Enhanced phylogenetic insights into the microbiome of chronic rhinosinusitis through the novel application of long read 16S rRNA gene amplicon sequencing.

INTRODUCTION: 16S rRNA next generation sequencing (NGS) has been the de facto standard of microbiome profiling. A limitation of this technology is the inability to accurately assign taxonomy to a species order. Long read 16S sequencing platforms, including Oxford Nanopore Technologies (ONT), have the potential to overcome this limitation. The paranasal sinuses are an ideal niche to apply this technology, being a low biomass environment where bacteria are implicated in disease propagation. Characterising the microbiome to a species order may offer new pathophysiological insights. METHODOLOGY: Cohort series comparing ONT and NGS biological conclusions. Swabs obtained endoscopically from the middle meatus of 61 CRSwNP patients underwent DNA extraction, amplification and dual sequencing (Illumina Miseq (NGS) and ONT GridION). Agreement, relative abundance, prevalence, and culture correlations were compared. RESULTS: Mean microbiome agreement between sequencers was 61.4%. Mean abundance correlations were strongest at a familial/genus order and declined at a species order where NGS lacked resolution. The most significant discrepancies applied to Corynebacterium and Cutibacterium, which were estimated in lower abundance by ONT. ONT accurately identified 84.2% of cultured species, which was significantly higher than NGS. CONCLUSIONS: ONT demonstrated superior resolution and culture correlations to NGS, but underestimated core sinonasal taxa. Future application and optimisation of this technology can advance our understanding of the sinonasal microenvironment.

Response of varied rice genotypes on cell membrane stability, defense system, physio-morphological traits and yield under transplanting and aerobic cultivation.

Aerobic rice cultivation progresses water productivity, and it can save almost 50% of irrigation water compared to lowland rice with the appropriate development of genotypes and management practices. Two field trials were conducted during 2020, and 2021 seasons to determine the validation of different rice varieties under aerobic cultivation based on their plant defense system, physio-morphological traits, stress indices, grain yield, and water productivity. The experiments were designed in a split-plot design with four replications. Two planting methods, transplanting and aerobic cultivation, were denoted as the main plots, and ten rice genotypes were distributed in the subplots. The results revealed that the planting method varied significantly in all measured parameters. The transplanting method with well watering had the highest value of all measured parameters except leaf rolling, membrane stability index, antioxidant, proline, and the number of unfilled grains. EHR1, Giza179 and GZ9399 as well as A22 genotypes a chief more antioxidant defense system that operated under aerobic conditions. Giza179, EHR1, GZ9399, and Giza178 showed high cell membrane stability and subsequently high validation under such conditions, and also showed efficiency in decreasing water consumption and improving water use efficiency. In conclusion, this study proves that Giza179, EHR1, GZ9399, Giza178, and A22 are valid genotypes for aerobic conditions.

Influence of Nano Silicon and Nano Selenium on Root Characters, Growth, Ion Selectivity, Yield, and Yield Components of Rice (Oryza sativa L.) under Salinity Conditions.

Rice production under salinity stress is a critical challenge facing many countries, particularly those in arid and semi-arid regions. This challenge could be handled by applying novel approaches to overcome yield limiting factors and improve resource use efficiency. The usage of nanoparticles (NPs) could be a beneficial approach to managing the growing problem of soil salinity. The aim of our study was to investigate the advantageous effects of soaking and foliar application of silicon (Si) and selenium (Se), (NPs-Si at 12.5 mg L-1 and NPs-Se at 6.25 mg L-1) on root characteristics, moropho-physiological traits, and yields of two rice varieties (i.e., Giza 177 as a salt sensitive and Giza 178 as a salt tolerant) grown in saline soil compared to untreated plants (control treatment). Results showed that soaking NPs-Se resulted in the highest value of root thickness for Giza 178 (0.90 mm, 0.95 mm) and root volume (153.30 cm3, 154.30 cm3), while Giza 177 recorded 0.83 mm, 0.81 mm for root thickness and 143.30 cm3, 141.30 cm3 for root volume in the 2018 and 2019 seasons, respectively. Soaking NPs-Se, NPs-Si and foliar application of NPs-Se at BT resulted in the highest relative water content and dry matter, while foliar application of NPs-Si at BT gave the highest leaf area index of rice plants compared to the other treatments. Giza 178 (i.e., salt tolerant variety) significantly surpassed Giza 177 (i.e., salt sensitive variety) in the main yield components such as panicle number and filled grains/ panicle, while Giza 177 significantly exceeded Giza 178 in the panicle weight, 1000-grain weight, and unfilled grains number/ panicle. Soaking NPs-Se and foliar application of NPs-Si at BT resulted in the highest grain yield of 5.41 and 5.34 t ha-1 during 2018 and 5.00 and 4.91 t ha-1 during 2019, respectively. The salt sensitive variety (Giza 177) had the highest Na+ leaf content and Na+/K+ ratio as well as the lowest K+ leaf content during both seasons. Applying nano nutrients such as NPs-Si and NPs-Se improved the yield components of the salt sensitive variety (Giza 177) by enhancing its ion selectivity. Both NPs-Si and NPs-Se had almost the same mode of action to mitigate the harmful salinity and enhance plant growth, and subsequently improved the grain yield. In summary, the application of NPs-Si and NPs-Se is recommended as a result of their positive influence on rice growth and yield as well as minimizing the negative effects of salt stress.

