Hasil untuk "Microbiology"

K. Maslowski, C. Mackay

J. Kuenen

A. I. Ihekoronye, P. O. Ngoddy

P. Walstra, J. Wouters, T. Geurts

Hannah F. Nicholson, Christopher Zdyrski, Christina M. Leyson et al.

Abstract High pathogenicity avian influenza viruses pose a growing threat to poultry, livestock, wildlife, and humans as they undergo accelerated expansion of host and geographical ranges. Since 2020, these viruses have driven a panzootic characterized by extensive viral diversification and spillover into species previously considered to be resistant. There is currently a lack of physiologically relevant in vitro models that can be used to screen the rapidly changing viral landscape. To address this need, we describe the first chicken lung organoids derived from adult stem cells of specific pathogen free White Leghorns. We analyze their gene expression with bulk RNA sequencing, confirm their cellular heterogeneity via single-nuclei RNA sequencing, and provide basic morphological characterization using hematoxylin and eosin staining, immunohistochemistry, and transmission electron microscopy. The results indicate that the organoids contained several cell types, including non-ciliated columnar, cuboidal, squamous, and mucin-producing cells, representative of different regions of the avian respiratory system. Furthermore, expression of genes relevant to influenza A virus infection and replication appeared to be conserved across organoid and tissue samples. Infections revealed that chicken lung organoids support robust replication of both low and high pathogenicity avian influenza A viruses, with high pathogenicity strains showing more rapid amplification. Therefore, these organoids have the potential to effectively model viral infection, enabling the investigation of viral pathogenesis and evolutionary potential, virus-host interactions, and antiviral targets.

Muhammad Waqas, Habibullah Nadeem, Ayshah Aysh Alrashidi et al.

Abstract Potassium (K+) is an essential nutrient for plants. It contributes to most physiological and biochemical pathways for plant metabolism, growth, and development. It is the most available plant nutrient, comprising 10–15% of plant weight. Plants have a sophisticated system of K+ transporters and channels for distribution in plant body. Apple is one of the most consumed fruits in the world. Its fruit quality and yield are positively affected by K+. However, limited information is available about K+ transport systems in Apple. In this study, 47 candidate genes (26 K+ transporters and 21 K+ channels) have been identified in Apple (Malus domestica) genome. The phylogenetic comparisons with other plants (Glycine max, Arabidopsis thaliana, and Oryza sativa) indicated that the K+ transport system is much conserved among different plants. The analysis of Gene structure showed the presence of specific introns and exon patterns for these gene families. Transcriptomic data analysis and RT-qPCR demonstrated significant variations in the transcript abundance of these genes in response to abiotic stresses. The current project represents the first report about the K+ transport system in Apple. Therefore, it may act as a starting point for further functional characterizations.

Taoxun Zhou, Bingying Zhang, Runxin Zhu et al.

Macrophages execute host defense against pathogens by releasing extracellular traps (METs) composed of DNA meshwork and antimicrobial proteins. Although MET-mediated pathogen immobilization is well documented, the induction mechanisms of MET generation by helminth parasites remain elusive. Here, we demonstrate that Strongyloides stercoralis larvae induce rapid chromatin extrusion in murine macrophages. Unlike neutrophil extracellular trap (NET) formation, MET formation does not require NADPH oxidase and exhibits distinct ultrastructural characteristics, including endoplasmic reticulum vesiculation, perinuclear space dilation, and inner nuclear membrane budding. Phosphoproteomic analysis revealed that MET formation is coordinately regulated by ERK and AKT signaling, F-actin cytoskeletal remodeling, histone acetylation, and phosphorylation of nuclear envelope (NE) proteins. Specifically, we show that protein kinase C zeta isoform (PKCζ)-mediated lamin A/C phosphorylation drives the NE budding and subsequent DNA expulsion. This work represents the first systematic delineation of the cellular dynamics and molecular machinery underlying MET formation, providing new insights into macrophage-directed anti-helminth immunity.

Orges Koci, Richard K. Russell, M. Guftar Shaikh et al.

Abstract Background Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration. Results In this study, we have developed a Java-based statistical framework ( https://github.com/KociOrges/cviewer ) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case–control relationships. Conclusions CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn’s disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract

Baraah T. Abu AlSel, Abdelrahman A. Mahmoud, Elham O. Hamed et al.

