Ultrastructural and morphological studies on variables affecting Escherichia coli with selected commercial antibiotics

Background

Many studies reported the effects of antibiotic exposure on E. coli bacterial growth and cell modification. However, scarce descriptive information on ultrastructural effects upon exposure of commercial antibiotics.

Methods

This study described the morphological and ultrastructural alterations caused by selected antibiotics (amoxicillin-clavulanate, ceftriaxone, polymyxin B, colistin, gentamicin, and amikacin) that targeted cell wall, plasma membrane, and cytoplasmic density, and also proteins synthesis. We determined extracellular morphological changes of exposure through scanning electron microscopy (FESEM) and intracellular activities through transmission electron microscopy (TEM) investigation.

Results

FESEM and TEM micrograph of E. coli exposed with selected antibiotics shows ultrastructural changes in beta-lactam class (amoxicillin-clavulanate, ceftriaxone) elongated the cells as the cell wall was altered as it inhibits bacterial cell wall synthesis, polymyxin class (polymyxin B, colistin) had plasmid and curli-fimbriae as it breaking down the plasma/cytoplasmic membrane, and aminoglycoside class (gentamicin, and amikacin) reduced ribosome concentration as it inhibits bacterial protein synthesis by binding to 30 s ribosomes.

Conclusion

Morphological and ultrastructural alterations of E. coli's mechanism of actions were translated and depicted. This study could be reference for characterization studies for morphological and ultrastructural of E. coli upon exposure to antimicrobial agents.

Discovery and technical validation of high-performance methylated DNA markers for the detection of cervical lesions at risk of malignant progression in low- and middle-income countries

BACKGROUND

Cervical cancer remains a leading cause of death, particularly in developing countries. WHO screening guidelines recommend human papilloma virus (HPV) detection as a means to identify women at risk of developing cervical cancer. While HPV testing identifies those at risk, it does not specifically distinguish individuals with neoplasia. We investigated whether a quantitative molecular test that measures methylated DNA markers could identify high-risk lesions in the cervix with accuracy.

RESULTS

Marker discovery was performed in TCGA-CESC Infinium Methylation 450 K Array database and verified in three other public datasets. The panel was technically validated using Quantitative Multiplex-Methylation-Specific PCR in tissue sections (N = 252) and cervical smears (N = 244) from the USA, South Africa, and Vietnam. The gene panel consisted of FMN2, EDNRB, ZNF671, TBXT, and MOS. Cervical tissue samples from all three countries showed highly significant differential methylation in squamous cell carcinoma (SCC) with a sensitivity of 100% [95% CI 74.12-100.00], and specificity of 91% [95% CI 62.26-99.53] to 96% [95% CI 79.01-99.78], and receiver operating characteristic area under the curve (ROC AUC) = 1.000 [95% CI 1.00-1.00] compared to benign cervical tissue, and cervical intraepithelial neoplasia 2/3 with sensitivity of 55% [95% CI 37.77-70.84] to 89% [95% CI 67.20-98.03], specificity of 93% [95% CI 84.07-97.38] to 96% [95% CI 79.01-99.78], and a ROC AUC ranging from 0.793 [95% CI 0.68-0.89] to 0.99 [95% CI 0.97-1.00] compared to CIN1. In cervical smears, the marker panel detected SCC with a sensitivity of 87% [95% CI 77.45-92.69], specificity 95% [95% CI 88.64-98.18], and ROC AUC = 0.925 [95% CI 0.878-0.974] compared to normal, and high-grade squamous intraepithelial lesion (HSIL) at a sensitivity of 70% (95% CI 58.11-80.44), specificity of 94% (95% CI 88.30-97.40), and ROC AUC = 0.884 (95% CI 0.822-0.945) compared to low-grade intraepithelial lesion (LSIL)/normal in an analysis of pooled data from the three countries. Similar to HPV-positive, HPV-negative cervical carcinomas were frequently hypermethylated for these markers.

CONCLUSIONS

This 5-marker panel detected SCC and HSIL in cervical smears with a high level of sensitivity and specificity. Molecular tests with the ability to rapidly detect high-risk HSIL will lead to timely treatment for those in need and prevent unnecessary procedures in women with low-risk lesions throughout the world. Validation of these markers in prospectively collected cervical smear cells followed by the development of a hypermethylated marker-based cervical cancer detection test is warranted.

Comparative analysis of the intestinal flora of BmNPV-resistant and BmNPV-sensitive silkworm varieties

Bombyx mori nucleopolyhedrovirus (BmNPV) is a very common and infectious virus that affects silkworms and hinders silk production. To investigate the intestinal flora of BmNPV-resistant and BmNPV-sensitive silkworm varieties, 16 S rDNA high-throughput sequencing was performed. The results of the cluster analysis showed that the intestinal flora of the resistant silkworm variety was more abundant than that of the sensitive silkworm variety. This was found even when infection with BmNPV caused a sharp decline in the number of intestinal floral species in both resistant and sensitive silkworm varieties. The abundances of the intestinal flora, including Aureimonas, Ileibacterium, Peptostreptococcus, Pseudomonas, Enterococcus, and Halomonas, in the resistant variety were considerably greater after infection with BmNPV than those in the sensitive variety. After infection with BmNPV, four kinds of important intestinal bacteria, namely, f_Saccharimonadaceae, Peptostreptococcus, Aureirmonas, and f_Rhizobiaceae, were found in the resistant silkworm variety. In the sensitive silkworm variety, only Faecalibaculum was an important intestinal bacterium. The differential or important bacteria mentioned above might be involved in immunoreaction or antiviral activities, especially in the intestines of BmNPV-resistant silkworms. By conducting a functional enrichment analysis, we found that BmNPV infection did not change the abundance of important functional components of the intestinal flora in resistant or sensitive silkworm varieties. However, some functional factors, such as the biosynthesis, transport, and catabolism of secondary metabolites (e.g., terpenoids and polyketides) and lipid transport and metabolism, were more important in the resistant silkworm variety than in the sensitive variety; thus, these factors may increase the resistance of the host to BmNPV. To summarize, we found significant differences in the composition, abundance, and function of the intestinal flora between resistant and sensitive silkworm varieties, especially after infection with BmNPV, which might be closely related to the resistance of resistant silkworm varieties to BmNPV.

Identifying Ontarians with Type 2 Diabetes Mellitus in Administrative Data: A Comparison of Two Case Definitions

INTRODUCTION

This study compared two previously validated sensitive and specific diabetes case definitions to explore the impact of different classification methods in Ontario ICES administrative data.

METHODS

This study included patients captured by the Ontario Diabetes Database with type 2 diabetes using either the sensitive cohort definition (≥ 2 physician visits for diabetes within 1 year or ≥ 1 drug claim for diabetes or ≥ 1 hospitalization with diabetes), or the specific cohort definition (≥ 3 physician visits for diabetes within 1 year), between October 1, 2013 to September 30, 2015. Each cohort's demographic and clinical features were described using descriptive analysis.

RESULTS

Using sensitive and specific definitions, 1,093,812 and 783,228 patients with type 2 diabetes were identified, respectively. Overall, the demographic and clinical characteristics were similar between cohorts. Patients in the sensitive cohort had mean age of 64.1 years and were 52.4% male, compared to 64.8 years and 53.6% male in the specific cohort. In the sensitive and specific cohorts respectively, 64.4% and 55.7% of patients reported one-year mean HbA1c of < 7% (53 mmol/mol) and 25.3% and 31.5% reported levels between 7.0-8.5% (53-69 mmol/mol).

CONCLUSIONS

Although sample sizes were different between sensitive and specific cohorts, demographic and clinical characteristics were similar.

An ultrasensitive and multiplexed miRNA one-step real time RT-qPCR detection system and its application in esophageal cancer serum

MicroRNAs (miRNAs) are increasingly recognized as promising biomarkers for early disease diagnosis and prognosis. Therefore, the need for rapid, robust methods for multiplex miRNA detection in biological research and clinical diagnosis is crucial. This study introduces a novel multiplex miRNA detection method, SMOS-qPCR (Sensitive and Multiplexed One-Step RT-qPCR). The method integrates multiplexed reverse transcription and TaqMan-based qPCR into a single tube, employing a one-step operation on a real-time PCR system. We investigated the effect of 3' end phosphorylation of the Linker, Linker concentration and probe concentration on the SMOS-qPCR, resulted in a wide linear range from 1 fM to 0.1 zM (R2 ≥ 0.99 for each miRNA), surpassing the capabilities of stem-loop RT-qPCR and SYBR Green One-step RT-qPCR. The method showed excellent performance in distinguishing mature miRNA from miRNA precursor, and successfully detected four miRNAs in a single tube without cross-interference. Its high specificity enables precise differentiation of less than 1% nonspecific signal. Finally, we demonstrated the effectiveness of the SMOS-qPCR system in detecting circulating miRNAs in serum samples, distinguishing between esophageal cancers and health individuals with high AUC values (>0.940). In conclusion, the proposed SMOS-qPCR system offers a straightforward and promising approach for miRNA profiling in future clinical applications.