Differential molecular and hormonal changes in oocytes, granulosa cells and follicular fluid of pregnant and non-pregnant camels.

This study aimed to compare the expression of genes regulating follicles development, survival and steroid hormones secretion in oocytes and granulosa cells (GCs) and study the correlation between their expression and follicular fluid (FF) levels of progesterone (P4) in pregnant and non-pregnant camels. In total, 138 ovarian pairs from slaughtered camels were used. Gene expression and hormonal assay were determined using real-time polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA), respectively. The obtained results revealed that the number of follicles (3-8 mm) was significantly (P < 0.05) lower in pregnant, compared with non-pregnant, camels. P4 level in the FF was significantly (P < 0.05) higher in pregnant, compared with non-pregnant, camels. However, no significant (P > 0.05) difference was noticed in the oestradiol (E2) level. STAR, PTEN, IGF1 and BCL2 mRNA levels were significantly higher in GCs and significantly lower in oocytes of pregnant, compared with non-pregnant, camels. However, follicle-stimulating hormone receptor (FSHR) mRNA level was significantly lower in GCs and oocytes, and the BMP15 mRNA level was significantly lower in oocytes of pregnant, compared with non-pregnant, camels. P4 level in FF was positively correlated with STAR, PTEN, IGF1 and BCL2 mRNA levels in GCs and negatively correlated with BMP15 mRNA levels in oocytes and FSHR mRNA levels in GCs and oocytes of pregnant camels. It could be concluded that pregnancy-induced variations in oocytes and GC expression of BMP15, IGF1, FSHR, STAR, BCL2, and PTEN genes might be associated with a decrease in the number of follicles and an increase in the FF level of P4.

The clinical outcomes of medical therapies in chronic rhinosinusitis are independent of microbiomic outcomes: a double-blinded, randomised placebo-controlled trial.

BACKGROUND: Oral and topical corticosteroids, and antibiotics form the mainstay medical treatment of chronic rhinosinusitis (CRS). Clinical outcomes vary depending on the chosen therapy, resident microbiome and disease phenotype. We conducted a double- blinded, placebo-controlled Randomised Controlled Trial (RCT) to investigate effects of medical therapy on clinical outcomes and associated microbiome shifts. METHODOLOGY: Fifty eligible patients (CRS with and without polyps) were treated for 3 weeks after randomisation into 3 arms: na- mely oral prednisolone, topical budesonide irrigations and oral doxycycline; each with appropriate placebo. Clinical scoring and microbiome swabs were performed on enrolment, at treatment completion and 3-weeks post treatment completion. Microbiome analysis was performed using the llumina-MiSeq next generation sequencing platform and QIME-2 pipeline. RESULTS: Significant improvement in clinical scores was observed in prednisolone and budesonide arms at treatment completion but not with antibiotic. Sub-group analysis showed more pronounced effects in patients with polyposis. Corynebacterium and Staphylococcus species predominated, with variable bacterial relative abundance among different treatments at all time-points. The only significant microbiome finding was an increase in bacterial diversity in topical budesonide group immediately after treatment, which returned to baseline 3-weeks post treatment. CONCLUSION: Clinical improvement was significant with oral and topical steroid but not empirical antibiotic. Although there were some associated microbiome changes with the various treatments, we could not ascertain the consistency of these and whether they do have a clinical significance at all.

