bluuebunny/crossref_metadata_2025 huggingface dataset:
Severe COVID-19 infection is associated with aberrant cytokine production by infected lung epithelial cells rather than by systemic immune dysfunction
Authors: Rouhani Sherin J , Trujillo Jonathan A , Pyzer Athalia R , Yu Jovian , Fessler Jessica , Cabanov Alexandra , Higgs Emily F , Cron Kyle R. , Zha Yuanyuan , Lu Yihao , Bloodworth Jeffrey C. , Abasiyanik Mustafa Fatih , Okrah Susan , Flood Blake A , Hatogai Ken , Leung Michael YK , Pezeshk Apameh , Kozloff Lara , Reschke Robin , Strohbehn Garth W. , Chervin Carolina Soto , Kumar Madan , Schrantz Stephen , Madariaga Maria Lucia , Beavis Kathleen G , Yeo Kiang-Teck J. , Sweis Randy F. , Segal Jeremy , Tay Savaş , Izumchenko Evgeny , Mueller Jeffrey , Chen Lin S , Gajewski Thomas F
Published: December 2021

The mechanisms explaining progression to severe COVID-19 remain poorly understood. It has been proposed that immune system dysregulation/over-stimulation may be implicated, but it is not clear how such processes would lead to respiratory failure. We performed comprehensive multiparameter immune monitoring in a tightly controlled cohort of 128 COVID-19 patients, and used the ratio of oxygen saturation to fraction of inspired oxygen (SpO2 / FiO2) as a physiologic measure of disease severity. Machine learning algorithms integrating 139 parameters identified IL-6 and CCL2 as two factors predictive of severe disease, consistent with the therapeutic benefit observed with anti-IL6-R antibody treatment. However, transcripts encoding these cytokines were not detected among circulating immune cells. Rather, in situ analysis of lung specimens using RNAscope and immunofluorescent staining revealed that elevated IL-6 and CCL2 were dominantly produced by infected lung type II pneumocytes. Severe disease was not associated with higher viral load, deficient antibody responses, or dysfunctional T cell responses. These results refine our understanding of severe COVID-19 pathophysiology, indicating that aberrant cytokine production by infected lung epithelial cells is a major driver of immunopathology. We propose that these factors cause local immune regulation towards the benefit of the virus.
Food for thought: Eating before saliva collection and interference with SARS-CoV-2 detection
Authors: Hernandez Matthew M. , Riollano-Cruz Mariawy , Boyle Mary C. , Banu Radhika , Shrestha Paras , Gray Brandon , Cao Liyong , Chen Feng , Shi Huanzhi , Paniz-Perez Daniel E. , Paniz-Perez Paul A. , Rishi Aryan L. , Dubinsky Jacob , Dubinsky Dylan , Dubinsky Owen , Baine Sophie , Baine Lily , Arinsburg Suzanne , Baine Ian , Ramirez Juan David , Cordon-Cardo Carlos , Sordillo Emilia Mia , Paniz-Mondolfi Alberto E.
Published: December 2021

Background

Saliva is an optimal specimen for detection of viruses that cause upper respiratory infections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to its cost-effectiveness and non-invasive collection. However, together with intrinsic enzymes and oral microbiota, children’s unique dietary habits may introduce substances that interfere with diagnostic testing.

Methods

To determine whether children’s dietary choices impact SARS-CoV-2 detection in saliva, we performed a diagnostic study that simulates testing of real-life specimens provided from healthy children (n=5) who self-collected saliva at home before and at 0, 20, and 60 minutes after eating from 20 foods they selected. Each of seventy-two specimens was split into two volumes and spiked with SARS-CoV-2-negative or -positive standards prior to side-by-side testing by reverse-transcription polymerase chain reaction matrix-assisted laser desorption ionization time-of-flight (RT-PCR/MALDI-TOF) assay.

Results

Detection of internal extraction control and SARS-CoV-2 nucleic acids was reduced in replicates of saliva collected at 0 minutes after eating 11 of 20 foods. Interference resolved at 20 and 60 minutes after eating all foods except hot dog in one participant. This represented a significant improvement in detection of nucleic acids compared to saliva collected at 0 minutes after eating (P=0.0005).

Conclusions

We demonstrate successful detection of viral nucleic acids in saliva self-collected by children before and after eating a variety of foods. Fasting is not required before saliva collection for SARS-CoV-2 testing by RT-PCR/MALDI-TOF, but waiting 20 minutes after eating is sufficient for accurate testing. These findings should be considered for SARS-CoV-2 testing and broader viral diagnostics in saliva specimens.
Coronavirus (COVID-19) Spike in Georgia: An Epidemiologic Study of Data, Modelling, and Policy Implications to Understand the Gender-and Race-Specific Variations
Authors: Mostafa Fahad , Ganji Riya , St. John Julie , Khan Hafiz
Published: December 2021

Objective

The purpose of this study was to investigate the gender-and race-specific predictive variations in COVID-19 cases and deaths in Georgia, USA.

Methods

The data were extracted from the Georgia Department of Public Health (GDPH). Statistical methods, such as descriptive statistics, Artificial neural networks (ANN), and Bayesian approach, were utilized to analyze the data.

