Development of a High-throughput Sequencing Platform for Detection of Viral Encephalitis Pathogens Based on Amplicon Sequencing.

Objective: Viral encephalitis is an infectious disease severely affecting human health. It is caused by a wide variety of viral pathogens, including herpes viruses, flaviviruses, enteroviruses, and other viruses. The laboratory diagnosis of viral encephalitis is a worldwide challenge. Recently, high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections. Thus, In this study, we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing. Methods: We designed nine pairs of specific polymerase chain reaction (PCR) primers for the 12 viruses by reviewing the relevant literature. The detection ability of the primers was verified by software simulation and the detection of known positive samples. Amplicon sequencing was used to validate the samples, and consistency was compared with Sanger sequencing. Results: The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×, and the sequence lengths were consistent with the sizes of the predicted amplicons. The sequences were verified using the National Center for Biotechnology Information BLAST, and all results were consistent with the results of Sanger sequencing. Conclusion: Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis. It is also a useful tool for the high-volume screening of clinical samples.

Guest adaptative supramolecular sensing strategy for warning the risky aflatoxins in contaminated cereals.

In the face of diversified analytes, it is a great challenge and infeasible task to design and synthesize corresponding macrocyclic hosts to realize the ideal supramolecular sensing. Herein, we proposed a novel supramolecular sensing strategy, guest adaptative assay (GAA), in which analyte was quantitatively transformed under mild conditions to perfectly adapt to macrocyclic host. As a health-threatening "landmine" in cereals, aflatoxins were converted by the aid of alkali hydrolysis to satisfactorily obtain aflatoxins transformants in ionic state, resulting in sensitive response by the guanidinocalix[5]arene•fluorescein reporter pair. Surprisingly, the established strategy not only exhibited effective practicality in screening out high-risk cereals contaminated with aflatoxins, but also relieved the laborious task of macrocycle design and screening in supramolecular sensing.

Non-Floquet engineering in periodically driven dissipative open quantum systems.

Floquet engineering plays a key role in realizing novel dynamical topological states. The conventional Floquet engineering, however, only applies to time-periodic non-dissipative Hermitian systems, and for the open quantum systems, non-Hermitian processes usually occur. So far, it remains unclear how to characterize the topological phases of time-periodic open quantum systems via the frequency space Floquet Hamiltonian. Here, we propose the non-Floquet theory to solve the problem and illustrate it by a continuously time-periodic non-Hermitian bipartite chain. In non-Floquet theory, a temporal non-unitary transformation is exercised on the Floquet states, and the transformed Floquet spectrum restores the form of the Wannier-Stark ladder. Besides, we also show that different choices of the starting points of the driving period can result in different localization behavior, effects of which can reversely be utilized to design quantum detectors of phases in dissipative oscillating fields. Our methods are capable of describing topological features in dynamical open quantum systems with various driving types and can find its applications to construct new types of dynamical topological materials.

Topological transition and Majorana zero modes in 2D non-Hermitian chiral superconductor with anisotropy.

We study a non-Hermitian chiral topological superconductor system on two dimensional square lattice, from which we obtained a rich topological phase diagram and established an exact relationship between topological charge flow of exceptional points in generalized Brillouin zone and change of topological properties. Its rich topological phase diagram is the result of competition between anisotropy and non-Hermitian effect. This system belongs to class D according to AZ classification of non-Hermitian systems. Each topological phase can be characterized by a 2DZnumber, which indicates the number of chiral edge modes, and two 1DZ2numbers, which indicate the existence of zero modes at edge dislocations.

Structurally screening calixarenes as peptide transport activators.

Calixarenes are reportedly excellent activators that can remarkably improve the transport efficiencies of cell penetrating peptides. We employed eight calixarenes to systematically study the influence of structure on activation efficiency, which revealed that the scaffold, head group, and alkyl chain are all significant factors for activation efficiency by affecting affinities with the peptide and membrane.