Metabolic syndrome (MetS) is a worldwide public health challenge. Accumulating evidence implicates elevated serum ferritin and disruptions in iron metabolism as potential elements linked to an increased risk of MetS. This study investigates the relationship between iron homeostasis—including hepcidin levels, serum iron concentration, unsaturated iron-binding capacity (UIBC), and the hepcidin/ferritin (H/F) ratio—and MetS. In this descriptive cross-sectional study, 209 participants aged 24–70 were categorized into two groups: 103 with MetS and 106 without MetS. All participants underwent medical assessment, including anthropometric measures, indices of glycemic control, lipid profiles, and iron-related parameters. Participants were further stratified by the Homeostasis Model Assessment—Insulin Resistance index into three subgroups: insulin-sensitive (IS) (<1.9), early insulin resistance (EIR) (>1.9 to <2.9), and significant insulin resistance (SIR) (>2.9). Notable increments in serum ferritin and hepcidin were observed in the SIR group relative to the IS and EIR groups, with a significant association between metabolic parameters. The UIBC and serum ferritin emerged as significant predictors of MetS, particularly in men, with an area under the curve (AUC) of 0.753 and 0.792, respectively (<i>p</i> ≤ 0.001). In contrast, hepcidin was notably correlated with MetS in women, with an AUC of 0.655 (<i>p</i> = 0.007). The H/F ratio showed superior predictive capability for MetS across both sexes (at cutoff level = 0.67). Among women, this ratio had an AUC of 0.639 (<i>p</i> = 0.015), and for men, it had an AUC of 0.792 (<i>p</i> < 0.001). Hypertension proved an independent risk factor for MetS, affirming its role in metabolic dysregulation. The findings highlight a significant interconnection between iron homeostasis parameters and MetS, with sex-specific variations underscoring the importance of personalized diagnostic criteria. The crucial role of the H/F ratio and the UIBC as emerging predictive markers for MetS indicates their potential utility in identifying at-risk individuals. Further longitudinal research is essential to establish causality and explore the interplay between these biomarkers and MetS.

Kun Wu, Xianjun Liu, Xianglong Meng et al.

ObjectiveThis study evaluated the effects of sauchinone on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) mice model and investigated the underlying mechanisms of the downstream pathway and gut microbiota.MethodsThe UC mice model was induced by DSS. The disease phenotypes were determined through pathological symptoms (body weight and disease activity index score), inflammation markers (histological and inflammatory factor detections), and colonic mucosal barrier damage (detection of tight junction proteins). The level of the NF-κB pathway was detected through marker proteins. Database and bioinformatics analyses were used to predict sauchinone-mediated downstream molecules that were previously identified by expression analysis. Mouse feces were collected to detect the V3–V4 region of the 16S rRNA gene.ResultsIn DSS-induced UC mice, sauchinone alleviated pathological symptoms, inhibited inflammation, and prevented mucosal barrier damage. Sauchinone further inhibited the NF-κB pathway by upregulating NAD (P) H dehydrogenase [quinone] 1 (NQO1) in DSS-induced UC mice. Moreover, sauchinone regulated the diversity and composition of the gut microbiota in mice, stimulating the growth of Firmicutes and inhibiting the growth of Proteobacteria and Bacteroidetes.ConclusionTherefore, sauchinone exerted therapeutic effects on UC in mice by regulating the NQO1/NF-κB pathway and altering the gut microbiota. This provides a theoretical basis for developing sauchinone as a therapeutic agent and extends our understanding of its bioactivity.

Nyasha Mafumo, Oliver K. I. Bezuidt, Wouter le Roux et al.

ABSTRACT Viruses are the most biologically abundant entities and may be ideal indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic ecosystem changes in rivers, leading to substantial shifts in chemical and biological attributes. Here, we evaluate the viability of using the presence of crAssphage as indicators of fecal contamination in South African rivers. Shotgun analysis revealed diverse crAssphage viruses in these rivers, which are impacted by chemical and biological pollution. Overall, the diversity and relative abundances of these viruses was higher in contaminated sites compared to pristine locations. In contrast to fecal coliform counts, crAssphage sequences were detected in pristine rivers, supporting the assertion that the afore mentioned marker may be a more accurate indicator of fecal contamination. Our data demonstrate the presence of diverse putative hosts which includes members of the phyla Bacteroidota, Pseudomonadota, Verrucomicrobiota, and Bacillota. Phylogenetic analysis revealed novel subfamilies, suggesting that rivers potentially harbor distinct and uncharacterized clades of crAssphage. These data provide the first insights regarding the diversity, distribution, and functional roles of crAssphage in rivers. Taken together, the results support the potential application of crAssphage as viable markers for water quality monitoring. IMPORTANCE Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. Waterborne viral outbreaks have been reported even after fecal indicator bacteria (FIB) were suggested to be absent or below regulated levels of coliforms. This indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination in two South African rivers. We assess the abundance, distribution, and diversity of these viruses in sites that had been predicted pristine or contaminated by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies were unrepresented in our data, suggesting that the diversity of these viruses may reflect geographic locality and dependence.

