Type I CRISPR-Cas-mediated microbial gene editing and regulation

There are six major types of CRISPR-Cas systems that provide adaptive immunity in bacteria and archaea against invasive genetic elements. The discovery of CRISPR-Cas systems has revolutionized the field of genetics in many organisms. In the past few years, exploitations of the most abundant class 1 type I CRISPR-Cas systems have revealed their great potential and distinct advantages to achieve gene editing and regulation in diverse microorganisms in spite of their complicated structures. The widespread and diversified type I CRISPR-Cas systems are becoming increasingly attractive for the development of new biotechnological tools, especially in genetically recalcitrant microbial strains. In this review article, we comprehensively summarize recent advancements in microbial gene editing and regulation by utilizing type I CRISPR-Cas systems. Importantly, to expand the microbial host range of type I CRISPR-Cas-based applications, these structurally complicated systems have been improved as transferable gene-editing tools with efficient delivery methods for stable expression of CRISPR-Cas elements, as well as convenient gene-regulation tools with the prevention of DNA cleavage by obviating deletion or mutation of the Cas3 nuclease. We envision that type I CRISPR-Cas systems will largely expand the biotechnological toolbox for microbes with medical, environmental and industrial importance

The efficacy and safety of condoliase for lumbar disc herniation: a systematic review and meta-analysis

Background: Chemonucleolysis is a minimally invasive treatment of lumbar disc herniation (LDH). However, the low specificity of the enzyme and the existence of serious adverse events limit the application of chemonucleolysis. Clinical studies in recent years have shown that Chondroitin sulfate ABC endolyase (condoliase) is a potential therapeutic enzyme for LDH. Aim. A meta-analysis was conducted to determine the efficacy and safety of condoliase in LDH treatment.Methods: We searched Web of Science, Embase, PubMed, and Cochrane Library databases. Two reviewers independently screened articles, extracted data, and assessed the risk of bias. The outcomes were the total effective rate, Oswestry Disability Index (ODI) score change, the proportion of lumbar surgery after condoliase treatment, herniated mass volume change, Pfirrmann grade change, and adverse events. Review Manager 5.3 and Stata 12.0 were used for meta-, sensitivity, and bias analysis.Results: Ten studies were included. A single-arm meta-analysis showed that the total effective rate was 78% [95% confidence interval (CI) 75%–81%], the proportion of surgery was 9% (95% CI 7%–12%), the proportion of Pfirrmann grade change was 43% (95%CI 38%–47%), and the adverse events were 4% (95% CI 2%–6%) after condoliase treatment. The two-arm meta-analysis showed that the ODI score change [standardized mean difference (SMD) −2.46, 95% CI −3.30 to −1.63] and the herniated mass volume change (SMD −16.97, 95% CI −23.92 to −10.03) of the condoliase treatment group were greater than those of the placebo control group, and there was no difference in adverse events between the two groups (OR 1.52, 95% CI 0.60–3.85). The results of sensitivity and publication bias analyses showed that the results were robust.Conclusion: Condoliase intradiscal injection has excellent eutherapeutic and safety for LDH, thus, has considerable potential as a treatment option besides conservative treatment and surgical intervention for LDH.Systematic Review Registration:https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022375492, PROSPERO (CRD42022375492)

Multidrug Efflux Systems in Microaerobic and Anaerobic Bacteria

Active drug efflux constitutes an important mechanism of antibiotic and multidrug resistance in bacteria. Understanding the distribution, expression, and physiological functions of multidrug efflux pumps, especially under physiologically and clinically relevant conditions of the pathogens, is the key to combat drug resistance. In animal hosts, most wounded, infected and inflamed tissues display low oxygen tensions. In this article, we summarize research development on multidrug efflux pumps in the medicinally relevant microaerobic and anaerobic pathogens and their implications in the effort to combat drug-resistant infections

Antibiotic influx and efflux in Pseudomonas aeruginosa: Regulation and therapeutic implications