Effect of high-fat diet for rats at different stages on glucose and lipid metabolism in offspring and related mechanisms. / å¤§é¼ ä¸åŒæ—¶æœŸé«˜è„‚é¥®é£Ÿå¯¹å­ä»£ç³–è„‚ä»£è°¢çš„å½±å“åŠæœºåˆ¶ç ”ç©¶.

OBJECTIVES: To study the effect of high-fat diet for maternal Sprague-Dawley rats at different stages on glucose and lipid metabolism in offspring and related mechanisms. METHODS: According to the diet before pregnancy and during pregnancy and lactation, maternal rats were randomly divided into four groups (n=9 each): CC (control diet before pregnancy and during pregnancy and lactation), HC (high-fat diet before pregnancy and control diet during pregnancy and lactation), CH (control diet before pregnancy and high-fat diet during pregnancy and lactation), and HH (high-fat diet before pregnancy and during pregnancy and lactation), and all offspring rats were given control diet after weaning. The body weight of maternal rats was recorded before and during pregnancy. Male offspring rats were selected from each group at the juvenile stage (3-week old) and the adult stage (12-week old) to measure the levels of fasting blood glucose (FBG) and fasting insulin (FINS) and the levels of triglyceride (TG) and total cholesterol (TC) in the liver. Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) index was calculated, and the area under the curve (AUC) was calculated for glucose tolerance test (GTT) and insulin tolerance test (ITT). Lipid deposition in the liver was observed, and the mRNA and protein expression levels of the key genes in glucose and lipid metabolism (IR, IRS, and AKT), FASN, SREBP1c, and PPARα in the liver were also measured. RESULTS: Compared with the control diet groups (CC and CH groups), the groups with high-fat diet before pregnancy (HC and HH groups) had a significant increase in body weight (P<0.001). Compared with the CC group, the HC, CH, and HH groups had a significantly greater increase in body weight (P<0.001). Compared with the CC group, the HC, CH, and HH groups had significant increases in body weight, the levels of TG and TC in the liver, and the mRNA and protein expression levels of FASN, SREBP1c, and PPARα in the offspring rats at week 3 after birth (P<0.05), as well as a significant increase in lipid deposition in the liver, with the most significant increase of the parameters in the HH group. Compared with the CC group, the HH group had significant increases in the levels of FBG and FINS, HOMA-IR index, GTT-AUC, ITT-AUC, and the protein expression level of p-IRS in the liver and significant reductions in the mRNA and protein expression levels of IR and IRS in the liver in the offspring rats at week 3 after birth (P<0.05). Compared with the CC group, the HC, CH, and HH groups had significant increases in body weight, the levels of FBG and FINS, HOMA-IR index, GTT-AUC, ITT-AUC, the levels of TG and TC in the liver, protein expression level of p-IRS in the liver, and the mRNA and protein expression levels of FASN, SREBP1c, and PPARα in the offspring rats at week 12 after birth (P<0.05), as well as a significant increase in lipid deposition in the liver, with the most increase of the parameters in the HH group. Compared with the CC group, the HC, CH, and HH groups had significant reductions in the mRNA expression levels of IR, IRS, and AKT and the protein expression levels of IR, IRS, and p-AKT in the offspring rats at week 12 after birth (P<0.05). There were no significant differences in the levels of glucose and lipid metabolism between the HC and CH groups at various stages (P>0.05). CONCLUSIONS: High-fat diet for rats at different stages before and after pregnancy has different effects on glucose and lipid metabolism of offspring rats, and high-fat diet before pregnancy and during pregnancy and lactation has the greatest effect. The effect of high-fat diet on glucose and lipid metabolism of offspring rats is considered associated with the changes in the expression of genes involved in glucose and lipid metabolism.

Detection of Pseudorabies Virus Antibodies in Human Encephalitis Cases.

