bluuebunny/crossref_metadata_2025 huggingface dataset:
In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing
Authors: Bourgonje Arno R. , Andreu-Sánchez Sergio , Vogl Thomas , Hu Shixian , Vila Arnau Vich , Gacesa Ranko , Leviatan Sigal , Kurilshikov Alexander , Klompus Shelley , Kalka Iris N. , van Dullemen Hendrik M. , Weinberger Adina , Visschedijk Marijn C. , Festen Eleonora A. M. , Faber Klaas Nico , Wijmenga Cisca , Dijkstra Gerard , Segal Eran , Fu Jingyuan , Zhernakova Alexandra , Weersma Rinse K.
Published: December 2021

Inflammatory bowel diseases (IBD), e.g. Crohn’s disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. We leveraged a high-throughput phage-displayed immunoprecipitation sequencing (PhIP-seq) workflow to identify antibodies against 344,000 antimicrobial, immune and food antigens in 497 IBD patients as compared to 1,326 controls. IBD was characterized by 373 differentially abundant antibodies (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD and 28% unique to UC. Antibodies against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (AUC=0.89), and similar discrimination was achieved when using only ten antibodies (AUC=0.87). IBD patients thus show a distinct antibody repertoire against selected peptides, allowing patient stratification and discovery of immunological targets.
LitRev: A data driven method for quick literature review from PubMed
Authors: Das Gourab
Published: December 2021

LitRev is a novel robust data driven approach, developed for quick literature review on a particular topic of interest. This method identifies common biological phrases that follow a power law distribution and important phrases which have the normalized point wise mutual information score greater than zero.

Contact

gourabdas0727@gmail.com
Stranded abroad during the COVID-19 pandemic: examining the psychological and financial impact of border restrictions
Authors: McDermid Pippa , Craig Adam , Sheel Meru , Blazek Katrina , Talty Siobhan , Seale Holly
Published: December 2021

Objective

With the easing of COVID-19-related international travel restrictions in late 2021 it is time to consider the direct and indirect social, emotional, and financial impacts that these border closures have had. The study aims to evaluate the psychological and financial distress reported by people stranded abroad due to international travel restrictions introduced in response to the COVID-19 pandemic.

Methods

Between July and September 2021, we implemented a cross-sectional online survey targeting individuals stranded abroad due to international travel restrictions. The survey collected data about COVID-19 travel restriction-related travel impacts; personal stress, anxiety, and depression (using the validated DASS-21tool); as well as impacts on housing and financial security; and demographic data.

Findings

We had 1054 participants complete the survey; most were trying to return to the Oceania region (75.4%), with 45% stranded in Europe. Overall, 64.2% reported financial distress while stranded abroad. 64.4% (x̄ =9.43, SD=5.81) reported either a moderate or severe (based on the DASS-21 classification) level of depression, 41.7% for anxiety (x̄ =5.46, SD=4.74), and 58.1% for stress (x̄ =10.64, SD=5.26). Statistically significant factors associated with moderate to extremely severe depression, anxiety, and stress were financial stress, an employment change, being <30yrs, having a high perceived risk of contracting COVID-19 abroad and being stranded for >2 months.

Conclusion

The study is among the first to explore the psychological and financial distress-related impacts associated with being stranded abroad due to COVID-19 travel restrictions. It highlights a range of unintended consequences that arise from pandemic-related travel restriction, identifies the health and social needs for a particularly vulnerable population, and provides clues as to the types of support that may be adopted to best support them. This research will assist policymakers in identifying support packages for people stranded abroad due to global disaster.
Trust in the scientific research community predicts intent to comply with COVID-19 prevention measures: An analysis of a large-scale international survey dataset
Authors: Han Hyemin
Published: December 2021

In the present study, I explored the relationship between people’s trust in different agents related to prevention of spread of COVID-19 and their compliance with pharmaceutical and non-pharmaceutical preventive measures. The COVIDiSTRESSII Global Survey dataset, which was collected from international samples, was analysed to examine the aforementioned relationship across different countries. For data-driven exploration, network analysis and Bayesian generalized linear model (GLM) analysis were performed. The result from network analysis demonstrated that trust in the scientific research community was most central in the network of trust and compliance. In addition, the outcome from Bayesian GLM analysis indicated that the same factor, trust in the scientific research community, was most fundamental in predicting participants’ intent to comply with both pharmaceutical and non-pharmaceutical preventive measures. I briefly discussed the implications of the findings, the importance of trust in the scientific research community in explaining people’s compliance with measure to prevent spread of COVID-19.
Measurement of SARS-CoV-2 antigens in plasma of pediatric patients with acute COVID-19 or MIS-C using an ultrasensitive and quantitative immunoassay
Authors: Sigal George B. , Novak Tanya , Mathew Anu , Chou Janet , Zhang Yubo , Manjula Navaratnam , Bathala Predeepthi , Joe Jessica , Padmanabhan Nikhil , Romero Daniel , Allegri-Machado Gabriella , Joerger Jill , Loftis Laura L. , Schwartz Stephanie P. , Walker Tracie C. , Fitzgerald Julie C. , Tarquinio Keiko M. , Zinter Matt S. , Schuster Jennifer E. , Halasa Natasha B. , Cullimore Melissa L. , Maddux Aline B. , Staat Mary A. , Irby Katherine , Flori Heidi R. , Coates Bria M. , Crandall Hillary , Gertz Shira J. , Randolph Adrienne G. , Pollock Nira R.
Published: December 2021