Scoping review of chronic rhinosinusitis proteomics.

BACKGROUND: Progressive advances in proteomic technology has improved our understanding of the chronic rhinosinusitis (CRS) pathogenesis and endotypes. This scoping review aims to present a comprehensive and descriptive analysis of nasal mucosa and mucus proteome of CRS patients. METHODOLOGY: Studies investigating the proteome of nasal mucosa and mucus from healthy and CRS patients via mass spectrometry were included. Critical appraisal of methodological quality was conducted with extraction of protein lists. Gene set enrichment analysis (GSEA) was performed on studies including CRS patients. RESULTS: 2962 proteins were identified in the 21 studies included in this review. Eleven studies investigated the nasal mucus proteome and ten studies investigated the nasal mucosa proteome. Studies demonstrated heterogeneity in patients, sampling and mass spectrometry methodology. Samples from CRS patients suggested a trend in enrichment of immune system and programmed cell death pathways. Increased expression of proteins involved in cellular components including the cytoskeleton and adherens junctions was also present in CRS. CONCLUSIONS: Alterations in the healthy sinonasal proteome may lead to the increased immunological, metabolic and tissue remodeling processes observed in CRS. However, it is difficult to draw significant conclusions from the GSEA due to the heterogeneity present in the limited literature available. These findings allow us to direct further research to better understand CRS pathogenesis and its endotypes.

The global transcriptomic signature in sinonasal tissues reveals roles for tissue type and chronic rhinosinusitis disease phenotype.

BACKGROUND: RNA sequencing (RNA-Seq) allows the characterization of a global transcriptomic signature in a least-biased fashion, but few studies have applied this method to investigate the pathophysiology of CRS. METHODS: We collected mucosal tissue samples from 6 CRS without nasal polyps (CRSsNP), 6 CRS with nasal polyps (CRSwNP), and 6 control patients. Additional matched polyp samples were collected from the 6 CRSwNP patients. RNA was extracted and sequenced on the Illumina HiSeq-2500. Differential gene expression and pathway analyses were performed. RESULTS: CRSsNP showed evidence of upregulated interferon-mediated immunity, MHC-class-I mediated antigen presentation, CXCR3 binding, neutrophil chemotaxis and degranulation, and potential downregulation of genes related to cilia movement and production. CRSwNP polyp tissue showed upregulation of B-cell mediated immune responses, but reduced expression of genes related to epithelial morphogenesis and haemostasis. Polyps also showed a generalized reduction of positive gene regulation. The sinonasal transcriptomic signature was largely determined by tissue type (polyp versus mucosa) and disease phenotype, with minimal signal originating from the individual patient. CONCLUSION: RNA-Seq is a useful tool to explore the complex pathophysiology of CRS. Our findings stress the importance of tissue selection in molecular research utilizing sinonasal tissue, and demonstrate the limitation of the sNP/wNP paradigm (and the importance of endotyping). On the other hand, classical CRSsNP/wNP disease phenotypes played some role in determining the global transcriptomic signature, and should not be hastily discarded. The value of RNA-Seq-described transcriptomic signatures in exploring endotypes is yet to be explored in future studies.

The persistence of intracellular Staphylococcus aureus in the sinuses: a longitudinal study.

BACKGROUND: Staphylococcus aureus (S. aureus) can reside within the sinonasal mucosa in chronic rhinosinusitis patients and causes recurrent infections. Within the host cell, S. aureus can evade host immune detection enabling its own survival. We hypothesise that S. aureus can persist within the sinonasal epithelium for a prolonged period without immune activation. METHODOLOGY: Patients with chronic rhinosinusitis with nasal polyps (CRSwNP) undergoing two sinus surgeries were included. Immunohistochemistry and Haematoxylin and Eosin stains were used to determine intracellular S. aureus (ICSA) status and inflammatory cell count, respectively. One-way ANOVA and paired t-tests were performed for comparison between ICSA subgroups and within each subgroup, respectively. RESULTS: Histopathological specimens from 34 patients (68 procedures) were included. ICSA positivity (ICSA+) was seen in 43 specimens (63.2%) from 26 (76%) patients. 18 (52.9%) of those were ICSA+ in both operations while 8 (23.5%) patients were ICSA+ in only one of the operations. 8 (23.5%) patients were ICSA negative in both operations. There was no difference in the number of eosinophils, lymphocyte and neutrophils between ICSA subgroups. CONCLUSIONS: This study demonstrated that S. aureus is found intracellularly within CRSwNP tissue at multiple time points without an increase in the number of eosinophils, lymphocytes and neutrophils. This finding supports our hypothesis that ICSA is able to escape from host detection and resides within the sinonasal mucosa despite intense treatment.

