bluuebunny/crossref_metadata_2025 huggingface dataset:
Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. isolated from coral tissue: proposal of two new families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov
Authors: Li Qiqi , Liu Cong , Xie Feiyang , Lyu Lina , Zhang Si , Li Jie
Published: June 2024

A genome-based polyphasic approach was used to determine the taxonomic status of two novel bacterial strains, SCSIO 12594T and SCSIO 12813T, isolated from tissues of a coral. Both strains were Gram-stain-negative and facultatively anaerobic. The genome sizes of strains SCSIO 12594T and SCSIO 12813T were 3.9 Mb and 4.1 Mb, respectively, and they possessed DNA G+C contents of 55.1 and 46.2 mol%, respectively . Both strains were found to be catalase- and oxidase-positive, while SCSIO 12594T also could hydrolyse starch. SCSIO 12594T was observed to grow at between 20 and 37 °C (optimally at 25 °C) and at a pH range from 6 to 7 and in the presence of 3–7 % (w/v) NaCl. The growth of SCSIO 12813T required seawater and occurred at 20–30 °C (optimum, 25 °C), pH 5–8 (optimum, pH 6–7) and in the presence of 3–3.7 % (w/v) NaCl. The results of 16S rRNA gene-based phylogenetic analysis indicated that SCSIO 12594T shared 92.97 % or less sequence similarity with its closest relatives Rhodobium gokarnense JA173T and other members of the order Hyphomicrobiales. The results of 16S rRNA sequences-based phylogenetic analysis of SCSIO 12813T indicated that Croceimicrobium hydrocarbonivorans A20-9T (89.34 %) was the most closely related species. SCSIO 12594T and SCSIO 12813T can be readily separated from their closest relatives, as indicated by the results of phylogenomic analysis, low average nucleotide indexes, average amino acid identity, digital DNA–DNA hybridisation (dDDH) similarities and associated phenotypic and chemical data. Consequently, the two coral isolates are considered to represent two novel genera and species for which the names Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. are proposed, the type strains are SCSIO 12594T (= JCM 35320T = GDMCC 1.3060T) and SCSIO 12813T (= JCM 35373T = GDMCC 1.3063T), respectively. In addition, two novel families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov are proposed to accommodate Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov., respectively.
Mitochondrial Dysfunction and Fatigue in Sjögren’s Disease
Authors: Kurien Biji T. , Ice John A. , Wood Rebecca , Pharaoh Gavin , Cavett Joshua , Lewis Valerie , Bhaskaran Shylesh , Rasmussen Astrid , Lessard Christopher J. , Farris Amy Darise , Sivils Kathy L. , Koelsch Kristi A. , Van Remmen Holly , Scofield R. Hal
Published: June 2024

Objectives

Sjögren’s disease (SjD) is a common exocrine disorder typified by chronic inflammation and dryness, but also profound fatigue, suggesting a pathological basis in cellular bioenergetics. In healthy states, damaged or dysfunctional mitochondrial components are broken down and recycled by mitophagy, a specialized form of autophagy. In many autoimmune disorders, however, evidence suggests that dysfunctional mitophagy allows poorly functioning mitochondria to persist and contribute to a cellular milieu with elevated reactive oxygen species. We hypothesized that mitophagic processes are dysregulated in SjD and that dysfunctional mitochondria contribute to overall fatigue. We sought to link fatigue with mitochondrial dysfunction directly in SjD, heretofore unexamined, and further sought to assess the pathogenic extent and implications of dysregulated mitophagy in SjD.

Methods

We isolated pan T cells via negative selection from the peripheral blood mononuclear cells of 17 SjD and 8 age-matched healthy subjects, all of whom completed fatigue questionnaires prior to phlebotomy. Isolated T cells were analyzed for mitochondrial oxygen consumption rate (OCR) and glycolysis using Seahorse, and linear correlations with fatigue measures were assessed. A mitophagy transcriptional signature in SjD was identified by reanalysis of whole-blood microarray data from 190 SjD and 32 healthy subjects. Differential expression analyses were performed by case/control and subgroup analyses comparing SjD patients by mitophagy transcriptional cluster against healthy subjects followed by bioinformatic interpretation using gene set enrichment analysis.

Results

Basal OCR, ATP-linked respiration, maximal respiration, and reserve capacity were significantly lower in SjD compared to healthy subjects with no observed differences in non-mitochondrial respiration, basal glycolysis, or glycolytic stress. SjD lymphocytic mitochondria show structural alterations compared to healthy subjects. Fatigue scores related to pain/discomfort in SjD correlated with the altered OCR. Results from subgroup analyses by mitophagic SjD clusters revealed highly variable inter-cluster differentially expressed genes (DEGs) and expanded the number of SjD-associated gene targets by tenfold within the same dataset.

