CRISPR/Cas12a-assisted visible fluorescence for pseudo dual nucleic acid detection based on an integrated chip.

BACKGROUND: A false negative result is one of the major problems in nucleic acid detection. Failure to screen positive samples for pathogens or viruses poses a risk to public health. This situation will lead to more serious consequences for infectious pathogens or viruses. At present, the common solution is to introduce exogenous or endogenous internal control. Because it amplifies and is detected separately from the target gene, it cannot avoid false negative results caused by DNA extraction failure or reagent inactivation. There is an urgent need for a simple and reliable method to solve the false negative problem of nucleic acid detection. RESULTS: We established a chip and an on-chip detection method for the integrated detection of target genes and internal control using the CRISPR system in LAMP amplification products. The chip is processed from a low-cost PMMA board and has three chambers and some channels. After adding the sample, the chip only needs to be rotated twice, and the sample enters three chambers successively depending on its gravity for dual LAMP reaction and CRISPR detections. With a portable LED blue light exciter, visual fluorescence detection is realized. Whether the detection result is positive, negative, or invalid can be determined according to the fluorescence in the CRISPR chamber for target gene and CRISPR chamber for internal control. In this study, the detection of Salmonella enterica in Fenneropenaeus chinensis was taken as an example. The results showed good specificity and sensitivity. It could detect as low as 15 copies/µL of Salmonella enterica. SIGNIFICANCE: The on-chip detection solves the problem of aerosol contamination and false negative results. It has the advantages of high sensitivity, high specificity, high accuracy, and low cost. This research will advance the development of nucleic acid detection technology, providing a new and reliable strategy for POCT detection of pathogenic bacteria and viruses.

Development of a convenient and effective hypertension risk prediction model and exploration of the relationship between Serum Ferritin and Hypertension Risk: a study based on NHANES 2017-March 2020.

Background: Hypertension is a major public health problem, and its resulting other cardiovascular diseases are the leading cause of death worldwide. In this study, we constructed a convenient and high-performance hypertension risk prediction model to assist in clinical diagnosis and explore other important influencing factors. Methods: We included 8,073 people from NHANES (2017-March 2020), using their 120 features to form the original dataset. After data pre-processing, we removed several redundant features through LASSO regression and correlation analysis. Thirteen commonly used machine learning methods were used to construct prediction models, and then, the methods with better performance were coupled with recursive feature elimination to determine the optimal feature subset. After data balancing through SMOTE, we integrated these better-performing learners to construct a fusion model based for predicting hypertension risk on stacking strategy. In addition, to explore the relationship between serum ferritin and the risk of hypertension, we performed a univariate analysis and divided it into four level groups (Q1 to Q4) by quartiles, with the lowest level group (Q1) as the reference, and performed multiple logistic regression analysis and trend analysis. Results: The optimal feature subsets were: age, BMI, waist, SBP, DBP, Cre, UACR, serum ferritin, HbA1C, and doctors recommend reducing salt intake. Compared to other machine learning models, the constructed fusion model showed better predictive performance with precision, accuracy, recall, F1 value and AUC of 0.871, 0.873, 0.871, 0.869 and 0.966, respectively. For the analysis of the relationship between serum ferritin and hypertension, after controlling for all co-variates, OR and 95% CI from Q2 to Q4, compared to Q1, were 1.396 (1.176-1.658), 1.499 (1.254-1.791), and 1.645 (1.360-1.989), respectively, with P < 0.01 and P for trend <0.001. Conclusion: The hypertension risk prediction model developed in this study is efficient in predicting hypertension with only 10 low-cost and easily accessible features, which is cost-effective in assisting clinical diagnosis. We also found a trend correlation between serum ferritin levels and the risk of hypertension.

A method of motion estimation of segmental ventricular wall with tracking of ultrasonic echocardiogram.

