Rapid detection of bacterial infections using nanotechnology-based point-of-care sensor with Raman spectroscopy

Background: Mass gathering is a risk factor for infectious diseases transmission. Therefore, rapid detection of infections is highly desirable. The current gold standard approach to detect bacterial infections in clinical samples (biological fluids) requires three days of bacterial culture to obtain the diagnosis and antibiotic sensitivity results1. This approach, although very accurate results in considerable delay in initiating proper treatment which increases the transmission of infection, mainly hospital-acquired infections. Therefore, rapid detection of infection would lead to rapid clinical interventions, which mitigate the spread of infection and support antibiotic stewardship consequently reducing the burden of hospital-acquired infections. The goal of this research is to develop a highly innovative sensor (point-of-care device) for rapid detection of bacterial infections in biological fluids. This project will also focus on identifying unique SERS spectra of bacterial infections commonly associated with mass gathering and early detection of antibiotic resistant bacteria. Methods: The proposed biosensor is a culture-free diagnostic method utilizing nanotechnology-based fabricated silver nanorod arrays (AgNR) as a substrate for the Surface Enhanced Raman Spectroscopy. Results: We reported the proof-of-concept study using this novel SERS-based diagnostic where we showed that rapid detection of bacterial biomarkers in sputum and exhaled breath condensates (EBC) from patients with cystic fibrosis2,3. We further identified unique SERS spectra of various bacterial siderophores and small molecule metabolites. Conclusion: This method is highly sensitive, fast, cheap, and can be implemented at the bedside using a portable (hand-held) Raman spectroscope.qscienc

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, [superscript 6m]A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(G[subscript PS] [superscript 6m]A) dinucleotides in the G[subscript PS] [superscript 6m]AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(G[subscript PS] A) motifs per genome, with [superscript 6m]A arising from a yet-to-be-identified methyltransferase. To further explore PT and 6m A in another consensus sequence, G[subscript PS] [superscript 6m]ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G[subscript PS] ATC) and Dam methyltransferase from E. coli DH10B ( [superscript 6m] A in G [superscript 6m] ATC). Based on this model, in vitro studies revealed reduced Dam activity in G PS ATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA revealed [superscript 6m] A in all 2,058 G[subscript PS] ATC sites (5% of 37,698 total GATC sites). This model system also revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited to discover that [superscript 6m] A can substitute for PT to confer resistance to restriction by the DndFGH system. These results point to complex but unappreciated interactions between DNA modification systems and raise the possibility of coevolution of interacting systems to facilitate the function of each

Prognostic Value of CD44 and Its Isoforms in Advanced Cancer: A Systematic Meta-Analysis With Trial Sequential Analysis

Objective: Cancer stem cell marker CD44 and its variant isoforms (CD44v) may be correlated with tumor growth, metastasis, and chemo-radiotherapy resistance. However, the prognostic power of CD44 and CD44v in advanced cancer remains controversial. Therefore, the purpose of our study was to generalize the prognostic significance of these cancer stem cell markers in advanced cancer patients.Methods: Hazard ratios (HRs) with 95% confidence intervals (95% CIs) were calculated from multivariable analysis to assess the associations among CD44, CD44v6, and CD44v9 positivity and overall survival (OS), disease-free survival (DFS), progression-free survival (PFS), cancer-specific survival (CSS), and recurrence-free survival (RFS). Trial sequential analysis (TSA) was also conducted.Results: We included 15 articles that reported on 1,201 patients with advanced cancer (CD44: nine studies with 796 cases, CD44v6: three studies with 143 cases, and CD44v9: three studies with 262 cases). CD44 expression was slightly linked to worse OS (HR = 2.03, P = 0.027), but there was no correlation between CD44 expression and DFS, RFS, or PFS. Stratified analysis showed that CD44 expression was not correlated with OS at ≥5 years or OS in patients receiving adjuvant therapy. CD44v6 expression was not associated with OS. CD44v9 expression was closely associated with poor 5-years CSS in patients treated with chemo/radiotherapy (HR = 3.62, P < 0.001). However, TSA suggested that additional trials were needed to confirm these conclusions.Conclusions: CD44 or CD44v9 might be novel therapeutic targets for improving the treatment of advanced cancer patients. Additional prospective clinical trials are strongly needed across different cancer types

Reactive Oxygen Species Released from Hypoxic Hepatocytes Regulates MMP-2 Expression in Hepatic Stellate Cells