Conclusion

Mitochondrial dysfunction, associated with fatigue, is a significant problem in SjD and warrants further investigation.
Centrosome Migration and Apical Membrane Formation in Polarized Epithelial Cells: Insights from the MDCK Cyst Model
Authors: Wang Po-Kai , Lin Keng-Hui , Tang Tang K.
Published: June 2024

Polarization is crucial for the proper functioning of epithelial cells. Early polarization features include the trafficking and enrichment of polarity molecules to form the apical membrane (AM) or cell-cell junctions, as well as the apical positioning of the centrosome. However, the dependencies among polarity molecules, AM formation, and centrosome positioning remain poorly understood. In conventional Matrigel-cultured epithelial cells,de novopolarization can occur when a single cell divides. At the exit of mitosis, centrosomes move to the location where the apical membrane will form, raising the question of the role of the centrosome in epithelial polarization. We perturb centrosomes and polarity regulators in Matrigel-cultured cells and also manipulate polarity direction in non-conventional culture to examine the relationship between polarity features. Surprisingly, the centrosome is not essential for AM formation but promotes formation efficiency. The polarity regulator Par3, rather than the trafficking of AM components, affects centrosome positioning. In non-conventional cultures, the centrosome migration is opposite to that of the AM direction, and Par3 exhibits a different pattern from Matrigel culture. Taken together, our work shows that polarity indicated by centrosome position is not universal and elucidates the upstream-downstream relationship between centrosome positioning and other polarization features, providing insights into epithelial polarization.

Impact statement

Single-cell observations refute the expectation that centrosome positioning is a critical factor in the polarization of epithelial cells, while showing that proper centrosome positioning enhances the efficiency of cell polarization.
Dynamics in the Intact fd Bacteriophage Revealed by Pseudo 3D REDOR-Based Magic Angle Spinning NMR
Authors: Lusky Orr Simon , Sherer Dvir , Goldbourt Amir
Published: June 2024

The development of robust NMR methodologies to probe dynamics on the atomic scale is vital to elucidate the close relations between structure, motion, and function in biological systems. Here we present an automated protocol to measure, using magic-angle spinning NMR, the effective13C-15N dipolar coupling constants between multiple spin pairs simultaneously with high accuracy. We use the experimental dipolar coupling constants to quantify the order parameters of multiple C-N bonds in the thousands of identical copies of the coat protein in intact fd-Y21M filamentous bacteriophage virus, and describe its overall dynamics on the sub-millisecond time scale. The method is based on combining three pseudo three-dimensional NMR experiments, where a rotational echo double resonance (REDOR) dephasing block, designed to measure internuclear distances, is combined with three complementary13C-13C mixing schemes: dipolar-assisted rotational resonance, through-bond transfer-based double quantum / single quantum correlation, and radio-frequency driven recoupling. These mixing schemes result in highly resolved carbon spectra with correlations that are created by different transfer mechanisms.

We show that the helical part of the coat protein undergoes a uniform small (∼30°) amplitude motion, while the N-terminus is highly flexible. In addition, our results suggest that the reduced mobility of lysine sidechains at the C-terminus are a signature of binding to the single stranded DNA.
Hierarchical global and local auxin signals coordinate cellular interdigitation inArabidopsis
Authors: Pérez-Henríquez Patricio , Li Hongjiang , Zhou Xiang , Pan Xue , Lin Wenwei , Tang Wenxin , Nagawa Shingo , Lin Deshu , Xu Tongda , Michniewicz Marta , Prigge Michael J. , Strader Lucia C. , Estelle Mark , Hayashi Ken-ichiro , Friml Jiří , Qi Linlin , Liu Zhongchi , Van Norman Jaimie , Yang Zhenbiao
Published: June 2024

The development of multicellular tissues requires both local and global coordination of cell polarization, however, the mechanisms underlying their interplay are poorly understood. In Arabidopsis, leaf epidermal pavement cells (PC) develop a puzzle-piece shape locally coordinated through apoplastic auxin signaling. Here we show auxin also globally coordinates interdigitation by activating the TIR1/AFB-dependent nuclear signaling pathway. This pathway promotes a transient maximum of auxin at the cotyledon tip, which then moves across the leaf activating local PC polarization, as demonstrated by locally uncaged auxin globally rescuing defects intir1;afb1;afb2;afb4;afb5mutant but not intmk1;tmk2;tmk3;tmk4mutants. Our findings show that hierarchically integrated global and local auxin signaling systems, which respectively depend on TIR1/AFB-dependent gene transcription in the nucleus and TMK-mediated rapid activation of ROP GTPases at the cell surface, control PC interdigitation patterns in Arabidopsis cotyledons, revealing a mechanism for coordinating a local cellular process with the development of whole tissues.
High throughput cell mechanotyping of cell response to cytoskeletal modulations using a microfluidic cell deformation system
Authors: Smith Ian M. , Ursitti Jeanine A. , Majeti Pranav , Givpoor Nikka , Stemberger Megan B. , Hengen Autumn , Banerjee Shohini , Stains Joseph , Martin Stuart S. , Ward Christopher , Stroka Kimberly M.
Published: June 2024