Nanoleaf-derived carbon materials as a sensitivity coating for solid‑phase microextraction of polycyclic aromatic hydrocarbons

Metal-organic framework-derived carbon materials have shown extensive application in the sensitive extraction of polycyclic aromatic hydrocarbons (PAHs), but more active sites for its adsorption were still a tireless pursuit. In this study, ZIF-nanoleaf-derived carbon (NLCs) was synthesized and developed as a solid-phase microextraction (SPME) fiber (NLCs-F). The extraction performance was compared with ZIF-dodecahedron-derived carbon (DHCs) coated fiber (DHCs-F), which was prepared by only changing the ratio of the reactants. The unique morphology of NLCs provided abundant adsorption active sites for the selected PAHs, while the large average aperture facilitated selective extraction of high molecular weight analytes. Additionally, the high carbon content enhanced the strong enrichment capability for hydrophobic PAHs. Hence, the prepared NLCs-F coupled with GC-MS showed a good correlation coefficient (0.9975) in a wide linear range, low limits of detection (0.3-1.8 ng L-1), satisfactory repeatability, and reproducibility, which made it apply in the enrichment of PAHs in actual tea and coffee samples.

What is the ideal combination therapy in de novo, oligometastatic, castration-sensitive prostate cancer?

PURPOSE

To review current evidence regarding the management of de novo, oligometastatic, castration-sensitive prostate cancer (PCa).

METHODS

A literature search was conducted on PubMed/Medline and a narrative synthesis of the evidence was performed in August 2022.

RESULTS

Oligometastatic disease is an intermediate state between localized and aggressive metastatic PCa defined by ≤ 3-5 metastatic lesions, although this definition remains controversial. Conventional imaging has limited accuracy in detecting metastatic lesions, and the implementation of molecular imaging could pave the way for a more personalized treatment strategy. However, oncological data supporting this strategy are needed. Radiotherapy to the primary tumor should be considered standard treatment for oligometastatic PCa (omPCa). However, it remains to be seen whether local therapy still has an additional survival benefit in patients with de novo omPCa when treated with the most modern systemic therapy combinations. There is insufficient evidence to recommend cytoreductive radical prostatectomy as local therapy; or stereotactic body radiotherapy as metastasis-directed therapy in patients with omPCa. Current data support the use of intensified systemic therapy with androgen deprivation therapy (ADT) and next-generation hormone therapies (NHT) for patients with de novo omPCa. Docetaxel has not demonstrated benefit in low volume disease. There are insufficient data to support the use of triple therapy (i.e., ADT + NHT + Docetaxel) in low volume disease.

CONCLUSION

The present review discusses current data in de novo, omPCa regarding its definition, the increasing role of molecular imaging, the place of local and metastasis-directed therapies, and the intensification of systemic therapies.

Development of sensitive magnetic nanoparticle assisted rapid sandwich assay(s-MARSA) to monitor Parkinson's disease and Schizophrenia pharmacotherapy

Parkinson's disease and Schizophrenia fall under low dopamine neurodegenerative and high dopamine psychiatric disorders respectively. Pharmacological interventions to correct mid-brain dopamine concentrations sometimes overshoots the physiological dopamine levels leading to psychosis in Parkinson's disease patients and, extra-pyramidal symptoms in schizophrenia patients. Currently no validated method is available to monitor side effects in such patients, Apolipoprotein E is one of the CSF biomarkers identified in the recent past that shows an inverse relation to mid-brain dopamine concentration. In this study, we have developed s-MARSA for the detection of Apolipoprotein E from ultra-small volume (2 μL) of CSF. s-MARSA exhibits a broad detection range (5 fg mL^-1 to 4 μg mL^-1) with a better detection limit and could be performed within an hour utilizing only a small volume of CSF sample. The values measured by s-MARSA strongly correlates with the values measured by ELISA. Our method has advantages over ELISA in having a lower detection limit, a broader linear detection range, shorter analysis time, and requiring a low volume of CSF samples. The developed s-MARSA method holds promise for the detection of Apolipoprotein E with clinical utility for monitoring pharmacotherapy of Parkinson's and Schizophrenia patients.

A colorimetric lateral flow immunoassay based on oriented antibody immobilization for sensitive detection of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). The high human-to-human transmission and rapid evolution of SARS-CoV-2 have resulted in a worldwide pandemic. To contain SARS-CoV-2, it is essential to efficiently control the transmission of the virus through the early diagnosis of infected individuals, including asymptomatic people. Therefore, a rapid and accurate assay is vital for the early diagnosis of SARS-CoV-2 in suspected individuals. In this study, we developed a colorimetric lateral flow immunoassay (LFIA) in which a CBP31-BC linker was used to immobilize antibodies on a cellulose membrane in an oriented manner. The developed LFIA enabled sensitive detection of cultured SARS-CoV-2 in 15 min with a detection limit of 5 × 10⁴ copies/mL. The clinical performance of the LFIA for detecting SARS-CoV-2 was evaluated using 19 clinical samples validated by reverse transcription-polymerase chain reaction (RT-PCR). The LFIA detected all the positive and negative samples accurately, corresponding to 100% accuracy. Importantly, patient samples with low viral loads were accurately identified. Thus, the proposed method can provide a useful platform for rapid and accurate point-of-care testing of SARS-CoV-2 in infected individuals to efficiently control the COVID-19 pandemic.

Rapid, sensitive, and specific detection of SARS-CoV-2 in nasopharyngeal swab samples of suspected patients using a novel one-step loop-mediated isothermal amplification (one-step LAMP) technique

BACKGROUND

In the absence of effective antiviral drugs or vaccines, early and accurate detection of SARS-CoV-2 infection is essential to the COVID-19 pandemic. This study developed and evaluated a novel rapid One-Step LAMP assay to directly detect the SARS-CoV-2 RNA from nasopharyngeal (NP) swab samples of patients with suspected SARS-CoV-2 infection living in deprived areas in comparison to One-Step Real-time PCR.

METHODS

Two hundred fifty-four NP swab samples from patients suspected of COVID-19 infection living in deprived western areas of Iran were tested by TaqMan One-Step RT-qPCR and fast One-Step LAMP assays. Tenfold serial dilutions of SARS-CoV-2 RNA standard strain where the viral copy number in each dilution was previously determined using the qPCR and various templates were used to investigate the analytical sensitivity and specificity of the One-Step LAMP assay in triplicate. Also, the efficacy and reliability of the method compared to TaqMan One-Step RT-qPCR were evaluated using SARS-CoV-2 positive and negative clinical samples.

RESULTS

The results of the One-Step RT-qPCR and One-Step LAMP tests were positive in 131 (51.6%) and 127 (50%) participants, respectively. Based on Cohen's kappa coefficient (κ), the agreement between the two tests was 97%, which was statistically significant (P < 0.001). The detection limit for the One-Step LAMP assay was 1 × 10¹ copies of standard SARS-CoV-2 RNA per reaction in less than an hour in triplicates. Negative results in all samples with non-SARS-CoV-2 templates represent 100% specificity.

CONCLUSIONS

The results showed that the One-Step LAMP assay is an efficient consistent technique for detecting SARS-CoV-2 among suspected individuals due to its simplicity, speed, low cost, sensitivity, and specificity. Therefore, it has great potential as a useful diagnostic tool for disease epidemic control, timely treatment, and public health protection, especially in poor and underdeveloped countries.

Ultra-sensitive molecular detection of gene fusions from RNA using ASPYRE

Background

RNA is a critical analyte for unambiguous detection of actionable mutations used to guide treatment decisions in oncology. Currently available methods for gene fusion detection include molecular or antibody-based assays, which suffer from either being limited to single-gene targeting, lack of sensitivity, or long turnaround time. The sensitivity and predictive value of next generation sequencing DNA-based assays to detect fusions by sequencing intronic regions is variable, due to the extensive size of introns. The required depth of sequencing and input nucleic acid required can be prohibitive; in addition it is not certain that predicted gene fusions are actually expressed.

Results

Herein we describe a method based on pyrophosphorolysis to include detection of gene fusions from RNA, with identical assay steps and conditions to detect somatic mutations in DNA [1], permitting concurrent assessment of DNA and RNA in a single instrument run.

Conclusion

The limit of detection was under 6 molecules/ 6 µL target volume. The workflow and instrumentation required are akin to PCR assays, and the entire assay from extracted nucleic acid to sample analysis can be completed within a single day.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01363-0.

Improving the accuracy of self-reported height and weight in surveys: an experimental study

Background

Many studies rely on self-reported height and weight. While a substantial body of literature exists on misreporting of height and weight, little exists on improving accuracy. The aim of this study was to determine, using an experimental design and a comparative approach, whether the accuracy of self-reported height and weight data can be increased by improving how these questions are asked in surveys, drawing on the relevant evidence from the psychology and survey research literatures.

