Metagenomic next-generation sequencing for detecting lower respiratory tract infections in sputum and bronchoalveolar lavage fluid samples from children

Lower respiratory tract infections are common in children. Bronchoalveolar lavage fluid has long been established as the best biological sample for detecting respiratory tract infections; however, it is not easily collected in children. Sputum may be used as an alternative yet its diagnostic accuracy remains controversial. Therefore, this study sought to evaluate the diagnostic accuracy of sputum for detecting lower respiratory tract infections using metagenomic next-generation sequencing. Paired sputum and bronchoalveolar lavage fluid samples were obtained from 68 patients; pathogens were detected in 67 sputum samples and 64 bronchoalveolar lavage fluid samples by metagenomic next-generation sequencing, respectively. The combined pathogen-detection rates in the sputum and bronchoalveolar lavage fluid samples were 80.90% and 66.2%, respectively. For sputum, the positive predictive values (PPVs) and negative predictive values (NPVs) for detecting bacteria were 0.72 and 0.73, respectively, with poor Kappa agreement (0.30; 95% confidence interval: 0.218–0.578, P < 0.001). However, viral detection in sputum had good sensitivity (0.87), fair specificity (0.57), and moderate Kappa agreement (0.46; 95% confidence interval: 0.231–0.693, P < 0.001). The PPVs and NPVs for viral detection in sputum were 0.82 and 0.67, respectively. The consistency between the sputum and bronchoalveolar lavage fluid was poor for bacterial detection yet moderate for viral detection. Thus, clinicians should be cautious when interpreting the results of sputum in suspected cases of lower respiratory tract infections, particularly with regards to bacterial detection in sputum. Viral detection in sputum appears to be more reliable; however, clinicians must still use comprehensive clinical judgment

Application of Nanotechnology in Immunity against Infection

The immune system has a physiological defense function, protecting the body from infectious diseases. Antibiotics have long been one of the most important means to treat infectious diseases, but in recent years, with the emergence of more and more multidrug-resistant (MDR) bacteria, it has become urgent to find new ways or drugs to treat infectious diseases. Nanoparticles (NPs) have attracted extensive attention owing to the special properties within the particle size range of 1–100 nanometers. In addition, NPs also have special shape symmetry and relative structural stability. The emergence of nanotechnology has brought new light to the widespread existence of MDR by its different antibacterial mechanisms. In addition to antibiotic nanocarriers being able to improve the antibacterial effect of antibiotics, some NPs also have certain antibacterial effect. What is more interesting is that linking functional groups on the surface of NPS as coatings can improve the stability of the whole system and improve the biocompatibility. The present review overviews the development of antimicrobial agents, so as to better understand the causes and mechanisms of antibiotic resistance in most microbial species, and to better think and explore new strategies to solve the problem. At the same time, this review introduces how nanotechnology can be applied to anti-infection immunity and its practical application and advantages in the treatment of infection

The effects of two free-floating plants (Eichhornia crassipes and Pistia stratiotes) on the burrow morphology and water quality characteristics of pond loach (Misgurnus anguillicaudatus) habitat

Loach exhibit conspicuous drilling behaviors in the mud of shallow waters, yet their burrow morphology and the factors affecting this behavior have received little attention. We characterized the burrow morphology and water quality of the pond loach Misgurnus anguillicaudatus in three scenarios: in tanks without plants, tanks with the free-floating plant water hyacinth Eichhornia crassipes, and tanks with water lettuce Pistia stratiotes. Water hyacinth effectively removed water TN, COD, NO3-N and NH4-N, and water lettuce removed water TP and NH4-N. Water hyacinth and water lettuce markedly reduced water turbidity and DO, increased TOC and EC. Water hyacinth purified water more effectively than water lettuce, providing a suitable habitat for loach feeding, living and burrowing. The burrow structures were V-shaped, Y-shaped, inverted L-shaped, or complicated dendritic networks composed of multiple V shapes. The hyacinth treatment was characterized by the greatest burrow volume, length, depth, and structural complexity, but the opening size was reduced by dense root mat coverage. Burrows in the water lettuce treatment were characterized by intermediate volume, length, branches and sinuosity, but they had the largest opening and pit size. The control treatment had a flat bottom with the smallest, shortest burrows. This study indicates that free-floating plants improve habitat suitability and change burrow morphology and may be used to improve loach breeding methods

Measurements of Gene Expression at Steady State Improve the Predictability of Part Assembly

Mathematical modeling of genetic circuits generally assumes that gene expression is at steady state when measurements are performed. However, conventional methods of measurement do not necessarily guarantee that this assumption is satisfied. In this study, we reveal a bi-plateau mode of gene expression at the single-cell level in bacterial batch cultures. The first plateau is dynamically active, where gene expression is at steady state; the second plateau, however, is dynamically inactive. We further demonstrate that the predictability of assembled genetic circuits in the first plateau (steady state) is much higher than that in the second plateau where conventional measurements are often performed. By taking the nature of steady state into consideration, our method of measurement promises to directly capture the intrinsic property of biological parts/circuits regardless of circuit–host or circuit–environment interactions

Automated Design of Genetic Toggle Switches with Predetermined Bistability

Synthetic biology aims to rationally construct biological devices with required functionalities. Methods that automate the design of genetic devices without post-hoc adjustment are therefore highly desired. Here we provide a method to predictably design genetic toggle switches with predetermined bistability. To accomplish this task, a biophysical model that links ribosome binding site (RBS) DNA sequence to toggle switch bistability was first developed by integrating a stochastic model with RBS design method. Then, to parametrize the model, a library of genetic toggle switch mutants was experimentally built, followed by establishing the equivalence between RBS DNA sequences and switch bistability. To test this equivalence, RBS nucleotide sequences for different specified bistabilities were <i>in silico</i> designed and experimentally verified. Results show that the deciphered equivalence is highly predictive for the toggle switch design with predetermined bistability. This method can be generalized to quantitative design of other probabilistic genetic devices in synthetic biology

Targeted Imaging of Brain Tumors with a Framework Nucleic Acid Probe

Development of agents for delivering drugs and imaging probes across the blood–brain barrier (BBB) remains a major challenge. In this study, we designed a biocompatible framework nucleic acid (FNA)-based imaging probe for brain tumor-targeting. We employed a typical type of FNAs, tetrahedral DNA nanostructures (TDNs), as the building block, which were modified with angiopep-2 (ANG), a 19-mer peptide derived from human Kunitz domain of aprotinin. This probe exhibited high binding efficiency with low-density lipoprotein receptor-related protein-1 (LRP-1) of BBB and glioma. We found that ANG-functionalized TDNs (ANG-TDNs) stayed intact for at least 12 h in serum, and that ANG modification effectively enhanced cellular uptake of TDNs in brain capillary endothelial cells and Uppsala 87 malignant glioma (U87MG) cells. Remarkably, studies in both in vitro and in vivo models revealed that ANG-TDNs could cross the BBB. Especially, in vivo imaging showed strong fluorescent signals in U87MG human glioblastoma xenograft in nude mice. This study establishes that the FNA-based platform provides a new theranostic tool for the study and therapy of brain tumors