Cellular mechanical properties influence cellular functions across pathological and physiological systems. The observation of these mechanical properties is limited in part by methods with a low throughput of acquisition or with low accessibility. To overcome these limitations, we have designed, developed, validated, and optimized a microfluidic cellular deformation system (MCDS) capable of mechanotyping suspended cells on a population level at a high throughput rate of ∼300 cells pers second. The MCDS provides researchers with a viable method for efficiently quantifying cellular mechanical properties towards defining prognostic implications of mechanical changes in pathology or screening drugs to modulate cytoskeletal integrity.
VPS34-IN1 inhibits cap-mediated translation and synergizes with STING to drive type-I IFN expression in human plasmacytoid DCs
Authors: Antas Paulo , Machado Mariana D. , Leite-Pinheiro Fátima , Barros Daniela , Ramalhinho Carlota , Mendes Andreia , Ferreira Beatriz H. , Carvoeiro Daniela , Reverendo Marisa , Duarte Iola F. , Narita Miwako , Su Bing , Argüello Rafael J. , Nal Beatrice , Pierre Philippe , Almeida Catarina R. , Gatti Evelina
Published: June 2024

Inhibition of the phosphatidylinositol kinase vacuolar protein sorting 34 (VPS34) with the pharmacological compound VPS34-IN1 has a range of effects on the dynamics of endosomes. While VPS34 inhibition has been suggested as a potential therapeutic approach for treating certain cancers, our findings indicate that it has minimal cytotoxic effects on leukemic blastic plasmacytoid dendritic cell neoplasms (BPDCN). VPS34-IN1, however, interferes with plasmacytoid dendritic cells (pDCs) function by blocking the recruitment of serum and glucocorticoid-regulated kinase 3 (SGK3) to endosomes, which is shown to be necessary for Toll-like receptor 7 (TLR7) signaling. In a contrasting parallel, VPS34-IN1 triggers the activation of the stimulator of interferon genes (STING) and significantly enhances pDCs’ response to the STING agonist 2’3’-cyclic guanosine monophosphate-adenosine monophosphate (2’3’-cGAMP). This cooperative action with VPS34-IN1 leads to strongly increased expression of type-I interferons (IFNs), associated with an alteration of STING degradation and importantly, inhibition of cap-mediated mRNA translation. Inhibition of protein synthesis by VPS34-IN1 appears to be central to this synergy with STING activation, notably by compromising the expression of IFIT1/ISG56, a negative regulator of innate signaling. Thus, despite their limited toxicity towards different cancer lines, inhibitors targeting VPS34 and SGK3 may present promising compounds for controlling the expression of type-I IFNs in response to various microbial stimuli and pathological contexts.

One-sentence summary

Pharmacological inhibition of VPS34 affects multiple signaling pathways downstream of innate immunity receptors and consequently can inhibit or potentiate type-I Interferon induction according to the danger or microbial stimuli received by plasmacytoid DCs.
Ensemblex: an accuracy-weighted ensemble genetic demultiplexing framework for population-scale scRNAseq sample pooling
Authors: Fiorini Michael R. , Amiri Saeid , Dilliott Allison A. , Ohki Cristine M. Yde , Smigielski Lukasz , Walitza Susanne , Fon Edward A. , Grünblatt Edna , Thomas Rhalena A. , Farhan Sali M.K.
Published: June 2024

Multiplexing samples from distinct individuals prior to sequencing is a promising step toward achieving population-scale single-cell RNA sequencing by reducing the restrictive costs of the technology. Individual genetic demultiplexing tools resolve the donor-of-origin identity of pooled cells using natural genetic variation but present diminished accuracy on highly multiplexed experiments, impeding the analytic potential of the dataset. In response, we introduce Ensemblex: an accuracy-weighted, ensemble genetic demultiplexing framework that integrates four distinct algorithms to identify the most probable subject labels. Using computationally and experimentally pooled samples, we demonstrate Ensemblex’s superior accuracy and illustrate the implications of robust demultiplexing on biological analyses.
Single-cell based integrative analysis of transcriptomics and genetics reveals robust associations and complexities for inflammatory diseases
Authors: Townsend Hope , Rosenberger Kaylee , Vanderlinden Lauren , Inamo Jun , Zhang Fan
Published: June 2024

Background

Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.

Methods

We present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases.First, we applied and compared the results of two recent algorithms, based on networks (scGWAS) or single-cell disease scores (scDRS), according to accuracy/sensitivity and interpretability (M. J. Zhang et al. 2022; Jia et al. 2022). While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,1,73 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC) (F. Zhang et al. 2023; Ishigaki et al. 2022; Smillie et al. 2019; de Lange et al. 2017).Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools’ resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas.Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.

Results

We first found that single-cell based tool scDRS called superior numbers of supported cell states, like MERTK+ myeloid cells in RA, which were overlooked by network-based scGWAS. While scGWAS was advantageous for gene exploration, scDRS captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5’ scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn’s disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.
Association of demographic factors with acute mountain sickness: a retrospective study in Litang
Authors: Zhao Haitong , Wang Hao , Wang Chao , Li Lifen , Zhang Xuan , Chen Ling , Ni Guohua , Yan Hui , Chen Lei , Luo Fengming
Published: June 2024

Objective

Acute mountain sickness (AMS) is a common clinical syndrome in high altitude areas, but the role of demographic factors in AMS has not been well-illucidated. This study aims to describe the relationship between demographic factors and AMS in Litang, one of the highest-altitude town in the world.