Background

Detection of SARS-CoV-2 antigens in blood has high sensitivity in adults with acute COVID-19, but sensitivity in pediatric patients is unclear. Recent data suggest that persistent SARS-CoV-2 spike antigenemia may contribute to multisystem inflammatory syndrome in children (MIS-C). We quantified SARS-CoV-2 nucleocapsid (N) and spike (S) antigens in blood of pediatric patients with either acute COVID-19 or MIS-C using ultrasensitive immunoassays (Meso Scale Discovery).

Methods

Plasma was collected from inpatients (<21 years) enrolled across 15 hospitals in 15 US states. Acute COVID-19 patients (n=36) had a range of disease severity and positive nasopharyngeal SARS-CoV-2 RT-PCR within 24 hours of blood collection. Patients with MIS-C (n=53) met CDC criteria and tested positive for SARS-CoV-2 (RT-PCR or serology). Controls were patients pre-COVID-19 (n=67) or within 24h of negative RT-PCR (n=43).

Results

Specificities of N and S assays were 95-97% and 100%, respectively. In acute COVID-19 patients, N/S plasma assays had 89%/64% sensitivity, respectively; sensitivity in patients with concurrent nasopharyngeal swab cycle threshold (Ct) ≤ 35 were 93%/63%. Antigen concentrations ranged from 1.28-3,844 pg/mL (N) and 1.65-1,071 pg/mL (S) and correlated with disease severity. In MIS-C, antigens were detected in 3/53 (5.7%) samples (3 N-positive: 1.7, 1.9, 121.1 pg/mL; 1 S-positive: 2.3 pg/mL); the patient with highest N had positive nasopharyngeal RT-PCR (Ct 22.3) concurrent with blood draw.

Conclusions

Ultrasensitive blood SARS-CoV-2 antigen measurement has high diagnostic yield in children with acute COVID-19. Antigens were undetectable in most MIS-C patients, suggesting that persistent antigenemia is not a common contributor to MIS-C pathogenesis.

Key points

In a U.S. pediatric cohort tested with ultrasensitive immunoassays, SARS-CoV-2 nucleocapsid antigens were detectable in most patients with acute COVID-19, and spike antigens were commonly detectable. Both antigens were undetectable in almost all MIS-C patients.
Empowering Engineered Muscle Function by Extending Connexin 43 Duration with Reduced Graphene Oxides
Authors: Ko Eunkyung , Aydin Onur , Li Zhengwei , Gapinske Lauren , Huang Kai-Yu , Saif Taher , Bashir Rashid , Kong Hyunjoon
Published: December 2021

Engineered skeletal muscle act as therapeutics invaluable to treat injured or diseased muscle and a “living” material essential to assemble biological machinery. For normal development, skeletal myoblasts should express connexin 43, one of the gap junction proteins that promote myoblast fusion and myogenesis, during the early differentiation stage. However, myoblasts cultured in vitro often down-regulate connexin 43 before differentiation, limiting myogenesis and muscle contraction. This study demonstrates that tethering myoblasts with reduced graphene oxide (rGO) slows connexin 43 regression during early differentiation and increases myogenic mRNA synthesis. The whole RNA sequencing also confirms that the rGO on cells increases regulator genes for myogenesis, including troponin, while decreasing negative regulator genes. The resulting myotubes generated a three-fold larger contraction force than the rGO-free myotubes. Accordingly, a valveless biohybrid pump assembled with the rGO-tethered muscle increased the fluid velocity and flow rate considerably. The results of this study would provide an important foundation for developing physiologically relevant muscle and powering up biomachines that will be used for various bioscience studies and unexplored applications.
Early neural activity changes associated with visual conscious perception
Authors: Khalaf Aya , Kronemer Sharif I. , Christison-Lagay Kate , Kwon Hunki , Li Jiajia , Wu Kun , Blumenfeld Hal
Published: December 2021