Methods

Two surveys from two separate studies were used to test our hypotheses (Science Survey, n = 1,200; Eating Behaviours Survey, n = 200). Participants were randomly assigned to one of six conditions, four of which were designed to improve the accuracy of the self-reported height and weight data (“preamble”), and two of which served as the control conditions ( “no preamble”). Four hypotheses were tested: (H1) survey participants read a preamble prior to being asked their height and weight will report lower heights and higher weights than those not read a preamble; (H2) the impact of question-wording (i.e., preamble vs. no preamble) on self-reported weight will be greater for participants with higher BMIs; (H3) the impact of question-wording on height will be greater for older participants; (H4) either version of the weight question – standard or “weight-specific”—may result in participants reporting more accurate self-reported weight. One-way MANOVA was conducted to test Hypothesis 1; two-way analysis of variance were conducted to test Hypothesis 2; moderation analysis was used to test Hypothesis 3; independent samples t-test was conducted to test Hypothesis 4.

Results

None of the hypotheses was supported.

Conclusions

This paper provides an important starting point from which to inform further work exploring how question wording can improve self-reported measurement of height and weight. Future research should explore how question preambles may or may not operationalise hypothesised underlying mechanisms, the sensitivity or intrusiveness of height and weight questions, individual beliefs about one’s height and weight, and survey context.

Rapid and simultaneous detection of multiple illegal additives in feed and food by SERS with reusable Cu2O-Ag/AF-C3N4 substrate

Illegal additives can bring the economic benefit, resulting in the continuous irregularities in the use of illegal additives. In this study, a method for rapid, sensitive, and simultaneous detection of multiple illegal additives including enrofloxacin, malachite green, nitrofurazone, and Sudan Ⅰ in feed and food samples by surface-enhanced Raman spectroscopy (SERS) with Cu₂O-Ag/AF-C₃N₄ composite substrate was developed. A Cu₂O-Ag/AF-C₃N₄ composite substrate was prepared by reacting Cu₂O modified by AF-C₃N₄ nanosheets with AgNO₃ solution. The substrate has a limit of detection (LOD) of 1.29 × 10^-6 mg/L, a good linear relationship of between 10^-6 and 10^-2 mg/L, and an R² value of 0.95 for Rhodamine B detection. Furthermore, the substrate showed high uniformity and reproducibility, with relative standard deviations (RSD) of 6.74% and 4.85%, respectively. Adding AF-C₃N₄ nanosheets not only increased the enhancement effect of the substrate, which was 4.4 times of that before addition, but also endowed it with good self-cleaning characteristics owing to its excellent photocatalytic activity. The substrate can be reused, with over 80% of the original Raman signal strength remaining after four repeat uses. The SERS based on the above substrate was used to detect the illegal additives, the LOD of enrofloxacin, malachite green, nitrofurazone, and Sudan Ⅰ can reach 4.67 × 10^-4 mg/L, 2.57 × 10^-5 mg/L, 5.7 × 10^-7 mg/L and 6.92 × 10^-5 mg/L. The results reveal that this substrate has great application potential in feed and food safety.

Reverse transcription recombinase-aided amplification assay for H5 subtype avian influenza virus

Background

The H5 subtype avian influenza virus (AIV) has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks.

Methods

In this study, we developed a reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of H5 subtype AIV. Assays were performed at a single temperature (39 °C), and the results were obtained within 20 min.

Results

The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 10³ RNA copies/μL at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse transcription quantitative real-time polymerase chain reaction assays, the κ value of the RT-RAA assay in 420 avian clinical samples was 0.983 (p < 0.001). The sensitivity for avian clinical sample detection was 97.26% (95% CI, 89.56–99.52%), and the specificity was 100% (95% CI, 98.64–100%).

Conclusions

These results indicated that our RT-RAA assay may be a valuable tool for detecting H5 subtype AIV.

Emergency Department Management of Chest Pain With a High-Sensitivity Troponin-Enabled 0/1-Hour Rule-Out Algorithm

OBJECTIVES

The analytical sensitivity of high-sensitivity cardiac troponin T (hsTnT) assays has enabled rapid myocardial infarction rule-out algorithms for emergency department (ED) presentations. Few studies have analyzed the real-world impact of hsTnT algorithms on outcomes and operations.

METHODS

Comparison of ED length of stay (LOS) and 30-day outcomes (return to ED, inpatient admission, and mortality) for patients presenting with chest pain during 2 separate 208-day periods using a 0/1-hour hsTnT-enabled algorithm or fourth-generation TnT.

RESULTS

Discharge, 30-day readmission, and 30-day mortality rates were not significantly different with fourth-generation TnT vs hsTnT. Thirty-day return rates were significantly decreased with hsTnT (17.4% vs 14.9%; P < .01). For encounters with TnT measured at least twice and resulting in discharge, median ED LOS decreased by 61 minutes with the use of hsTnT (488 vs 427 minutes; P < .0001). Median time between first and second TnT results decreased by 82 minutes with hsTnT (202 vs 120 minutes; P < .0001), suggesting that the 0/1-hour algorithm was incompletely adopted.

CONCLUSIONS

Implementation of the hsTnT algorithm was associated with decreased 30-day return rates and decreased ED LOS for a subset of patients, despite incomplete adoption of the 0/1-hour algorithm.

"Lighting-up" methylene blue-embedded zirconium based organic framework triggered by Al3+ for advancing the sensitivity of E. coli O157:H7 analysis in dual-signal lateral flow immunochromatographic assay

The sensitive detection of foodborne pathogens is of great significance for ensuring food safety and quality. Herein, on the basis of methylene blue-embedded zirconium based organic framework (UIO@MB) as the remarkable capture carrier and signal indicator, with the Al³⁺-assisted the fluorescent signal response, we developed a label-free and dual-signal lateral flow immunochromatographic assay (LDLFIA) for sensitive detection of Escherichia coli (E. coli) O157:H7. The UIO@MB sensing carrier without monoclonal antibodies (mAbs) was manufactured, which adhered to bacteria to form the UIO@MB-E. coli O157:H7 conjugate, resulting in visible blue band. Then the fluorescent response of the OH-rich UIO@MB was excited by introducing Al³⁺, arising from capturing of Al³⁺ by -OH through coordination and electrostatic affinity, thus generating a green fluorescent band. Impressively, a smartphone-based portable reading system was developed that can reflect the test results of UIO@MB-LDLFIA immediately. Under optimum conditions, UIO@MB-LDLFIA can complete colorimetric and fluorescent mode detection within 90 min, with a detection sensitivity of 10³ CFU/mL, which were 100 times lower than traditional gold nanoparticles-based LFIA and polymerase chain reaction (PCR). Moreover, the feasibility of the method was further evaluated by the determination of E. coli O157: H7 in drinking water and cabbage with average recoveries of 85.1-123.0%.

Noninvasive Measurement of Retinal Microvascular Permeability During Loss of Endothelial Quiescence

In the retina EC dysfunction and angiogenesis are driven by an altered microenvironment e.g., diabetes, leading to hypoxia and inflammation in the retinal layers, resulting in excessive vascular leakage and growth. The gold standard for measuring blood-retinal barrier permeability in response to disease and or therapy has been the gold standard Evans blue (EB) assay. However, this technique has limitations in vivo, including nonspecific tissue binding and toxicity. Here we describe a novel imaging methodology combining sodium fluorescein fundus angiography (FFA) with mathematical quantification allowing retinal permeability to be noninvasively and accurately measured at multiple time points in the same animal, minimizing animal use in line with the 3Rs framework. In addition, this technique is a nontoxic, high throughput, sensitive, and cost-effective alternative technique to the Evans blue assay. Moreover, this technique can be translated to other species.

Comparative analysis of four malaria diagnostic tools and implications for malaria treatment in southwestern Nigeria

OBJECTIVES

One of the problems encountered in malaria control and elimination is inaccurate diagnosis, resulting from the degree of sensitivity of the different malaria diagnostic tools. Even though microscopy remains the gold standard for malaria diagnosis, more sensitive and robust diagnostic tools such as polymerase chain reactions (PCR) are used in research settings to monitor interventions and track sub-microscopic infections due to some of the drawbacks of microscopy. Since diagnosis is a critical determinant for rational malaria treatment, it is imperative that accurate diagnosis must be assured for an effective treatment plan. Therefore, this study compared two routinely used point of care malaria diagnostic tools with two molecular tools and discussed their implication for malaria treatment.

DESIGN

In this study, 436 individuals with suspected malaria were sampled and systematically tested using four methods, namely rapid diagnostic test (henceforth referred to as malaria RDT- mRDT), microscopy, nested PCR (nPCR), and quantitative PCR (qPCR). Test sensitivities and specificities were compared, and their level of concordance was determined.

RESULTS

With nPCR as the gold standard, a false positivity rate of 42.2%, 8.9%, and 57.8% was obtained for mRDT, microscopy, and qPCR. Similarly, false negativity rates of 12.5%, 62.5%, and 0.8% were obtained for each of the methods mentioned above, respectively. Of all the tools assessed, qPCR gave the highest sensitivity (99.2%) and moderate specificity (42.2%), followed by the mRDT kit used (87.5%).

CONCLUSIONS

With the detection of a high false positivity rate based on mRDT and a substantial proportion of sub-microscopic carriers in this study area by nested/quantitative PCR, we recommend that these molecular tools should be in specialized laboratories within the region to (i) track and treat sub-microscopic carriers to prevent their contribution to malaria transmission; (ii) provide reliable epidemiological data using high throughput testing tools for evaluating malaria interventions.