Methods

Demographic data of patients diagnosed with AMS from January 2022 to December 2023 were collected from the information management system of Litang County People’s Hospital, including gender, age, onset time, ethnicity, current residence and its altitude. Descriptive statistical methods were used to describe these factors.

Results

7,290 AMS patients were included, among which 62.37% (4,547/7,290) were male and 37.63% (2,743/7,290) were female; 90.41% (6,591/7,290) were non-Tibetan, and 9.59% (699/7,290) were Tibetan; the age group 20-29 had the highest number of patients (2,422, 39.08%), and the incidence of AMS generally decreased with age; the proportion of AMS occurring from May to August reached 51.99% (3,790/7,290); the percentage from lower altitude areas was 79.05% (4,333/7,150).

Conclusions

These data from Litang suggest higher incidence of AMS may be detected in males, non-Tibetans, young people, summer time and residents from lower altitude. Special attention should be paid to these demographic factors for preventing the occurrence of AMS.
Whole exome-seq and RNA-seq data reveal unique neoantigen profiles in Kenyan breast cancer patients
Authors: Wagutu Godfrey , Gitau John , Mwangi Kennedy , Murithi Mary , Melly Elias , Harris Alexandra R. , Sayed Shahin , Ambs Stefan , Makokha Francis
Published: June 2024

Background

The immune response against tumors relies on distinguishing between self and non-self, the basis of cancer immunotherapy. Neoantigens from somatic mutations are central to many immunotherapeutic strategies and understanding their landscape in breast cancer is crucial for targeted interventions. We aimed to profile neoantigens in Kenyan breast cancer patients using genomic DNA and total RNA from paired tumor and adjacent non-cancerous tissue samples of 23 patients.

Methods

We sequenced the genome-wide exome (WES) and RNA, from which somatic mutations were identified and their expression quantified, respectively. Neoantigen prediction focused on human leukocyte antigens (HLA) crucial to cancer, HLA type I. HLA alleles were predicted from WES data covering the adjacent non-cancerous tissue samples, identifying four alleles that were present in at least 50% of the patients. Neoantigens were deemed potentially immunogenic if their predicted median IC50 binding scores were ≤500nM and were expressed [transcripts per million (TPM) >1] in tumor samples.

Results

An average of 1465 neoantigens covering 10260 genes had ≤500nM median IC50 binding score and >1 TPM in the 23 patients and their presence significantly correlated with the somatic mutations (R2=0.570,P=0.001). Assessing 58 genes reported in the catalog of somatic mutations in cancer (COSMIC, v99) to be commonly mutated in breast cancer, 44 (76%) produced >2 neoantigens among the 23 patients, with a mean of 10.5 ranging from 2 to 93. For the 44 genes, a total of 477 putative neoantigens were identified, predominantly derived from missense mutations (88%), indels (6%), and frameshift mutations (6%). Notably, 78% of the putative breast cancer neoantigens were patient-specific. HLA-C*06:01 allele was associated with the majority of neoantigens (194), followed by HLA-A*30:01 (131), HLA-A*02:01 (103), and HLA-B*58:01 (49). Among the genes of interest that produced putative neoantigens wereMUC17,TTN,MUC16,AKAP9,NEB,RP1L1,CDH23,PCDHB10,BRCA2,TP53,TG, andRB1.

Conclusions

The unique neoantigen profiles in our patient group highlight the potential of immunotherapy in personalized breast cancer treatment as well as potential biomarkers for prognosis. The unique mutations producing these neoantigens, compared to other populations, provide an opportunity for validation in a much larger sample cohort.
The effect of circulating neutralizing antibodies on the replication of SARS-CoV-2 variants following post-vaccination infections
Authors: Garcia-Knight Miguel A. , Kelly J. Daniel , Lu Scott , Tassetto Michel , Goldberg Sarah A. , Zhang Amethyst , Pineda-Ramirez Jesus , Anglin Khamal , Davidson Michelle C. , Chen Jessica Y. , Fortes-Cobby Maya , Park Sara , Martinez Ana , So Matthew , Donovan Aidan , Viswanathan Badri , Richardson Eugene T. , McIlwain David R. , Gaudilliere Brice , Rutishauser Rachel L. , Chenna Ahmed , Petropoulos Christos , Wrin Terri , Deeks Steve G. , Abedi Glen R. , Saydah Sharon , Martin Jeffrey N. , Briggs-Hagen Melissa , Midgley Claire M. , Peluso Michael J. , Andino Raul
Published: June 2024