The neural mechanisms of visual conscious perception have been investigated for decades. However, the spatiotemporal dynamics associated with the earliest neural responses following consciously perceived stimuli are still poorly understood. Using a dataset of intracranial EEG recordings, the current study aims to investigate the neural activity changes associated with the earliest stages of visual conscious perception. Subjects (N=10, 1,693 grey matter electrode contacts) completed a continuous performance task in which individual letters were presented in series and subjects were asked to press a button when they saw a target letter. Broadband gamma power (40-115Hz) dynamics were analyzed in comparison to baseline prior to stimulus and contrasted for target trials with button presses and non-target trials without button presses. Regardless of event type, we observed early gamma power changes within 30-150 ms from stimulus onset in a network including increases in bilateral occipital, fusiform, frontal (including frontal eye fields), and medial temporal cortex, increases in left lateral parietal-temporal cortex, and decreases in the right anterior medial occipital cortex. No significant differences were observed between target and non-target stimuli until >150 ms post-stimulus, when we saw greater gamma power increases in left motor and premotor areas, suggesting a possible role of these later signals in perceptual decision making and/or motor responses with the right hand. The early gamma power findings suggest a broadly distributed cortical visual detection network that is engaged at early times tens of milliseconds after signal transduction from the retina.
Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance
Authors: Salamzade Rauf , Manson Abigail L. , Walker Bruce J. , Brennan-Krohn Thea , Worby Colin J. , Ma Peijun , He Lorrie L. , Shea Terrance P. , Qu James , Chapman Sinéad B. , Howe Whitney , Young Sarah K. , Wurster Jenna I. , Delaney Mary L. , Kanjilal Sanjat , Onderdonk Andrew B. , Pironti Alejandro , Bittencourt Cassiana E. , Gussin Gabrielle M. , Kim Diane , Peterson Ellena M. , Ferraro Mary Jane , Hooper David C. , Shenoy Erica S. , Cuomo Christina A. , Hung Deborah T. , Cosimi Lisa A. , Huang Susan S. , Kirby James E. , Pierce Virginia M. , Bhattacharyya Roby P. , Earl Ashlee M.
Published: December 2021

Background

Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms.

Methods

To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem susceptible Enterobacterales, isolated from patients from four U.S. hospitals over nearly five years.

Results

Our CRE collection comprised a diverse range of species, lineages and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events.

Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment.

Conclusions

Collectively, the framework we developed provides a clearer, high resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.
The price of defence: toxins, visual signals and oxidative state in an aposematic butterfly
Authors: Blount Jonathan D. , Rowland Hannah M. , Mitchell Christopher , Speed Michael P. , Ruxton Graeme D. , Endler John A. , Brower Lincoln P.
Published: December 2021

In a variety of aposematic species, the conspicuousness of an individual’s warning signal and the quantity of its chemical defence are positively correlated. This apparent honest signalling is predicted by resource competition models which assume that the production and maintenance of aposematic defences compete for access to antioxidant molecules that have dual functions as pigments and in protecting against oxidative damage. We raised monarch butterflies (Danaus plexippus) on their milkweed host-plants (Apocynaceae) with increasing quantities of cardenolides to test whether (1) the sequestration of secondary defences is associated with costs in the form of oxidative lipid damage and reduced antioxidant defences; and (2) that reduced oxidative state can decrease the capacity of individuals to produce aposematic displays. In male monarchs conspicuousness was explained by an interaction between oxidative damage and sequestration: males with high levels of oxidative damage become less conspicuous with increased sequestration of cardenolides, whereas those with low oxidative damage become more conspicuous with increased levels of cardenolides. There was no significant effect of oxidative damage or concentration of sequestered cardenolides on female conspicuousness. Our results demonstrate a physiological linkage between the production of coloration and protection from autotoxicity, and differential costs of signalling in monarch butterflies.
Mutations in the spike RBD of SARS-CoV-2 omicron variant may increase infectivity without dramatically altering the efficacy of current multi-dosage vaccinations
Authors: Li Bingrui , Lu Xin , McAndrews Kathleen M. , Kalluri Raghu
Published: December 2021

