Fast and Accurate Pneumocystis Pneumonia Diagnosis in Human Samples Using a Label-Free Plasmonic Biosensor

Pneumocystis jirovecii is a fungus responsible for human Pneumocystis pneumonia, one of the most severe infections encountered in immunodepressed individuals. The diagnosis of Pneumocystis pneumonia continues to be challenging due to the absence of specific symptoms in infected patients. Moreover, the standard diagnostic method employed for its diagnosis involves mainly PCR-based techniques, which besides being highly specific and sensitive, require specialized personnel and equipment and are time-consuming. Our aim is to demonstrate an optical biosensor methodology based on surface plasmon resonance to perform such diagnostics in an efficient and decentralized scheme. The biosensor methodology employs poly-purine reverse-Hoogsteen hairpin probes for the detection of the mitochondrial large subunit ribosomal RNA (mtLSU rRNA) gene, related to P. jirovecii detection. The biosensor device performs a real-time and label-free identification of the mtLSU rRNA gene with excellent selectivity and reproducibility, achieving limits of detection of around 2.11 nM. A preliminary evaluation of clinical samples showed rapid, label-free and specific identification of P. jirovecii in human lung fluids such as bronchoalveolar lavages or nasopharyngeal aspirates. These results offer a door for the future deployment of a sensitive diagnostic tool for fast, direct and selective detection of Pneumocystis pneumonia disease.

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Molecular detection of DHFR gene polymorphisms in Pneumocystis jirovecii isolates from Indian patients

The Journal of Infection in Developing Countries ◽

10.3855/jidc.6810 ◽

2015 ◽

Vol 9 (11) ◽

pp. 1250-1256 ◽

Cited By ~ 3

Author(s):

Yogita Singh ◽

Bijay Ranjan Mirdha ◽

Randeep Guleria ◽

Shehla Khalil ◽

Ashutosh Panda ◽

...

Keyword(s):

Gene Polymorphisms ◽

Large Subunit ◽

Tertiary Care ◽

Pneumocystis Jirovecii ◽

Clinical Samples ◽

Rrna Gene ◽

Dhfr Gene ◽

Pcr Assay ◽

Nucleotide Substitutions ◽

Lsu Rrna

Introduction: Pneumocystis pneumonia (PCP) is an opportunistic life-threatening infection, especially for immunocompromised individuals. A trimethoprim-sulfamethoxazole (TMP-SMX) combination is commonly used for the treatment of PCP, targeting both dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) enzymes. Several studies have already shown that polymorphisms in the DHPS gene are associated with drug resistance. The present study analyzed DHFR gene polymorphisms in Pneumocystis jirovecii recovered from clinical samples from patients admitted to a tertiary care health center in New Delhi, India. Methodology: Detection of P. jirovecii was performed using Gomori methenamine silver staining (GMS) and nested polymerase chain reaction (PCR) assay targeting the mitochondrial large subunit ribosomal RNA (mt LSU rRNA) gene. The DHFR gene was amplified using nested PCR protocol and was sequenced for detection of polymorphisms. Results: Of 180 clinical samples, only 4% (7/180) were positive by GMS staining, and 10% (18/180) were positive by mt LSU rRNA PCR assay. Of these 18 positive samples, only 77% (14/18) were amplified by the DHFR gene PCR assay. A total of 16 nucleotide substitutions were observed in 42% (6/14) samples targeted for the DHFR gene, of which 8 nucleotide substitutions were synonymous and the rest were non-synonymous. Conclusions: The DHFR gene mutations found in this study may possibly indicate an association of process likely to contribute to therapeutic failure or an evolutionary process, and warrant continuous monitoring.

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Faculty Opinions recommendation of Detection of a biomarker for Alzheimer's disease from synthetic and clinical samples using a nanoscale optical biosensor.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1024067.284859 ◽

2005 ◽

Author(s):

Jon Zubieta

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Optical Biosensor ◽

Clinical Samples

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Sarocladium and Lecanicillium Associated with Maize Seeds and Their Potential to Form Selected Secondary Metabolites

Biomolecules ◽

10.3390/biom11010098 ◽

2021 ◽

Vol 11 (1) ◽

pp. 98

Author(s):

Lidia Błaszczyk ◽

Agnieszka Waśkiewicz ◽

Karolina Gromadzka ◽

Katarzyna Mikołajczak ◽

Jerzy Chełkowski

Keyword(s):

Large Subunit ◽

Solid Substrate ◽

Rrna Gene ◽

Decenoic Acid ◽

Bioactive Substances ◽

Lecanicillium Lecanii ◽

Maize Seeds ◽

Internally Transcribed Spacer ◽

First Time

The occurrence and diversity of Lecanicillium and Sarocladium in maize seeds and their role in this cereal are poorly understood. Therefore, the present study aimed to investigate Sarocladium and Lecanicillium communities found in endosphere of maize seeds collected from fields in Poland and their potential to form selected bioactive substances. The sequencing of the internally transcribed spacer regions 1 (ITS 1) and 2 (ITS2) and the large-subunit (LSU, 28S) of the rRNA gene cluster resulted in the identification of 17 Sarocladium zeae strains, three Sarocladium strictum and five Lecanicillium lecanii isolates. The assay on solid substrate showed that S. zeae and S. strictum can synthesize bassianolide, vertilecanin A, vertilecanin A methyl ester, 2-decenedioic acid and 10-hydroxy-8-decenoic acid. This is also the first study revealing the ability of these two species to produce beauvericin and enniatin B1, respectively. Moreover, for the first time in the present investigation, pyrrocidine A and/or B have been annotated as metabolites of S. strictum and L. lecanii. The production of toxic, insecticidal and antibacterial compounds in cultures of S. strictum, S. zeae and L. lecanii suggests the requirement to revise the approach to study the biological role of fungi inhabiting maize seeds.