The impact of pre-existing neutralizing antibodies (NAbs) titers on SARS-CoV-2 viral shedding dynamics in post-vaccination infection (PVI) are not well understood. We characterized viral shedding longitudinally in nasal specimens in relation to baseline (pre/peri-infection) serum neutralizing antibody titers in 125 participants infected with distinct SARS-CoV-2 variants. Among 68 participants who had received vaccinations, we quantified the effect of baseline serum NAb titers on maximum viral RNA titers and on the duration of infectivity. Baseline NAb titers were higher and efficiently targeted a broader range of variants in participants who received one or two monovalent ancestral booster vaccinations compared to those with a full primary vaccine series. In participants with Delta variant infections, baseline NAb titers targeting Delta were negatively correlated with maximum viral RNA copies. Per log10increase in baseline NAb IC50, maximum viral load was reduced -2.43 (95% confidence interval [CI] -3.76, -1.11) log10 N copies and days of infectious viral shedding were reduced -2.79 [95% CI: -4.99, -0.60] days. By contrast, in those with Omicron infections (BA.1, BA.2, BA.4 or BA.5 lineages) baseline NAb responses against Omicron lineages did not predict viral outcomes. Our results provide robust estimates of the effect of baseline NAbs on the magnitude and duration of nasal viral replication after PVI (albeit with an unclear effect on transmission) and show how immune escape variants efficiently evade these modulating effects.
tbea: tools for pre- and post-processing in Bayesian evolutionary analyses
Authors: Ballen Gustavo A. , Reinales Sandra
Published: June 2024

1

Estimating phylogenies in which branch lengths are expressed in units of absolute time is crucial for testing hypotheses in modern evolutionary biology. However, bioinformatic tools to process data from bayesian divergence time estimation analyses are often not easily adaptable, and documenting methodological choices is not a generalized practice.

The R package tbea is a toolset to integrate biological, geological and paleontological information to optimize the specification of models, their parameters and prior distributions in divergence times estimation analyses. tbea implements statistical models to (i) better translate time information in dating sources into the specified calibration densities, (ii) improve comparisons between prior and posterior distributions for parameters of interest, (iii) carry out inference on origination times for a collection of posterior distributions, (iv) summarize different distributions into a single one, useful e.g. when building secondary calibrations, and (v) improve the reproducibility of divergence time estimation analyses allowing users to document methodological choices.

We illustrate the package functionalities by carrying out two worked examples. One on the phylogenetic relationships and divergence time estimation of South American Saber-Tooth Characins of the family Cynodontidae, and another one on the separation time of drainages East and West of the Andes in South America during the Neogene.

It is expected that the tools herein available will be key when estimating events in time from collections of point estimates, as well as the combination of different posterior densities from the same parameter are useful to justifying the selection of secondary calibration points, or discussing the timing of biogeographic events when multiple sources are available.
A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity
Authors: Madhuprakash Jogi , Toghani AmirAli , Contreras Mauricio P. , Posbeyikian Andres , Richardson Jake , Kourelis Jiorgos , Bozkurt Tolga O. , Webster Michael , Kamoun Sophien
Published: June 2024

NRCs are essential helper NLR (nucleotide-binding domain and leucine-rich repeat) proteins that execute the immune response triggered by disease resistance proteins, also known as sensor NLRs. The structure of the resting state of NbNRC2 was recently revealed to be a homodimer. However, the sensor-activated state has not yet been elucidated. In this study, we used cryo-EM to determine the structure of sensor-activated NbNRC2, which forms a hexameric inflammasome-like structure known as resistosome. To confirm the functional significance of the hexamer, we mutagenized the interfaces involved in oligomerization and found that mutations in three nucleotide-binding domain interface residues abolish oligomerization and immune signalling. Comparative structural analyses between the resting state NbNRC2 homodimer and the sensor-activated homohexamer revealed significant structural rearrangements before and after activation, providing insights into NLR activation mechanisms. Furthermore, structural comparisons between the NbNRC2 hexamer and previously reported CC-NLR pentameric assemblies revealed features in NbNRC2 that allow for the integration of an additional protomer. We also used the NbNRC2 hexamer structure to assess the recently released AlphaFold 3 for the prediction of activated CC-NLR oligomers. This revealed that AlphaFold 3 allows for high-confidence modelling of the N-terminalα1-helices of NbNRC2 and other CC-NLRs, a region that has proven difficult to fully resolve using structural approaches. Overall, our work sheds light on the structural and biochemical mechanisms underpinning NLR activation and expands our understanding of NLR structural diversity.
Sex differences and immune correlates of Long COVID development, persistence, and resolution
Authors: Hamlin Rebecca E. , Pienkos Shaun M. , Chan Leslie , Stabile Mikayla A. , Pinedo Kassandra , Rao Mallika , Grant Philip , Bonilla Hector , Holubar Marisa , Singh Upinder , Jacobson Karen B. , Jagannathan Prasanna , Maldonado Yvonne , Holmes Susan P. , Subramanian Aruna , Blish Catherine A.
Published: June 2024