Kotaro Soeda, Takayoshi Sasako, Kenichiro Enooku et al.

Abstract Diabetes is known to increase the risk of nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC). Here we treat male STAM (STelic Animal Model) mice, which develop diabetes, NASH and HCC associated with dysbiosis upon low-dose streptozotocin and high-fat diet (HFD), with insulin or phlorizin. Although both treatments ameliorate hyperglycemia and NASH, insulin treatment alone lead to suppression of HCC accompanied by improvement of dysbiosis and restoration of antimicrobial peptide production. There are some similarities in changes of microflora from insulin-treated patients comorbid with diabetes and NASH. Insulin treatment, however, fails to suppress HCC in the male STAM mice lacking insulin receptor specifically in intestinal epithelial cells (ieIRKO), which show dysbiosis and impaired gut barrier function. Furthermore, male ieIRKO mice are prone to develop HCC merely on HFD. These data suggest that impaired gut insulin signaling increases the risk of HCC, which can be countered by restoration of insulin action in diabetes.

Rasheeda Mohamedali, Suvradeep Mitra, Swarnendu Mandal et al.

Background: Enhancer of zeste homolog 2 (EZH2) is one of the major epigenetic modifiers involved in the transcriptional repression of target genes through trimethylation of H3K27 (lysine 27 residue of histone H3). Deregulated expression of both EZH2 and H3K27me3 has been implicated in the biological behavior and prognostic outcome of various malignancies. Aim: To assess the role of EZH2 and H3K27me3 in the carcinogenesis of urothelial carcinoma of urinary bladder. Materials and Methods: One hundred fifty consecutive urothelial carcinoma cases of urinary bladder (54.7% high-grade) were included in this study. Immunohistochemical analysis for EZH2 and H3K27me3 was performed on whole tissue sections. A multiplication score obtained by multiplying staining intensity and proportion of positively stained neoplastic cells was used for assessment. Results: EZH2 showed a significant correlation with the tumor grade and lamina propria invasion (p < 0.001). The cases with high EZH2 expression showed a significantly high proliferative index (Mean- 32.7%; p < 0.001). In contrast, negative and low expression of H3K27me3 was significantly more common in high-grade cases (p = 0.006). The expression of H3K27me3 was significantly associated with lamina propria (p = 0.01) and deep muscle invasion (p = 0.007). EZH2 showed a significantly higher expression in the high-grade invasive areas as compared to the high-grade non-invasive areas of the same tumor (p = 0.03). Conclusions: This study establishes an important role of the key epigenetic regulators EZH2 and H3K27me3 in the pathobiology of urothelial carcinomas. Strong expression of EZH2 and weak expression of H3K27me3 are associated with higher grade, proliferative index and invasive behavior.

Guadalein Tanunliong, Aaron C. Liu, Samantha Kaweski et al.

BackgroundOlder adults have been disproportionately affected during the SARS-CoV-2 pandemic, including higher risk of severe disease and long-COVID. Prior exposure to endemic human coronaviruses (HCoV) may modulate the response to SARS-CoV-2 infection and contribute to age-related observations. We hypothesized that cross-reactive antibodies to SARS-CoV-2 are associated with antibodies to HCoV and that both increase with age.MethodsTo assess SARS-CoV-2 unexposed individuals, we drew upon archived anonymized residual sero-surveys conducted in British Columbia (BC), Canada, including before SARS-CoV-2 emergence (May, 2013) and before widespread community circulation in BC (May, 2020). Fifty sera, sex-balanced per ten-year age band, were sought among individuals ≤10 to ≥80 years old, supplemented as indicated by sera from March and September 2020. Sera were tested on the Meso Scale Diagnostics (MSD) electrochemiluminescent multiplex immunoassay to quantify IgG antibody against the Spike proteins of HCoV, including alpha (HCoV-229E, HCoV-NL63) and beta (HCoV-HKU1, HCoV-OC43) viruses, and the 2003 epidemic beta coronavirus, SARS-CoV-1. Cross-reactive antibodies to Spike, Nucleocapsid, and the Receptor Binding Domain (RBD) of SARS-CoV-2 were similarly measured, with SARS-CoV-2 sero-positivity overall defined by positivity on ≥2 targets.ResultsSamples included 407 sera from 2013, of which 17 were children ≤10 years. The 2020 samples included 488 sera, of which 88 were children ≤10 years. Anti-Spike antibodies to all four endemic HCoV were acquired by 10 years of age. There were 20/407 (5%) sera in 2013 and 8/488 (2%) in 2020 that were considered sero-positive for SARS-CoV-2 based on MSD testing. Of note, antibody to the single SARS-CoV-2 RBD target was detected in 329/407 (81%) of 2013 sera and 91/488 (19%) of 2020 sera. Among the SARS-CoV-2 overall sero-negative population, age was correlated with anti-HCoV antibody levels and these, notably 229E and HKU1, were correlated with cross-reactive anti-SARS-CoV-2 RBD titres. SARS-CoV-2 overall sero-positive individuals showed higher titres to HCoV more generally.ConclusionMost people have an HCoV priming exposure by 10 years of age and IgG levels are stable thereafter. Anti-HCoV antibodies can cross-react with SARS-CoV-2 epitopes. These immunological interactions warrant further investigation with respect to their implications for COVID-19 clinical outcomes.

