Diverse Body Fluids Research Articles

Detection of Free-Living Amoeba in a tertiary care hospital

This study aims to investigate the presence of Free-Living Amoebae (FLA), particularly Acanthamoeba spp., in diverse water systems and body fluids within a hospital. Water and body fluid samples were collected from various locations. Cultivation of FLA was performed using Non-Nutrient Agar (NNA) culture with Escherichia coli, and microscopic observations after staining. Microscopic observations revealed the presence of Acanthamoeba spp. in pre-dialysis tank water and dental flush water samples. The identification of Acanthamoeba in specific water sources underscores the importance of continuous monitoring and preventive strategies to mitigate potential health risks.

Diagnosis of malignant body fluids via cancer-universal methylation in cell-free DNA.

BACKGROUNDDifferentiating malignant from nonmalignant body fluids remains a clinical challenge because of the unsatisfying performance of conventional cytology. We aimed to improve the sensitivity and ubiquity of cancer cell detection by assaying universal cancer-only methylation (UCOM) markers in supernatant cell-free DNA (cfDNA).METHODSAn observational prospective cohort including 1,321 nonmalignant and malignant body fluids of multiple cancers was used to develop and validate a cfDNA UCOM methylation diagnostic assay. All samples were divided into 2 portions for cytology and supernatant cfDNA methylation analysis.RESULTSThe significant hypermethylation of a potentially novel UCOM marker, TAGMe, together with the formerly reported PCDHGB7, was identified in the cfDNA of malignant body fluid samples. The combined model, cell-free cancer-universal methylation (CUE), was developed and validated in a prospective multicancer cohort with markedly elevated sensitivity and specificity, and was further verified in a set containing additional types of malignant body fluids and metastases. In addition, it remained hypersensitive in detecting cancer cells in cytologically negative malignant samples.CONCLUSIONcfDNA methylation markers are robust in detecting tumor cells and are applicable to diverse body fluids and tumor types, providing a feasible complement to current cytology-based diagnostic analyses.TRIAL REGISTRATIONThis study was registered at Chictr.org.cn (ChiCTR2200060532).FUNDINGNational Natural Science Foundation of China (32270645, 31872814, 32000505, 82170088), the National Key R&D Program of Ningxia Hui Autonomous region (2022BEG01003), Shanghai Municipal Key Clinical Specialty (shslczdzk02201), Science and Technology Commission of Shanghai Municipality (20DZ2261200, 20DZ2254400), and Major Special Projects of Basic Research of Shanghai Science and Technology Commission (18JC1411101).

Assessment of the Specificity and Stability of Micro-RNAs as a Forensic Gene Marker

Abstract Background: Forensic investigations depend on bodily fluid analysis to identify the perpetrators. Identifying perpetrators requires knowledge about suspects’ body fluids. Due to their durability and tissue-specific expression patterns, miRNAs may be forensic indicators. However, miRNA expression patterns in various bodily fluids are seldom compared. This study examined miR-372, miR-135p, miR-124-3p, miR-16, and miR-10b expression in seminal fluids, blood stains, and vaginal secretions using quantitative PCR using SNORD-47 as a reference gene. This research compared miRNA expression levels in diverse body fluids to assess their potential as forensic biomarkers. MicroRNAs were isolated from forensic blood, seminal fluids, and vaginal mixed stains. Methods: Quantitative PCR measured miR-372, miR-135p, miR-124-3p, miR-16, and miR-10b gene expression. Normalization utilized SNORD-47. These miRNAs were compared in various bodily fluids. Results: The analysis of the results revealed that three bodily fluids have unique miRNA expression patterns. Seminal fluids expressed considerably more miR-135b and miR-10b than vaginal secretions. Vaginal fluids expressed more miR-372 and miR-124-3p than seminal fluids. Blood fluids expressed more miR-126 and miR-16 than seminal and vaginal fluids. Conclusion: MiR-126, miR-16, miR-372, and miR-124-3p were considerably more significant than SNORD-47 in blood, vaginal secretions, and seminal fluids.

Recycling COVID-19 health care wastes in bitumen modification: a case of disposable medical gloves.