Ratiometric fluorescent sensing of ethanol based on copper nanoclusters with tunable dual emission

Copper nanoclusters (Cu NCs) have attracted a surge of interest in fluorescent sensors as their outstanding physicochemical and optical properties. However, most of the reports have focused on single-signal fluorescent sensors, which are susceptible to background interferences and affect accuracy of the results. Herein, we constructed a facile ratiometric fluorescent sensor for monitoring ethanol based on Cu NCs with tunable dual emission. Polyvinylpyrrolidone (PVP)-modified Cu NCs were simply prepared in water, which exhibit ratiometric dual emission, including a strong green emission at 520 nm and a weak blue emission at 450 nm. The PVP-Cu NCs in water with strong green emission display monodisperse state due to the formation of hydration shell around Cu NCs. In ethanol where the hydration shell is destructed, Cu NCs tend to aggregate and show strong blue emission. This emission shift might attribute to the enhancement of Cu-Cu metallophilic interaction with the aggregation of Cu NCs, which induces the excited-state level increasing. Thus, a ratiometric fluorescent probe for ethanol based on the PVP-Cu NCs is fabricated, which possesses rapid response (<1 min), and realize full-range detection from 0 to 100%. In addition, this ratiometric probe is successfully applied to determine the alcohol strength of alcohol beverages, demonstrating the great potential in practical application.

Ratiometric fluorescence for sensitive detection of phosphate species based on mixed lanthanide metal organic framework

Phosphate (PO₄^3-) plays a major role in aquatic ecosystems and biosystems. Developing a highly sensitive and selective ratiometric fluorescence probe for detection of PO₄^3- is of great significance to the ecological environment and human health. In this work, a novel dual lanthanide metal organic framework was synthesized via hydrothermal reaction based on Tb³⁺ and Ce³⁺ as the center metal ions and terephthalic acid as the organic ligand (designated as Tb-Ce-MOFs). The fluorescence of Tb-Ce-MOFs shows emission at 375 nm. In the presence of PO₄^3-, with increased concentration of PO₄^3-, the fluorescence intensity of Tb-Ce-MOFs at 500 nm and 550 nm increased, while the intensity at 375 nm was reduced. Hence, ratiometric fluorescence detecting of PO₄^3- can be achieved by measuring the ratio of fluorescence at 550 nm (FL₅₅₀) to 375 nm (FL₃₇₅) in the fluorescent spectra of the Tb-Ce-MOFs. In this sensing approach, the Tb-Ce-MOFs probe exhibits highly sensitive and selective for detection of PO₄^3-. The limit of detection is calculated to be 28 nM and the detection range is 0.1 to 10 μM. In addition, the Tb-Ce-MOFs were used in the detection of PO₄^3- in real samples. We design and synthesize a mixed lanthanide metal organic framework fluorescence probe (Tb-Ce-MOFs) for ratiometric fluorescence for the detection of PO₄^3- based on Tb³⁺ and Ce³⁺ as the center metal ions and terephthalic acid as the organic ligand.

Rapid and sensitive detection of melanin using glutathione conjugated gold nanocluster based fluorescence quenching assay

In the present study, a rapid, facile, and highly sensitive assay based on glutathione conjugated gold nanocluster (GSH-AuNCs) is developed for the detection of melanin. The analysis of melanin which is linked to several diseases is crucial. The current methods for melanin estimation are complex and long, thus demands an alternative technology. In general, melanin exhibits photoactive properties, thus, it might have fluorescence quenching properties through the phenomenon of fluorescence resonance energy transfer. To verify our assumption, we have developed the fluorescence quenching assay based on gold nanocluster and melanin interaction. As a result, under the optimized condition, the developed quenching assay demonstrated the high selectivity and sensitivity toward melanin with a limit of detection and correlation coefficient of 0.060 μg/mL and 0.993, respectively. Moreover, the whole process represented the rapid assay time of 30 min to complete. To validate the performance of our assay on real samples, B16F1 cells lysate, and hair samples were tested that provided satisfactory results. Therefore, we believe that our assay due to good sensitivity and short assay time could be beneficial for the clinical diagnosis of melanin in the future study.

Highly Sensitive Fluorescent Probe for Detection of Paraquat Based on Nanocrystals

Paraquat is one of the most toxic materials widely applied in agriculture in most countries. In the present study, a simple, innovative and inexpensive nano biosensor which is based on a thioglycolic acid (TGA) - CdTe@CdS core-shell nanocrystals (NCs) to detect paraquat, is suggested. The NCs based biosensor shows a linear working range of 10-100 nM, and limited detection of 3.5 nM. The proposed sensor that has been well used for the detection and determination of paraquat in natural water samples is collected from corn field and a canal located near to the corn field yielding recoveries as high as 98%. According to our findings, the developed biosensor shows reproducibility and high sensitivity to determine paraquat in natural water samples in which the amount of paraquat has low levels. The suggested method is efficiently applied to paraquat determination in the samples of natural water that are collected from a tap water and a canal located near to the cornfield.

Risk factors for the development of post-infectious bronchiolitis obliterans after Mycoplasma pneumoniae pneumonia in the era of increasing macrolide resistance

BACKGROUND

The prevalence of macrolide-resistant Mycoplasma pneumoniae (MP) pneumonia has been rapidly increased. MP pneumonia is a risk factor for the development of post-infectious bronchiolitis obliterans (PIBO). The aim of the present study was to identify the risk factors for the development of PIBO after MP pneumonia in the era of increasing macrolide resistance of MP.

MATERIALS AND METHODS

This retrospective study enrolled 150 children with a mean age of 6.0 years admitted to the hospital due to MP pneumonia between May 2019 and February 2020 at a tertiary hospital. The clinical, radiologic, and laboratory data were obtained using retrospective chart review.

RESULTS

Eighteen children (12%) were diagnosed with PIBO after MP pneumonia. PIBO was diagnosed after a mean duration of 100.0 days (range, 6-268 days) from symptom onset. The respiratory virus co-infection (adjusted odds ratio [aOR], 4.069; 95% confidence interval [95% CI], 1.224-13.523), adenovirus co-infection (aOR, 5.607; 95% CI, 1.801-17.454), longer duration between symptom onset and admission (aOR, 1.150; 95% CI, 1.020-1.298), higher levels of serum lactate dehydrogenase (LDH) at the time of admission (aOR, 1.001; 95% CI, 1.000-1.003), and poor response to stepwise treatment increased the risk for development of PIBO after MP pneumonia. However, macrolide resistance of MP was not associated with development of PIBO after MP pneumonia.

CONCLUSION

The present study suggests that respiratory virus co-infection, including adenovirus, poor response to the treatment of MP pneumonia, and higher levels of serum LDH, but not macrolide resistance of MP, are risk factors of PIBO after MP pneumonia.

A Sensitive and High-Throughput Flow Cytometry-Based Assay for Measuring Antibody Neutralization of Human Adenovirus Type 3

The assessment of neutralization activity is an important step in the evaluation of neutralizing antibodies (NAbs). The traditional methods for measuring the antibody neutralization of human adenovirus type 3 (HAdV-3) are the microneutralization (MN) assay, which has insufficient sensitivity, and the plaque reduction neutralization test (PRNT), which is not suitable for high-throughput screening. Herein, we describe the development of a flow cytometry-based neutralization (FCN) assay for measuring the neutralization of sera, cell culture supernatants, and chimeric antibodies against HAdV-3 on the basis of a recombinant HAdV-3 (rHAdV-3) construct expressing the enhanced green fluorescent protein (EGFP). For flow cytometry-based assays, the optimal cell confluence was determined as 90%, and the virus was titrated using the assay. The established FCN assay follows the percentage law and an optimal MOI of not less than 5 × 10^-4 was determined by using a purified chimeric antibody. In addition, comparison of the anti-HAdV-3 NAb titers of 72 human serum samples by the MN and FCN assays, showed that both assays correlated strongly with each other. Our FCN assay was an improvement over the MN assay because the observation period was reduced from 3 to 1 days and data analysis could be performed objectively and robotically. Importantly, the newly established FCN assay allows measurement of the neutralization activity of chimeric antibodies expressed in cell culture supernatants. Thus, this sensitive and high-throughput FCN assay is a useful alternative to the MN assay for measuring the antibody neutralization of HAdV-3 and for screening anti-HAdV-3 NAbs in cell culture supernatants.