BACKGROUND: Ultrasonic echocardiography is commonly used for monitoring myocardial dysfunction. However, it has limitations such as poor quality of echocardiography images and subjective judgment of doctors. METHODS: In this paper, a calculation model based on optical flow tracking of echocardiogram is proposed for the quantitative estimation motion of the segmental wall. To improve the accuracy of optical flow estimation, a method based on confidence-optimized multiresolution(COM) optical flow model is proposed to reduce the estimation errors caused by the large amplitude of myocardial motion and the presence of "shadows" and other image quality problems. In addition, motion vector decomposition and dynamic tracking of the ventricular region of interest are used to extract information regarding the myocardial segmental motion. The proposed method was validated using simulation images and 50 clinical cases (25 patients and 25 healthy volunteers) for myocardial motion analysis. RESULTS: The results demonstrated that the proposed method could track the motion information of myocardial segments well and reduce the estimation errors of optical flow caused due to the use of low-quality echocardiogram images. CONCLUSIONS: The proposed method improves the accuracy of motion estimation for the cardiac ventricular wall.

Phenotypic comparison and DNA sequencing analysis of a wild-type and a pediocin-resistant mutant of Listeria ivanovii.

Listeria ivanovii is one of the two pathogenic species within the genus Listeria, the other being Listeria monocytogenes. In this study, we generated a stable pediocin resistant mutant Liv-r1 of a L. ivanovii strain, compared phenotypic differences between the wild-type and the mutant, localised the pediocin-induced mutations in the chromosome, and analysed the mechanisms behind the bacteriocin resistance. In addition to pediocin resistance, Liv-r1 was also less sensitive to nisin. The growth of Liv-r1 was significantly reduced with glucose and mannose, but less with cellobiose. The cells of Liv-r1 adsorbed less pediocin than the wild-type cells. Consequently, with less pediocin on the cell surface, the mutant was also less leaky, as shown as the release of intracellular lactate dehydrogenase to the supernatant. The surface of the mutant cells was more hydrophobic than that of the wild-type. Whole genome sequencing revealed numerous changes in the Liv-r1 chromosome. The mutations were found e.g., in genes encoding sigma-54-dependent transcription regulator and internalin B, as well as in genes involved in metabolism of carbohydrates such as glucose and cellobiose. Genetic differences observed in the mutant may be responsible for resistance to pediocin but no direct evidence is provided.

MAL62 Overexpression Enhances Freezing Tolerance of Baker's Yeast in Lean Dough by Enhancing Tps1 Activity and Maltose Metabolism.

Trehalose plays a crucial role in response to freezing stress in baker's yeast. MAL62, a gene involved in the adenosine diphosphoglucose-dependent trehalose synthesis pathway, can increase trehalose content. However, the difference between MAL62-related trehalose synthesis and traditional uridine diphosphoglucose-dependent trehalose synthesis is not well-understood. MAL62 overexpression showed less effect in enhancing intracellular trehalose compared to TPS1 overexpression. However, MAL62 overexpression elicited trehalose synthesis before fermentation with enhanced maltose metabolism and had a similar effect on cell viability after freezing. Furthermore, MAL62 and TPS1 overexpression in the NTH1 deletion background further strengthened freezing tolerance and improved leavening ability. Our results suggest that the enhancement in freezing tolerance by MAL62 overexpression may involve multiple pathways rather than simply enhancing trehalose synthesis. The results reveal valuable insights into the relationship between maltose metabolism and freezing tolerance and may help to develop better yeast strains for enhancing fermentation characteristics of frozen dough.

MAL62 overexpression and NTH1 deletion enhance the freezing tolerance and fermentation capacity of the baker's yeast in lean dough.

BACKGROUND: Trehalose is related to several types of stress responses, especially freezing response in baker's yeast (Saccharomyces cerevisiae). It is desirable to manipulate trehalose-related genes to create yeast strains that better tolerate freezing-thaw stress with improved fermentation capacity, which are in high demand in the baking industry. RESULTS: The strain overexpressing MAL62 gene showed increased trehalose content and cell viability after prefermention-freezing and long-term frozen. Deletion of NTH1 in combination of MAL62 overexpression further strengthens freezing tolerance and improves the leavening ability after freezing-thaw stress. CONCLUSIONS: The mutants of the industrial baker's yeast with enhanced freezing tolerance and leavening ability in lean dough were developed by genetic engineering. These strains had excellent potential industrial applications.

Attachment of Escherichia coli to Listeria monocytogenes for pediocin-mediated killing.