Disposable medical gloves (DMGs) have long been used to mitigate the risk of direct exposure to diverse microorganisms and body fluids; hence, they are a critical weapon to protect patients and healthcare staff from infectious diseases. Measures to control the spread of COVID-19 have sparked the production of an excessive number of DMGs, most of which are eventually being disposed of in landfills. Untreated DMGs in landfills do not only pose a direct risk of transmitting coronavirus and other pathological germs but also pollute air, water, and soil dramatically. As a healthier alternative, recycling discarded polymer-rich DMGs into bitumen modification is considered to be a prospective waste management strategy applicable to the asphalt pavement industry. In this study, this conjecture is tested by examining two common DMGs - latex gloves and vinyl gloves - at four different percentages (1%, 2%, 3%, and 4% by weight). The morphological characteristics of DMG-modified specimens were inspected by using a high-definition scanning electron microscope (SEM) equipped with an energy dispersive X-ray analyzer (EDX). A wide range of laboratory tests including penetration, softening point temperature, ductility, and elastic recovery were undertaken to evaluate the impact of waste gloves on the conventional engineering properties of bitumen. Moreover, viscoelastic behavior and modification processing were studied by conducting the dynamic shear rheometer (DSR) test and the Fourier transform infrared spectroscopy (FTIR) analysis. Test results have revealed the outstanding potential of recycled DMG waste for modifying neat asphalt binder. More specifically, bitumens modified with 4% latex glove and 3% vinyl glove were seen as capable of superiorly withstanding permanent deformations caused by heavy axle loads at high service temperatures. Furthermore, it has been shown that 1.2 tons of modified binder would embed approximately 4000 pairs of recycled DMGs. This study shows that DMG waste can be used as a viable modifier, which would help open a new avenue for mitigating the environmental pollution arising from the COVID-19 pandemic.

Textile One-Component Organic Electrochemical Sensor for Near-Body Applications.

The need for more efficient health services and the trend of a healthy lifestyle pushes the development of smart textiles. Since textiles have always been an object of everyday life, smart textiles promise an extensive user acceptance. Thereby, the manufacture of electrical components based on textile materials is of great interest for applications as biosensors. Organic electrochemical transistors (OECTs) are often used as biosensors for the detection of saline content, adrenaline, glucose, etc., in diverse body fluids. Textile-based OECTs are mostly prepared by combining a liquid electrolyte solution with two separate electro-active yarns that must be precisely arranged in a textile structure. Herein, on the other hand, a biosensor based on a textile single-component organic electrochemical transistor with a hardened electrolyte was developed by common textile technologies such as impregnation and laminating. Its working principle was demonstrated by showing that the herein-produced transistor functions similarly to a switch or an amplifier and that it is able to detect ionic analytes of a saline solution. These findings support the idea of using this new device layout of textile-based OECTs as biosensors in near-body applications, though future work must be carried out to ensure reproducibility and selectivity, and to achieve an increased level of textile integration.

ExRNAdisease: An extracellular RNA transcriptome atlas in human diseases

Extracellular RNAs (exRNAs) are types of RNAs that present outside of the cells with highly stable features. exRNAs have been shown to play important roles in aiding intercellular communication and regulating cellular processes. In clinical settings, exRNAs have the potential to serve as biomarkers indicating the presence of a disease.Recently, the high-throughput technologies such as RNA sequencing (RNAseq) and microarray have generated abundant exRNA expression data about various diseases. Thus, it is highly desirable to have a comprehensive database for disease-related exRNA transcriptome data detected in diverse body fluids. Here, a total of 88 previously published exRNA transcriptome datasets were collected. We developed a web-accessible database, exRNADisease, which is designed as a central repository for exRNAs from body fluids in human diseases and healthy controls. In the current version, a total of 18,265 samples were collected, which includes 10 body fluids and 78 human disease types. Six different types of RNAs were included (messenger RNAs, circular RNAs, long noncoding RNAs, microRNAs, transfer RNA fragments and PIWI-interacting RNA). Literature is also included to provide the robust evidence about the relationship between exRNAs and diseases. A user-friendly interface was constructed to conveniently search and browse disease-related exRNAs. exRNADisease will become a useful platform to provide genome-wide view of exRNA deregulation in human diseases and help to identify novel biomarkers.Availability and implementation: exRNAdisease can be freely accessible at http://www.origin-gene.cn/database/exRNAdisease/.