A Facile and Sensitive DNA Sensing of Harmful Algal Blooms Based on Graphene Oxide Nanosheets

Gene detection has important applications in biology, biomedical engineering, clinical, environmental, and marine fields. Rapid, sensitive, and selective recognition of specific genes is essential in practical applications. In this study, we describe a facile and sensitive DNA sensing platform for specific and quantitative detection of Heterosigma akashiwo, which is one of the causative agents of red tides. Fast and sensitive detection is achieved by using chemically synthesized graphene oxide (GO) nanosheets. Probe DNA is designed according to the specific DNA fragments of harmful algae and labeled with fluorescent molecules FAM (fluorescein-based dye). GO nanosheet solution is made, in which the strong interaction between FAM-labeled probe and GO nanosheets keeps them in close proximity, facilitating the fluorescence quenching of the fluorophore by GO nanosheets. In the presence of a complementary target DNA, the FAM-labeled DNA probe and the target DNA hybridize and desorb from the surface of GO nanosheets, resulting in restoration of fluorophore fluorescence. The concentration of target DNA fragments is analyzed by the fluorescence intensity at ~ 520 nm with emission wavelength of 480 nm. The sensitive detecting platform achieved stable measurement of 1 pM specific genes from Heterosigma akashiwo. Our GO nanosheet-based DNA-sensing platform performs fast and sensitive detection of trace amount of DNA, and enables quantitative recognition of harmful algae, which has promising applications in real-time monitoring in the marine environment of red tide generative dynamics, allowing effective control, particularly in relation to marine aquaculture.

Exonuclease I and III improve the detection efficacy of hepatitis B virus covalently closed circular DNA

BACKGROUND

Hepatitis B virus covalently closed circular DNA (HBV cccDNA) is an important biomarker of hepatitis B virus infection. However, the current methods are not specific and sensitive. The present study aimed to develop a specific and sensitive assay method for the quantification of HBV cccDNA.

METHODS

Exonuclease I (Exo I) & Exonuclease III (Exo III) and specific primer probes are used in real-time PCR. The virus particles isolated from peripheral blood mononuclear cells were used as negative control and HBV1.3 recombinant plasmid 3.2 kb circular DNA fragment was used as positive control. The methods of cccDNA detection were evaluated in cell lines, plasmid, animal model, patient serum and liver biopsies.

RESULTS

A linear range of 10¹-10⁷ copies/assay using specific primers for HBV cccDNA was established. HBV cccDNA were only detected in cell lines, animal model and liver tissue. It cannot be detected in serum samples. Intrahepatic HBV cccDNA level had good correlation with intrahepatic total HBV DNA level (r = 0.765, P < 0.001).

CONCLUSIONS

The real-time quantitative PCR is an effective and feasible method for sensitive and specific detection of low copy number of cccDNA. The novel detection method is fast, provides high sensitivity and specificity and can be used in clinical practice.

Intraspecific variation in sensitivity of high yielding rice varieties towards UV-B radiation

Effective screening of thirteen commonly cultivated rice (Oryza sativa L.) varieties was carried out to evaluate the varietal-specific differences in morphological, physiological and biochemical responses to various doses of UV-B irradiation (7, 14, 21 and 28 kJ m-2d-1). Determination of UV-B tolerant rice varieties would be helpful in selecting a suitable variety for the areas experiencing higher influx of UV-B radiation. Based on the initial screening of thirteen rice varieties, carried out by analyzing shoot length, fresh weight, photosynthetic pigments and the rate of lipid peroxidation under various doses of UV-B, it was found that Mangalamahsuri, Aathira, Kanchana, Jyothi and Annapoorna were tolerant lines and Neeraja, Swetha, Swarnaprabha and Aiswarya were the sensitive ones. Further screening of these nine varieties was done by analyzing primary metabolites (total protein, soluble sugar and proline content) and non enzymatic antioxidants (ascorbate and glutathione) involved in free radical scavenging mechanism to mitigate the negative effects of UV-B irradiation. Based on the cumulative stress response index (CSRI), the sum of relative individual component responses (total protein, soluble sugar, proline, ascorbate and glutathione content) at each UV-B treatment and total stress response index (TSRI), the sum of CSRI of all the four UV-B treatments for each variety, nine rice varieties selected after primary screening were classified as tolerant (Mangalamahsuri, Aathira and Kanchana), intermediate (Jyothi, Annapoorna, Neeraja and Swetha) and sensitive (Swarnaprabha and Aiswarya).

Quantitative real-time PCR with high-throughput automatable DNA preparation for molecular screening of Nosema spp. in Antheraea pernyi

Accurate diagnosis of pathogenic Nosema spp. in Antheraea pernyi samples is considered especially useful for reducing economic losses in sericulture and improving food safety by maintaining pathogen-free pupae. However, microscopy and immunologic methods have poor diagnostic sensitivity, while the more sensitive PCR methods remain costly and time-consuming for template preparation. To address this issue, we introduce a sensitive ALMS-qPCR method that combines fast, simple DNA extraction using Alkali Lysis followed by Magnetic bead Separation (ALMS) and quantitative real-time PCR (qPCR). This approach is especially fit for large-scale pathogen molecular screening, because the DNA preparation procedure is fast (<0.94 min per sample) and is high-throughput (performs on a 96-well plate). It is cost-effective, since the most expensive materials can be made in the lab and can be recycled, while the automated procedure can help to minimize labor cost. Though the DNA preparation procedure was substantially simplified, common PCR inhibitory factors were not observed. The sensitivity of ALMS-qPCR is high and the limit of detection is 0.045 parasites/μL. Large-scale screening of Nosema spp. in 3000 Antheraea pernyi samples confirmed the efficacy of the ALMS-qPCR method. Sensitivity is much higher than clinical microscopy, especially for host groups with low infection prevalence and levels. High-throughput ALMS-qPCR, combining automated DNA preparation and sensitive qPCR, provides an enhanced approach for pébrine screening and epidemiological studies. The application of ALMS-qPCR in the sericulture industry will help to strengthen pébrine control and breed pathogen-free species, which means much safer food provision and better genetic resource conservation.

Development and validation of an assay to measure cannabidiol and Δ9-tetrahydrocannabinol in human EDTA plasma by UHPLC-MS/MS

The therapeutic use of cannabinoids has increased with providers often recommending cannabinoid-containing products with limited pre-clinical and clinical pharmacokinetic studies. An ultra-performance liquid chromatography with triple quadrupole mass spectrometry method was developed and validated for the determination of cannabidiol and Δ9-tetrahydrocannabinol in human ethylenediaminetetraacetic acid (EDTA) plasma. The cannabinoids are extracted from plasma with a liquid-liquid procedure utilizing methyl tert-butyl ether. UHPLC Separation was achieved with a Waters Acquity HSS T3 column (100 × 2.1 mm, 1.8 μm) under isocratic conditions (18:82:0.02 water:methanol:formic acid v/v/v). The run time was 8.5 min. Detection of analytes was achieved using electrospray ionization and triple quadrupole selected reaction monitoring. Standard curve concentrations ranged from 0.5 to 250 ng/mL for cannabidiol and Δ9-tetrahydrocannabinol. The intra- and inter-day accuracy (% bias) and precision (relative standard deviation) were <9.20% in low, medium, and high quality control samples. The validated method was applied to the analysis of donated human EDTA plasma. The assay provides an important patient monitoring capability to determine variability in clinical pharmacokinetics during use of cannabinoid-containing products.

Selective and sensitive spectrophotometric method to determine trace amounts of copper metal ions using Amaranth food dye

Copper is an essential element in some biological processes in organisms, so it was important to find ways to identify trace amounts of it. Minimal amounts of copper ions can be determined in aqueous solutions in the spectrophotometric method suggested in this study. The method depends on the reaction between Cu(II) and Amaranth dye at the pH 6.0. The gradual disappearance of Amaranth colour at 520 nm occurring with an increase of Cu(II) concentration from 0.13 up to 2.0 μg cm^-3. The molar absorptivity coefficient and Sandell's sensitivity of the complex are found to be 0.94 × 10⁴ L mol^-1 cm^-1, 6.8 ng cm^-2 respectively. The advantages of this method are simple, selective, and highly sensitive. The method was used for determination of copper ions in aqueous solutions containing several metal ions, where excellent agreements between reported and obtained results were achieved in aqueous solutions containing copper metal ions only. The postulated method is in an excellent agreement with the determination of Cu(II) ion concentrations by atomic absorption spectroscopy (AAS). The interference was studied to determine the copper metal ions concentration, and do not interfere with eleven of other metal ions.

Theoretical study for anisotropic responses of the condensed-phase RDX under shock loadings

We have performed quantum-based molecular dynamics (MD) simulations in conjunction with multiscale shock technique (MSST) to investigate the initial chemical processes and the anisotropy of shock sensitivity of the RDX under shock loading applied along the different directions. The results show that there is a difference between x (or y)-direction and z-direction in the response to a shock wave velocity of 12 km/s. It was shown that detonation temperature and pressure in the z-direction lags behind that of x-direction (or y-direction). Moreover, from the time evolution of the population of various key fragments, we also observe that along with z-direction significantly later than that of x (or y)-direction, which the reaction rate is also slower. Thus, we draw a conclusion that sensitive for shock propagation along x or y-direction, but less sensitive for shock propagation along z-direction.