Sex differences have been observed in acute COVID-19 and Long COVID (LC) outcomes, with greater disease severity and mortality during acute infection in males and a greater proportion of females developing LC. We hypothesized that sex-specific immune dysregulation contributes to the pathogenesis of LC. To investigate the immunologic underpinnings of LC development and persistence, we used single-cell transcriptomics, single-cell proteomics, and plasma proteomics on blood samples obtained during acute SARS-CoV-2 infection and at 3 and 12 months post-infection in a cohort of 45 patients who either developed LC or recovered. Several sex-specific immune pathways were associated with LC. Specifically, males who would develop LC at 3 months had widespread increases inTGF-βsignaling during acute infection in proliferating NK cells. Females who would develop LC demonstrated increased expression ofXIST, an RNA gene implicated in autoimmunity, and increasedIL1signaling in monocytes at 12 months post infection. Several immune features of LC were also conserved across sexes. Both males and females with LC had reduced co-stimulatory signaling from monocytes and broad upregulation ofNF-κBtranscription factors. In both sexes, those with persistent LC demonstrated increased LAG3, a marker of T cell exhaustion, reducedETS1transcription factor expression across lymphocyte subsets, and elevated intracellular IL-4 levels in T cell subsets, suggesting that ETS1 alterations may drive an aberrantly elevated Th2-like response in LC. Altogether, this study describes multiple innate and adaptive immune correlates of LC, some of which differ by sex, and offers insights toward the pursuit of tailored therapeutics.

One Sentence Summary

This multi-omic analysis of Long COVID reveals sex differences and immune correlates of Long COVID development, persistence, and resolution.
The Establishment and Potential Spread ofOsmia cornuta(Hymenoptera: Megachilidae) in North America
Authors: Getz Michael P , Best Lincoln R , Melathopoulos Andony P , Warren Timothy L
Published: June 2024

Mason bees, subgenusOsmiaPanzer (Hymenoptera: Megachilidae), are economically and ecologically significant pollinators. In eastern North America, the rapid spread of two non-native species from Asia,O. cornifronsRadoszkowski andO. taurusSmith, has coincided with declines in nativeOsmiapopulations, raising concern about the effects of further exotic invasions. Here we investigate the recent establishment in British Columbia, Canada of the European orchard bee,O. cornutaLatreille, previously thought to be limited to Europe and its periphery. We documentO. cornutarecords ranging over 170 km, including sightings of live adults and the discovery of a multigenerational nest with hundreds of cocoons. We tested whether theseO. cornutacocoons could be discriminated from otherOsmiaspecies by training a machine learning classifier on features extracted from images. The best performing model could not reliably discriminate cocoons by species, raising the possibilityO. cornutacould be inadvertently intermingled in future commercial shipments. Spatially isolated records ofO. cornifronsandO. taurusfurther suggest ongoing anthropogenic dispersal of these species. To determine environmentally suitable regions forO. cornutato spread in North America, we estimated its climate niche using native-range occurrence data. This analysis indicated broad regions of the Pacific Northwest and eastern North America contain potentially suitable habitat. Together, our findings document the establishment ofO. cornutain North America and the potential for it to spread broadly. Our study demonstrates the utility of accessible biodiversity data archives and public observation programs in tracking biological invasions and highlights the need for future monitoring of exoticOsmia.
Reduction of fungal dysbiosis is involved in the attenuation of Dextran Sodium Sulfate-Induced Mouse Colitis Mediated by GILZ protein and yeast extract compound
Authors: Gentili Marco , Nunzi Emilia , Sabbatini Samuele , Lusenti Eleonora , Cari Luigi , Mencacci Antonella , Ballet Nathalie , Migliorati Graziella , Riccardi Carlo , Ronchetti Simona , Monari Claudia
Published: June 2024

Inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis, have a complex and multifactorial pathogenesis that remains not fully elucidated. Recent research suggests that intestinal fungal dysbiosis may contribute to the development and persistence of IBD. In this study, we explored, for the first time, the effects of the glucocorticoid-induced leucine zipper (GILZ) protein, known to have protective effects on the gut mucosa in preclinical IBD models, in combination with a yeast extract, which supports the growth of beneficial microorganisms, in a mouse model of ulcerative colitis. The combined treatment produced significant protection against severe disease outcomes in the mice, including the restoration of intestinal barrier integrity and the reduction of pro-inflammatory cytokines. Specifically, GILZ primarily acted on the gut permeability, while the yeast extract mainly reduced pro-inflammatory cytokines. Notably, both treatments were effective in restoring the intestinal burden of clinically importantCandidaand formerCandidaspecies. Analysis of the intestinal fungal communities revealed that both treatments were able to reduce colitis-associated fungal dysbiosis, promoting a fungal composition similar to that of healthy mice. This effect was mainly the result of a decreased abundance of theMeyerozimagenus, which was dominant in the colitic mice. Thus, combined treatment regimens with the GILZ protein and yeast extract could represent a new strategy for the treatment of inflammatory bowel diseases, by targeting multiple mechanisms at the basis of IBD, including the fungal dysbiosis.