Real time imaging of single extracellular vesicle pH regulation in a microfluidic cross-flow filtration platform

Extracellular vesicles (EVs) are cell-derived membranous structures carrying transmembrane proteins and luminal cargo. Their complex cargo requires pH stability in EVs while traversing diverse body fluids. We used a filtration-based platform to capture and stabilize EVs based on their size and studied their pH regulation at the single EV level. Dead-end filtration facilitated EV capture in the pores of an ultrathin (100 nm thick) and nanoporous silicon nitride (NPN) membrane within a custom microfluidic device. Immobilized EVs were rapidly exposed to test solution changes driven across the backside of the membrane using tangential flow without exposing the EVs to fluid shear forces. The epithelial sodium-hydrogen exchanger, NHE1, is a ubiquitous plasma membrane protein tasked with the maintenance of cytoplasmic pH at neutrality. We show that NHE1 identified on the membrane of EVs is functional in the maintenance of pH neutrality within single vesicles. This is the first mechanistic description of EV function on the single vesicle level.

Alpha-synuclein as a biomarker in Parkinson's disease: focus on neural derived extracelluar vesicles.

Alpha-synuclein as a biomarker in Parkinson's disease: focus on neural derived extracelluar vesicles.

ExoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids.

Extracellular vesicles (EVs) are small membranous vesicles that contain an abundant cargo of different RNA species with specialized functions and clinical implications. Here, we introduce an updated online database (http://www.exoRBase.org), exoRBase 2.0, which is a repository of EV long RNAs (termed exLRs) derived from RNA-seq data analyses of diverse human body fluids. In exoRBase 2.0, the number of exLRs has increased to 19 643 messenger RNAs (mRNAs), 15 645 long non-coding RNAs (lncRNAs) and 79 084 circular RNAs (circRNAs) obtained from ∼1000 human blood, urine, cerebrospinal fluid (CSF) and bile samples. Importantly, exoRBase 2.0 not only integrates and compares exLR expression profiles but also visualizes the pathway-level functional changes and the heterogeneity of origins of circulating EVs in the context of different physiological and pathological conditions. Our database provides an attractive platform for the identification of novel exLR signatures from human biofluids that will aid in the discovery of new circulating biomarkers to improve disease diagnosis and therapy.

Nanoconfined 3D redox capacitor-based electrochemical sensor for ultrasensitive monitoring of metabolites in bacterial communication

The ability to monitor metabolites related to cell communication is important for understanding bacterial physiology, identifying bacterial species in a cellular community, and providing insights into the stage of infection. Here, we developed a nanostructured electrochemical sensor comprising a 3D-redox-capacitor-coated electrode, which was prepared by grafting a redox capacitor molecule, catechol/o-quinone, at high density to a chitosan layer. It provided high sensitivity in detecting redox-active bacterial metabolites through a redox cycling reaction in the nanoconfined structures of the electrode. We used it to monitor the secretion of signalling-related metabolites at different growth phases of Pseudomonas aeruginosa. We also used the electrode to detect signalling-related metabolites in diverse simulated body fluids mixed with P. aeruginosa culture. It was able to provide information on bacterial communication and help in sensitive diagnostic monitoring of bacterial infection.

Urinary Alpha1-Microglobulin: A New Predictor for In-Hospital Mortality in Patients with ST-Segment Elevation Myocardial Infarction.

