bluuebunny/crossref_metadata_2025 huggingface dataset:
Saliva-based detection of COVID-19 infection in a real-world setting using reagent-free Raman spectroscopy and machine learning
Authors: Ember Katherine , Daoust François , Mahfoud Myriam , Dallaire Frédérick , Zamani Esmat , Tran Trang , Plante Arthur , Diop Mame-Kany , Nguyen Tien , St-Georges-Robillard Amélie , Ksantini Nassim , Lanthier Julie , Filiatrault Antoine , Sheehy Guillaume , Quach Caroline , Trudel Dominique , Leblond Frédéric
Published: September 2021

Significance

The primary method of COVID-19 detection is reverse transcription polymerase chain reaction (RT-PCR) testing. PCR test sensitivity may decrease as more variants of concern arise.

Aim

We aimed to develop a reagent-free way to detect COVID-19 in a real-world setting with minimal constraints on sample acquisition.

Approach

We present a workflow for collecting, preparing and imaging dried saliva supernatant droplets using a non-invasive, label-free technique – Raman spectroscopy – to detect changes in the molecular profile of saliva associated with COVID-19 infection.

Results

Using machine learning and droplet segmentation, amongst all confounding factors, we discriminated between COVID-positive and negative individuals yielding receiver operating coefficient (ROC) curves with an area under curve (AUC) of 0.8 in both males (79% sensitivity, 75% specificity) and females (84% sensitivity, 64% specificity). Taking the sex of the saliva donor into account increased the AUC by 5%.

Conclusion

These findings may pave the way for new rapid Raman spectroscopic screening tools for COVID-19 and other infectious diseases.
Comparative analysis of human immune responses following SARS-CoV-2 vaccination with BNT162b2, mRNA-1273, or Ad26.COV2.S
Authors: Barbeau Dominique J. , Martin Judith M. , Carney Emily , Dougherty Emily , Doyle Joshua D. , Dermody Terence S. , Hoberman Alejandro , Williams John V. , Michaels Marian G. , Alcorn John F. , Duprex W. Paul , McElroy Anita K.
Published: September 2021

Background

Three SARS-CoV-2 vaccines, two based on mRNA, BNT162b2 and mRNA-1273, and one based on an adenovirus platform, Ad26.COV2.S, received emergency use authorization by the U.S. Food and Drug Administration in 2020/2021. These vaccines displayed clinical efficacy in initial studies against confirmed COVID-19 of 95.0%, 94.1%, and 66.9%, respectively.

Methods

Individuals receiving one of these vaccines were invited to participate in a prospective longitudinal comparative study of immune responses elicited by the three vaccines. In this observational cohort study, humoral responses were evaluated using a SARS-CoV-2 receptor-binding domain (RBD) ELISA and a SARS-CoV-2 virus neutralization assay at mean of 21-31 days and 45-63 days following each initial vaccination. IFN-γ ELISPOT assays were conducted with peripheral blood mononuclear cells obtained at a median of 45-63 days after each initial vaccination.

Results

The two mRNA-based platforms elicited similar RBD ELISA responses and neutralizing antibody responses. The adenovirus-based vaccine elicited significantly lower RBD ELISA and SARS-CoV-2 virus neutralization activity. The mRNA-1273 vaccine elicited significantly higher spike glycoprotein-specific T cell responses than either the BNT162b2 or the Ad26.COV2.S vaccines.

Conclusions

Both mRNA based vaccines elicited higher magnitude humoral responses than Ad26.COV2.S and mRNA1273 elicited the highest magnitude of T cell response. Neutralizing antibody titers correlated with reported estimates of vaccine efficacy.

Summary of key points

We compared antigen specific humoral and T cell responses following vaccination with BNT162b2, mRNA-1273, or Ad26.COV2.S. Both mRNA based vaccines elicited higher magnitude humoral responses than Ad26.COV2.S and mRNA1273 elicited the highest magnitude of T cell response.
Automated Detection of Candidate Subjects with Cerebral Microbleeds using Machine Learning
Authors: Sundaresan Vaanathi , Arthofer Christoph , Zamboni Giovanna , Dineen Robert A. , Rothwell Peter M. , Sotiropoulos Stamatios N. , Auer Dorothee P. , Tozer Daniel , Markus Hugh S. , Miller Karla L. , Dragonu Iulius , Sprigg Nikola , Alfaro-Almagro Fidel , Jenkinson Mark , Griffanti Ludovica
Published: September 2021

Cerebral microbleeds (CMBs) appear as small, circular, well defined hypointense lesions of a few mm in size on T2*-weighted gradient recalled echo (T2*-GRE) images and appear enhanced on susceptibility weighted images (SWI). Due to their small size, contrast variations and other mimics (e.g. blood vessels), CMBs are highly challenging to detect automatically. In large datasets (e.g. the UK Biobank dataset), exhaustively labelling CMBs manually is difficult and time consuming. Hence it would be useful to preselect candidate CMB subjects in order to focus on those for manual labelling, which is essential for training and testing automated CMB detection tools on these datasets. In this work, we aim to detect CMB candidate subjects from a larger dataset, UK Biobank, using a machine learning-based, computationally light pipeline. For our evaluation, we used 3 different datasets, with different intensity characteristics, acquired with different scanners. They include the UK Biobank dataset and two clinical datasets with different pathological conditions. We developed and evaluated our pipelines on different types of images, consisting of SWI or GRE images. We also used the UK Biobank dataset to compare our approach with alternative CMB preselection methods using non-imaging factors and/or imaging data. Finally, we evaluated the pipeline’s generalisability across datasets. Our method provided subject-level detection accuracy>80% on all the datasets (withindataset results), and showed good generalisability across datasets, providing a consistent accuracy of over 80%, even when evaluated across different modalities.
Real-world Effectiveness of 2-dose SARS-CoV-2 Vaccination in Kidney Transplant Recipients
Authors: McEvoy Caitríona M. , Lee Anna , Misra Paraish S. , Lebovic Gerald , Wald Ron , Yuen Darren A.
Published: September 2021