Quantitation of tadalafil in human plasma using a sensitive and rapid LC-MS/MS method for a bioequivalence study

A highly sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the determination of tadalafil (TAD) in human plasma. TAD and its deuterated internal standard (IS), tadalafil-d3, were extracted from 200 µL plasma using Phenomenex Strata-X-C 33 µ extraction cartridges. Chromatographic analysis was carried out on Synergi™ Hydro-RP C18 (100 mm × 4.6 mm, 4 µm) column with a mobile phase consisting of methanol and 10 mM ammonium formate, pH 4.0 (90:10, v/v), delivered at a flow rate of 0.9 mL/min. Quantitation of the protonated analyte was done on a triple quadrupole mass spectrometer using multiple reaction monitoring via electrospray ionization. The precursor to product ions transitions monitored for TAD and TAD-d3 were m/z 390.3 → 268.2 and m/z 393.1 → 271.2, respectively. The calibration curve was linear over the concentration range of 0.50-500 ng/mL with correlation coefficient, r2 ≥ 0.9994. Acceptable intra-batch and inter-batch precision (≤ 3.7%) and accuracy (97.8% to 104.1%) were obtained at five concentration levels. The recovery of TAD from spiked plasma was highly precise and quantitative (98.95% to 100.61%). Further, the effect of endogenous matrix components was minimal. TAD was found to be stable under different storage conditions in human plasma and also in whole blood samples. The validated method was successfully used to determine TAD plasma concentration in a bioequivalence study with 20 mg TAD tablets in 24 healthy volunteers. Method performance was evaluated by reanalyzing 115 study samples.

An ambient temperature stable and ready-to-use loop-mediated isothermal amplification assay for detection of toxigenic Vibrio cholerae in outbreak settings

Cholera, caused by Vibrio cholerae is a foodborne disease that frequently reported in food and water related outbreak. Rapid diagnosis of cholera infection is important to avoid potential spread of disease. Among available diagnostic platforms, loop-mediated isothermal amplification (LAMP) is regarded as a potential diagnostic tool due to its rapidity, high sensitivity and specificity and independent of sophisticated thermalcycler. However, the current LAMP often requires multiple pipetting steps, hence is susceptible to cross contamination. Besides, the strict requirement of cold-chain during transportation and storage make its application in low resource settings to be inconvenient. To overcome these problems, the present study is aimed to develop an ambient-temperature-stable and ready-to-use LAMP assay for the detection of toxigenic Vibrio cholerae in low resource settings. A set of specific LAMP primers were designed and tested against 155 V. cholerae and non-V. cholerae strains. Analytical specifity showed that the developed LAMP assay detected 100% of pathogenic V. cholerae and did not amplified other tested bacterial strains. Upon testing against stool samples spiked with toxigenic V. cholerae outbreak isolates, the LAMP assay detected all of the spiked samples (n = 76/76, 100%), in contrast to the conventional PCR which amplified 77.6% (n = 59/76) of the tested specimens. In term of sensitivity, the LAMP assay was 100-fold more sensitive as compared to the conventional PCR method, with LOD of 10 fg per μL and 10 CFU per mL. Following lyophilisation with addition of lyoprotectants, the dry-reagent LAMP mix has an estimated shelf-life of 90.75 days at room temperature.

A rapid and sensitive colorimetric assay for the determination of adenosine kinase activity

Adenosine kinase (ADK) plays an important role in the growth and development of organisms. A convenient, quick, reliable, sensitive and low-cost assay for ADK activity is of great significance. Here, we found the reaction system with bromothymol blue as the pH indicator had a maximum absorption peak at 614 nm. The absorbance change in 614 nm was positively correlated with the generated hydrogen ions in the reaction catalyzed by ADK. Then, we demonstrated this assay was feasible for ADK activity. Further, we analyzed the effects of buffer, bromothymol blue concentrations on the sensitivity of the assay, and investigated the sensitivity of ADK contents and adenosine concentration on the assay. Finally, we calculated the K_m and Vmax of ADK from Bombyx mori with this assay. Our results suggested this assay was quick, convenient, reliable, sensitive and economic for the activity of ADK. It is an excellent alternative for the conventional ADK assays.

Bioindicator responses and performance of plant species along a vehicular pollution gradient in western Himalaya

Loss of green cover, and increasing pollution is a prime global concern. The problem calls for screening of pollution-tolerant tree species that can be integrated into plantation drives. Recognizing this, the study analyzed bio-indicator responses and performance of commonly occurring plant species along a pollution gradient in western Himalaya. Based on distance from the road, three sites viz., highly polluted (HP), moderately polluted (MP), and least polluted (LP), were identified. From these sites, leaves of commonly occurring 26 tree species were collected and analyzed for dust accumulation, total chlorophyll, relative water content (RWC), ascorbic acid, and pH using standard protocols. Later, assessment of Air Pollution Tolerance Index (APTI) and Anticipated Performance Indices (API) was carried out. The results revealed variations in biochemical characteristics. The pH, RWC, and total chlorophyll increased with decreasing pollution while ascorbic acid increased with increasing pollution. Dust capturing potential of Ficus carica (1.191 mg/m²) and Toona ciliata (0.820 mg/m²) was relatively higher. Based on the results of APTI, Grevillea robusta was classified as tolerant. It scored significantly higher values (21.06, 21.19, and 19.61 in LP, MP, and HP sites, respectively). Quercus floribunda, G. robusta (68.75% each), Juglans regia (68.7%), and T. ciliata (62.50%) were good performers in HP sites. Acer caesium, Betula utilis, and Morus alba that had low API scores (43.75%) were predicted as poor performers. Thus, G. robusta, Q. floribunda, J. regia, T. ciliata, and F. carica were evaluated as best performers. They could be integrated into plantations drives for environmental management.

Sensitive and rapid determination of amantadine without derivatization in human plasma by LC-MS/MS for a bioequivalence study

A highly sensitive, rapid and rugged liquid chromatography-tandem mass spectrometry (LC-ESI-MS/MS) method was developed for reliable estimation of amantadine (AMD), an antiviral drug in human plasma. The analyte and internal standard (IS), amantadine-d6 (AMD-d6), were extracted from 200 µL plasma by solid phase extraction on Phenomenex Strata-X-C 33 µ cartridges. Chromatography was performed on Synergi™ Hydro-RP C₁₈ (150 mm × 4.6 mm, 4 µm) analytical column using a mixture of acetonitrile and 10 mM ammonium formate, pH 3.0 (80:20, v/v) as the mobile phase. Detection and quantitation was done by multiple reaction monitoring in the positive ionization mode for AMD (m/z 152.1 → 135.1) and IS (m/z 158.0 → 141.1) on a triple quadrupole mass spectrometer. The assay was linear in the concentration range of 0.50–500 ng/mL with correlation coefficient (r²) ≥ 0.9969. The limit of detection of the method was 0.18 ng/mL. The intra-batch and inter-batch precisions were ≤ 5.42% and the accuracy varied from 98.47% to 105.72%. The extraction recovery of amantadine was precise and quantitative in the range of 97.89%–100.28%. IS-normalized matrix factors for amantadine varied from 0.981 to 1.012. The stability of AMD in whole blood and plasma was evaluated under different conditions. The developed method was successfully applied for a bioequivalence study with 100 mg of AMD in 32 healthy volunteers. The reproducibility of the assay was determined by reanalysis of 134 subject samples.

Bacteriological Profile and Antimicrobial Susceptibility Pattern in Chronic Suppurative Otitis Media: A 1-Year Cross-Sectional Study

Inadequate antibiotic treatment, misuse/improper choice of antibiotic and poor compliance of patients have resulted in changes in susceptibility to antibiotics of the causative organisms and also development of resistance to commonly used antibiotics. Thus, this study aimed to identify the bacteriological profile and determine antibiotic susceptibility pattern in CSOM patients. This 1-year cross-sectional study was conducted on 120 clinically diagnosed cases of CSOM attending ear, nose, and throat outpatient department. Ear discharges obtained were processed for bacterial culture (aerobic and anaerobic). Antimicrobial susceptibility testing was done by Kirby-Bauer disc diffusion method. Demographic and clinical characteristics of the patients were recorded. Of total 120 cases, pathogens were isolated from 116 cases. The commonest aerobic organism isolated was Pseudomonas aeruginosa (38.79%) followed by Staphylococcus aureus (32.75%). Staphylococcus aureus showed maximum sensitivity to erythromycin (71.05%), followed by cotrimoxazole (63.15%) and ampicillin (55.26%). Maximum resistance was observed for ciprofloxacin (78.9%), followed by amoxiclave (55.26%). Pseudomonas aeruginosa showed maximum sensitivity to piperacillin (91.11%) followed by gentamicin (71.11%), amikacin (71.11%), moderate sensitivity to ceftazidime (51.11%); however resistance to carbpenicillin (60%). Ciprofloxacin was the most prescribed topical agent showing an increase in resistance to common organisms of CSOM. Hence, it is mandatory to study each case of CSOM bacteriologically to formulate local antibiotic policy for appropriate use of antibiotics. This will certainly help in achieving a safe ear and to control the organisms developing resistance to prevalent antibiotics.

