raheel , Crotty-Alexander Laura , Ware Lorraine B. , Aldaz C. Marcelo , Jacobson Jeffrey R. , Dudek Steven M. , Natarajan Viswanathan , Machado Roberto F. , Singla Sunit
Published: July 2020

RATIONALE

A history of chronic cigarette smoking is known to increase risk for ARDS, but the corresponding risks associated with chronic e-cigarette use are largely unknown. The chromosomal fragile site gene, WWOX, is highly susceptible to genotoxic stress from environmental exposures, and thus an interesting candidate gene for the study of exposure-related lung disease.

METHODS AND RESULTS

Lungs harvested from current versus former/never smokers exhibited a 47% decrease in WWOX mRNA levels. Exposure to nicotine-containing e-cigarette vapor resulted in an average 57% decrease in WWOX mRNA levels relative to vehicle treated controls. In separate studies, endothelial (EC)-specific WWOX KO versus wild type mice were examined under ARDS-producing conditions. EC WWOX KO mice exhibited significantly greater levels of vascular leak and histologic lung injury. ECs were isolated from digested lungs of untreated EC WWOX KO mice using sorting by flow cytometry for CD31+CD45- cells. These were grown in culture, confirmed to be WWOX-deficient by RT-PCR and Western blotting, and analyzed by electric cell impedance sensing (ECIS) as well as a FITC dextran transwell assay for their barrier properties during MRSA or LPS exposure. WWOX KO ECs demonstrated significantly greater declines in barrier function relative to wild type cells during either MRSA or LPS treatment as measured by both ECIS and the transwell assay.

CONCLUSION

The increased risk for ARDS observed in chronic smokers may be mechanistically linked, at least in part, to lung WWOX downregulation, and this phenomenon may also manifest in the near future in chronic users of e-cigarettes.
A gene-level methylome-wide association analysis identifies novel Alzheimer’s disease genes
Authors: Wu Chong , Bradley Jonathan , Li Yanming , Wu Lang , Deng Hong-Wen
Published: July 2020

Motivation

Transcriptome-wide association studies (TWAS) have successfully facilitated the discovery of novel genetic risk loci for many complex traits, including late-onset Alzheimer’s disease (AD). However, most existing TWAS methods rely only on gene expression and ignore epigenetic modification (i.e., DNA methylation) and functional regulatory information (i.e., enhancer-promoter interactions), both of which contribute significantly to the genetic basis of AD.

Results

This motivates us to develop a novel gene-level association testing method that integrates genetically regulated DNA methylation and enhancer-target gene pairs with genome-wide association study (GWAS) summary results. Through simulations, we show that our approach, referred to as the CMO (cross methylome omnibus) test, yielded well controlled type I error rates and achieved much higher statistical power than competing methods under a wide range of scenarios. Furthermore, compared with TWAS, CMO identified an average of 124% more associations when analyzing several brain imaging-related GWAS results. By analyzing to date the largest AD GWAS of 71,880 cases and 383,378 controls, CMO identified six novel loci for AD, which have been ignored by competing methods.

Availability and implementation

Software:https://github.com/ChongWuLab/CMO

Contact

cwu3@fsu.edu

Supplementary information

Supplementary data are available at Bioinformatics online.