The humoral response to two doses of SARS-CoV-2 (Covid-19) vaccine among transplant recipients is inferior to immunocompetent individuals.1 Data on the ‘real-world’ effectiveness of vaccination in kidney transplant recipients [KTRs] are lacking. We performed a cohort study to investigate the impact of vaccination on Covid-19 infection and outcomes in our kidney transplant program.
A new multi-species Protein A-ELISA assay for plague diagnosis in humans and other mammal hosts
Authors: Bezerra Matheus Filgueira , Xavier Camila Cavalcanti , de Almeida Alzira Maria Paiva , de Souza Reis Christian Robson
Published: September 2021

Background

The Hemagglutination assay (HA) is widely used in plague diagnosis, however, it has a subjective interpretation and demands high amounts of antigen and other immunobiological supplies. Conventional IgG-ELISA is limited by the need of specific conjugates for multiple plague hosts.

Methods

Thus, we developed an ELISA Protein A-peroxidase method to detect anti-F1 antibodies across several species, including humans. To determine the cut-off and performance rates, HA results from 288 samples (81 rabbits, 64 humans, 66 rodents and 77 dogs) were used as reference.

Results

Optimal conditions were found with 250ng/well of F1 and 1:500 serum dilution. Protein A-ELISA showed high repeatability and reproducibility. The positive/negative OD ratios were higher in Protein A-ELISA and there was no significant cross-reaction with other pathogenic yersiniae. The overall sensitivity/specificity, area under the curve and Kappa rates for Protein A-ELISA were 93.9/98.9%; 0.993 and 0.938, respectively. Similar results were observed in each species separately. There was a strong agreement between Protein A and IgG assays (kappa=0.973) in independent analysis (n=487).

Conclusions

Altogether, the Protein A-ELISA showed high performance when compared both to HA and IgG-ELISA, with a polyvalent single protocol that requires reduced amounts of antigen and can be employed to any plague hosts.
The slower antibody response in myelofibrosis patients after two doses of mRNA SARS-CoV-2 vaccine calls for a third dose
Authors: Fiorino Fabio , Sicuranza Anna , Ciabattini Annalisa , Santoni Adele , Pastore Gabiria , Simoncelli Martina , Polvere Jacopo , Galimberti Sara , Auddino Stefano , Baratè Claudia , Montagnani Francesca , Sammartano Vincenzo , Bocchia Monica , Medaglini Donata
Published: September 2021

Immunization with mRNA SARS-CoV-2 vaccines has been highly recommended and prioritized in fragile categories with higher risk of mortality after COVID-19 disease compared to healthy people, including patients with myelofibrosis (MF). Available data on the vaccine immune response developed by MF patients, and the impact of the treatment with the inhibitor of JAK-STAT signaling ruxolitimib, are still fragmented to support an informed decision for a third dose for this category of subjects. Here, we show that 76% of MF patients develop spike-specific IgG after the second vaccine dose, but the response has a slower kinetic compared to healthy subjects, suggesting a reduced capability of their immune system to promptly react to vaccination. A reduced ACE2/RBD inhibition binding activity of spike-specific antibodies was also observed, especially in ruxolitimib treated patients. Our results contribute to answer the open question on the induction of the antibody responses in MF patients following vaccination with COVID-19 mRNA vaccines, showing a slow kinetic that support the need for a third dose of SARS-CoV-2 mRNA vaccines.
Immune profile and responses of a novel Dengue DNA vaccine encoding EDIII-NS1 consensus design based on Indo-African sequences
Authors: Sankaradoss Arun , Jagtap Suraj , Nazir Junaid , E-Moula Shefta , Modak Ayan , Fialho Joshuah , Iyer Meenakshi , Shastri Jayanthi S , Dias Mary , Gadepalli Ravisekhar , Aggarwal Alisha , Vedpathak Manoj , Agrawal Sachee , Pandit Awadhesh , Nisheetha Amul , Kumar Anuj , Shafi Mohamed , Balachandra Swathi , Damodar Tina , Masika Moses Muia , Mwaura Patrick , Anzala Omu , Muthumani Kar , Sowdhamini Ramanathan , Medigeshi Guruprasad R. , Roy Rahul , Pattabiraman Chitra , Krishna Sudhir , Sreekumar Easwaran
Published: September 2021

