A CRISPR/Cas12a-mediated sensitive DNA detection system for gene-edited rice

BACKGROUND

In recent years, genome editing technology represented by CRISPR/Cas9 has been developed and applied in transgenic research and development, and transgenic products have been developed for a variety of applications. Gene editing products, unlike traditional genetically modified crops, which are generally obtained by target gene deletion, insertion, base mutation, etc., may not differ significantly at the gene level from conventional crops, which increases the complexity of testing.

OBJECTIVE

We established a specific and sensitive CRISPR/Cas12a-mediated gene-editing system to detect target fragments in a variety of transgenic rice lines and commercial rice-based processing products.

METHOD

In this study, the CRISPR-Cas12a visible detection system was optimized for the visualization of nucleic acid detection in gene-edited rice. The fluorescence signals were detected by both gel electrophoresis and fluorescence-based methods.

RESULT

The detection limit of the CRISPR-Cas12a detection system established in this study was more precise at 101 copies, demonstrating that CRISPR-Cas12a detection technology is better for low-concentration samples. In addition to achieving single-base detection in gene-edited rice, we showed that different base mutations in the target sequence have different detection efficiencies by sitewise variant compact analysis. The CRISPR-Cas12a system was verified via a common transgenic rice strain and commercial rice sources. The results proved that the detection method could not only be tested in samples with multiple mutation types but could also effectively detect target fragments in commercial rice products.

CONCLUSION

We have developed a set of efficient detection methods with CRISPR-Cas12a for gene-edited rice detection to provide a new technical basis for rapid field detection of gene-edited rice.

HIGHLIGHTS

The CRISPR/Cas12a-mediated visual detection method used to detect gene-edited rice was evaluated for its specificity, sensitivity, and robustness.

Biomarkers for differentiation of coronavirus disease 2019 or extracorporeal membrane oxygenation related inflammation and bacterial/fungal infections in critically ill patients: A prospective observational study

Secondary infections in coronavirus disease 2019 (COVID-19) patients are difficult to distinguish from inflammation associated with COVID-19 and/or extracorporeal membrane oxygenation (ECMO). Therefore, highly specific and sensitive biomarkers are needed to identify patients in whom antimicrobial therapy can be safely withheld. In this prospective monocentric study, 66 COVID-19 patients admitted to the intensive care unit (ICU) for ECMO evaluation were included. A total of 46 (70%) patients with secondary infections were identified by using broad microbiological and virological panels and standardized diagnostic criteria. Various laboratory parameters including C-reactive protein (CRP), interleukin (IL)-6, procalcitonin (PCT), and IL-10 were determined at time of study inclusion. The best test performance for differentiating bacterial/fungal secondary infections and COVID-19 and/or ECMO associated inflammation was achieved by IL-10 (ROC-AUC 0.84) and a multivariant step-wise regression model including CRP, IL-6, PCT, and IL-10 (ROC-AUC 0.93). Data obtained in the present study highlights the use of IL-10 to differentiate secondary bacterial/fungal infections from COVID-19 and/or ECMO associated inflammation in severely ill COVID-19 patients.

The Role of Ga-68-PSMA PET/CT in the Initial Staging of Prostate Cancer - A Single Center 4 Year Experience

Background

Recommended imaging modalities for prostate cancer staging have disappointing sensitivities, whereas [68Ga]-PSMA PET/CT (PET-PSMA) shows promising sensitivities and specificities in the initial management of prostate cancer. Recent studies have revealed that a significant change of management when PET-PSMA was used, with favorable negative predictive values.

Methods

In this retrospective study, we analyzed every PET-PSMA performed in our center for initial staging of intermediate and high-risk prostate cancer. Patients were divided into two groups based on whether imaging modalities other than PET-PSMA were performed. In patients submitted to radical prostatectomy, PET-PSMA findings were compared to histological analysis of the specimen.

Results

PET-PSMA results of 57 patients were gathered, with 77.2% (n=44) having performed CT scan or bone scan (BS) prior to PET-PSMA. Prostate cancer management strategy was changed in 61.4% (n=27), when PET-PSMA was performed following CT and BS. BS and CT results were consistent with PET-PSMA in 43.2% and 44.8%, respectively. In 30 cases, a curative strategy was used based on PET-PSMA findings. PET-PSMA revealed a negative predictive value of 95.2% in 23 patients submitted to radical prostatectomy with bilateral pelvic lymphadenectomy. Prostate SUV values on preoperative PET-PSMA correlated with initial PSA, ISUP grade, PC risk staging and presence of extraprostatic lesions.

Conclusions

PET-PSMA is a key element for prostate cancer staging and management, with high diagnostic accuracy. More prospective studies need to be implemented to determine its role as a first-line staging tool.

Reflectance confocal microscopy: Principles, basic terminology, clinical indications, limitations, and practical considerations

Reflectance confocal microscopy (RCM) is a noninvasive imaging tool used for in vivo visualization of the skin. It has been extensively studied for use in the evaluation of equivocal cutaneous neoplasms to decrease the number of biopsy procedures in patients with benign lesions. Furthermore, its applications are broadening to include presurgical cancer margin mapping, tumor recurrence surveillance, monitoring of ablative and noninvasive therapies, and stratification of inflammatory disorders. With the approval of category I Current Procedural Terminology reimbursement codes for RCM image acquisition and interpretation, use of this technology has been increasingly adopted by dermatologists. The first article in this 2-part continuing medical education series highlights basic terminology, principles, clinical applications, limitations, and practical considerations in the clinical use of RCM technology.