An advanced uracil DNA glycosylase-supplemented loop-mediated isothermal amplification (UDG-LAMP) technique used in the sensitive and specific detection of Cryptosporidium parvum, Cryptosporidium hominis, and Cryptosporidium meleagridis in AIDS patients

The rapid and accurate detection of Cryptosporidium spp. is critically important for the prevention and timely treatment of cryptosporidiosis in AIDS patients (APs). This study was conducted to examine a UDG-LAMP technique for the first time to diagnose cryptosporidiosis in APs. After collecting demographic and clinical data, three stool samples were collected from the participants (120 volunteering APs). The microscopic examination of stained smears using the acid-fast method and the UDG-LAMP assay were performed for each sample. 10% of APs were infected with Cryptosporidium spp. The number of detected cryptosporidiosis cases using the acid-fast staining and UDG-LAMP methods were significantly different (P < 0.001). Diarrhea and weight loss were found to be significantly associated with cryptosporidiosis in patients (P < 0.05). The pretreatment of LAMP reagents with UDG successfully eliminated the likelihood of product re-amplification remaining from previous reactions. The UDG-LAMP technique could detect cryptosporidiosis in APs with high sensitivity and rapidity without carryover contamination.

Blood pressure responses to dietary sodium: Association with autonomic cardiovascular function in normotensive adults

Blood pressure responses to dietary sodium vary widely person-to-person. Salt sensitive rodent models display altered autonomic function, a trait thought to contribute to poor cardiovascular health. Thus, we hypothesized that increased salt sensitivity (SS) in normotensive humans would be associated with increased muscle sympathetic nerve activity (MSNA), decreased high frequency heart rate variability (HF-HRV), and decreased baroreflex sensitivity. Healthy normotensive men and women completed 1week of high (300mmol·day^-1) and 1week of low (20mmol·day^-1) dietary sodium (random order) with 24h mean arterial pressure (MAP) assessed on the last day of each diet to assess SS. Participants returned to the lab under habitual sodium conditions for testing. Forty-two participants are presented in this analysis, 19 of which successful MSNA recordings were obtained (n=42: age 39±2yrs., BMI 24.3±0.5kg·(m²)^-1, MAP 83±1mmHg, habitual urine sodium 93±7mmol·24h^-1; n=19: MSNA burst frequency 20±2 bursts·min^-1). The variables of interest were linearly regressed over the magnitude of SS. Higher SS was associated with increased MSNA (burst frequency: r=0.469, p=0.041), decreased HF-HRV (r=-0.349, p=0.046), and increased LF/HF-HRV (r=0.363, p=0.034). SS was not associated with sympathetic or cardiac baroreflex sensitivity (p>0.05). Multiple regression analysis accounting for age found that age, not SS, independently predicted HF-HRV (age adjusted no longer significant; p=0.369) and LF/HF-HRV (age adjusted p=0.273). These data suggest that age-related salt sensitivity of blood pressure in response to dietary sodium is associated with altered resting autonomic cardiovascular function.

A retrospective study of amrubicin monotherapy for the treatment of relapsed small cell lung cancer in elderly patients

Purpose

Amrubicin is one of the most active chemotherapeutic drugs for small cell lung cancer (SCLC). Previous studies reported its effectiveness and severe hematological toxicity. However, the efficacy of amrubicin monotherapy in elderly patients with SCLC has not been described. The objective of this study was to investigate the feasibility of amrubicin monotherapy in elderly patients and its efficacy for relapsed SCLC.

Methods

A retrospective cohort study design was used. We retrospectively evaluated the clinical effects and adverse events of amrubicin treatment in elderly (≥70 years) SCLC patients with relapsed SCLC.

Results

Between November 2003 and September 2015, 86 patients (aged ≥70 years) received amrubicin monotherapy for relapsed SCLC at four institutions. There were 42 cases of sensitive relapse (S) and 44 of refractory relapse (R). S cases with median age of 75 years (range 70–85 years) and R cases with median age of 74 years (range 70–84 years) were included in our analysis. The median number of treatment cycles was three (range 1–9), and the response rate was 33.7% (40.5% in the S and 27.2% in the R cases). Median progression-free survival time was 4.0 months in the S and 2.7 months in the R patients (p = 0.013). Median survival time from the start of amrubicin therapy was 7.6 months in the S and 5.5 months in the R cases (p = 0.26). The frequencies of grade ≥3 hematological toxicities were as follows: leukopenia, 60.4%; neutropenia, 74.4%; anemia, 11.6%; thrombocytopenia, 16.2%; and febrile neutropenia, 17.4%. Treatment-related death was observed in one patient.

Conclusion

Although hematological toxicities, particularly neutropenia, were severe, amrubicin showed favorable efficacy, not only in the S but also in the R cases, as shown in previous studies. Amrubicin could be a preferable standard treatment in elderly patients with relapsed SCLC. These results warrant further evaluation of amrubicin in elderly patients with relapsed SCLC by a prospective trial.

Electronic supplementary material

The online version of this article (doi:10.1007/s00280-017-3403-9) contains supplementary material, which is available to authorized users.

Imaging-guided synergetic therapy of orthotopic transplantation tumor by superselectively arterial administration of microwave-induced microcapsules

It is an ambitious target to improve overall Hepatocellular Carcinoma therapeutic effects. Recently, MW ablation has emerged as a powerful thermal ablation technique, affording favorable survival with excellent local tumor control. To achieve better therapeutic effects of MW ablation, MW sensitizers are prepared for enhanced MW ablation to preferentially heat tumor territory. However, it is still not practicable for treatment of the orthotopic transplantation tumor. Herein, biocompatible and degradable methoxy poly(ethylene glycol)-poly(lactic-co-glycolic acid) (mPEG-PLGA) microcapsules with hierarchical structure have been designed for microwave-induced tumor therapy. Chemical drug doxorubicin hydrochloride (DOX·HCl), microwave (MW) sensitizers and CT imaging contrast MoS₂ nanosheets and MR imaging contrast Fe₃O₄ nanoparticles are co-incorporated into the microcapsules. In vitro/vivo MR/CT dual-modal imaging results prove the potential application for guiding synergetic therapy and predicting post-therapy tumor progression in the orthotopic transplantation tumor model. After blocking the tumor-feeding arteries, these microcapsules not only exclude the cooling effect by cutting off the blood flow but also enhance MW heating conversion at tumor site. The focused MW heating makes microcapsules mollescent or ruptured and releases DOX·HCl from the microcapsules, achieving the controlled release of drugs for chemical therapy. Compared with MW ablation, 29.4% increase of necrosis diameter of normal liver in rabbit is obtained under MW ablation combined with transcatheter arterial blocking, and the average size of necrosis and inhibition rate of VX-2 liver orthotopic transplantation tumor in rabbit has increased by 129.33% and 73.46%. Moreover, it is proved that the superselectively arterial administration of the as-prepared microcapsules has no recognizable toxicity on the animals. Therefore, this research provides a novel strategy for the construction of MW-induced microcapsules for orthotopic transplantation tumor ablation with the properties of MW sensitizing, superselective arterial blocking, control release and enhanced accumulation of DOX·HCl, and MR/CT dual-modal imaging, which exhibits great potential applications in the field of HCC therapy.

An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS

One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, "What can the organisms in the sample do?" Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here, we present SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with real metagenomes, and the results show that it accurately predicts the subsystems present in the profiled microbial communities, is computationally efficient, and up to 1000 times faster than other tools. SUPER-FOCUS is freely available at http://edwards.sdsu.edu/SUPERFOCUS .

A novel, sensitive and selective method of UPLC/MS-MS for rapid simultaneous determination of midodrine and its active metabolite desglymidodrine in human plasma: Application to support bioequivalence study in healthy human volunteers

A specific, rapid, sensitive and selective ultra-performance liquid chromatography - tandem mass spectrometry has been developed for the simultaneous determination of midodrine and desglymidodrine in human plasma. The analytes and its deuterated analogs were quantitatively extracted from 100μL of human plasma by solid phase extraction technique. Separation of analytes was achieved on the Waters Acquity UPLC BEH C18 (50×2.1mm, 1.7μm) column using acetonitrile-4.0mM ammonium formate, pH 2.5(90:10, v/v) as mobile phase. The protonated analytes were quantified by selected reaction monitoring in the positive ionization mode by triple quadrupole mass spectrometer. The calibration plots were linear over the concentration range of 0.050-50.0ng/mL. The intra-batch and inter-batch precision (%CV) across quality control levels was <4.0 and the% mean relative recovery was ≥96%. Various other parameters like stability in different conditions; matrix effect and reproducibility of the method were performed in accordance with the guidelines specified by the USFDA for bioanalytical method development and validation. The developed method was successfully administered to the pharmacokinetics study of 5 mg midodrine tablet in 12 healthy subjects. Reproducibility of assay was proved by reanalysis of 48 incurred samples.

Association between HLA genes and dust mite sensitivity in a Brazilian population

BACKGROUND

Type I hypersensitivity, also known as IgE-mediated allergy, is a complex, multifactorial condition whose onset and severity are influenced by both genetic and environmental factors. Mite allergens stimulate the production of humoral response (IgE), especially in children, which is closely involved in atopic asthma and rhinitis.

OBJECTIVE

This study aimed to investigate the association between HLA class I (-A, -B, and -C), and HLA class II (-DRB1) genes in individuals sensitive to dust mites (Dermatophagoides farinae, Dermatophagoides pteronyssinus, or Blomia tropicalis) and mite-insensitive controls.

METHODS

396 participants were grouped as mite-sensitive and mite-insensitive according to immediate hypersensitivity as determined by skin-prick tests, and to HLA genotyping by polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO).