Results

More Whites died from COVID-19 than African-Americans/Blacks in Cobb, Hall, Gwinnett, and non-Georgia residents; however, more Blacks died in Dekalb and Fulton counties. The highest posterior mean for female deaths was obtained in Gwinnett County (77.17; 95% CI, 74.23–80.07) and for male deaths in Fulton County (73.48; 95% CI, 72.18–74.49). For overall race/ethnicity, Whites had the highest posterior mean for deaths (183.18; 95% CI, 128.29–238.27) compared with Blacks (162.48; 95% CI, 127.15– 197.42). Assessing the classification of the chronic medical conditions using ANN, Cobb and Hall Counties showed the highest mean AUC-ROC of the models (78% and 79%, respectively).

Conclusions

The predictive models of COVID-19 transmission will help public health practitioners and researchers to better understand the course of the COVID-19 pandemic. The study findings are generalizable to populations with geographic and racial/ethnic similarities and may be used to determine gender/race-specific future virus models for effective interventions or policy modifications.

Human Subjects

No personal identifiable information was obtained.
Rule-based and stimulus-based cues bias auditory decisions via different computational and physiological mechanisms
Authors: Tardiff Nathan , Suriya-Arunroj Lalitta , Cohen Yale E. , Gold Joshua I.
Published: December 2021

Expectations, such as those arising from either learned rules or recent stimulus regularities, can bias subsequent auditory perception in diverse ways. However, it is not well understood if and how these diverse effects depend on the source of the expectations. Further, it is unknown whether different sources of bias use the same or different computational and physiological mechanisms. We examined how rule-based and stimulus-based expectations influenced behavior and pupil- linked arousal, a marker of certain forms of expectation-based processing, of human subjects performing an auditory frequency-discrimination task. Rule-based cues consistently biased choices and response times (RTs) toward the more-probable stimulus. In contrast, stimulus-based cues had a complex combination of effects, including choice and RT biases toward and away from the frequency of recently presented stimuli. These different behavioral patterns also had: 1) distinct computational signatures, including different modulations of key components of a novel form of a drift-diffusion decision model and 2) distinct physiological signatures, including substantial bias- dependent modulations of pupil size in response to rule-based but not stimulus-based cues. These results imply that different sources of expectations can modulate auditory processing via distinct mechanisms: one that uses arousal-linked, rule-based information and another that uses arousal- independent, stimulus-based information to bias the speed and accuracy of auditory perceptual decisions.

Author summary

Prior information about upcoming stimuli can bias our perception of those stimuli. Whether different sources of prior information bias perception in similar or distinct ways is not well understood. We compared the influence of two kinds of prior information on tone-frequency discrimination: rule-based cues, in the form of explicit information about the most-likely identity of the upcoming tone; and stimulus-based cues, in the form of sequences of tones presented before the to-be-discriminated tone. Although both types of prior information biased auditory decision- making, they demonstrated distinct behavioral, computational, and physiological signatures. Our results suggest that the brain processes prior information in a form-specific manner rather than utilizing a general-purpose prior. Such form-specific processing has implications for understanding decision biases real-world contexts, in which prior information comes from many different sources and modalities.
Emergence of the Delta Variant and risk of SARS-CoV-2 infection in secondary school students and staff: prospective surveillance in 18 schools, England
Authors: Ladhani Shamez N. , Ireland Georgina , Baawuah Frances , Beckmann Joanne , Okike Ifeanyichukwu O , Ahmad Shazaad , Garstang Joanna , Brent Andrew J , Brent Bernadette , Aiano Felicity , Amin-Chowdhury Zahin , Kall Meaghan , Borrow Ray , Linley Ezra , Zambon Maria , Poh John , Warrener Lenesha , Lackenby Angie , Ellis Joanna , Amirthalingam Gayatri , Brown Kevin E , Ramsay Mary E
Published: December 2021

Background

The role of educational settings on SARS-CoV-2 infection and transmission remains controversial. We investigated SARS-CoV-2 infection, seroprevalence and seroconversions rates in secondary schools during the 2020/21 academic year, which included the emergence of the more transmissible Alpha and Delta variants, in England.

Methods

The UK Health Security Agency (UKHSA) initiated prospective surveillance in 18 urban English secondary schools. Participants had nasal swabs for SARS-CoV-2 RT-PCR and blood sampling for SARS-CoV-2 Nucleoprotein and Spike protein antibodies at the start (Round 1: September-October 2020) and end (Round 2: December 2021) of the autumn term, when schools reopened after national lockdown was imposed in January 2021 (Round 3: March-April) and end of the academic year (Round 4: May-July).

Findings

We enrolled 2,314 participants (1277 students, 1037 staff). In-school testing identified 31 PCR-positive participants (20 students, 11 staff). Another 247 confirmed cases (112 students, 135 staff) were identified after linkage with national surveillance data, giving an overall positivity rate of 12.0% (278/2313; staff [14.1%, 146/1037] vs students [10.3%, 132/1276; p=0.006). Nucleoprotein-antibody seroprevalence increased for students and staff between Rounds 1-3 but changed little in Round 4, when the Delta variant was the dominant circulating strain. Overall, Nucleoprotein-antibody seroconversion was 18.4% (137/744) in staff and 18.8% (146/778) in students, while Spike-antibody seroconversion was higher in staff (72.8% (525/721) than students (21.3%, 163/764) because of vaccination.