Yao Su, Yao Su, Jianyang Liu et al.

Mumps, a disease caused by the mumps virus (MuV), has been spread widely across the world, especially among children and adolescents. Recent frequent local mumps outbreaks were reported worldwide, which may be caused by the decline in the neutralization ability of the existing attenuated live mumps vaccines against circulating MuV strains which were different from the genotype A or B vaccine strains. There is an urgent need to understand the genotypes of MuV strains currently circulated globally and in China. The gene sequences of MuV strains circulated globally were collected and phylogenetic trees were constructed using different strategies. The results showed that the MuV strains previously circulated globally were predominantly genotype G, while genotype F was predominantly circulated in China, followed by genotype G. The molecular evolution of genotype F MuV strains circulated in China is at a low genetic mutation rate, and the analysis of population dynamics pattern indicates that the incidence of genotype F mumps in China showed a rebound trend. These findings provide a basis for the selection or design of vaccine strains, and the decision of the evaluation strains for immunogenicity and protective efficacy, which laid the foundation for the research and development, as well as the application of next-generation MuV vaccines.

W. F. Harrigan, M. McCance

Carmen Espinosa, Carmen Espinosa, Meritxell Abril et al.

In recent decades, human activity coupled with climate change has led to a deterioration in the quality of surface freshwater. This has been related to an increase in the appearance of algal blooms, which can produce organic compounds that can be toxic or can affect the organoleptic characteristics of the water, such as its taste and odor. Among these latter compounds is geosmin, a metabolite produced by certain cyanobacteria that confers an earthy taste to water and which can be detected by humans at very low concentrations (nanogram per liter). The difficulty and cost of both monitoring the presence of this compound and its treatment is a problem for drinking water treatment companies, as the appearance of geosmin affects consumer confidence in the quality of the drinking water they supply. In this field study, the evaluation of four sampling sites with different physicochemical conditions located in the upper part of the Ter River basin, a Mediterranean river located in Catalonia (NE Spain), has been carried out, with the aim of identifying the main triggers of geosmin episodes. The results, obtained from 1 year of sampling, have made it possible to find out that: (i) land uses with a higher percentage of agricultural and industrial activity are related to high nutrient conditions in river water, (ii) these higher nutrient concentrations favor the development of benthic cyanobacteria, (iii) in late winter–early spring, when these cyanobacteria are subjected to both an imbalance of the dissolved inorganic nitrogen and soluble reactive phosphorus ratio, guided by a phosphorus concentration increase, and to cold–mild temperatures close to 10°C, they produce and release geosmin, and (iv) 1–2 weeks after cyanobacteria reach a high relative presence in the whole biofilm, an increase in geosmin concentration in water is observed, probably associated with the cyanobacteria detachment from cobbles and consequent cell lysis. These results could serve as a guide for drinking water treatment companies, indicating under what conditions they can expect the appearance of geosmin episodes and implement the appropriate treatment before it reaches consumers’ tap.

Satoshi Ikegame, Mohammed N. A. Siddiquey, Chuan-Tien Hung et al.

Here, the authors characterize the neutralization capacity of post-Sputnik V vaccination sera against SARS-CoV-2 variants of concern B.1.1.7 (alpha) and B.1.351 (beta), showing the latter to exhibit resistance to neutralization in vitro.

W. E. Moore

Toni Glymph