Hypoxia is a common environmental stress factor and is associated with fibrogenesis. Matrix metalloproteinase-2 (MMP-2), produced by hepatic stellate cells (HSCs), plays an important role in liver fibrogenesis. However, inconsistent results have been reported on the impact of hypoxia on MMP-2 expression and activity in HSCs. We speculated that cell–cell interaction is involved in the regulation of MMP-2 expression and activity at low oxygen level in vivo. Therefore, in this report we investigated the mechanism by which hypoxic hepatocytes regulates MMP-2 expression in HSCs. Our results showed that the conditioned medium from hypoxia-treated rat hepatocytes strongly induced the expression of MMP-2 mRNA and protein in rat HSC-T6 cells. Reduced glutathione neutralized ROS released from hypoxic hepatocytes, leading to reduced MMP-2 expression in HSC-T6 cells. In addition, phospho-IκB-α protein level was increased in HSC-T6 cells treated with hypoxia conditioned medium, and NF-κB signaling inhibitor inhibited MMP-2 expression in HSC-T6 cells. Taken together, our data suggest that ROS is an important factor released by hypoxic hepatocytes to regulate MMP-2 expression in HSCs, and NF-κB signaling is crucially involved in ROS-induced MMP-2 expression in HSCs. Our findings suggest that strategies aimed at antagonizing the generation of ROS in hypoxic hepatocytes and inhibiting NF-κB signaling in HSCs may represent novel therapeutic options for liver fibrosis

Twenty Novel Disease Group-Specific and 12 New Shared Macrophage Pathways in Eight Groups of 34 Diseases Including 24 Inflammatory Organ Diseases and 10 Types of Tumors.

The mechanisms underlying pathophysiological regulation of tissue macrophage (Mφ) subsets remain poorly understood. From the expression of 207 Mφ genes comprising 31 markers for 10 subsets, 45 transcription factors (TFs), 56 immunometabolism enzymes, 23 trained immunity (innate immune memory) enzymes, and 52 other genes in microarray data, we made the following findings. (1) When 34 inflammation diseases and tumor types were grouped into eight categories, there was differential expression of the 31 Mφ markers and 45 Mφ TFs, highlighted by 12 shared and 20 group-specific disease pathways. (2) Mφ in lung, liver, spleen, and intestine (LLSI-Mφ) express higher M1 Mφ markers than lean adipose tissue Mφ (ATMφ) physiologically. (3) Pro-adipogenic TFs C/EBPα and PPARγ and proinflammatory adipokine leptin upregulate the expression of M1 Mφ markers. (4) Among 10 immune checkpoint receptors (ICRs), LLSI-Mφ and bone marrow (BM) Mφ express higher levels of CD274 (PDL-1) than ATMφ, presumably to counteract the M1 dominant status via its reverse signaling behavior. (5) Among 24 intercellular communication exosome mediators, LLSI- and BM- Mφ prefer to use RAB27A and STX3 than RAB31 and YKT6, suggesting new inflammatory exosome mediators for propagating inflammation. (6) Mφ in peritoneal tissue and LLSI-Mφ upregulate higher levels of immunometabolism enzymes than does ATMφ. (7) Mφ from peritoneum and LLSI-Mφ upregulate more trained immunity enzyme genes than does ATMφ. Our results suggest that multiple new mechanisms including the cell surface, intracellular immunometabolism, trained immunity, and TFs may be responsible for disease group-specific and shared pathways. Our findings have provided novel insights on the pathophysiological regulation of tissue Mφ, the disease group-specific and shared pathways of Mφ, and novel therapeutic targets for cancers and inflammations

Analysis of Fungal Diversity before and after Discoloration of Rubberwood in Xishuangbanna

The discoloration problem of rubber wood caused by the discoloration fungi has caused the degradation of rubber wood and greatly reduced its economic value, and the prevention and control of rubber wood discoloration have become the top priority of basic research on rubber wood protection and modification. To determine the fungal community diversity and dominant groups before and after discoloration of rubber wood, nine rubber wood samples were subjected to ITS sequencing using Illumina high-throughput sequencing technology. The results showed that the detected fungal communities comprised 5 phyla, 18 classes, 58 orders, 137 families, 218 genera, and 297 species. Discoloration of rubber wood is not caused by a single species, with the dominant genera for discolored rubber wood being Huntiella, Ceratocystis, and Acremonium and for undiscolored rubber wood, Phomopsis. Furthermore, the diversity, uniformity of species distribution, and richness of discolored rubber wood were found to be higher than those of undiscolored rubber wood. In conclusion, understanding the change trends in the structure of these fungal communities is essential for studying the biological control of rubberwood discoloration