Development of novel aptamer-based enzyme-linked apta-sorbent assay (ELASA) for rapid detection of mariculture pathogen Vibrio alginolyticus

As the major opportunistic pathogen to both marine animals and humans, Vibrio alginolyticus (V. alginolyticus) has caused heavy economic losses to mariculture. ssDNA aptamer VA2 targeting live V. alginolyticus was generated by systematic evolution of ligands by exponential enrichment (SELEX) technology in our previous study. In this study, we first developed aptamer (VA2)-based enzyme-linked apta-sorbent assay (VA2-ELASA) for rapid detection of mariculture pathogen V. alginolyticus. The VA2-ELASA could achieve the rapid detection for V. alginolyticus infection with high specificity and sensitivity. The VA2-ELASA could specifically identify V. alginolyticus, but not other non-target bacterial strains. VA2-ELASA could detect V. alginolyticus at the concentration of 5 × 10⁴ /ml, the incubation time short to 1 min and the incubation temperature as high as 45°C, which proved sensitivity and stability of the novel VA2-ELASA in this study. It took less than one hour to accomplish the detection process by VA2-ELASA. The characteristics of specificity, sensitivity and easy operation make VA2-ELASA a novel useful technology for the rapid diagnosis of pathogen V. alginolyticus in mariculture.

Comparison of Scoring Systems in Predicting Success of Percutaneous Nephrolithotomy

Background:

Scoring systems are useful to inform the patients about the success and complication rates of the operation prior the surgery.

Aims:

To determine the applicability of the popular scoring systems (Guy’s, stone size, tract length, obstruction, number of involved calices, and essence/stone density and Clinical Research Office of the Endourological Society) by means of examining preoperative data of patients treated with percutaneous nephrolithotomy.

Study Design:

Cross sectional study.

Methods:

We retrospectively reviewed files of the patients who had undergone percutaneous nephrolithotomy in our center between 2011 and 2015. Excluded from the study were patients aged <18 years, and those who were not assessed preoperatively with computed tomography. Preoperative computed tomography images of all patients were assessed by a single observer, and patients were graded based on three scoring system. Demographic data were analyzed along with perioperative data (operation, fluoroscopy, length of hospital stay, changes in hematocrit values, location, and number of access sites, stone-free and complication rates).

Results:

A total of 298 patients who had been treated with 300 procedures were enrolled into the study. Mean age, stone burden, number of stones, and density were 48.1±12.9 years, 663.5±442.8 mm², 1.8±1.1 and 888.3±273 HU respectively. Scores of the cases based on Guy’s, stone size, tract length, obstruction, number of involved calices, and essence/stone density, and Clinical Research Office of the Endourological Society scoring system were calculated as 2, 7.6, and 222.1 points respectively. 81.6% of the patients were stone-free. Complications were detected in 30 (9.9%) patients. Based on receiver operating characteristic curve analysis a positive correlation was detected between success rate and scoring systems, i.e., Guy’s (p=<0.001, r=-0.309), stone size, tract length, obstruction, number of involved calices, and essence/stone density (p=<0.001, r=-0.295), and Clinical Research Office of the Endourological Society (p=<0.001, r=0.426). The Clinical Research Office of the Endourological Society scoring system had the highest predictive value. The sensitivity rates rates for Guy’s, Clinical Research Office of the Endourological Society and Stone scoring system were as 78.78%, 80% and 82.34% respectively.

Conclusion:

All of scoring systems predicted correctly the success of the percutaneous nephrolithotomy procedures. The Clinical Research Office of the Endourological Society scoring system had the highest predictive value.

Evolution of proteomic biomarker for chronic liver disease: Promise into reality

Liver is the vital organ for synthesis of proteins whose concentration in blood reflects liver dysfunction. Variations in protein domain can generate clinically significant biomarkers. Biomarker pipeline includes discovery of candidates, qualification, verification, assay optimization, and validation. Advances in proteomic approach can discover protein biomarker candidates based on “up-or-down” regulation or fold change in expression which is correlated with disease state. Despite numerous biomarker candidates been discovered, only few are useful in clinical practice which indicates the need for well-established validation regimen. Hence, the main purpose of this review is to understand the protein biomarker development and pitfalls. Companion diagnostics provide insights into potential cost-effective diagnosis for chronic liver disease.

Identification of circulating protein biomarkers in patients with hepatocellular carcinoma concomitantly infected with chronic hepatitis C virus

CONTEXT

The incidence rate of hepatocellular carcinoma (HCC) is higher in developing countries, and most cases are associated with chronic hepatitis C virus (HCV) infection.

OBJECTIVE

To evaluate the circulating proteins as liver biomarkers for the identification of HCC associated with HCV infection in Egyptian patients using LC-MS/MS analysis.

METHODS

Blood sera were collected from 31 HCC patients and the fractionated proteins were subjected to LC-MS/MS analysis. Protein candidates were validated by enzyme-linked immunosorbent assay (ELISA).

RESULTS

Thirty-three proteins were significantly identified in the sera of HCC patients with persistent HCV infection. These proteins are involved in several biological processes including acute phase response, complement activation, hemostasis process and lipid metabolism. The level of lectin galactoside-binding soluble 3 binding protein (LGALS3BP), Kininogen-1 (KNG1), serum amyloid A2 (SAA2) and paraoxonase 1 (PON1) and alpha-fetoprtoein (AFP) were elevated in serum.

CONCLUSION

In HCC patients with chronic HCV infection, we identified a group of differentially expressed circulating proteins involved in regulating different cellular mechanisms.