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Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

International Journal of Molecular Sciences ◽

10.3390/ijms21197330 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7330

Author(s):

Roberta Noberini ◽

Cristina Morales Torres ◽

Evelyn Oliva Savoia ◽

Stefania Brandini ◽

Maria Giovanna Jodice ◽

...

Keyword(s):

Mass Spectrometry ◽

Histone H1 ◽

Histone Variants ◽

Linker Histone ◽

Clinical Samples ◽

Label Free ◽

Complex Samples ◽

Linker Histone H1 ◽

Ideal Tool ◽

Free Quantification

Epigenetic aberrations have been recognized as important contributors to cancer onset and development, and increasing evidence suggests that linker histone H1 variants may serve as biomarkers useful for patient stratification, as well as play an important role as drivers in cancer. Although traditionally histone H1 levels have been studied using antibody-based methods and RNA expression, these approaches suffer from limitations. Mass spectrometry (MS)-based proteomics represents the ideal tool to accurately quantify relative changes in protein abundance within complex samples. In this study, we used a label-free quantification approach to simultaneously analyze all somatic histone H1 variants in clinical samples and verified its applicability to laser micro-dissected tissue areas containing as low as 1000 cells. We then applied it to breast cancer patient samples, identifying differences in linker histone variants patters in primary triple-negative breast tumors with and without relapse after chemotherapy. This study highlights how label-free quantitation by MS is a valuable option to accurately quantitate histone H1 levels in different types of clinical samples, including very low-abundance patient tissues.

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Phylogeny of the Australian freshwater crayfish Cherax destructor-complex (Decapoda : Parastacidae) inferred from four mitochondrial gene regions

Invertebrate Systematics ◽

10.1071/is04021 ◽

2005 ◽

Vol 19 (3) ◽

pp. 209 ◽

Cited By ~ 6

Author(s):

Thuy T. T. Nguyen ◽

Christopher M. Austin

Keyword(s):

16S Rrna ◽

Cytochrome Oxidase ◽

Mitochondrial Gene ◽

Large Subunit ◽

Strong Support ◽

Interspecific Variation ◽

Rrna Gene ◽

Freshwater Crayfish ◽

Cherax Destructor ◽

Australian Freshwater

The phylogenetic relationships among 32 individuals of Australian freshwater crayfish belonging to the Cherax destructor-complex were investigated using a dataset comprising sequences from four mitochondrial gene regions: the large subunit rRNA (16S rRNA), cytochrome oxidase I (COI), adenosine triphosphatase 6 (ATPase 6), and cytochrome oxidase III (COIII). A total of 1602 bp was obtained, and a combined analysis of the data produced a tree with strong support (bootstrap values 94–100%) for three divergent lineages, verifying the phylogenetic hypotheses of relationships within the C. destructor species-complex suggested in previous studies. Overall, sequences from the 16S rRNA gene showed the least variation compared to those generated from protein coding genes, which presented considerably greater levels of divergence. The level of divergence within C. destructor was found to be greater than that observed in other species of freshwater crayfish, but interspecific variation among species examined in the present study was similar to that reported previously.

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Label-free optical biosensor based on a dual-core microstructured polymer optical fiber

Optik ◽

10.1016/j.ijleo.2015.07.019 ◽

2015 ◽

Vol 126 (21) ◽

pp. 2930-2933 ◽

Cited By ~ 1

Author(s):

Nai-Fei Ren ◽

Bing Sun ◽

Ming-Yang Chen

Keyword(s):

Optical Fiber ◽

Optical Biosensor ◽

Label Free ◽

Polymer Optical Fiber ◽

Dual Core

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Sympodiomyces attinorum sp. nov., a yeast species associated with nests of the leaf-cutting ant Atta sexdens

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63200-0 ◽

2004 ◽

Vol 54 (5) ◽

pp. 1891-1894 ◽

Cited By ~ 27

Author(s):

Solange C. Carreiro ◽

Fernando C. Pagnocca ◽

Maurício Bacci ◽

Marc-André Lachance ◽

Odair C. Bueno ◽

...

Keyword(s):

Yeast Species ◽

Novel Species ◽

Large Subunit ◽

Growth Characteristics ◽

Rrna Gene ◽

The Novel ◽

Atta Sexdens ◽

Leaf Cutting ◽

Large Subunit Rrna ◽

Waste Deposit

Four strains of a novel yeast species were isolated from laboratory nests of the leaf-cutting ant Atta sexdens in Brazil. Three strains were found in older sponges and one was in a waste deposit in the ant nests. Sequencing of the D1/D2 region of the large-subunit rRNA gene showed that the novel species, named Sympodiomyces attinorum sp. nov., is phylogenetically related to Sympodiomyces parvus. Unlike Sympodiomyces parvus, Sympodiomyces attinorum can ferment glucose, assimilate methyl α-d-glucoside, salicin and citrate, and grow at 37 °C, thus enabling these two species to be distinguished. Differentiation from other related species is possible on the basis of other growth characteristics. The type strain of Sympodiomyces attinorum is UNESP-S156T (=CBS 9734T=NRRL Y-27639T).

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