Association between group 2 innate lymphoid cells enrichment, nasal polyps and allergy in chronic rhinosinusitis.

BACKGROUND: Group 2 innate lymphoid cells (ILC2s) were shown to be involved in the initiation and coordination of Th2-type immune responses in allergic disease animal models. Recently, ILC2s enrichment was noted in chronic rhinosinusitis (CRS) patients; however, the role of ILC2s in coordinating the Th2 response in CRS remains to be elucidated. Here, we characterize the ILC2 compartment in CRS by investigating the correlations between ILC2s, Th2 cells and Th2 cytokines expression in CRS patients. METHODS: We used flow cytometric analysis of sinonasal mucosal tissues of 29 CRS patients and 5 controls to quantify ILC2s and Th2 cells. Messenger RNA expression levels of IL-5, IL-13, IL-25, IL-33, TSLP and GATA3 were determined using qRT-PCR. RESULTS: ILC2s were significantly enriched in nasal polyps (CRSwNP) patients. Multivariate linear regression showed a significant positive association of ILC2 numbers with CRSwNP and allergic CRS and a negative association with the number of previous endoscopic sinus surgeries. Group 2 innate lymphoid cell numbers significantly correlated with Th2 cell frequencies. Messenger RNA expression levels of IL-5 and IL-13 were increased in CRSwNP compared with controls, while mRNA levels of IL-25 and GATA3 were significantly reduced. CONCLUSIONS: Our results characterize the complex interactions between ILC2s and other Th2 response elements in the context of CRS and suggest that ILC2 enrichment occurs in CRSwNP and in allergic CRS patients.

New type of left ventricular rupture during redo mitral valve replacement. A case report.

We report the case of a 41 years old woman who presented with massive bleeding after redo mitral valve replacement. A Left ventricular rupture, different from the three known types of wall rupture was hardly identified and controlled with extreme difficulty. The patient died eight days postoperatively due to disseminated intravascular coagulopathy. Retrospective analysis of the Echocardiographic examination was highly suggestive of abnormal position of the previously implanted mitral valve bioprosthesis with left ventricular outflow tract obstruction and weakness of the posterior wall of the left ventricular outflow tract.

Immunohistochemical expression of CD95 (Fas), c-myc and epidermal growth factor receptor in hepatitis C virus infection, cirrhotic liver disease and hepatocellular carcinoma.

Gene product expression in normal and chronic hepatitis C virus infection was determined in an attempt to improve our understanding of the molecular events leading to the development of cirrhosis and liver carcinoma. Activation of CD95 (Fas) causes apoptosis of cells and liver failure in mice and has been associated with human liver disorders. c-myc is involved in cell proliferation and EGFR in regeneration of cells. The material of the current study included 50 cases of chronic hepatitis C (CHC) (and negative hepatitis B virus infection), 29 cases of liver cirrhosis and HCV (LC), and 19 cases of hepatocellular carcinoma and HCV (HCC) admitted to the Theodor Bilharz Research Institute (TBRI) during the years 2003-2004. Ten wedge liver biopsies - taken during laparoscopic cholecystectomy - were included in the study as normal controls. Laboratory investigations, including liver function tests, serological markers for viral hepatitis and serum alpha fetoprotein level (alpha-FP), were determined for all cases. Histopathological study and immunohistochemistry using monoclonal antibodies for CD95, c-myc and EGFR were also done. In CHC cases, the histological activity index (HAI) revealed more expression of Fas antigen in liver tissues with active inflammation than in those without active inflammation (p < 0.01). EGFR and c-myc act synergistically in liver tumorigenesis. Upregulation of Fas in chronic hepatitis C infection and of c-myc & EGFR in malignant transformation was concluded from this study. c-myc expression may obstruct the induction of apoptosis of HCC cells and lead to uncontrolled cell growth.