With the continuous evolution of SARS-CoV-2, variants of concern (VOCs) and their mutations are a focus of rapid assessment. Vital mutations in the VOC are found in spike protein, particularly in the receptor binding domain (RBD), which directly interacts with ACE2 on the host cell membrane, a key determinant of the binding affinity and cell entry. With the reporting of the most recent VOC, omicron, we performed amino acid sequence alignment of the omicron spike protein with that of the wild type and other VOCs. Although it shares several conserved mutations with other variants, we found that omicron has a large number of unique mutations. We applied the Hopp-Woods scale to calculate the hydrophilicity scores of the amino acid stretches of the RBD and the entire spike protein, and found 3 new hydrophilic regions in the RBD of omicron, implying exposure to water, with the potential to bind proteins such as ACE2 increasing transmissibility and infectivity. However, careful analysis reveals that most of the exposed domains of spike protein can serve as antigenic epitopes for generating B cell and T cell-mediated immune responses. This suggests that in the collection of polyclonal antibodies to various epitopes generated after multiple doses of vaccination, some can likely still bind to the omicron spike protein and the RBD to prevent severe clinical disease. In summary, while the omicron variant might result in more infectivity, it can still bind to a reasonable repertoire of antibodies generated by multiple doses of current vaccines likely preventing severe disease. Effective vaccines may not universally prevent opportunistic infections but can prevent the sequelae of severe disease, as observed for the delta variant. This might still be the case with the omicron variant, albeit, with increased frequency of infection.
Role of anterior insula cortex in context-induced relapse of nicotine-seeking
Authors: Ghareh Hussein , Alonso-Lozares Isis , Schetters Dustin , Herman Rae J. , Heistek Tim S. , van Mourik Yvar , Jean-Richard-dit-Bressel Philip , Zernig Gerald , Mansvelder Huibert D. , de Vries Taco J. , Marchant Nathan J.
Published: December 2021

Tobacco use is the leading cause of preventable death worldwide, and relapse during abstinence remains the key barrier to successful treatment of tobacco addiction. During abstinence, environmental contexts associated with nicotine use can induce craving and contribute to relapse. The insular cortex (IC) is thought to be a critical substrate of nicotine addiction and relapse. However, its specific role in context-induced relapse of nicotine-seeking is not fully known. In this study, we report a novel rodent model of context-induced relapse to nicotine-seeking after punishment-imposed abstinence, which models self-imposed abstinence through increasing negative consequences of excessive drug use. Using the neuronal activity marker Fos we find that the anterior (aIC), but not the middle or posterior IC, shows increased activity during context-induced relapse. Combining Fos with retrograde labelling of aIC inputs, we show projections to aIC from contralateral aIC and basolateral amygdala exhibit increased activity during context-induced relapse. Next, we used fiber photometry in aIC and observed phasic increases in aIC activity around nicotine-seeking responses during self-administration, punishment, and the context-induced relapse tests. Next, we used chemogenetic inhibition in both male and female rats to determine whether activity in aIC is necessary for context-induced relapse. We found that chemogenetic inhibition of aIC decreased context-induced nicotine-seeking after either punishment- or extinction-imposed abstinence. These findings highlight the critical role nicotine-associated contexts play in promoting relapse, and they show that aIC activity is critical for this context-induced relapse following both punishment and extinction imposed abstinence.
Hierarchical length and sequence preferences establish a single major piRNA 3’-end
Authors: Stoyko Daniel , Genzor Pavol , Haase Astrid D.
Published: December 2021

PIWI-interacting RNAs (piRNAs) guard germline genomes against the deleterious action of retroviruses and other mobile genetic elements. How piRNAs faithfully discriminate between self and non-self to restrict all mobile elements while sparing essential genes remains a key outstanding question in genome biology. PiRNAs use extensive base-pairing to recognize their targets and variable 3’ends could change the specificity and efficacy of piRNA silencing. Here, we identify conserved rules that ensure the generation of a single major piRNA 3’end in flies and mice. Our data suggest that the PIWI proteins initially define a short interval on pre-piRNAs that grants access to the ZUC-processor complex. Within this Goldilocks zone, the preference of the ZUC-processor to cut in front of a Uridine determines the ultimate processing site. We observe a mouse-specific roadblock that relocates the Goldilocks zone and generates an opportunity for consecutive trimming by PNLDC1. Our data reveal a conserved hierarchy between length and sequence preferences that controls the piRNA sequence space. The unanticipated precision of 3’end formation bolsters the emerging understanding that the functional piRNA sequence space is tightly controlled to ensure effective defense.

Key findings

Every piRNA has a single major 3’end

Length preference trumps sequence preference during 3’end formation.

Relocation of the Goldilocks zone generates opportunity for trimming of mouse piRNAs.
scMARK an ‘MNIST’ like benchmark to evaluate and optimize models for unifying scRNA data
Authors: Swechha  , Mendonca Dylan , Focsa Octavian , Díaz-Mejía J. Javier , Cooper Samuel
Published: December 2021

Today’s single-cell RNA analysis tools provide enormous value in enabling researchers to make sense of large single-cell RNA (scRNA) studies, yet their ability to integrate different studies at scale remains untested. Here we present a novel benchmark dataset (scMARK), that consists of 100,000 cells over 10 studies and can test how well models unify data from different scRNA studies. We also introduce a two-step framework that uses supervised models, to evaluate how well unsupervised models integrate scRNA data from the 10 studies. Using this framework, we show that the Variational Autoencoder, scVI, represents the only tool tested that can integrate scRNA studies at scale. Overall, this work paves the way to creating large scRNA atlases and ‘off-the-shelf’ analysis tools.
Label-free imaging to track reprogramming of human somatic cells
Authors: Molugu Kaivalya , Battistini Giovanni A. , Heaster Tiffany M. , Rouw Jacob , Guzman Emmanuel C. , Skala Melissa C. , Saha Krishanu
Published: December 2021