BackgroundAlpha1-microglobulin (A1MG) is a small molecular protein related to oxidation and inflammation. It exists in diverse body fluids, including urine. Results from urine tests are sometimes neglected when predicting in-hospital prognosis. It remains unclear whether urinary A1MG (UA1MG) can predict short-term prognosis of ST-elevated myocardial infarction (STEMI).Material/MethodsA total of 1854 hospitalized patients with acute STEMI were retrospectively enrolled in our study. Medical records were used to obtain patient demographic and clinical information, UA1MG values (which were used to divide patients into groups of low, medium, or high), and other laboratory parameters. Principal clinical outcomes of interest were all-cause in-hospital deaths, cardiac deaths, and major adverse cardiac events (MACEs).ResultsAmong the 1854 enrolled patients, 43 (2.3%) died in the hospital, of which 33 (1.8%) were cardiac deaths. MACEs were noted in 113 patients (6.1%) during hospitalization. The group with the highest UA1MG value showed a significantly higher frequency of in-hospital deaths, cardiac deaths, and MACEs, compared to those of the lowest UA1MG value group (4.4% vs. 1.0%, P<0.001; 3.1% vs. 0.6%, P<0.005; and 8.6% vs. 4.7%, P=0.007, respectively). Multivariate regression analysis revealed that UA1MG levels (odds ratio 1.109, 95% confidence interval (CI) 1.027–1.197, P=0.008) independently predicted all-cause in-hospital mortality. A UA1MG value of 3.23 mg/dL was considered as an optimal cutoff point in STEMI to predict all-cause mortality after receiver operating characteristic curve analysis (area under the curve 0.73, 95% CI 0.65–0.80, P<0.001).ConclusionsThe UA1MG value at hospital admission could be an independent prognostic factor of all-cause in-hospital mortality in patients with STEMI.

Extracellular microRNA 3’ end modification across diverse body fluids

ABSTRACT microRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene regulation. The presence of miRNAs in extracellular biofluids is increasingly recognized. However, most previous characterization of extracellular miRNAs focused on their overall expression levels. Alternative sequence isoforms and modifications of miRNAs were rarely considered in the extracellular space. Here, we developed a highly accurate bioinformatic method, called miNTA, to identify 3’ non-templated additions (NTAs) of miRNAs using small RNA-sequencing data. Using miNTA, we conducted an in-depth analysis of miRNA 3’ NTA profiles in 1047 extracellular RNA-sequencing data sets of 4 types of biofluids. This analysis identified hundreds of miRNAs with 3’ uridylation or adenylation, with the former being more prevalent. Among these miRNAs, up to 53% (22%) had an average 3’ uridylation (adenylation) level of at least 10% in a specific biofluid. Strikingly, we found that 3’ uridylation levels enabled segregation of different types of biofluids, more effectively than overall miRNA expression levels. This observation suggests that 3’ NTA levels possess fluid-specific information relatively robust to batch effects. In addition, we observed that extracellular miRNAs with 3’ uridylations are enriched in processes related to angiogenesis, apoptosis, and inflammatory response, and this type of modification may stabilize base-pairing between miRNAs and their target genes. Together, our study provides a comprehensive landscape of miRNA NTAs in human biofluids, which paves way for further biomarker discoveries. The insights generated in our work built a foundation for future functional, mechanistic, and translational discoveries.

Detection of viral RNA in diverse body fluids in an SFTS patient with encephalopathy, gastrointestinal bleeding and pneumonia: a case report and literature review

BackgroundSevere fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease that commonly has a lethal course caused by the tick-borne Huaiyangshan banyang virus [former SFTS virus (SFTSV)]. The viral load in various body fluids in SFTS patients and the best infection control measure for SFTS patients have not been fully established.Case presentationA 79-year-old man was bitten by a tick while working in the bamboo grove in Nagasaki Prefecture in the southwest part of Japan. Due to the occurrence of impaired consciousness, he was referred to Nagasaki University Hospital for treatment. The serum sample tested positive for SFTSV-RNA in the genome amplification assay, and he was diagnosed with SFTS. Furthermore, SFTSV-RNA was detected from the tick that had bitten the patient. He was treated with multimodal therapy, including platelet transfusion, antimicrobials, antifungals, steroids, and continuous hemodiafiltration. His respiration was assisted with mechanical ventilation. On day 5, taking the day on which he was hospitalized as day 0, serum SFTSV-RNA levels reached a peak and then decreased. However, the cerebrospinal fluid collected on day 13 was positive for SFTSV-RNA. In addition, although serum SFTSV-RNA levels decreased below the detectable level on day 16, he was diagnosed with pneumonia with computed tomography. SFTSV-RNA was detected in the bronchoalveolar lavage fluid on day 21. By day 31, he recovered consciousness completely. The pneumonia improved by day 51, but SFTSV-RNA in the sputum remained positive for approximately 4 months after disease onset. Strict countermeasures against droplet/contact infection were continuously conducted.ConclusionsEven when SFTSV genome levels become undetectable in the serum of SFTS patients in the convalescent phase, the virus genome remains in body fluids and tissues. It may be possible that body fluids such as respiratory excretions become a source of infection to others; thus, careful infection control management is needed.