Interpretation

SARS-CoV-2 infection and transmission in secondary schools remained low when community infection rates were low because of national lockdown, even after the emergence of the Delta variant

Funding

DHSC
Vitamin D Supplementation is Associated with Slower Epigenetic Aging
Authors: Vetter Valentin Max , Sommerer Yasmine , Kalies Christian Humberto , Spira Dominik , Bertram Lars , Demuth Ilja
Published: December 2021

Adverse effects of low vitamin D level on mortality and morbidity are controversially discussed. Especially older people are at risk for vitamin D deficiency and therefore exposed to its potentially harmful influence on the aging process. A way of measuring differences in the biological age is through DNA methylation age (DNAm age) and its deviation from chronological age, DNAm age acceleration (DNAmAA). We previously reported on an association between vitamin D deficiency and higher 7-CpG DNAmAA in participants of the Berlin Aging Study II (BASE-II).

In this study, we employ a quasi-interventional study design to assess the relationship between DNAmAA of five epigenetic clocks and vitamin D supplementation. Longitudinal data were available for 1,036 participants of BASE-II that were reexamined on average 7.4 years later in the GendAge study (mean age at follow-up: 75.6 years, SD = 3.8 years, age range: 64.9 – 94.1 years, 51.9 % female). DNAmAA was estimated with the 7-CpG clock, Horvath’s clock, Hannum’s clock, PhenoAge and GrimAge. Methylation data were obtained through methylation-sensitive single nucleotide primer extension (MS-SNuPE) or Illumina’s Infinium “MethylationEPIC” array.

Vitamin D deficient participants who chose to start vitamin D supplementation after baseline examination showed a 2.6 year lower 7-CpG DNAmAA (p=0.011) and 1.3-year lower Horvath DNAmAA (p=0.042) compared to untreated and vitamin D deficient participants. DNAmAA did not statistically differ between participants with successfully treated vitamin D deficiency and healthy controls (p>0.16).

Therefore, we conclude that intake of vitamin D supplement is associated with lower DNAmAA in participants with vitamin D deficiency. Additionally, our findings suggest that sufficient vitamin D supplementation can compensate and potentially reverse the increase in 7-CpG DNAmAA that we found in in vitamin D deficient participants.
Knockout of liver fluke granulin, Ov-grn-1, impedes malignant transformation during chronic infection with Opisthorchis viverrini
Authors: Chaiyadet Sujittra , Tangkawattana Sirikachorn , Smout Michael J. , Ittiprasert Wannaporn , Mann Victoria H. , Deenonpoe Raksawan , Arunsan Patpicha , Loukas Alex , Brindley Paul J. , Laha Thewarach
Published: December 2021

Infection with the food-borne liver fluke Opisthorchis viverrini is the principal risk factor for cholangiocarcinoma (CCA) in the Mekong Basin countries of Thailand, Lao PDR, Vietnam, Myanmar and Cambodia. Using a novel model of CCA, involving infection with gene-edited liver flukes in the hamster during concurrent exposure to dietary nitrosamine, we explored the role of the fluke granulin-like growth factor Ov-GRN-1 in malignancy. We derived RNA-guided gene knockout flukes (ΔOv-grn-1) using CRISPR/Cas9/gRNA materials delivered by electroporation. Genome sequencing confirmed programmed Cas9-catalyzed mutations of the targeted genes, which was accompanied by rapid depletion of transcripts and the proteins they encode. Gene-edited parasites colonized the biliary tract of hamsters and developed into adult flukes, however less hepatobiliary tract disease manifested during chronic infection with ΔOv-grn-1 worms in comparison to hamsters infected with control gene-edited and non-edited parasites. Specifically, immuno- and colorimetric-histochemical analysis of livers revealed markedly less periductal fibrosis surrounding the flukes and less fibrosis globally within the hepatobiliary tract during infection with ΔOv-grn-1 genotype worms, minimal biliary epithelial cell proliferation, and significantly fewer mutations of TP53 in biliary epithelial cells. Moreover, fewer hamsters developed high-grade CCA compared to controls. The clinically relevant, pathophysiological phenotype of the hepatobiliary tract confirmed a role for this secreted growth factor in malignancy and morbidity during opisthorchiasis.

Author summary

Infection with the human liver flukes, Opisthorchis viverrini, O. felineus and Clonorchis sinensis remains a public health concern in regions where these parasites are endemic. O. viverrini is endemic in the Mekong River drainage countries of including Thailand and the Lao People’s Democratic Republic. Infection follows the consumption of undercooked freshwater fish harboring the parasite. Liver fluke infection, opisthorchiasis, is associated with diseases of the liver and bile ducts including cancer of the biliary tract, cholangiocarcinoma, a cancer with a poor prognosis. This report characterizes for the first time experimental infection with gene-edited O. viverrini liver flukes during concurrent exposure to nitrosamine in a rodent model of liver fluke infection-associated cancer. Cancer development was slowed in hamsters infected with the parasite following CRISPR-based knock-out mutation and loss of a parasite gene known to stimulate growth of cells lining the bile ducts. These findings describe a new model for investigation of risk factors for infection-associated cholangiocarcinoma and to assess efficacy of anti-infection/anti-cancer vaccines.
SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling
Authors: Biering Scott B. , Sousa Francielle Tramontini Gomes de , Tjang Laurentia V. , Pahmeier Felix , Ruan Richard , Blanc Sophie F. , Patel Trishna S. , Worthington Caroline M. , Glasner Dustin R. , Castillo-Rojas Bryan , Servellita Venice , Lo Nicholas T.N. , Wong Marcus P. , Warnes Colin M. , Sandoval Daniel R. , Clausen Thomas Mandel , Santos Yale A. , Ortega Victoria , Aguilar Hector C. , Esko Jeffrey D. , Chui Charles Y. , Pak John E. , Beatty P. Robert , Harris Eva
Published: December 2021

Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated with barrier dysfunction, the triggers of this pathology are unclear. Here, we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to trigger barrier dysfunction in vitro and vascular leak in vivo, independently of viral replication and the ACE2 receptor. We identify an S-triggered transcriptional response associated with extracellular matrix reorganization and TGF-β signaling. Using genetic knockouts and specific inhibitors, we demonstrate that glycosaminoglycans, integrins, and the TGF-β signaling axis are required for S-mediated barrier dysfunction. Our findings suggest that S interactions with barrier cells are a contributing factor to COVID-19 disease severity and offer mechanistic insight into SARS-CoV-2 triggered vascular leak, providing a starting point for development of therapies targeting COVID-19 pathogenesis.
Mechanisms underlying melanoma invasion as a consequence of MLK3 loss
Authors: Balinda Henriette U. , Sedgwick Alanna , D’Souza-Schorey Crislyn
Published: December 2021

Invasive melanoma is an aggressive form of skin cancer with high incidence of mortality. The process of invasion is a crucial primary step in the metastatic cascade, yet the mechanisms involved are still under investigation. Here we document a critical role for MLK3 (MAP3K11) in the regulation of melanoma cell invasion. We report that cellular loss of MLK3 in melanoma cells promotes cell invasion. Knock down of MLK3 expression results in the hyperactivation of ERK, which is linked to the formation of a BRAF/Hsp90/Cdc37 protein complex. ERK hyperactivation leads to enhanced phosphorylation and inactivation of GSK3β and the stabilization of c-Jun and JNK activity. Blocking of ERK and JNK signaling as well as Hsp90 activity downstream of MLK3-silencing significantly reduces melanoma invasion. Furthermore, our studies show that ERK activation in the aforementioned context is coupled to MT1-MMP transcription as well as the TOM1L1-dependent localization of the membrane protease to invadopodia at the invasive front. These studies provide critical insight into the mechanisms that couple MLK3 loss with BRAF hyperactivation and its consequence on melanoma invasion.
Multiple ETS Factors Participate in the Transcriptional Control of TERT Mutant Promoter in Thyroid Cancers
Authors: Thornton Caitlin E.M. , Hao Jingzhu , Tamarapu Prasanna P. , Landa Iñigo
Published: December 2021

Hotspot mutations in the TERT (telomerase reverse transcriptase) gene are key determinants of thyroid cancer progression. TERT promoter mutations (TPM) create de novo consensus binding sites for the ETS (“E26 transforming sequence”) family of transcription factors. In this study, we systematically knocked down each of the 20 ETS factors expressed in thyroid tumors and screened their effects on TERT expression in seven thyroid cancer cell lines with defined TPM status. We observed that, unlike in other TPM-carrying cancers such as glioblastomas, ETS factor GABPA does not unambiguously regulate transcription from the TERT mutant promoter in thyroid specimens. In fact, multiple members of the ETS family impact TERT expression, and they typically do so in a mutation-independent manner. In addition, we observe that partial inhibition of MAPK, a central pathway in thyroid cancer transformation, is more effective at suppressing TERT transcription in the absence of TPMs. Taken together, our results show a more complex scenario of TERT regulation in thyroid cancers compared to other lineages, suggest that compensatory mechanisms by ETS and other regulators likely exist and advocate for the need of a more comprehensive understanding of the mechanisms of TERT deregulation in thyroid tumors before eventually exploring TPM-specific therapeutic strategies.

Graphical Abstract
EraSOR: Erase Sample Overlap in polygenic score analyses
Authors: Choi Shing Wan , Mak Timothy Shin Heng , Hoggart Clive J. , O’Reilly Paul F.
Published: December 2021

Background

Polygenic risk score (PRS) analyses are now routinely applied in biomedical research, with great hope that they will aid in our understanding of disease aetiology and contribute to personalized medicine. The continued growth of multi-cohort genome-wide association studies (GWASs) and large-scale biobank projects has provided researchers with a wealth of GWAS summary statistics and individual-level data suitable for performing PRS analyses. However, as the size of these studies increase, the risk of inter-cohort sample overlap and close relatedness increases. Ideally sample overlap would be identified and removed directly, but this is typically not possible due to privacy laws or consent agreements. This sample overlap, whether known or not, is a major problem in PRS analyses because it can lead to inflation of type 1 error and, thus, erroneous conclusions in published work.

Results

Here, for the first time, we report the scale of the sample overlap problem for PRS analyses by generating known sample overlap across sub-samples of the UK Biobank data, which we then use to produce GWAS and target data to mimic the effects of inter-cohort sample overlap. We demonstrate that inter-cohort overlap results in a significant and often substantial inflation in the observed PRS-trait association, coefficient of determination (R2) and false-positive rate. This inflation can be high even when the absolute number of overlapping individuals is small if this makes up a notable fraction of the target sample. We develop and introduce EraSOR (Erase Sample Overlap and Relatedness), a software for adjusting inflation in PRS prediction and association statistics in the presence of sample overlap or close relatedness between the GWAS and target samples. A key component of the EraSOR approach is inference of the degree of sample overlap from the intercept of a bivariate LD score regression applied to the GWAS and target data, making it powered in settings where both have sample sizes over 1,000 individuals. Through extensive benchmarking using UK Biobank and HapGen2 simulated genotype-phenotype data, we demonstrate that PRSs calculated using EraSOR-adjusted GWAS summary statistics are robust to inter-cohort overlap in a wide range of realistic scenarios and are even robust to high levels of residual genetic and environmental stratification.