Pseudorabies virus (PRV), a veterinary pathogen that infects domestic animals as well as wild animals such as wild boar and feral swine, was recently reported to infect human and led to endophthalmitis and encephalitis. A retrospective seroepidemiologic survey was conducted using 1,335 serum samples collected from patients with encephalitis and ELISA positive rates were 12.16%, 14.25%, and 6.52% in 2012, 2013, and 2017, respectively. The virus neutralizing antibody titers of positive samples correlated well with ELISA results. The pseudorabies virus antibody positive rate of patients with encephalitis were higher than that of healthy people in 2017. The above results suggest that some undefined human encephalitis cases may be caused by PRV infection.

Distribution of Microbiota in Fine Particulate Matter Particles in Guangzhou, China.

OBJECTIVE: High PM 2.5 concentration is the main feature of increasing haze in developing states, but information on its microbial composition remains very limited. This study aimed to determine the composition of microbiota in PM 2.5 in Guangzhou, a city located in the tropics in China. METHODS: In Guangzhou, from March 5 th to 10 th, 2016, PM 2.5 was collected in middle volume air samplers for 23 h daily. The 16S rDNA V4 region of the PM 2.5 sample extracted DNA was investigated using high-throughput sequence. RESULTS: Among the Guangzhou samples, Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Actinobacteria were the dominant microbiota accounting for more than 90% of the total microbiota, and Stenotrophomonas was the dominant gram-negative bacteria, accounting for 21.30%-23.57%. We examined the difference in bacterial distribution of PM 2.5 between Beijing and Guangzhou at the genus level; Stenotrophomonas was found in both studies, but Escherichia was only detected in Guangzhou. CONCLUSION: In conclusion, the diversity and specificity of microbial components in Guangzhou PM 2.5 were studied, which may provide a basis for future pathogenicity research in the tropics.

Robust Majorana edge modes with low frequency multiple time periodic driving.

Floquet Majorana edge modes capture the topological features of periodically driven p-wave superconductors. We present a Kitaev chain with multiple time periodic driving terms. Our results demonstrate how multiple driving will affect Floquet bands in frequency space, leading to more robust Floquet Majorana edge modes against driving frequency ω in comparison with the single driving scenario. Meanwhile, we have proposed how to predict Majorana edge modes via the Zak phase of Floquet bands. Besides, in contrast to the cases with single driving term, where the constant phase can be gauged out by properly choosing the initial time, we have shown the relative phase between multiple driving can not be gauged out and will play a dominant role in deciding topological phase transitions. For the sake of completeness, we also investigate the high frequency limit. Analytical results on effective Hamiltonian can be obtained via Magnus expansion and relative phase induced topological transitions can be shown explicitly.

Topological supersolidity of dipolar Fermi gases in a spin-dependent optical lattice.

We investigate the topological supersolid states of dipolar Fermi gases trapped in a spin-dependent 2D optical lattice. Our results show that topological supersolid states can be achieved via the combination of topological superfluid states with the stripe order. Different from the general held belief that supersolid state in fermionic system can only survive with simultaneous coexistence of the repulsive and attractive dipolar interaction. We demonstrate that it can be maintained when the dipolar interaction is attractive in both x and y direction. By adjusting the ratio of hopping amplitude between different directions and dipolar interaction strength U, the system will undergo a phase transition among p x + ip y superfluid state, p y -wave superfluid state, and the topological supersolid state. The supersolid state in the attractive environment is proved to be stable by the positive sign of the inverse compressibility. We also design an experimental protocol to realize the staggered next-next-nearest-neighbor hopping via the laser assisted tunneling technique, which is the key to simulate the spin-dependent potential.

New Insight into the Role of Exosomes in Pancreatic Cancer.