Following the recent clinical clearance of an Indian DNA COVID-19 vaccine, India and Africa are potential regions where DNA vaccines may become a major delivery system subject to a range of immunological and regulatory scrutiny. The ongoing COVID pandemic highlights the need to tackle viral variants and expand the number of antigens and assess diverse delivery systems. To address some of these key issues, we have created a Dengue DNA vaccine candidate with the EDIII region as the key antigen given the promise of this segment in not causing ADE, a challenge with this disease. In addition, we have added the NS1 region to broaden the immune response. Following a large Dengue viral sequencing exercise in India, complemented with data from east Africa, our approach was to generate a consensus of four serotypes ED3-NS1 vaccine to explore tackling the issue of diversity. OurIn silicostructural analysis of EDIII consensus vaccine sequence revealed that epitopes are structurally conserved and immunogenic across HLA diversity. Vaccination of mice with this construct induced pan-serotype neutralizing antibodies and antigen-specific T cell responses. Furthermore, the DNA vaccination confers protection against DENV challenge in AG129 mice. Finally, assaying of intracellular staining for IFN-γ, immunoglobulin IgG2(a/c) /IgG1 ratios as well as immune gene profiling suggested a strong Th1-dominant immune response. Our Dengue DNA platform with a focus on Indo-African sequences offers an approach for assessing cross reactive immunity in animal models and lays the foundation for human vaccine roll out either as a stand-alone or mix and match strategy.
Metatranscriptomic Signatures of Lung Function in Pediatric Hematopoietic Cell Transplant Candidates
Authors: Zinter Matt S. , Versluys Birgitta A. , Lindemans Caroline A. , Mayday Madeline Y. , Reyes Gustavo , Sunshine Sara , Chan Marilynn , Fiorino Elizabeth , Cancio Maria , Prevaes Sabine , Sirota Marina , Matthay Michael A. , Kharbanda Sandhya , Dvorak Christopher C. , Boelens Jaap J. , DeRisi Joseph L.
Published: September 2021

Rationale

Impaired baseline lung function is associated with mortality after allogeneic hematopoietic cell transplantation (HCT). Limited knowledge of the molecular pathways that characterize pre-transplant lung function has hindered the development of lung-targeted interventions.

Objectives

To elucidate the biologic and microbiologic correlates of impaired lung function in pediatric allogeneic HCT candidates.

Methods

Between 2005-2016, 104 patients with malignant and non-malignant disorders ages 4-19 years underwent paired pulmonary function testing (PFT) and bronchoalveolar lavage (BAL) a median of 1-2 weeks prior to allogeneic transplant in Utrecht, the Netherlands. Cryopreserved BAL underwent RNA sequencing followed by alignment to microbial and human reference genomes for microbiome and gene expression analyses.

Measurements and Main Results

Abnormal pulmonary function was recorded in more than half the cohort, consisted most commonly of restriction and impaired diffusion, and was associated with both all-cause and lung-injury related mortality after HCT. BAL microbiome depletion of commensal supraglottic taxa such as Haemophilus and enrichment of nasal and skin taxa such as Staphylococcus were associated with worse measures of lung capacity and gas diffusion. In addition, impaired lung capacity and diffusion were also associated with gene expression signatures of alveolar epithelial proliferation, epithelial-mesenchymal transition, and downregulated immunity, suggesting a post-injury pro-fibrotic response. Detection of microbial depletion and abnormal epithelial gene expression in BAL enhanced the prognostic utility of pre-HCT PFTs for the outcome of post-HCT mortality.

Conclusions

These findings suggest a novel and potentially actionable connection between microbiome depletion, alveolar injury, and pulmonary fibrosis in the pathogenesis of pre-HCT lung dysfunction.
A computational model of CAR T-cell immunotherapy predicts leukemia patient responses at remission, resistance, and relapse
Authors: Liu Lunan , Ma Chao , Zhang Zhuoyu , Chen Weqiang
Published: September 2021

Adaptive CD19-targeted CAR (Chimeric Antigen Receptor) T-cell transfer has become a promising treatment for leukemia. Though patient responses vary across different clinical trials, there currently lacks reliable early diagnostic methods to predict patient responses to those novel therapies. Recently, computational models achieve to in silico depict patient responses, with prediction application being limited. We herein established a computational model of CAR T-cell therapy to recapitulate key cellular mechanisms and dynamics during treatment based on a set of clinical data from different CAR T-cell trials, and revealed critical determinants related to patient responses at remission, resistance, and relapse. Furthermore, we performed a clinical trial simulation using virtual patient cohorts generated based on real clinical patient dataset. With input of early-stage CAR T-cell dynamics, our model successfully predicted late responses of various virtual patients compared to clinical observance. In conclusion, our patient-based computational immuno-oncology model may inform clinical treatment and management.
A Comparison of Weighted Stochastic Simulation Methods
Authors: Thomas Payton J , Ahmadi Mohammad , Zheng Hao , Myers Chris J.
Published: September 2021

1

Rare events are of particular interest in biology because rare biochemical events may be catastrophic to a biological system. To estimate the probability of rare events, several weighted stochastic simulation methods have been developed. Unfortunately, the robustness of these methods is questionable. Here, an analysis of weighted stochastic simulation methods is presented. The methods considered here fail to accomplish the task of rare event simulation, in general, suggesting that new methods are necessary to adequately study rare biological events.
The dynamical Matryoshka model: 1. Incoherent neutron scattering functions for lipid dynamics in bilayers
Authors: Bicout Dominique J. , Cisse Aline , Matsuo Tatsuhito , Peters Judith
Published: September 2021