IMPORTANCE

Inflammatory bowel diseases (IBD), including Crohn’s disease and ulcerative colitis, are characterized by chronic inflammation and have a complex, multifactorial pathogenesis that is not yet fully understood. Currently, no established therapeutic strategy can consistently manage IBD effectively. Recent research indicates that intestinal fungal dysbiosis could potentially contribute to the development and persistence of chronic IBD, highlighting the importance of investigating alternative therapeutic strategies able to attenuate fungal dysbiosis in the context of intestinal inflammation. In this study, we demonstrate that a combination of a recombinant protein (GILZp) and a compound with prebiotic properties could represent a new therapeutic strategy for the treatment of IBD, as it not only decreases inflammation and restores the integrity of the epithelial barrier, but reduces fungal dysbiosis associated with DSS-induced colitis.
Exotoxins secreted byClostridium septicuminduce macrophage death:implications for bacterial immune evasion mechanisms at infection sites
Authors: Ortiz Flores RM , Cáceres CS , Cortiñas TI , Gomez Mejiba SE , Sasso CV , Ramirez DC , Mattar Domínguez MA
Published: June 2024

The induction of macrophage death is regarded as a potential mechanism by which components secreted byClostridium septicumare used to evade the innate immune response and cause tissue damage. This study aimed to determine the effect of partially purified fractions of extracellular proteins secreted byC. septicumon the death of mouse peritoneal macrophages. Elicited mouse peritoneal macrophages were incubated with partially purified fractions of proteins secreted byC. septicuminto the culture medium. After incubation, we found that the protein fraction with a molecular weight ≥ 100 kDa caused significant cell death in macrophages, changed cell morphology, increased markers of apoptosis and autophagy, and increased the expression (protein and mRNA) of IL-10 and TNFα Our data suggest that the proteins secreted byC. septicum(MW, ≥ kDa) induce cell death in macrophages by promoting autophagy- triggered apoptosis. This study may contribute to our understanding of the molecular mechanism of immune evasion byC. septicumat the infection site.
Exploring self-reported quality of life in developmental language disorder
Authors: Larson Caroline
Published: June 2024

Purpose

Developmental language disorder (DLD) is a lifelong condition associated with poorer outcomes than neurotypical peers, yet relatively little is known about long-term quality of life in DLD. This preliminary study adopts a neurodiversity-informed approach by exploringself-reportedquality of life in an adolescent and young adult DLD sample, as well as linguistic and risk factors contributing to quality of life.

Method

Participants were five individuals with DLD aged 12-20 years (M = 15.60; SD = 3.05). I administered two self-report quality of life scales, a language assessment, an experimental morphosyntax task, and measures of risk factors. Data were analyzed descriptively.

Results

Participants generally reported positive views about their quality of life, though accessing accommodations and health services emerged as barriers. Relatively better grammaticality judgement performance appeared to be linked with poorer ratings of happiness and the ability to ‘be yourself.’ Nonverbal ability represented a potential risk factor, though there may be a stronger cumulative role for risk factors.

Conclusions

DLD participants reported relatively good quality of life. Exploratory findings suggest barriers to quality of life in some contexts, as well as roles for individual differences in language and risk factors. These descriptive findings should be examined in larger scale studies and may represent areas of consideration when clinicians address functional challenges that impact mental health and wellbeing in individuals with DLD.
Minimizing biological risk for novel inhibitory drug targets: One knockout is all you need
Authors: Dimitriev Alan , Postovit Lynne-Marie , Simpson Amber L. , Wong Gane Ka-Shu
Published: June 2024

We argue that biological risk for novel inhibitory drug targets can be minimized, almost eliminated, by a computational analysis of the healthcare records and DNA sequences in resources like UK Biobank or All-of-Us. The key insight is that an inhibitory drug is functionally equivalent to a loss-of-function (LOF) variant in the targeted gene. It is a special case of what has been called an “experiment of nature”. To demonstrate, we considered all available clinical trials (58 in total) and inhibitory drugs (15 in total) for 5 cardiovascular drug targets: PCSK9, APOC3, ANGPTL3, LPA, and ASGR1. The results were shocking. Every biomarker assessed in these clinical trials was successfully predicted, i.e. directionality and proportionality of effect, but not the magnitude since that varies with dosage. This concept has not been widely adopted because geneticists believe that homozygous LOFs, which are exceedingly rare, would be needed to observe a significant phenotypic effect from most genetic knockouts. Our study shows that, to the contrary, given a sufficiently large biobank, counting both carriers and non-carriers, heterozygous LOFs alone can inform drug development.
Augmenting maternal clinical cohort data with administrative laboratory dataset linkages: a validation study
Authors: Rossouw Laura , Ngcobo Nkosinathi , Clouse Kate , Nattey Cornelius , Technau Karl-Günter , Maskew Mhairi
Published: June 2024

Background

The use of big data and large language models in healthcare can play a key role in improving patient treatment and healthcare management, especially when applied to large-scale administrative data. A major challenge to achieving this is ensuring that patient confidentiality and personal information is protected. One way to overcome this is by augmenting clinical data with administrative laboratory dataset linkages in order to avoid the use of demographic information.