The process of reprogramming patient samples to human induced pluripotent stem cells (iPSCs) is stochastic, asynchronous, and inefficient leading to a heterogeneous population of cells. Here, we track the reprogramming status of single patient-derived cells during reprogramming with label-free live-cell imaging of cellular metabolism and nuclear morphometry to identify high-quality iPSCs. Erythroid progenitor cells (EPCs) isolated from human peripheral blood showed distinct patterns of autofluorescence lifetime for the reduced form of nicotinamide adenine dinucleotide (phosphate) [NAD(P)H] and flavin adenine dinucleotide (FAD) during reprogramming. Random forest models classified starting EPCs, partially-reprogrammed intermediate cells, and iPSCs with ∼95% accuracy. Reprogramming trajectories resolved at the single cell level indicated significant reprogramming heterogeneity along different branches of cell state. This combination of micropatterning, autofluorescence imaging, and machine learning provides a unique non-destructive method to assess the quality of iPSCs in real-time for various applications in regenerative medicine, cell therapy biomanufacturing, and disease modeling.
SV2A-Syt1 interaction controls surface nanoclustering and access to recycling synaptic vesicles
Authors: Small Christopher , Harper Callista , Kontaxi Christiana , Davenport Elizabeth , Wallis Tristan , Malapaka Anusha , Yak Nyakuoy , Joensuu Merja , Martínez-Mármol Ramon , Cousin Michael A. , Meunier Frédéric A.
Published: December 2021

Following exocytosis, the recapture of vesicular proteins stranded at the plasma membrane in recycling synaptic vesicles (SVs) is essential to sustain neurotransmission. Nanoclustering is emerging as a mechanism through which proteins may be ‘pre-assembled’ prior to endocytosis, to ensure high fidelity of retrieval for subsequent rounds of vesicle fusion. Here, we used single molecule imaging to examine the nanoclustering of synaptotagmin-1 (Syt1) and synaptic vesicle protein 2A (SV2A). Syt1 forms surface nanoclusters through interaction of its C2B domain (K326/K328) with SV2A, as demonstrated by mutating Syt1 (K326A/K328A) and knocking down endogenous SV2A. Blocking cognate interaction with Syt1 (SV2AT84A) also decreased SV2A clustering. Impaired nanoclustering of Syt1 and SV2A leads to accelerated endocytosis of Syt1, altered intracellular sorting and decreased trafficking of Syt1 to a Rab5-positive endocytic pathway. We conclude that the interaction between SV2A and Syt1 locks both molecules into surface nanoclusters, controlling their entry into recycling SVs.
Primary infection by E. multilocularis induces distinct patterns of crosstalk between hepatic regulatory T and natural killer T cells in mice
Authors: Yarahmadov Tural , Wang Junhua , Sanchez-Taltavull Daniel , Alvarez Rojas Cristian A. , Brodie Tess , Büchi Isabel , Keogh Adrian , Gottstein Bruno , Stroka Deborah , Beldi Guido
Published: December 2021

The larval stage of the helminthic cestode Echinococcus multilocularis can inflict tumor-like hepatic lesions that cause the parasitic disease alveolar echinococcosis in humans, with high mortality in untreated patients. Recently, opportunistic properties of the disease have been proposed based on the increased incidence in immunocompromised patients and mouse models, indicating that an appropriate adaptive immune response is required for the control of the disease. However, little is known about how the local hepatic immune responses modulate the infection with E. multilocularis. In a mouse model of oral infection that mimics the normal infection route in human patients, the adaptive immune response in the liver was assessed using single-cell RNA sequencing of isolated hepatic CD3+ T cells at different infection stages. We observed an early significant increase in regulatory T and natural killer T cells in parallel with an active downregulation of CD4+ and CD8+ T cells. Early interactions between regulatory T cells and natural killer T cells indicate a promotion of the formation of hepatic lesions and later contribute to suppression of the resolution of parasite-induced pathology. The obtained data provides a fresh insight on the adaptive immune responses and local regulatory pathways at different infection stages of E. multilocularis in mice.