Fluid lipid bilayers are the building blocks of biological membranes. Although there is a large amount of experimental data using inconsistent quasi-elastic neutron scattering (QENS) techniques to study membranes, very little theoretical works have been developed to study the local dynamics of membranes. The main objective of this work is to build a theoretical framework to study and describe the local dynamics of lipids and derive analytical expressions of inconsistent diffusion functions (ISF) for QENS. As results, we developed the dynamical Matryoshka model which describes the local dynamics of lipid molecules in membrane layers as a nested hierarchical convolution of three motional processes: (i) individual motions described by the vibrational motions of H-atoms; (ii) internal motions including movements of the lipid backbone, head groups and tails, and (iii) molecule movements of the lipid molecule as a whole. The analytical expressions of the ISF associated with these movements are all derived. For use in analyzing the QENS experimental data, we also derived an analytical expression for the aggregate ISF of the Matryoshka model which involves an elastic term plus three inelastic terms of well-separated time scales and whose amplitudes and rates are functions of the lipid motions. And as an illustrative application, we used the aggregated ISF to analyze the experimental QENS data on a lipid sample of multilamellar bilayers of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine). It is clear from this analysis that the dynamical Matryoshka model describes very well the experimental data and allow extracting the dynamical parameters of the studied system.
Recombinant Fasciola hepatica fatty acid binding protein (Fh15) as a novel anti-inflammatory biotherapeutic in an acute gram-negative non-human primate sepsis model
Authors: Rosado-Franco Jose J. , Armina-Rodriguez Albersy , Marzan-Rivera Nicole , Burgos Armando G. , Spiliopoulos Natalie , Dorta-Estremera Stephanie M. , Mendez Loyda B. , Espino A.M.
Published: September 2021

Abstract

Due to their phylogenetic proximity to human, non-human primates (NHP) are considered an adequate choice for basic and pre-clinical model of sepsis. Gram-negative bacteria are the primary causative of sepsis. During infection bacteria continuously release the potent toxin lipopolysaccharide (LPS) into the bloodstream, which triggers an uncontrolled systemic inflammatory response leading to death. Our previous research has demonstrated in vitro and in vivo using a mouse model of septic shock that Fh15, a recombinant variant of the Fasciola hepatica fatty acid binding protein, acts as an antagonist of TLR4 suppressing the LPS-induced pro-inflammatory cytokine storm. The present study aimed to demonstrate that Fh15 suppress the cytokine storm and other inflammatory markers during the early phase of an endotoxemia induced in rhesus macaques by i.v. infusion with lethal doses of live E. coli. Fh15 was administrated as isotonic infusion 30 min prior to the bacterial infusion. Among the novel findings reported in this communication, I) Fh15 significantly prevented bacteremia, suppressed LPS levels in plasma and the production of C-reactive protein and procalcitonin, which are key signature of inflammation and bacterial infection, respectively, II) notably reduced the production of pro-inflammatory cytokines, and III) increased innate immune cell populations in blood, which suggest a role in promoting a prolonged steady state in rhesus macaques even in the presence of inflammatory stimuli. This is the first report demonstrating that a F. hepatica-derived molecule possesses potential as anti-inflammatory drug against endotoxemia in an NHP-model.

Tweet

This is the first communication demonstrating that a F. hepatica-derived molecule possesses potential as anti-inflammatory drug against endotoxemia in an NHP-model.

Importance

Sepsis caused by Gram-negative bacteria affect 1.7 million adults annually in the United States and is one of the most important causes of death at intensive care units. Although the effective use of antibiotics has resulted in improved prognosis of sepsis, the pathological and deathly effects has been attributed to the persistent inflammatory cascade. There is a present need to develop anti-inflammatory agents that can suppress or neutralize the inflammatory responses and prevent the lethal consequences of sepsis. We demonstrated herein that a small molecule of 14.5kDa can suppress the bacteremia, endotoxemia and many other inflammatory markers in a rhesus macaque model. These results reinforce the notion that Fh15 constitute an excellent candidate for drug development against sepsis.
Transcriptomics reveals how minocycline-colistin synergy overcomes antibiotic resistance in multidrug-resistant Klebsiella pneumoniae
Authors: Brennan-Krohn Thea , Grote Alexandra , Rodriguez Shade , Kirby James E. , Earl Ashlee M.
Published: September 2021

Multidrug resistant gram-negative bacteria are a rapidly growing public health threat, and the development of novel antimicrobials has failed to keep pace with their emergence. Synergistic combinations of individually ineffective drugs present a potential solution, yet little is understood about the mechanisms of most such combinations. Here, we show that the combination of colistin (polymyxin E) and minocycline has a high rate of synergy against colistin-resistant and minocycline-intermediate or -resistant strains of Klebsiella pneumoniae. Furthermore, using RNA-Seq, we characterized the transcriptional profiles of these strains when treated with the drugs individually and in combination. We found a striking similarity between the transcriptional profiles of bacteria treated with the combination of colistin and minocycline at individually subinhibitory concentrations and those of the same isolates treated with minocycline alone. We observed a similar pattern with the combination of polymyxin B nonapeptide (a polymyxin B analogue that lacks intrinsic antimicrobial activity) and minocycline. We also found that genes involved in polymyxin resistance and peptidoglycan biosynthesis showed significant differential gene expression in the different treatment conditions, suggesting possible mechanisms for the antibacterial activity observed in the combination. These findings suggest that the synergistic activity of this combination against bacteria resistant to each drug alone involves sublethal outer membrane disruption by colistin, which permits increased intracellular accumulation of minocycline.