Host derived exosomes-pathogens interactions: Potential functions of exosomes in pathogen infection.

As bilayer vesicular corpuscles secreted by different living cells, exosomes can be found in diverse body fluids and are rich in lipids, proteins, nucleic acids and other complicated components. Exosomes offer a potent mechanism for participation in intercellular transportation, such as targeted transmission of inclusions to nearby or distant cells or tissues, and assistance in intercellular information communication to change physiological functions and properties. Exosomes take part in antigen presentation for activation of immune cells and stimulate the release of inflammatory factors and the expression of immune molecules, thus modulating the immune responses of host cells. In the microbial infection of host cells, exosomes can strengthen innate and specific immune responses and thereby the immune resistance against the invading microbes through natural killer cells, macrophages and activated T cells by the presentation of pathogens including viral factors and bacteria, but exosomes are also capable of immunosuppression during pathogens infection. Exosomes are considerably valuable in research and clinical defense of microbial infection, given their biological activities in intercellular transportation, information communication and cell-mediated immunity modulation after microbial infection.

Mining Exosomal Genes for Pancreatic Cancer Targets.

Exosomes, cell-derived vesicles encompassing lipids, DNA, proteins coding genes and noncoding RNAs (ncRNAs) are present in diverse body fluids. They offer novel biomarker and drug therapy potential for diverse diseases, including cancer. Using gene ontology, exosomal genes database and GeneCards metadata analysis tools, a database of cancer-associated protein coding genes and ncRNAs (n=2,777) was established. Variant analysis, expression profiling and pathway mapping were used to identify putative pancreatic cancer exosomal gene candidates. Five hundred and seventy-five protein-coding genes, 26 RNA genes and one pseudogene directly associated with pancreatic cancer were identified in the study. Nine open reading frames (ORFs) encompassing enzymes, apoptosis and transcriptional regulators, and secreted factors and five cDNAs (enzymes) emerged from the analysis. Among the ncRNA class, 26 microRNAs (miRs), one pseudogene, one long noncoding RNA (LNC) and one antisense gene were identified. Furthermore, 22 exosome-associated protein-coding targets (a cytokine, enzymes, membrane glycoproteins, receptors, and a transporter) emerged as putative leads for pancreatic cancer therapy. Seven of these protein-coding targets are FDA-approved and the drugs-based on these could provide repurposing opportunities for pancreatic cancer. The database of exosomal genes established in this study provides a framework for developing novel biomarkers and drug therapy targets for pancreatic cancer.

Viral shedding from diverse body fluids in a patient with severe fever with thrombocytopenia syndrome

BackgroundSevere fever with thrombocytopenia syndrome (SFTS) is a tick-borne disease characterized by high fever, thrombocytopenia, leukopenia, and multiple organ failure and is caused by a novel bunyavirus. Human-to-human transmission has been reported previously, but the mode of transmission has not been clarified thoroughly. Study designWe identified a case of a 73-year-old woman with SFTS and performed a semi-quantitative real-time reverse transcription PCR (real-time RT-PCR) assay on her blood, tracheal aspirate, gastric aspirate and urine to detect SFTS virus (SFTSV). ResultsDuring 7-day hospitalization, all the serum samples showed positive Ct values lower than 35 in both the S and M segments, suggesting the presence of the SFTSV RNA. After initiation of plasma exchange, serum SFTSV load markedly decreased, but still remained positive. The SFTS viral RNA was also detected in other body fluids, including tracheal aspirate and gastric aspirate. ConclusionThese results suggest that droplet transmission can occur through close contact with infected patients.

Statistical Aspects in Proteomic Biomarker Discovery.

In the pursuit of a personalized medicine, i.e., the individual treatment of a patient, many medical decision problems are desired to be supported by biomarkers that can help to make a diagnosis, prediction, or prognosis. Proteomic biomarkers are of special interest since they can not only be detected in tissue samples but can also often be easily detected in diverse body fluids. Statistical methods play an important role in the discovery and validation of proteomic biomarkers. They are necessary in the planning of experiments, in the processing of raw signals, and in the final data analysis. This review provides an overview on the most frequent experimental settings including sample size considerations, and focuses on exploratory data analysis and classifier development.