Author summary

Alveolar echinococcosis is an endemic parasitic infection leading to slowly growing but potentially lethal liver lesions if untreated. Transmission by increasing populations of urban foxes and the raise of immunosuppressed patients in mainly industrializsed endemic zones are the main causes responsible for increased incidence of alveolar echinococcosis. Observations in humans and mice indicate that reactions of the adaptive immune system are required to control the disease and to protect from a chronic infection. Therefore, we analysed the responses of T cells in the liver at single-cell resolution in a murine model mimicking the typical route of infection in humans. This so called single-cell RNA sequencing revealed specific temporal changes of T cell subsets such as natural killer T cells and regulatory T cells, indicating that these two cell types are recruited in the early phase to try to protect from parasite proliferation and are subsequently inhibited in the late phase of infection thus indicating immune escape mechanisms of the parasite. This study shows temporal changes of the immune cell profile in the liver over the course of a natural infection with E. multilocularis at the single cell level and reveals putative targets for novel therapeutic approaches for human AE and possibly other (parasitic/helminthic) diseases.
Strain variation inClostridioides difficiletoxin activity associated with genomic variation at both PaLoc and non-PaLoc loci
Authors: Saund Katie , Pirani Ali , Lacy D. Borden , Hanna Philip C. , Snitkin Evan
Published: December 2021

Clinical disease fromClostridioides difficileinfection can be mediated by two toxins and their neighboring regulatory genes encoded within the five-gene pathogenicity locus (PaLoc). We provide several lines of evidence that the toxin activity ofC. difficilemay be modulated by genomic variants outside of the PaLoc. We used a phylogenetic tree-based approach to demonstrate discordance between toxin activity and PaLoc evolutionary history, an elastic net method to show the insufficiency of PaLoc variants alone to model toxin activity, and a convergence-based bacterial genome-wide association study (GWAS) to identify correlations between non-PaLoc loci with changes in toxin activity. Combined, these data support a model ofC. difficiledisease wherein toxin activity may be strongly affected by many non-PaLoc loci. Additionally, we characterize multiple otherin vitrophenotypes relevant to human infections including germination and sporulation. These phenotypes vary greatly in their clonality, variability, convergence, and concordance with genomic variation. Lastly, we highlight the intersection of loci identified by GWAS for different phenotypes and clinical severity. This strategy to identify the overlapping loci can facilitate the identification of genetic variation linking phenotypic variation to clinical outcomes.

IMPORTANCE

Clostridioides difficilehas two major disease mediating toxins, A and B, encoded within the pathogenicity locus (PaLoc). In this study we demonstrate via multiple approaches that genomic variants outside of the PaLoc are associated with changes in toxin activity. These genomic variants may provide new avenues of exploration in the hunt for novel disease modifying interventions. Additionally, we provide insight into the evolution of several additional phenotypes also critical to clinical infection such as sporulation, germination, and growth rate. Thesein vitrophenotypes display a range of responses to evolutionary pressures and as such vary in their appropriateness for certain bacterial genome wide association study approaches. We used a convergence-based association method to identify the genomic variants most correlated with both changes in these phenotypes and disease severity. These overlapping loci may be important to both bacterial function and human clinical disease.
Superspreading of SARS-CoV-2 infections: A Systematic Review and Meta-analysis
Authors: Du Zhanwei , Wang Chunyu , Liu Caifen , Bai Yuan , Pei Sen , Adam Dillon C. , Wang Lin , Wu Peng , Lau Eric H. Y. , Cowling Benjamin J.
Published: December 2021

Superspreading in transmission is a feature of SARS-CoV-2 transmission. We conducted a systematic review and meta-analysis on globally reported dispersion parameters of SARS-CoV-2. The pooled estimate was 0.55 (95% CI: 0.30, 0.79). The study location and method were found to be important drivers for its diversity.
Surveillance of COVID-19 vaccine effectiveness – a real-time case-control study in southern Sweden
Authors: Björk Jonas , Bonander Carl , Moghaddassi Mahnaz , Rasmussen Magnus , Malmqvist Ulf , Kahn Fredrik , Inghammar Malin
Published: December 2021

The extensive register infrastructure available for COVID-19 surveillance in Scania county, Sweden, makes it possible to classify cases with respect to hospitalization and disease severity, stratify on time since last dose and demographic factors, account for prior infection, and extract data for population controls automatically. Estimated vaccine effectiveness 0-3 months after the last dose remained stable during the study period but waned markedly 6 months after the last dose in older persons.
Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study
Authors: Ayoubkhani Daniel , Bermingham Charlotte , Pouwels Koen B. , Glickman Myer , Nafilyan Vahé , Zaccardi Francesco , Khunti Kamlesh , Alwan Nisreen A. , Walker A. Sarah
Published: December 2021

Objective

To estimate associations between COVID-19 vaccination and Long Covid symptoms in adults who were infected with SARS-CoV-2 prior to vaccination.

Design

Observational cohort study using individual-level interrupted time series analysis.

Setting

Random sample from the community population of the UK.