IMPORTANCE

Few treatment options exist for multidrug resistant gram-negative bacteria. Synergistic antimicrobial combinations (in which two individually inactive drugs regain activity when used in combination) can overcome resistance. In susceptible bacteria, minocycline acts inside the cell by preventing protein synthesis, while colistin disrupts the outer membrane. Even in bacteria resistant to both drugs, the combination of the two is active. To understand this activity, we studied Klebsiella pneumoniae isolates resistant to both drugs. We extracted messenger RNA during treatment with each drug alone and with the combination, then performed RNA sequencing to analyze gene expression levels. Bacteria treated with the combination had an expression profile similar to bacteria treated with minocycline alone. Our findings suggest that synergy results from low-level, subinhibitory membrane disruption by colistin, which permits sufficient accumulation of minocycline in the cell to overcome resistance. Understanding this pathway will facilitate further development of synergistic antimicrobial combination regimens.
Astrocytic C-X-C motif chemokine ligand-1 mediates β-amyloid-induced synaptotoxicity
Authors: Perez-Nievas Beatriz Gomez , Johnson Louisa , Beltran-Lobo Paula , Hughes Martina M. , Gammallieri Luciana , Tarsitano Francesca , Myszczynska Monika A , Vazquez-Villasenor Irina , Jimenez-Sanchez Maria , Troakes Claire , Wharton Stephen B. , Ferraiuolo Laura , Noble Wendy
Published: September 2021

Background

Pathological interactions between β-amyloid (Aβ) and tau drive the synapse loss that underlies neural circuit disruption and cognitive decline in Alzheimer’s disease (AD). Reactive astrocytes, displaying altered functions, are also a prominent feature of AD brain. This large and heterogeneous population of cells are increasingly recognised as contributing to early phases of disease. However, the contribution of astrocytes to detrimental Aβ-tau interactions in AD is not well understood.

Methods

Mouse and human astrocyte cultures were stimulated with concentrations and species of human Aβ that mimic those in human AD brain. Astrocyte conditioned medium was collected and immunodepleted of Aβ before being added to rodent or human neuron cultures. Cytokines, identified in unbiased screens were also applied to neurons, including following the pre-treatment of neurons with chemokine receptor antagonists. Tau mislocalisation, synaptic markers and dendritic spine numbers were measured in cultured neurons and organotypic brain slice cultures.

Results

Conditioned medium from astrocytes stimulated with Aβ induces tau mislocalisation and exaggerated synaptotoxicity that is recapitulated following spiking of neuron culture medium with recombinant C-X-C motif chemokine ligand-1 (CXCL1), a chemokine we show to be upregulated in Alzheimer’s disease brain. Antagonism of neuronal C-X-C motif chemokine receptor 2 (CXCR2) prevented tau mislocalisation and synaptotoxicity in response to CXCL1 and Aβ-stimulated astrocyte secretions.

Conclusions

Our data indicate that astrocytes exacerbate tau mislocalisation and the synaptotoxic effects of Aβ via interactions of astrocytic CXCL1 and neuronal CXCR2 receptors, highlighting this chemokine-receptor pair as a novel target for therapeutic intervention in AD.
A new oomycete metabarcoding method using therps10gene
Authors: Foster Zachary S. L. , Albornoz Felipe E. , Fieland Valerie J. , Larsen Meredith M. , Jones F. Andrew , Tyler Brett M. , Nguyen Hai D. T. , Burgess Treena I. , Riddell Carolyn , Voglmayr Hermann , Martin Frank N. , Grünwald Niklaus J.
Published: September 2021

Oomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed for rapid and accurate characterization of oomycete communities using DNA metabarcoding. We have identified the mitochondrial 40S ribosomal protein S10 gene (rps10) as a locus useful for oomycete metabarcoding and provide primers predicted to amplify all oomycetes based on available reference sequences from a wide range of taxa. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental samples and a mock community using Illumina MiSeq. Amplified sequence variants (ASVs) and operational taxonomic units (OTUs) were identified per community. Both the sequence and predicted taxonomy of ASVs and OTUs were compared to the known composition of the mock community. Bothrps10and ITS yielded ASVs with sequences matching 21 of the 24 species in the mock community and matching all 24 when allowing for a 1 bp difference. Taxonomic classifications of ASVs included 23 members of the mock community forrps10and 17 for ITS1. Sequencing results for the environmental samples suggest the proposedrps10locus results in substantially less amplification of non-target organisms than the ITS1 method. The amplifiedrps10region also has higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchablerps10reference database for species identification and all protocols needed for oomycete metabarcoding. Therps10barcode and methods described herein provide an effective tool for metabarcoding oomycetes using short-read sequencing.