Listeria phage endolysin cell wall-binding domain (CBD) from the Listeria phage A500 was fused with flagellar subunit FliC in Escherichia coli, aiming at binding of E. coli cells to Listeria cells, followed by enhanced killing of Listeria by pediocin production. FliC::CBD chimeric flagella were expressed and detected by Western blot. However, only few chimeric flagella could be isolated from the recombinant cells compared with sufficient amount of wild-type flagella obtained from the host cells. Interestingly, wild-type flagella extract showed capacity of binding Listeria cells. Pediocin-secreting E. coli cells with Listeria-binding flagella killed approximately 40 % of the Listeria cells, whereas cell-free spent growth medium with the same pediocin concentration only inhibited Listeria growth. These results suggested that binding the Listeria to bacteriocin-secreting cells improves killing.

Modelling growth and bacteriocin production by Pediococcus acidilactici PA003 as a function of temperature and pH value.

To investigate the effect of pH and temperature on the cell growth and bacteriocin production of Pediococcus acidilactici PA003, a lactic acid bacterium isolated from traditionally fermented cabbage, the kinetic behaviour of P. acidilactici PA003 was simulated in vitro during laboratory fermentations by making use of MRS broth. Firstly, primary models were developed for cell growth, glucose consumption, lactic acid and bacteriocin production for a given set of environmental conditions. Based on primary models, further study was undertaken to fit secondary models to describe the influence of temperature and pH on microbial behaviour. The models were validated successfully for all components. The results from the cell yield coefficient for lactic acid production reflected the homofermentative nature of P. acidilactici PA003. Both cell growth and bacteriocin production were very much influenced by changes in temperature and pH. The optimal condition for specific growth rate and biomass concentration was almost the same at pH 6.5 and 35 °C. At 35 °C and pH 6.1, the maximal bacteriocin activity was also achieved. The kinetic models provide useful tools for elucidating the mechanisms of temperature and pH on the kinetic behaviour of P. acidilactici PA003. The information obtained in this paper may be very useful for the selection of suitable starter cultures for a particular fermentation process and is a first step in the optimization of food fermentation processes and technology as well.

Cell immobilization studies using a cellulose-binding domain fused to PrtP in Lactococcus lactis.

The cellulose-binding domain (CBD) of XylA was fused with PrtP, NisP and AcmA anchors derived from Lactococcus lactis under P45 promoter and Usp45 secretion signal. The fusion construct with the anchor PrtP (334 aa) was shown to exhibit the most efficient immobilization. The CBD-PrtP construct on the other hand was not efficiently attached to the cell wall and as such was found mainly in the supernatant. Results also showed that expression of the CBD-NisP anchor fusion led to a similar result. This raised the question if more efficient binding of the anchor to the cell wall by sortase could enhance the efficiency of cell immobilization to the cellulosic material. However, expressing sortase with the CBD-PrtP fusion did not improve the immobilization of the cells to cellulose.  

Fusion expression of pedA gene to obtain biologically active pediocin PA-1 in Escherichia coli.

Two heterologous expression systems using thioredoxin (trxA) as a gene fusion part in Escherichia coli were developed to produce recombinant pediocin PA-1. Pediocin PA-1 structural gene pedA was isolated from Pediococcus acidilactici PA003 by the method of polymerase chain reaction (PCR), then cloned into vector pET32a(+), and expressed as thioredoxin-PedA fusion protein in the host strain E. coli BL21 (DE3). The fusion protein was in the form of inclusion body and was refolded before purification by nickel-iminodiacetic acid (Ni-IDA) agarose resin column. Biological activity of recombinant pediocin PA-1 was analyzed after cleavage of the fusion protein by enterokinase. Agar diffusion test revealed that 512-arbitrary unit (AU) recombinant pediocin PA-1 was obtained from 1 ml culture medium of E. coli (pPA003PED1) using Listeria monocytogenes as the indicator strain. Thioredoxin-PedA fusion gene was further cloned into pET20b(+). Thioredoxin-PedA fusion protein was detected in both the periplasmic and cytoplasmic spaces. The recombinant pediocin PA-1 from the soluble fraction attained 384 AU from 1 ml culture medium of E. coli (pPA003PED2). Therefore, biologically active pediocin PA-1 could be obtained by these two hybrid gene expression methods.