Methods

We explored an alternative method to examine patient files from a large administrative dataset in South Africa (the National Health Laboratory Services, or NHLS), by linking external data to the NHLS database using specimen barcodes associated with laboratory tests. This offers us with a deterministic way of performing data linkages without accessing demographic information. In this paper, we quantify the performance metrics of this approach.

Results

The linkage of the large NHLS data to external hospital data using specimen barcodes achieved a 95% success. Out of the 1200 records in the validation sample, 87% were exact matches and 9% were matches with typographic correction. The remaining 5% were either complete mismatches or were due to duplicates in the administrative data.

Conclusions

The high success rate indicates the reliability of using barcodes for linking data without demographic identifiers. Specimen barcodes are an effective tool for deterministic linking in health data, and may provide a method of creating large, linked data sets without compromising patient confidentiality.
Network meta-analysis made simple: a composite likelihood approach
Authors: Liu Yu-Lun , Zhang Bingyu , Chu Haitao , Chen Yong
Published: June 2024

Network meta-analysis, also known as mixed treatments comparison meta-analysis or multiple treatments meta-analysis, extends conventional pairwise meta-analysis by simultaneously synthesizing multiple interventions in a single integrated analysis. Despite the growing popularity of network meta-analysis within comparative effectiveness research, it comes with potential challenges. For example, within-study correlations among treatment comparisons are rarely reported in the published literature. Yet, these correlations are pivotal for valid statistical inference. As demonstrated in earlier studies, ignoring these correlations can inflate mean squared errors of the resulting point estimates and lead to inaccurate standard error estimates. This paper introduces a composite likelihood-based approach that ensures accurate statistical inference without requiring knowledge of the within-study correlations. The proposed method is computationally robust and efficient, with substantially reduced computational time compared to the state-of-the-science methods implemented in R packages. The proposed method was evaluated through extensive simulations and applied to two important applications including a network meta-analysis comparing interventions for primary open-angle glaucoma, and another comparing treatments for chronic prostatitis and chronic pelvic pain syndrome.

Highlights

What is already known?

Network meta-analysis extends conventional pairwise meta-analysis by simultaneously synthesizing multiple interventions in a single integrated analysis.

A significant challenge in network meta-analysis is the lack of reported within-study correlations among treatment comparisons in the published studies.

What is new?

We propose a new method for network meta-analysis that ensures vaild statistical inference without the need for knowledge of within-study correlations.

The proposed method employs a composite likelihood and a sandwich-type robust variance estimator, offering a computationally efficient and scalable solution, particularly for network meta-analysis with a large number of treatments and studies.

Potential impact forResearch Synthesis Methodsreaders

The proposed method can be easily applied to any univariate network meta-analysis project without requiring knowledge of within-study correlations among treatment comparisons.
Patient and public experience and views on digital systems for sharing records for health and care preferences at the end of life
Authors: Birtwistle J. , Russell AM , Relton S. , Easdown H. , Grieve U. , Allsop M.
Published: June 2024

Objective

To explore patient and public experiences of and priorities for the use of shared patient health records for advance care planning.

Methods

A convergent-parallel mixed method design was used. An online national survey of patients and the public gathered data on experiences and views of sharing health and advance care planning information to support care at the end of life. Descriptive statistics were used to analyse rating scale responses (5 or 10-point scale) and thematic analysis applied to free-text responses.

Results

Responses (N=1728) included participants in 103 UK counties, including people with a terminal condition (n=33), long-term condition (n=442), who provide or have provided care to a person with a long-term or terminal illness (n=229), and who identified as healthy and interested in planning for the future (n=1024). Confidence that recorded care preferences would be accessed when needed was low for carers (median= 2, IQR 1-4) and moderate for patients (median=3, IQR 1-4). Four themes derived from free-text responses included: i) Experience of sharing health information; ii) Preparation, communication and understanding; iii) Concerns, unknowns and assurance seeking, and; iv) Preserving Dignity and Respect: Understanding individual contexts.

Conclusions

Whilst recognising the potential of sharing health records, respondents and in particular carers, doubted that patient information would be accessed by relevant health professionals when needed. Future research is required to explore whether patient and carer access to the record influences their confidence in the accuracy of the content and the likelihood of care being delivered in line with their wishes.

What is already known on this topic

Digital systems can support documentation and sharing of health information, wishes and preferences for the end of life.

What this study adds

Patients and carers perceive the documentation of advance care plans as a burdensome and complex process, that can lead to confusion about the purpose of documentation.

Respondents expressed doubts about the accuracy of documented information, uncertainty about whether health professionals could access their records when needed and concerns that documented wishes and preferences would be ignored.

How this study might affect research, practice or policy

Patient and public views must be considered in the design and implementation of digital systems. In particular, efforts should be made to build confidence and clarify the expectations of patients and members of the public around the documentation of their wishes and preferences for care alongside the subsequent sharing and use of this information.