Interpretive summary

Oomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed to rapidly characterize the diversity of oomycete species found in environmental samples. We have identified the mitochondrial 40S ribosomal protein S10 gene (rps10) as being useful for oomycete community sequencing. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental samples and a community we synthesized in the laboratory. The amplifiedrps10region is predicted to have a higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchablerps10reference database for species identification and all protocols needed for oomycete community sequencing. Therps10barcode and methods described herein provide an effective tool for characterizing oomycetes using environmental DNA sequencing.
Glucosyltransferase-dependent and independent effects of Clostridioides difficile toxins during infection
Authors: Peritore-Galve F. Christopher , Shupe John A. , Cave Rory J. , Washington M. Kay , Kuehne Sarah A. , Lacy D. Borden
Published: September 2021

Clostridioides difficile infection (CDI) is the leading cause of nosocomial diarrhea and pseudomembranous colitis in the USA. In addition to these symptoms, patients with CDI can develop severe inflammation and tissue damage, resulting in life-threatening toxic megacolon. CDI is mediated by two large homologous protein toxins, TcdA and TcdB, that bind and hijack receptors to enter host cells where they use glucosyltransferase (GT) enzymes to inactivate Rho family GTPases. GT-dependent intoxication elicits cytopathic changes, cytokine production, and apoptosis. At higher concentrations TcdB induces GT-independent necrosis in cells and tissue by stimulating production of reactive oxygen species via recruitment of the NADPH oxidase complex. Although GT-independent necrosis has been observed in vitro, the relevance of this mechanism during CDI has remained an outstanding question in the field. In this study we generated novel C. difficile toxin mutants in the hypervirulent BI/NAP1/PCR-ribotype 027 R20291 strain to test the hypothesis that GT-independent epithelial damage occurs during CDI. Using the mouse model of CDI, we observed that epithelial damage occurs through a GT-independent process that is does not involve immune cell influx. The GT-activity of either toxin was sufficient to cause severe edema and inflammation, yet GT activity of both toxins was necessary to produce severe watery diarrhea. These results indicate that both TcdA and TcdB contribute to infection when present. Further, while inactivating GT activity of C. difficile toxins may suppress diarrhea and deleterious GT-dependent immune responses, the potential of severe GT-independent epithelial damage merits consideration when developing toxin-based therapeutics against CDI.

SIGNIFICANCE

Clostridioides difficile is the leading cause of antibiotic-associated diarrhea in hospitals worldwide. This bacterium produces two virulence factors, TcdA and TcdB, which are large protein toxins that enter host colon cells to cause inflammation, fluid secretion, and cell death. The enzymatic domain of TcdB is a target for novel C. difficile infection (CDI) therapeutics since it is considered the major factor in causing severe CDI. However, necrotic cell death due to non-enzymatic TcdB-host interactions have been reported in cell culture and intoxicated tissue. Here, we generated C. difficile strains with enzyme-inactive toxins to evaluate the role of each toxin in an animal model of CDI. We observe an additive role for TcdA and TcdB in disease and both glucosyltransferase-dependent and independent phenotypes. These findings are expected to inform the development of toxin-based CDI therapeutics.
Identifying The “Core” Transcriptome of SARS-CoV-2 Infected Cells
Authors: Nour Elanood Tageldin , Tran Ryan , Afravi Ayda , Pei Xinyue , Davidian Angela , Kadandale Pavan
Published: September 2021

In 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first emerged, causing the COVID-19 pandemic. Consequently, ongoing research has focused on better understanding the mechanisms underlying the symptoms of this disease. Although COVID-19 symptoms span a range of organ systems, the specific changes in gene regulation that lead to the variety of symptoms are still unclear. In our study, we used publicly available transcriptome data from previous studies on SARS-CoV-2 to identify commonly regulated genes across cardiomyocytes, human bronchial epithelial cells, alveolar type II cells, lung adenocarcinoma, human embryonic kidney cells, and patient samples. Additionally, using this common “core” transcriptome, we could identify the genes that were specifically and uniquely regulated in bronchial epithelial cells, embryonic kidney cells, or cardiomyocytes. For example, we found that genes related to cell metabolism were uniquely upregulated in kidney cells, providing us with the first mechanistic clue about specifically how kidney cells may be affected by SARS-CoV-2. Overall, our results uncover connections between the differential gene regulation in various cell types in response to the SARS-CoV-2 infection and help identify targets of potential therapeutics.
Cell-Intrinsic and Extrinsic Effects of Galectin-1 and Galectin-3 in B-Cell Precursor Acute Lymphoblastic Leukemia
Authors: Fei Fei , Joo Eun Ji , Yang Lu , Groffen John , Heisterkamp Nora
Published: September 2021

Acute lymphoblastic leukemias arising from the malignant transformation of B-cell precursors (BCP-ALLs) are protected against chemotherapy by both intrinsic factors as well as by interactions with bone marrow stromal cells. Galectin-1 and Galectin-3 have overlapping expression patterns and potentially common functions in these cells. We used Galectin-1 and Galectin-3 double null mutant murine BCP-ALL cells to examine the effect of loss endogenous Galectins. We also tested the effect of dual Galectin inhibition by use of plant-derived natural compounds GM-CT-01 and GR-MD-02 in human BCP-ALL cells in co-culture with stroma. Transformed wild type and Galectin-1 x Galectin-3 double knockout BCP-ALL cells were similar in immunophenotype and active intracellular signaling. However, compared to wild type cells, they showed impaired migration, significantly reduced proliferation and increased sensitivity to drug treatment. GM-CT-01 and GR-MD-02 attenuated intracellular signal transduction and sensitized human BCP-ALL cells to chemotherapy including vincristine and the targeted tyrosine kinase inhibitor nilotinib. Our data show endogenous and extracellular Galectins contribute positively to the growth and survival of BCP-ALL cells. Strategies that would efficiently ablate these two Galectins at both locations would decrease microenvironmental protection and reduce BCP-ALL persistence in the protective bone marrow niche after chemotherapy.
Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor
Authors: Danziger Oded , Patel Roosheel S , DeGrace Emma J , Rosen Mikaela R , Rosenberg Brad R
Published: September 2021