Conclusion

The results of all PRS analyses for which sample overlap cannot be definitively ruled out should be considered with caution given high type 1 error observed in the presence of even low overlap between base and target cohorts. Given the strong performance of EraSOR in eliminating inflation caused by sample overlap in PRS studies with large (>5k) target samples, we recommend that EraSOR be used in all future such PRS studies to mitigate the potential effects of inter-cohort overlap and close relatedness.
Synthesis and Evaluation of Acridone and Xanthone Epoxides with Anti-MRSA and Anti-MSSA Activity
Authors: Chittepu Padmaja , Yang Junshu , Benoit Adam , Salomon Christine E. , Ji Yinduo , Ferguson David M.
Published: December 2021

A series of acridone and xanthone-based compounds bearing 1,2-epoxypropyl or 1,2-propanediol substituents were synthesized and evaluated for activity against MRSA and MSSA bacterial strains. The results indicate a correlation exists between the number of epoxide groups and activity, with peak MIC values observed for bis-epoxy derivatives. Both activity and heathy cell toxicity was shown to decrease with the addition of a third epoxy group. The corresponding ring-opened diol analogs were devoid of activity, demonstrating the critical function of the epoxide in mediating antimicrobial activity. The most active compounds were also screened using a regulated antisense RNA expression library. The results show no increase in activity against cells sensitized by down-regulation of the most common drug targets, including DNA gyrase, DNA topoisomerase, tRNA synthetase, and the fatty acid biosynthesis pathway. The compounds are postulated to function as membrane disrupting agents, similar to the xanthone natural product α-mangostin.
Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution
Authors: Pessi Igor S. , Rutanen Aino , Hultman Jenni
Published: December 2021

Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analysed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus “UBA10452”, an uncultured lineage of putative AOA in the order Nitrososphaerales (“terrestrial group I.1b”), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographical, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographical/habitat clusters.
Brassica napus genes Rlm4 and Rlm7, conferring resistance to Leptosphaeria maculans, are alleles of the Rlm9 wall-associated kinase-like resistance locus
Authors: Haddadi Parham , Larkan Nicholas J. , Van de Wouw Angela , Zhang Yueqi , Neik Ting Xiang , Beynon Elena , Bayer Philipp , Edwards Dave , Batley Jacqueline , Borhan M. Hossein
Published: December 2021

Brassica napus (canola/rapeseed) race specific resistance genes against blackleg disease, caused by the ascomycete fungus Leptosphaeria maculans, have been commonly used in canola breeding. To date; LepR3, Rlm2 and Rlm9 R genes against L. maculans have been cloned from B. napus. LepR3 and Rlm2 are Receptor Like Proteins (RLP) and the recently reported Rlm9 is a Wall Associated Kinase-Like (WAKL) protein. Rlm9 located on chromosome A07 is closely linked with Rlm3, Rlm4, RLm7 genes. Recognition of AvrLm5-9 and AvrLm3 by their corresponding Rlm9 and Rlm3 proteins is masked in the presence of AvrLm4-7. Here we report cloning of Rlm4 and Rlm7 by generating genome sequence of the doubled haploid (DH) B. napus cv Topas DH16516 introgression lines Topas-Rlm4 and Topas-Rlm7. Candidate Rlm4 and Rlm7 genes were identified form the genome sequence and gene structures were determined by mapping RNA-sequence reads, generated from infected cotyledon tissues, to the genome of Topas-Rlm4 and Topas-Rlm7. Rlm4 and Rlm7 genomic constructs with their native promoters were transferred into the blackleg susceptible B. napus cv Westar N-o-1. Complementation of resistance response in the transgenic Westar:Rlm4 and Westar:Rlm7 that were inoculated with L. maculans transgenic isolates 2367:AvrRlm4-7 or 2367:AvrLm7 confirmed the function of Rlm4 and Rlm7 genes. Wild type L. maculans isolate 2367 that does not contain AvrLm4-7 or AvrLm7, and transgenic 2367:AvrLm3 and 2367:AvrLm5-9 did not induce resistance proving the specificity of Rlm4 and Rlm7 response. Rlm4 and Rlm7 alleles are also allelic to Rlm9. Rlm4 and Rlm7 genes encode WAKL proteins. Comparison of highly homologous sequences of Rlm4 and Rlm7 with each other and with the sequence of additional alleles, using whole genome sequencing of additional 128 lines, identified a limited number of point mutation located within the predicted extracellular receptor domains.
There and Back to the Present: An Evolutionary Tale on Biological Diversity
Authors: Duarte Leandro , Nakamura Gabriel , Debastiani Vanderlei , Maestri Renan , Pereira Maria João Ramos , Cianciaruso Marcus , Diniz-Filho José Alexandre F.
Published: December 2021