Participants

28,356 COVID-19 Infection Survey participants (mean age 46 years, 56% female, 89% white) aged 18 to 69 years who received at least their first vaccination after test-confirmed infection.

Main outcome measures

Presence of long Covid symptoms at least 12 weeks after infection over the follow-up period 3 February to 5 September 2021.

Results

Median follow-up was 141 days from first vaccination (among all participants) and 67 days from second vaccination (84% of participants). First vaccination was associated with an initial 12.8% decrease (95% confidence interval: −18.6% to −6.6%) in the odds of Long Covid, but increasing by 0.3% (−0.6% to +1.2%) per week after the first dose. Second vaccination was associated with an 8.8% decrease (−14.1% to −3.1%) in the odds of Long Covid, with the odds subsequently decreasing by 0.8% (−1.2% to −0.4%) per week. There was no statistical evidence of heterogeneity in associations between vaccination and Long Covid by socio-demographic characteristics, health status, whether hospitalised with acute COVID-19, vaccine type (adenovirus vector or mRNA), or duration from infection to vaccination.

Conclusions

The likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose. Vaccination may contribute to a reduction in the population health burden of Long Covid, though longer follow-up time is needed.

Summary box

What is already known on this topic

COVID-19 vaccines are effective at reducing rates of SARS-CoV-2 infection, transmission, hospitalisation, and death

The incidence of Long Covid may be reduced if infected after vaccination, but the relationship between vaccination and pre-existing long COVID symptoms is unclear, as published studies are generally small and with self-selected participants

What this study adds

The likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose

There was no evidence of differences in this relationship by socio-demographic characteristics, health-related factors, vaccine type, or duration from infection to vaccination

Although causality cannot be inferred from this observational evidence, vaccination may contribute to a reduction in the population health burden of Long Covid; further research is needed to understand the biological mechanisms that may ultimately contribute to the development of therapeutics for Long Covid
Minor intron splicing efficiency increases with the development of lethal prostate cancer
Authors: Augspach Anke , Drake Kyle D. , Roma Luca , Qian Ellen , Lee Se Ri , Clarke Declan , Kumar Sushant , Jaquet Muriel , Gallon John , Bolis Marco , Triscott Joanna , Galván José A. , Chen Yu , Thalmann George , Julio Marianna Kruithof-de , Theurillat Jean-Philippe P. , Wuchty Stefan , Gerstein Mark , Piscuoglio Salvatore , Kanadia Rahul N. , Rubin Mark A.
Published: December 2021

Here we explored the role of minor spliceosome (MiS) function and minor intron-containing gene (MIG) expression in prostate cancer (PCa). We show MIGs are enriched as direct interactors of cancer-causing genes and their expression discriminates PCa progression. Increased expression of MiS U6atac snRNA, including others, and 6x more efficient minor intron splicing was observed in castration-resistant PCa (CRPC) versus primary PCa. Notably, androgen receptor signalling influenced MiS activity. Inhibition of MiS through siU6atac in PCa caused minor intron mis-splicing and aberrant expression of MIG transcripts and encoded proteins, which enriched for MAPK activity, DNA repair and cell cycle. Single cell-RNAseq confirmed cell cycle defects and lineage dependency on the MiS from primary to CRPC and neuroendocrine PCa. siU6atac was ∼50% more efficient in lowering tumor burden of CRPC cells and organoids versus current state-of-the-art combination therapy. In all, MiS is a strong therapeutic target for lethal PCa and potentially other cancers.

Graphical Abstract

U6atac expression, MiS activity, and minor intron splicing correlate with PCa therapy resistance and PCa progression to CRPC-adeno and transdifferentiation to CRPC-NE. One major MiS regulator during that process is the AR-axis, which is re-activated during CRPC-adeno and blocked in CRPC-NE. Molecularly, an increase in MiS dependent splicing promotes changes of transcriptome and proteome. This results in cell cycle activation, increased MAPK signalling and increased DNA repair. U6atac mediated MiS inhibition renders MiS splicing error-prone through increased intron retention and alternative splicing events, which results in cell cycle block and decreased MAPK signalling and DNA repair. MiS inhibition blocks all stages of PCa. Figure created withBioRender.com.
Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes
Authors: Nagy László G. , Vonk Peter Jan , Künzler Markus , Földi Csenge , Virágh Máté , Ohm Robin A. , Hennicke Florian , Bálint Balázs , Csernetics Árpád , Hegedüs Botond , Hou Zhihao , Liu Xiao-Bin , Nan Shen , Pareek Manish , Sahu Neha , Szathmári Benedek , Varga Torda , Wu Hongli , Yang Xiao , Merényi Zsolt
Published: December 2021