RESULTS

After chi-square heterogeneity testing no significant differences were observed in HLA-A, B, and C genes, except for the HLA-DRB1 locus, which, showed a negative association for DRB1∗04, between mite-sensitive and mite-insensitive individuals. In high resolution, DRB1∗04:11 allele was significantly different from all other results (P=0.0042, OR=0.26, and 95%CI=0.09-0.70). The analysis stratified by etiologic agent confirmed these associations.

CONCLUSION

Our results suggest a possible association between HLA-DRB1 genes and hypersensitivity to dust mites.

A rapid and sensitive LC-MS/MS method for determination of lercanidipine in human plasma and its application in a bioequivalence study in Chinese healthy volunteers

A rapid and highly sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been developed and validated for the determination of lercanidipine (LER) in human plasma. The plasma sample was deproteinized with methanol after addition of diazepam (internal standard, IS) and separated on a 38°C Hedera ODS-2 analytical column with a mobile phase of methanol and 5mM ammonium acetate buffer solution containing 0.1% formic acid at an isocratic flow rate of 400μL/min. The detection was performed on an API 4000 tandem mass spectrometer coupled with electrospray ionization (ESI) source in positive ESI mode. Quantification was conducted by multiple reaction monitoring (MRM) of the transitions of m/z 612.2→280.2 for LER and m/z 285.1→193.1 for IS, respectively. The method exhibited high sensitivity (LLOQ of 0.015ng/mL) and good linearity over the concentration range of 0.015-8.0ng/mL. No matrix effect and carry-over effect were observed. The values on both the occasions (intra- and inter-day) were all within 15% at three concentration levels. This robust method was successfully applied in a bioequivalence study to evaluate the pharmacokinetics of LER in 59 healthy male Chinese volunteers after a single oral administration of 10mg LER.

Self-locked aptamer probe mediated cascade amplification strategy for highly sensitive and selective detection of protein and small molecule

In this work, a novel self-locked aptamer probe mediated cascade amplification strategy has been constructed for highly sensitive and specific detection of protein. First, the self-locked aptamer probe was designed with three functions: one was specific molecular recognition attributed to the aptamer sequence, the second was signal transduction owing to the transduction sequence, and the third was self-locking through the hybridization of the transduction sequence and part of the aptamer sequence. Then, the aptamer sequence specific recognized the target and folded into a three-way helix junction, leading to the release of the transduction sequence. Next, the 3'-end of this three-way junction acted as primer to trigger the strand displacement amplification (SDA), yielding a large amount of primers. Finally, the primers initiated the dual-exponential rolling circle amplification (DE-RCA) and generated numerous G-quadruples sequences. By inserting the fluorescent dye N-methyl mesoporphyrin IX (NMM), enhanced fluorescence signal was achieved. In this strategy, the self-locked aptamer probe was more stable to reduce the interference signals generated by the uncontrollable folding in unbounded state. Through the cascade amplification of SDA and DE-RCA, the sensitivity was further improved with a detection limit of 3.8 × 10(-16) mol/L for protein detection. Furthermore, by changing the aptamer sequence of the probe, sensitive and selective detection of adenosine has been also achieved, suggesting that the proposed strategy has good versatility and can be widely used in sensitive and selective detection of biomolecules.

Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards

Absolute quantitative strategies are emerging as a powerful and preferable means of deriving concentrations in biological samples for systems biology applications. Method development is driven by the need to establish new-and validate current-protein biomarkers of high-to-low abundance for clinical utility. In this chapter, we describe a methodology involving two-dimensional (2D) reversed-phase liquid chromatography (RPLC), operated under alkaline and acidic pH conditions, combined with multiple reaction monitoring (MRM)-mass spectrometry (MS) (also called selected reaction monitoring (SRM)-MS) and a complex mixture of stable isotope-labeled standard (SIS) peptides, to quantify a broad and diverse panel of 253 proteins in human blood plasma. The quantitation range spans 8 orders of magnitude-from 15 mg/mL (for vitamin D-binding protein) to 450 pg/mL (for protein S100-B)-and includes 31 low-abundance proteins (defined as being <10 ng/mL) of potential disease relevance. The method is designed to assess candidates at the discovery and/or verification phases of the biomarker pipeline and can be adapted to examine smaller or alternate panels of proteins for higher sample throughput. Also detailed here is the application of our recently developed software tool-Qualis-SIS-for protein quantitation (via regression analysis of standard curves) and quality assessment of the resulting data. Overall, this chapter provides the blueprint for the replication of this quantitative proteomic method by proteomic scientists of all skill levels.

Measuring Chitinase and Protease Activity in Cultures of Fungal Entomopathogens

Entomopathogenic fungi produce a variety of destructive enzymes and metabolites to overcome the unique defense mechanisms of insects. In a first step, fungal chitinases and proteinases need to break down the insect's cuticle. Both enzyme classes support the infection process by weakening the chitin barrier and by producing nutritional cleavage products for the fungus. In a second step, the pathogen can now mechanically penetrate the weakened cuticle and reach the insect's hemolymph where it starts proliferating. The critical enzymes chitinase and proteinase are also excreted into the supernatants of fungal cultures and can be used as indicators of virulence. Chromogenic assays adapted for 96-well microtiter plates that measure these enzymes provide a sensitive, fast, and easy screening method for evaluating the potential biocontrol activity of fungal isolates and may be considered as an alternative to laborious and time-consuming bioassays. Furthermore, monitoring fungal enzyme production in dependence of time, nutrient sources, or other factors can facilitate in establishing optimal growth and harvesting conditions for selected isolates with the aim of achieving maximum biocontrol activity.

Pesticides in Ichkeul Lake-Bizerta Lagoon Watershed in Tunisia: use, occurrence, and effects on bacteria and free-living marine nematodes

This study aimed to identify the most commonly used agricultural pesticides around Ichkeul Lake-Bizerta Lagoon watershed. First survey of pesticide use on agricultural watershed was performed with farmers, Regional Commissioner for Agricultural Development, and pesticide dealers. Then, sediment contamination by pesticides and response of benthic communities (bacteria and free-living marine nematode) were investigated. The analysis of 22 active organochlorine pesticides in sediments was performed according to quick, easy, cheap, effective, rugged, and safe (QuEChERS) method, biodiversity of indigenous bacterial community sediment was determined by terminal restriction fragment length polymorphism (T-RFLP), and free-living marine nematodes were counted. The results of the field survey showed that iodosulfuron, mesosulfuron, 2,4-dichlorophenoxyacetic acid (2,4 D), glyphosate, and fenoxaprops were the most used herbicides, tebuconazole and epoxiconazole the most used fungicides, and deltamethrin the most used insecticide. Sixteen organochlorine pesticide compounds among the 22 examined were detected in sediments up to 2 ppm in Ichkeul Lake, endrin, dieldrin, and hexachlorocyclohexane being the most detected molecules. The most pesticide-contaminated site in the lake presented the higher density of nematode, but when considering all sites, no clear correlation with organochlorine pesticide (OCP) content could be established. The bacterial community structure in the most contaminated site in the lake was characterized by the terminal restriction fragments (T-RFs) 97, 146, 258, 285, and 335 while the most contaminated site in the lagoon was characterized by the T-RFs 54, 263, 315, 403, and 428. Interestingly, T-RFs 38 and 143 were found in the most contaminated sites of both lake and lagoon ecosystems, indicating that they were resistant to OCPs and able to cope with environmental fluctuation of salinity. In contrast, the T-RFs 63, 100, 118, and 381 in the lake and the T-RFs 40, 60, 80, 158, 300, 321, and 357 in the lagoon were sensitive to OCPs. This study highlighted that the intensive use of pesticides in agriculture, through transfer to aquatic ecosystem, may disturb the benthic ecosystem functioning of the protected area. The free-living marine nematodes and bacterial communities represent useful proxy to follow the ecosystem health and its capacity of resilience.

Highly selective and sensitive surface enhanced Raman scattering nanosensors for detection of hydrogen peroxide in living cells

Determination of hydrogen peroxide (H2O2) with high sensitivity and selectivity in living cells is a challenge for evaluating the diverse roles of H2O2 in the physiological and pathological processes. In this work, we present novel surface enhanced Raman scattering (SERS) nanosensors, 4-carboxyphenylboronic acid (4-CA) modified gold nanoparticles (Au NPs/4-CA), for sensing H2O2 in living cells. The nanosensors are based on that the H2O2-triggered oxidation reaction with the arylboronate on Au NPs would liberate the phenol, thus causing changes of the SERS spectra of the nanosensors. The results show the nanosensors feature higher selectivity for H2O2 over other reactive oxygen species, abundant competing cellular thiols and biologically relevant species, as well as excellent sensitivity with a low detection limit of 80 nM, which fulfills the requirements for detection of H2O2 in a biological system. In addition, the SERS nanosensors exhibit long term stability against time and pH, and high biocompatibility. More importantly, the presented nanosensors can be successfully used for monitoring changes of H2O2 levels within living biological samples upon oxidative stress, which opens up new opportunities to study its cellular biochemistry.