Ecologists often agree on the importance of macroevolution for niche-mediated distribution of biological diversity along environmental gradients. Yet, macroevolutionary diversification and dispersal in time and space generate uneven geographic distribution of phylogenetic pools, which affects the imprint let by macroevolution on local species pools. In this article we introduce an individual-based simulation approach coupled to Approximate Bayesian Computation (ABC) that allows to parameterize the adaptation rate of species’ niche positions along the evolution of a monophyletic lineage, and the intensity of dispersal limitation, associated with the distribution of biological diversity between assemblages potentially connected by dispersal (metacommunity). The analytical tool was implemented in an R package calledmcfly. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate and dispersal limitation parameters. Further, we evaluated the role played by niche evolution and dispersal limitation on species diversity distribution of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and the distribution of biological diversity, and thereby improved our understanding of evolutionary imprints on ecological patterns. Perhaps more importantly, it offers new possibilities for solving the eco-evolutionary puzzle.
High temporal resolution systems profiling reveals distinct patterns of interferon response after Covid-19 mRNA vaccination and SARS-CoV2 infection
Authors: Rinchai Darawan , Deola Sara , Zoppoli Gabriele , Ahamed Kabeer Basirudeen Syed , Taleb Sara , Pavlovski Igor , Maacha Selma , Gentilcore Giusy , Toufiq Mohammed , Mathew Lisa , Liu Li , Vempalli Fazulur Rehaman , Mubarak Ghada , Lorenz Stephan , Sivieri Irene , Cirmena Gabriella , Dentone Chiara , Cuccarolo Paola , Giacobbe Daniele Roberto , Baldi Federico , Garbarino Alberto , Cigolini Benedetta , Cremonesi Paolo , Bedognetti Michele , Ballestrero Alberto , Bassetti Matteo , Hejblum Boris P. , Augustine Tracy , Panhuys Nicholas Van , Thiebaut Rodolphe , Branco Ricardo , Chew Tracey , Shojaei Maryam , Short Kirsty , Feng Carl ,   PREDICT-19 consortium, Zughaier Susu M. , Maria Andrea De , Tang Benjamin , Hssain Ali Ait , Bedognetti Davide , Grivel Jean-Charles , Chaussabel Damien
Published: December 2021

Knowledge of the mechanisms underpinning the development of protective immunity conferred by mRNA vaccines is fragmentary. Here we investigated responses to COVID-19 mRNA vaccination via ultra-low-volume sampling and high-temporal-resolution transcriptome profiling (23 subjects across 22 timepoints, and with 117 COVID-19 patients used as comparators). There were marked differences in the timing and amplitude of the responses to the priming and booster doses. Notably, we identified two distinct interferon signatures. The first signature (A28/S1) was robustly induced both post-prime and post-boost and in both cases correlated with the subsequent development of antibody responses. In contrast, the second interferon signature (A28/S2) was robustly induced only post-boost, where it coincided with a transient inflammation peak. In COVID19 patients, a distinct phenotype dominated by A28/S2 was associated with longer duration of intensive care. In summary, high-temporal-resolution transcriptomic permitted the identification of post- vaccination phenotypes that are determinants of the course of COVID-19 disease.
Mechanism Driven Early Stage Identification and Avoidance of Antisense Oligonucleotides Causing TRL9 Mediated Inflammatory Responses in Bjab cells
Authors: Pollak Adam J. , Cauntay Patrick , Machemer Todd , Paz Suzanne , Damle Sagar , Henry Scott P. , Burel Sebastien A.
Published: December 2021

Nucleic acid-based PS-ASOs have the potential to activate cellular innate immune responses, and the level of activation can vary quite dramatically with sequence. Minimizing degree of proinflammatory effect is one of the main selection criteria for compounds intended to move into clinical trials. While a recently developed hPBMC-based assay showed excellent ability to detect innate immune active PS-ASOs, which can then be discarded from the developmental process, this assay is highly resource-intensive and easily affected by subject variability. This compelled us to develop of a more convenient high-throughput assay. Here, we describe a new in vitro assay, utilizing a cultured human Bjab cell line, which was developed and validated to identify PS-ASOs that may cause innate immune activation. The assay was calibrated to replicate results from the hPMBC assay. The Bjab assay was designed to be high throughput and more convenient by using RT-qPCR readout of mRNA of the chemokine Ccl22. The Bjab assay was also shown to be highly reproducible and to provide a large dynamic range in determining the immune potential of PS-ASOs via comparison to known benchmark PS-ASO controls that were previously shown to be either safe or inflammatory in clinical trials. In addition, we demonstrate that Bjab cells can be used to provide mechanistic information on PS-ASO-TLR9 dependent innate immune activation.
Protective effect of peroxisome proliferator-activated receptor-α in regulating the early inflammation response to extended hepatectomy from a comparative transcriptomic analysis
Authors: Shi Cheng-Cheng , Bai Yang , Yan Xin , Cheng Nuo , Guo Wen-Zhi , Zhang Shui-Jun , Shi Ji-Hua
Published: December 2021