Interferons establish an antiviral state in responding cells through the induction of hundreds of interferon-stimulated genes (ISGs). ISGs antagonize viral pathogens directly through diverse mechanisms acting at different stages of viral life cycles, and indirectly by modulating cell cycle and promoting programmed cell death. The mechanisms of action and viral specificities for most ISGs remain incompletely understood. To enable the high throughput interrogation of ISG antiviral functions in pooled genetic screens while mitigating the potentially confounding effects of endogenous IFN and potential antiproliferative/proapoptotic ISG activities, we adapted a CRISPR-activation (CRISPRa) system for inducible ISG induction in isogenic cell lines with and without the capacity to respond to IFN. Engineered CRISPRa cell lines demonstrated inducible, robust, and specific gRNA-directed expression of ISGs, which are functional in restricting viral infection. Using this platform, we screened for ISGs that restrict SARS-CoV-2, the causative agent of the COVID-19 pandemic. Results included ISGs previously described to restrict SARS-CoV-2 as well as multiple novel candidate antiviral factors. We validated a subset of candidate hits by complementary targeted CRISPRa and ectopic cDNA expression infection experiments, which, among other hits, confirmed OAS1 as a SARS-CoV-2 restriction factor. OAS1 exhibited strong antiviral effects against SARS-CoV-2, and these effects required OAS1 catalytic activity. These studies demonstrate a robust, high-throughput approach to assess antiviral functions within the ISG repertoire, exemplified by the identification of multiple novel SARS-CoV-2 restriction factors.
Confined Migration Induces Heterochromatin Formation and Alters Chromatin Accessibility
Authors: Hsia Chieh-Ren , McAllister Jawuanna , Hasan Ovais , Judd Julius , Lee Seoyeon , Agrawal Richa , Chang Chao-Yuan , Soloway Paul , Lammerding Jan
Published: September 2021

During migration, cells often squeeze through small constrictions, requiring extensive deformation. We hypothesized that the nuclear deformation associated with such confined migration could alter chromatin organization and function. Studying cells migrating through microfluidic devices that mimic interstitial spaces in vivo, we found that confined migration results in increased H3K9me3 and H3K27me3 heterochromatin marks that persist for several days. This “confined migration-induced heterochromatin” (CMiH) was distinct from heterochromatin formation during migration initiation. Confined migration predominantly decreased chromatin accessibility at intergenic regions near centromeres and telomeres, suggesting heterochromatin spreading from existing heterochromatin sites. Consistent with the overall decrease in chromatin accessibility, global transcription was decreased during confined migration. Intriguingly, we also identified increased accessibility at promoter regions of genes linked to chromatin silencing, tumor invasion, and DNA damage response. Inhibiting CMiH reduced migration speed, suggesting that CMiH promotes confined migration. Together, our findings indicate that confined migration induces chromatin changes that regulate cell migration and other cellular functions.
Placental mammals acquired the functional region and domain in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation
Authors: Lestari Beni , Naito Satomi , Endo Akinori , Nishihara Hidenori , Kato Akira , Watanabe Erika , Denda Kimitoshi , Komada Masayuki , Fukushima Toshiaki
Published: September 2021

The molecular evolution processes underlying the acquisition of the placenta in eutherian ancestors are not fully understood. Mouse NCK-interacting kinase (NIK)-related kinase (NRK) is expressed highly in the placenta and plays a role in preventing placental hyperplasia. Here, we show the molecular evolution of NRK, which confers its function for inhibiting placental cell proliferation. Comparative genome analysis identified NRK orthologues across vertebrates, which share the kinase and citron homology (CNH) domains. Evolutionary analysis revealed that NRK underwent extensive amino acid substitutions in the ancestor of placental mammals and has been since conserved. Biochemical analysis of mouse NRK revealed that the CNH domain binds to phospholipids, and a region in NRK binds to and inhibits casein kinase-2 (CK2), which we named the CK2-inhibitory region (CIR). Cell culture experiments suggest the following: (1) mouse NRK is localised at the plasma membrane via the CNH domain, where the CIR inhibits CK2. (2) This mitigates CK2-dependent phosphorylation and inhibition of PTEN, and (3) leads to the inhibition of AKT signalling and cell proliferation. Nrk deficiency increased phosphorylation levels of PTEN and AKT in mouse placenta, supporting our hypothesis. Unlike mouse NRK, chicken NRK did not bind to phospholipids and CK2, decrease phosphorylation of AKT, or inhibit cell proliferation. Both the CNH domain and CIR have evolved under purifying selection in placental mammals. Taken together, our study suggests that placental mammals acquired the phospholipid-binding CNH domain and CIR in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation.
Structural Insights into Bifunctional Thaumarchaeal Crotonyl-CoA Hydratase and 3-Hydroxypropionyl-CoA Dehydratase from Nitrosopumilus maritimus
Authors: Destan Ebru , Yuksel Busra , Tolar Bradley B. , Ayan Esra , Deutsch Sam , Yoshikuni Yasuo , Wakatsuki Soichi , Francis Christopher A. , DeMirci Hasan
Published: September 2021

The ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3- hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar_1308 reduces the total number of enzymes necessary for CO2 fixation in Thaumarchaeota, reducing the overall cost for biosynthesis. Here, we present the first high-resolution crystal structure of this bifunctional enzyme with key catalytic residues in the thaumarchaeal 3HP/4HB pathway.
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing
Authors: Begik Oguzhan , Diensthuber Gregor , Liu Huanle , Delgado-Tejedor Anna , Kontur Cassandra , Niazi Adnan Muhammad , Valen Eivind , Giraldez Antonio J. , Beaudoin Jean-Denis , Mattick John S. , Novoa Eva Maria
Published: September 2021

RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here, we develop Nanopore 3’ end-capture sequencing (Nano3P-seq), a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition and tail length dynamics at per-read resolution. By employing a template switching-based sequencing protocol, Nano3P-seq can sequence any given RNA molecule from its 3’ end, regardless of its polyadenylation status, without the need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P-seq captures a wide diversity of RNA biotypes, providing quantitative estimates of RNA abundance and tail lengths in mRNA, lncRNA, sn/snoRNA, scaRNA, and rRNA molecules. We find that, in addition to mRNA and lncRNA, polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform-specific level, correlating with mRNA decay. Finally, we identify non-A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall, Nano3P-seq is a simple and robust method for accurately estimating transcript levels, tail lengths, and tail composition heterogeneity in individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.
A curcumin direct protein (DiPro) biosensor for cell-free prototyping
Authors: Lesniewska Agata , Griffin Guy , Freemont Paul S , Polizzi Karen M , Moore Simon J
Published: September 2021

In synthetic biology, biosensors are routinely coupled to a gene expression cascade for detecting small molecules and physical signals. We posit that an alternative direct protein (DiPro) biosensor mechanism, could provide a new opportunity for rapid detection of specific chemicals. Herein, we reveal a fluorescent curcumin DiPro biosensor, based on the Escherichia coli double bond reductase (EcCurA) as a detection system. We characterise the EcCurA DiPro biosensor and propose enhanced curcumin fluorescence is generated through π-π stacking between protein and ligand. Using a cell-free synthetic biology approach, we use the EcCurA DiPro biosensor to fine tune 10 reaction parameters (cofactor, substrate, and enzyme levels) for cell-free biosynthesis, assisted through acoustic liquid handling robotics. Overall, we increase EcCurA-curcumin fluorescence by 80-fold. We speculate that a generic DiPro biosensor fluorescence mechanism can be further exploited for a wider range of chemicals that share intrinsic fluorescence and have a suitable binding protein.
Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB
Authors: Tian Yannan , Zeng Fuxing , Raybarman Adrika , Carruthers Amy , Li Qingrong , Fatma Shirin , Huang Raven H.
Published: September 2021

In bacteria, rescue of stalled ribosomes due to 3’-truncated mRNAs is carried out by the ubiquitous trans-translation system as well as alternative ribosome-rescue factors such as ArfA and ArfB. It is unclear, however, how the stalled ribosomes caused by ribosomal damages are rescued. Here, we report that a bacterial system composed of PrfH and RtcB not only rescues a stalled ribosome resulting from a specific damage in the decoding center but also repairs the damage afterwards. Peptide release assays reveal that PrfH is only active with the damaged ribosome, but not with the intact one. A 2.55-angstrom cryo-EM structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into specific recognition of the damage site by PrfH. RNA repair assays demonstrate that PrfH-coupled RtcB efficiently repairs the damaged 30S ribosomal subunit, but not the damaged tRNAs. Thus, our studies have uncovered a biological operation by a pair of bacterial enzymes, aiming to reverse the potentially lethal damage inflicted by an invading ribotoxin for cell survival.
Identification of touch neurons underlying dopaminergic pleasurable touch and sexual receptivity
Authors: Elias Leah J. , Schaffler Melanie , Succi Isabella , Foster William , Gradwell Mark , Bohic Manon , Ejoh Lindsay , Abraira Victoria , Abdus-Saboor Ishmail
Published: September 2021

Pleasurable touch during social behavior is the key to building familial bonds and meaningful connections. One form of social touch occurs during sexual encounters. Although sexual behavior is initiated in part by touch, and touch is ongoing throughout copulation, the identity and role of sensory neurons that transduce sexual touch remain unknown. A population of sensory neurons labeled by the G-protein coupled receptor Mrgprb4 detect stroking touch in mice, however, these neurons have never been implicated in any natural social behaviors. Here, we study the social relevance of Mrgprb4-lineage neurons by genetically engineering mice to allow activation or ablation of this population and reveal that these neurons are required for sexual receptivity and sufficient to induce dopamine release in the brain. Even in social isolation, optogenetic stimulation of Mrgprb4-lineage neurons through the back skin is sufficient to induce a conditioned place preference and a striking dorsiflexion resembling the lordotic copulatory posture in females. In the absence of Mrgprb4-lineage neurons, female mice no longer find male mounts rewarding: sexual receptivity is supplanted by aggression and a coincident decline in dopaminergic release in the mesolimbic reward pathway. In addition to sexual behavior, Mrgprb4-lineage neurons are also required for social postures induced by female-to-female back touch. Together, these findings establish that Mrgprb4-lineage neurons are the first neurons of a skin-to-brain circuit encoding the rewarding quality of social touch.