Abstract Pseudomonas aeruginosa is a notorious multidrug‐resistant pathogen that poses a serious and growing threat to the worldwide public health. The expression of resistance determinants is exquisitely modulated by the abundant regulatory proteins and the intricate signal sensing and transduction systems in this pathogen. Downregulation of antibiotic influx porin proteins and upregulation of antibiotic efflux pump systems owing to mutational changes in their regulators or the presence of distinct inducing molecular signals represent two of the most efficient mechanisms that restrict intracellular antibiotic accumulation and enable P. aeruginosa to resist multiple antibiotics. Treatment of P. aeruginosa infections is extremely challenging due to the highly inducible mechanism of antibiotic resistance. This review comprehensively summarizes the regulatory networks of the major porin proteins (OprD and OprH) and efflux pumps (MexAB‐OprM, MexCD‐OprJ, MexEF‐OprN, and MexXY) that play critical roles in antibiotic influx and efflux in P. aeruginosa. It also discusses promising therapeutic approaches using safe and efficient adjuvants to enhance the efficacy of conventional antibiotics to combat multidrug‐resistant P. aeruginosa by controlling the expression levels of porins and efflux pumps. This review not only highlights the complexity of the regulatory network that induces antibiotic resistance in P. aeruginosa but also provides important therapeutic implications in targeting the inducible mechanism of resistance

Nonlinearity association of serum calcium with the risk of anaemia in US adults

ABSTRACTBackground Calcium plays a key role in many bio-homeostasis functions. Previous studies indicated that serum calcium is associated with diseases such as anaemia. However, the evidence on the association between serum calcium levels and anaemia risk is limited. Thus, the purpose of our study is to investigate the relationship between serum calcium and anaemia in US adults.Methods This cross-sectional study used data from the National Health and Nutrition Examination Survey (NHANES) including 15,519 participants, aged ≥18 years. The analyses were performed using multivariate logistic regression and a generalized additive model (GAM). Subgroup analysis, stratified by gender and age, was also performed.Results Among the sample of 15,519 individuals, 1565 (10.8%) had been diagnosed with anaemia. Both the univariate logistic regression model and multivariate logistic regression model showed a reverse relationship between serum calcium and anaemia risk. Moreover, a non-linear association between serum calcium and anaemia risk was observed using GAM and smooth curve fitting. The inflection point of serum calcium was at 2.3 mmol/L. GAM with penalized splines suggested a reverse association between serum calcium and the prevalence of anaemia when the concentration of serum calcium was below 2.3 mmol/L. In contrast, we found no statistically significant difference when serum calcium concentration was higher than the inflection point (2.3 mmol/L).Conclusion Lower serum calcium levels were associated with increased risk of anaemia risk. Moreover, we observed non-linear associations between serum calcium and anaemia risk. Our results need to be confirmed in future prospective studies

Distribution Contract Analysis on e-Platform by Considering Channel Role and Good Complementarity

Although suppliers can sell their goods on e-retailers’ e-platforms through either a wholesale or agency contract, suppliers that produce complementary goods and have different channel roles have been confused as to how to choose an optimal distribution contract. This paper aims to study this problem by considering the combined impacts of suppliers’ channel roles, e-retailer’s referral fees, goods’ differences in the level of complementarity and goods’ differences in potential demand. Our results show that, regardless of one supplier’s distribution contract choice, the other supplier always prefers agency contract, which is independent of two suppliers’ channel roles, the e-retailer’s referral fees, two goods’ differences in the level of complementarity and two goods’ differences in the potential demand. Moreover, when two suppliers use different distribution contracts to sell goods with different levels of complementarity on the same e-retailer’s e-platform, low-complementarity goods have a larger optimal retail price only if the two goods’ differences in the level of complementarity are sufficiently high, and the supplier can obtain more profits by producing low-complementarity goods regardless of the supplier’s distribution contract and channel role

Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853

Abstract Background Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome. Results Here we sequenced and assembled the complete genome of P. aeruginosa ATCC 27853 using the Pacific Biosciences SMRT (PacBio) technology and Illumina sequencing platform. We found that accessory genes of ATCC 27853 including prophages and genomic islands (GIs) mainly contribute to the difference between P. aeruginosa ATCC 27853 and other P. aeruginosa strains. Seven prophages were identified within the genome of P. aeruginosa ATCC 27853. Of the predicted 25 GIs, three contain genes that encode monoxoygenases, dioxygenases and hydrolases that could be involved in the metabolism of aromatic compounds. Surveying virulence-related genes revealed that a series of genes that encode the B-band O-antigen of LPS are lacking in ATCC 27853. Distinctive SNPs in genes of cellular adhesion proteins such as type IV pili and flagella biosynthesis were also observed in this strain. Colony morphology analysis confirmed an enhanced biofilm formation capability of ATCC 27853 on solid agar surface compared to Pseudomonas aeruginosa PAO1. We then performed transcriptome analysis of ATCC 27853 and PAO1 using RNA-seq and compared the expression of orthologous genes to understand the functional genome and the genomic details underlying the distinctive colony morphogenesis. These analyses revealed an increased expression of genes involved in cellular adhesion and biofilm maturation such as type IV pili, exopolysaccharide and electron transport chain components in ATCC 27853 compared with PAO1. In addition, distinctive expression profiles of the virulence genes lecA, lasB, quorum sensing regulators LasI/R, and the type I, III and VI secretion systems were observed in the two strains. Conclusions The complete genome sequence of P. aeruginosa ATCC 27853 reveals the comprehensive genetic background of the strain, and provides genetic basis for several interesting findings about the functions of surface associated proteins, prophages, and genomic islands. Comparative transcriptome analysis of P. aeruginosa ATCC 27853 and PAO1 revealed several classes of differentially expressed genes in the two strains, underlying the genetic and molecular details of several known and yet to be explored morphological and physiological potentials of P. aeruginosa ATCC 27853

Rapid Identification of Rainbow Trout Adulteration in Atlantic Salmon by Raman Spectroscopy Combined with Machine Learning

This study intends to evaluate the utilization potential of the combined Raman spectroscopy and machine learning approach to quickly identify the rainbow trout adulteration in Atlantic salmon. The adulterated samples contained various concentrations (0–100% w/w at 10% intervals) of rainbow trout mixed into Atlantic salmon. Spectral preprocessing methods, such as first derivative, second derivative, multiple scattering correction (MSC), and standard normal variate, were employed. Unsupervised algorithms, such as recursive feature elimination, genetic algorithm (GA), and simulated annealing, and supervised K-means clustering (KM) algorithm were used for selecting important spectral bands to reduce the spectral complexity and improve the model stability. Finally, the performances of various machine learning models, including linear regression, nonlinear regression, regression tree, and rule-based models, were verified and compared. The results denoted that the developed GA–KM–Cubist machine learning model achieved satisfactory results based on MSC preprocessing. The determination coefficient (R2) and root mean square error of prediction sets (RMSEP) in the test sets were 0.87 and 10.93, respectively. These results indicate that Raman spectroscopy can be used as an effective Atlantic salmon adulteration identification method; further, the developed model can be used for quantitatively analyzing the rainbow trout adulteration in Atlantic salmon

Mechanical Properties of RTM-made Composite Cross-joints

AbstractTension and shear tests are carried out on composite cross-joints, produced by resin transfer moulding (RTM), stitch-RTM and cobonding techniques separately, to investigate the influences of different production methods on their mechanical properties and their failure mechanism. It is concluded from test results that, in terms of mechanical properties, the RTM-made cross-joint holds superiority over other two, and both stitch-RTM and cobonding methods have significant adverse effects on mechanical properties. Experimental observation and finite element (FE) numerical simulation show that the delamination first takes place at the upper triangle-like resin-rich zone of joints, then propagates along the interface between the zone and the curved webs/flanges to the bottom plate, and grows along the horizontal bottom plate till failure of the joint accurs at last. Results demonstrate that there is a good agreement between the FE model and the tests