The regulation mechanism of small-for-size syndrome remains unclear. Thus, we aimed to analyze the molecular profiles following extended hepatectomy and identify the therapeutic target. Major hepatectomy and extended hepatectomy were performed in the rat model, and the remnant livers were obtained dynamically for the high-throughput transcriptome analysis to identify the differentially expressed genes (DEGs). The general framework for weighted gene co-expression network analysis (WGCNA) was employed to explore the expression patterns of DEGs. As result, WGCNA identified 10 distinct gene co-expression modules according to the correlation between module eigengene and different postoperative time-points. The magenta module (gene count: 289) and the lightcyan module (gene count: 484) were found positively correlated with major hepatectomy instead of extended hepatectomy. In the lightcyan module, peroxisome proliferator-activated receptor-α (PPARα) was selected and found the down-regulation in the remnant liver following extended (marginal) hepatectomy in rats and humans. Besides, administration of PPARα agonist attenuated hepatic inflammation injury while PPARα antagonist increased liver inflammation injury after extended hepatectomy in rats, marked by the significantly changed aminotransferases, tumor necrosis factor-α and interleukin-6 levels in the plasm, and histological Suzuki criteria. Consequently, DEGs and their molecular profiles after extended hepatectomy were identified, and PPARα might be a potential therapy target for small-for-size syndrome.
Age dependent changes in circulating Tfh cells influence the development of functional antibodies to malaria in children
Authors: Chan Jo-Anne , Loughland Jessica R , de la Parte Lauren , Okano Satomi , Ssewanyana Isaac , Nalubega Mayimuna , Nankya Felistas , Musinguzi Kenneth , Rek John , Arinaitwe Emmanuel , Tipping Peta , Bourke Peter , Andrew Dean , Dooley Nicholas , SheelaNair Arya , Wines Bruce D , Hogarth Mark , Beeson James , Greenhouse Bryan , Dorsey Grant , Kamya Moses , Hartel Gunter , Minigo Gabriela , Feeney Margaret , Jagannathan Prasanna , Boyle Michelle J
Published: December 2021

T-follicular helper (Tfh) cells are key drivers of antibodies that protect from malaria. However, little is known regarding the host and parasite factors that influence Tfh and functional antibody development. Here, we use samples from a large cross-sectional study of children residing in an area of high malaria transmission in Uganda to characterize Tfh cells and functional antibodies to multiple parasites stages. We identify a dramatic re-distribution of the Tfh cell compartment with age that is independent of malaria exposure, with Th2-Tfh cells predominating in early childhood, while Th1-Tfh cell gradually increase to adult levels over the first decade of life. Functional antibody acquisition is age-dependent and hierarchical acquired based on parasite stage, with merozoite responses followed by sporozoite and gametocyte antibodies. Antibodies were boosted in children with current infection, and were higher in females. The children with the very highest antibody levels had increased Tfh cell activation and proliferation, consistent with a key role of Tfh cells in antibody development. Together, these data reveal a complex relationship between the circulating Tfh compartment, antibody development and protection from malaria.
biPACT: a method for three-dimensional visualization of mouse spinal cord circuits of long segments with high resolution
Authors: Nakanishi Katsuyuki , Shinozaki Munehisa , Nagoshi Narihito , Nakamura Masaya , Okano Hideyuki
Published: December 2021

Background

The spatial complexity of neuronal circuits in the central nervous system is a hurdle in understanding and treating brain and spinal cord injuries. Although several methods have recently been developed to render the spinal cord transparent and label specific neural circuits, three-dimensional visualization of long segments of spinal cord with high resolution remains challenging.

New Method

We present a method that combines tissue staining of neuronal tracts traced with biotinylated dextran amine (BDA) and a modified passive clarity clearing protocol to describe individual fibers in long segments of mouse spinal cord.

Results

Corticospinal tract was traced with BDA with a mouse model of thoracic spinal cord injury. The spinal cord was stained and cleared in two weeks with four solutions: staining solution, hydrogel solution, clearing solution, and observation solution. The samples were observed with a light-sheet microscope, and three-dimensional reconstruction was performed with ImageJ software. High resolution-images comparable with tissue sections were obtained continuously and circumferentially. By tiling, it was possible to obtain high-resolution images of long segments of the spinal cord. The tissue could be easily re-stained in case of fading,

Comparison with Existing Methods

The present method does not require special equipment, can label specific circuits without genetic technology, and re-staining rounds can be easily implemented. It enables to visualize individual neural fiber of specific neural circuit in long spinal cord segments.

Conclusions

By using simple neural staining, and clearing methods, it was possible to acquire a wide range of high-resolution three-dimensional images of the spinal cord.

Highlights

No special devices or genetic tracers are required for a new clearing method

Neuronal fibers are individually depicted in long segments of mouse spinal cord.

Re-staining of neuronal fiber is possible.

Stereotaxic observation is achieved by 3-D reconstruction with open-source software.
Insights into the role of lipoteichoic acids and MprF function in Bacillus subtilis
Authors: Guyet Aurélie , Alofi Amirah , Daniel Richard A.
Published: December 2021

Gram-positive bacterial cells are protected from the environment by a cell envelope which comprises of layers of peptidoglycan that maintain the cell shape and teichoic acids polymers whose biological function remains unclear. In Bacillus subtilis, loss of all Class A Penicillin-Binding Proteins (aPBPs) which function in peptidoglycan synthesis is conditionally lethal. Here we show that this lethality is associated with an alteration of the lipoteichoic acids (LTA) and the accumulation of the major autolysin LytE in the cell wall. Our analysis provides further evidence that the length and abundance of LTA acts to regulate the cellular level and activity of autolytic enzymes, specifically LytE. Importantly, we identify a novel function for the aminoacyl-phosphatidylglycerol synthase MprF in the modulation of LTA biosynthesis in B. subtilis and Staphylococcus aureus. This finding has implications for our understanding of antimicrobial resistance (particularly daptomycin) in clinically relevant bacteria and the involvement of MprF in the virulence of pathogens, such as methicillin resistant S. aureus.
Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients
Authors: Lu Lu , Mok Bobo Wing-Yee , Chen Linlei , Chan Jacky Man-Chun , Tsang Owen Tak-Yin , Lam Bosco Hoi-Shiu , Chuang Vivien Wai-Man , Chu Allen Wing-Ho , Chan Wan-Mui , Ip Jonathan Daniel , Chan Brian Pui-Chun , Zhang Ruiqi , Yip Cyril Chik-Yan , Cheng Vincent Chi-Chung , Chan Kwok-Hung , Hung Ivan Fan-Ngai , Yuen Kwok-Yung , Chen Honglin , To Kelvin Kai-Wang
Published: December 2021

Background

The SARS-CoV-2 Omicron variant, designated as a Variant of Concern(VOC) by the World Health Organization, carries numerous spike protein mutations which have been found to evade neutralizing antibodies elicited by COVID-19 vaccines. The susceptibility of Omicron variant by vaccine-induced neutralizing antibodies are urgently needed for risk assessment.