Extracellular RNAs: development as biomarkers of human disease

Ten ongoing studies designed to test the possibility that extracellular RNAs may serve as biomarkers in human disease are described. These studies, funded by the NIH Common Fund Extracellular RNA Communication Program, examine diverse extracellular body fluids, including plasma, serum, urine and cerebrospinal fluid. The disorders studied include hepatic and gastric cancer, cardiovascular disease, chronic kidney disease, neurodegenerative disease, brain tumours, intracranial haemorrhage, multiple sclerosis and placental disorders. Progress to date and the plans for future studies are outlined.

Neurodegenerative Diseases: Phenome to Genome Analysis

Genome-Wide Association Studies (GWAS) tools are an attractive starting point for disease target discovery. Genetic association evidence provides a strong link to disease phenotypes across diverse human DNAs. The National Center for Biotechnology Information (NCBI) Phenome-Genome Integrator tool (PheGenI) was used to identify genes associated with neurodegenerative disease phenotypes (NeuroGenes). Four hundred ninty-nine known proteins and 30 uncharacterized proteins were found to be associated with diverse neurological diseases including Alzeheimer’s, amyotrophic lateral sclerosis (ALS), epilepsy, multiple scelerosis, stroke and Parkinson’s. The NeuroGenes also were associated with other diseases and associated disorders. Using diverse bioinformatics and proteomics tools, an atlas of the NeuroGenes was created to facilitate rational biomarker and drug target discovery. NeuroGenes protein expression was detected in diverse body fluids. The NeuroGenes were categorized into functional classes of proteins using protein motif and domains analysis tools. Expression Quantitative Trait Loci (eQTL) analysis identified single nucleotide polymorphisms (SNPs) associated with mRNA expression across diverse sets of samples from Alzheimer’s disease, Parkinson’s disease, brain infarction, multiple sclerosis, schizophrenia, stroke, mental retardation and neurological cancers. Thirty uncharacterized proteins encompassing structural protein, translation initiation factor, GDP/GTP exchange factor (GEF), transmembrane proteins, tubulin/histonebinding and a lysosomal hydrolase were identified as putative proteins for dementia, Parkinson’s, neurobehavior, multiple scelerosis and ALS. These results may provide new biomarkers for neurological diseases.

Ebola-Associated Genes in the Human Genome: Implications for Novel Targets

Ebola Virus Disease (EVD) is a major healthcare challenge facing the globe today and if left unchecked could become a pandemic. A limited knowledgebase exists about the Ebola virus with no U.S. Federal Drug Agency (FDA) approved drugs. Ebolaspecific proteins, antibodies and vaccines are being explored currently for therapy. In an attempt to first develop an understanding of the human proteins involved in the EVD and potentially create a pipeline of targets for evaluation, the human genome was mined for EVD association using 1) genetic association, 2) disease-oriented knowledge database text mining, 3) transcriptome-based Meta Analysis and 4) pathway enrichment analysis. Forty-five human proteins (29 known proteins and 16 novel previously uncharacterized proteins) were identified which were associated with EVD. Mining the proteomic expression databases revealed the detection of these 45 proteins in diverse body fluids. Detailed bioinformatics and proteomic analyses of these EVD associated proteins shed light on pathways, nature and class of the proteins and their association with diverse diseases including other infectious diseases. Mining the drug banks for association with the 45 genes reveals putative drugs including antineoplastics, anti-inflammatory drugs, leukotrienes, interferons, anticoagulants, nucleoside analogues, retinoic acid and statins to add to the currently meager options for therapy and supportive care. Putative targets of interest include a chemokine (C-C motif) ligand 8 (CCL8), enzymes (indoleamine 2,3-dioxygenase 1|IDO1, cytochrome c oxidase| COA6) and Short-chain dehydrogenase/reductase, SDR) and members of the receptor family, killer cell immunoglobulin-like receptor, cytoplasmic tail (KIR). Using knockout technology, the 45 proteins identified in this study can be rapidly verified for therapeutic potential. The association of these proteins with other diseases potentially expands the scope to diverse use. The results presented in this study provide a further example of harnessing the human genome to identify disease relevant proteins for subsequent research and development.