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes ofCoprinopsis cinerea, and their orthologs inAgaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus,andSchizophyllum commune, providing functional hypotheses for ∼10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi.
eIF5B and eIF1A remodel human translation initiation complexes to mediate ribosomal subunit joining
Authors: Lapointe Christopher P. , Grosely Rosslyn , Sokabe Masaaki , Alvarado Carlos , Wang Jinfan , Montabana Elizabeth , Villa Nancy , Shin Byung-Sik , Dever Thomas E. , Fraser Christopher S. , Fernández Israel S. , Puglisi Joseph D.
Published: December 2021

Joining of the ribosomal subunits at a translation start site on a messenger RNA during initiation commits the ribosome to synthesize a protein. Here, we combined single-molecule spectroscopy and structural methods using anin vitroreconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when universally-conserved eukaryotic initiation factors (eIFs) eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we examined initiation complexes that contained both eIF1A and eIF5B using single-particle electron cryo-microscopy. The resulting structure illuminated how eukaryote-specific contacts between eIF1A and eIF5B remodel the initiation complex to orient initiator tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during human translation initiation.
Programmable in vivo CRISPR activation elucidates the oncogenic and immunosuppressive role of MYC in lung adenocarcinoma
Authors: Thege Fredrik I. , Rupani Dhwani N. , Barathi Bhargavi B. , Manning Sara L. , Maitra Anirban , Rhim Andrew D. , Wörmann Sonja M.
Published: December 2021

Conventional genetically engineered mouse models (GEMMs) are time consuming, laborious and offer limited spatio-temporal control. Here, we describe the development of a streamlined platform for in vivo gene activation using CRISPR activation (CRISPRa) technology. Unlike conventional GEMMs, our model system allows for flexible, sustained and timed activation of one or more target genes using single or pooled lentiviral guides. Using Myc and Yap1 as model oncogenes, we demonstrate gene activation in primary pancreatic organoid cultures in vitro and enhanced tumorigenic potential in Myc-activated organoids when transplanted orthotopically. By implementing our model as an autochthonous lung cancer model, we show that transduction-mediated Myc activation leads to accelerated tumor progression and significantly reduced overall survival relative to non-targeted tumor controls. Furthermore, we found that Myc-activation led to the acquisition of an immune suppressive “cold” tumor microenvironment. Through cross-species validation of our results using publicly available RNA/DNA-seq data sets, we were able to link MYC to a previously described, immunosuppressive transcriptomic subtype in patient tumors, thus identifying a patient cohort that may benefit from combined MYC/immune-targeted therapies. Overall, our work demonstrates how CRISPRa can be used for rapid functional validation of putative oncogenes and may allow for the identification and evaluation of potential metastatic and oncogenic drivers through competitive screening.
CD4+and CD8+regulatory T cells characterization in the rat using a unique transgenicFoxp3-EGFPmodel
Authors: Ménoret Séverine , Tesson Laurent , Remy Séverine , Gourain Victor , Sérazin Céline , Usal Claire , Guiffes Aude , Chenouard Vanessa , Ouisse Laure-Hélène , Gantier Malika , Heslan Jean-Marie , Fourgeux Cynthia , Poschmann Jeremie , Guillonneau Carole , Anegon Ignacio
Published: December 2021

Background

CD4+and CD8+regulatory T cells (Treg) in diverse species include different subsets from different origins. In all species, CD8+Treg have been poorly characterized. CD4+and CD8+Treg in rats have only partially been characterized and there is no rat model in which FOXP3+Treg are genetically tagged.

Results

We generated a rat transgenic line using the CRISPR/Cas9 system in which EGFP was inserted in frame on the 3’ end of theFoxp3gene using a 2A self-cleaving peptide. EGFP was exclusively expressed by CD4+and CD8+T cells in similar proportion as observed with anti-FOXP3 antibodies. CD4+EGFP+Treg were 5-10 times more frequent than CD8+EGFP+Treg. CD4+and CD8+EGFP+Treg expressed both the CD25highCD127lowCD45RClow/-markers. The suppressive activity of CD4+and CD8+Treg was largely confined to EGFP+cells. RNAseq analyses showed similarities but also differences among CD4+and CD8+EGFP+cells and provided the first description of the natural FOXP3+CD8+Treg transcriptome. In vitro culture of CD4+and CD8+EGFP-cells with TGFbeta and IL-2 resulted in the induction of EGFP+Treg. Preferential expansion of CD4+and CD8+EGFP+Treg could be detected upon in vivo administration of a low dose of IL-2.

Conclusions

This new and uniqueFoxp3-EGFPrat line constitutes a useful model to identify and isolate viable natural and induced CD4+and CD8+Treg. Additionally, it allows to identify new molecules expressed in CD8+Treg that may allow to better define their phenotype and function not only in rats but also in other species.