Methods

Omicron variant strains HKU691 and HKU344-R346K were isolated from patients using TMPRSS2-overexpressing VeroE6 cells. Whole genome sequence was determined using nanopore sequencing. Neutralization susceptibility of ancestral lineage A virus and the Omicron, Delta and Beta variants to sera from 25 BNT162b2 and 25 Coronavac vaccine recipients was determined using a live virus microneutralization assay.

Results

The Omicron variant strain HKU344-R346K has an additional spike R346K mutation, which is present in 8.5% of strains in GISAID database. Only 20% and 24% of BNT162b2 recipients had detectable neutralizing antibody against the Omicron variant HKU691 and HKU344-R346K, respectively, while none of the Coronavac recipients had detectable neutralizing antibody titer against either Omicron isolates. For BNT162b2 recipients, the geometric mean neutralization antibody titers(GMT) of the Omicron variant isolates(5.43 and 6.42) were 35.7-39.9-fold lower than that of the ancestral virus(229.4), and the GMT of both omicron isolates were significantly lower than those of the beta and delta variants. There was no significant difference in the GMT between HKU691 and HKU344-R346K.

Conclusions

Omicron variant escapes neutralizing antibodies elicited by BNT162b2 or CoronaVac. The additional R346K mutation did not affect the neutralization susceptibility. Our data suggest that the Omicron variant may be associated with lower COVID-19 vaccine effectiveness.
Quality-adjusted life expectancy norms for the English population
Authors: Schneider Paul , McNamara Simon , Love-Koh James , Doran Tim , Gutacker Nils
Published: December 2021

Objective

The National Institute for Health and Care Excellence in England has proposed severity-of-disease modifiers that give greater weight to health benefits accruing to patients who experience a larger shortfall in quality-adjusted life years (QALYs) under current standard of care compared to healthy individuals. This requires an estimate of quality-adjusted life expectancy (QALE) of the general population by age and sex. Previous QALE population norms are based on nearly 30-year old assessments of HRQoL in the general population. This study provides updated QALE estimates for the English population by age and sex.

Methods

EQ-5D-5L data for 14,412 participants from the Health Survey for England (waves 2017 and 2018) were pooled and HRQoL population norms were calculated. These norms were combined with official life tables from the Office for National Statistics for 2017-2019 using the Sullivan method to derive QALE estimates by age and sex. Values were discounted using 0%, 1.5% and 3.5% discount rates.

Results

QALE at birth is 68.04 QALYs for men and 68.48 QALYs for women. These values are lower than previously published QALE population norms based on older HRQoL data. Additional data tables and figures are made available through an interactive web application: https://r4scharr.shinyapps.io/shortfall/.

Conclusions

This study provides new QALE population norms for England that serve to establish absolute and relative QALY shortfalls for the purpose of health technology assessments.
Differential impact of Covid-19 on incidence of diabetes mellitus and cardiovascular diseases in acute, post-acute and long Covid-19: population-based cohort study in the United Kingdom
Authors: Rezel-Potts Emma , Douiri Abdel , Sun Xiaohui , Chowienczyk Phillip J , Shah Ajay M , Gulliford Martin C
Published: December 2021

Objective

This study aimed to estimate the incidence of new diabetes mellitus (DM) and cardiovascular diseases (CVD) up to one year after Covid-19 compared with matched controls.

Methods

A cohort study was conducted using electronic records for 1,473 family practices with a population of 14.9 million. Covid-19 patients without DM or CVD were individually matched with controls and followed up to October 2021. A difference-in-difference analysis estimated the net effect of Covid-19 allowing for baseline differences and covariates.

Results

There were 372,816 Covid-19 patients, with 2,935 CVD and 3,139 DM events, and 372,816 matched controls with 1,193 CVD and 1,861 DM events following the index date. Net incidence of DM increased in acute Covid-19 up to four weeks from index date (adjusted rate ratio, RR 1.71, 1.40 to 2.10) and remained elevated in post-acute (five to 12 weeks from index date; RR 1.17, 1.01 to 1.36) and long-Covid-19 (13 to 52 weeks, 1.20, 1.09 to 1.31). Acute Covid-19 was associated with net increased CVD incidence (RR 6.02, 95% confidence interval 4.84 to 7.47) including pulmonary embolism (RR 14.5, 7.72 to 27.4), atrial arrythmias (6.58, 3.78 to 11.4) and venous thromboses (5.44, 3.22 to 9.17). CVD incidence declined in post-acute Covid-19 (1.68, 1.41 to 2.01) and showed no net increase in long Covid-19 (0.95, 0.85 to 1.06).

Conclusions

DM incidence remains elevated up to one year following Covid-19. CVD is increased early after Covid-19 mainly from pulmonary embolism, atrial arrhythmias and venous thromboses.