Pancreatic cancer is one of the most lethal diseases among solid malignancies. Most patients are diagnosed in the late stage or after metastasis. Notably, pancreatic cancer is resistant to chemotherapy and lacks efficient target therapy methods. Given that, investigating the mechanism of metastasis, finding biomarkers for early detection and identifying novel therapeutic target of pancreatic cancer are needed. Exosomes, which are one type of extracellular vesicules, play an important role in intercellular communication. It has been confirmed that exosomes can be released by all types of cells and are significantly associated with multifaceted cancer, including pancreatic cancer. It has been suggested that they correlate with biogenesis, progression, metastasis, and tumor immunity in pancreatic cancer. Meanwhile, exosomes have the potential to be non-invasive biomarkers for early detection of pancreatic cancer. In this review, we retrospectively assess the discovery and evolvement of exosomes and highlight the multiple roles of exosomes in pancreatic cancer. Exosomes, as intercellular messengers, are projected to be a novel strategy for early detection and targeted therapy in pancreatic cancer.

Targeting TF-AKT/ERK-EGFR Pathway Suppresses the Growth of Hepatocellular Carcinoma.

Tissue factor (TF) is a transmembrane glycoprotein to initiate blood coagulation and frequently overexpressed in a variety of tumors. Our previous study has showed that the expression of TF is upregulated and correlated with prognosis in hepatocellular carcinoma (HCC). However, the role and molecular mechanism of TF in the growth of HCC are still unclear. In vitro and in vivo functional experiments were performed to determine the effect of TF on the growth of HCC cells. A panel of biochemical assays was used to elucidate the underlying mechanisms. TF could promote the growth of HCC in vitro and in vivo by activating both ERK and AKT signaling pathways. TF induced EGFR upregualtion, and inhibition of EGFR suppressed TF-mediated HCC growth. In addition, TF protein expression was correlated with EGFR in HCC tissues. TF promotes HCC growth by upregulation of EGFR, and TF as well as EGFR may be potential therapeutic targets of HCC.

Serological Survey of Zika Virus in Humans and Animals in Dejiang Prefecture, Guizhou Province, China.

OBJECTIVE: The current outbreak of Zika virus (ZIKV) poses a severe threat to human health. Two ZIKV strains were isolated from mosquitoes collected from the Dejiang prefecture in China in 2016, which was the first isolation of ZIKV in nature in China. METHODS: In this study, serum samples were collected from 366 healthy individuals and 104 animals from Dejiang prefecture in 2017, and the plaque reduction neutralization test (PRNT) was used to evaluate the seroprevalence of ZIKV. RESULTS: None of the 366 residents from whom the samples were collected were seropositive for ZIKV. None of the 11 pigs from whom the samples were collected were seropositive for ZIKV, while 1 of 63 (1.59%) chickens and 2 of 30 (6.67%) sheep were seropositive for ZIKV. CONCLUSION: The extremely low seropositivity rate of ZIKV antibodies in animals in the Dejiang prefecture, Guizhou province in this study indicates that ZIKV can infect animals; however, there is a low risk of ZIKV circulating in the local population.

Development of an Internally Controlled Reverse Transcription Recombinase-aided Amplification Assay for the Rapid and Visual Detection of West Nile Virus.

West Nile virus (WNV) causes West Nile fever and West Nile encephalitis. Because infection by WNV creates serious public health problems, its simple, rapid, and visual detection is very important in clinical practice, especially in resource-limited laboratories. We have developed a rapid, specific, and highly sensitive internally controlled reverse transcription recombinase-aided amplification (RTRAA) assay to detect WNV, using both real-time fluorescence and the lateral flow dipstick (LFD) at 39.0 °C for 30 min. The analytical sensitivity of the RT-RAA assay was 10 plasmid copies and 1.6 pfu per reaction with real-time fluorescence, and 1,000 plasmid copies per reaction with the LFD. No crossreaction with other control viruses was observed. Compared with the RT-qPCR assay, the RT-RAA assay demonstrated 100% sensitivity and 100% specificity for WNV.

TaqMan Real-time RT-PCR Assay for Detecting and Differentiating Japanese Encephalitis Virus.

OBJECTIVE: To detect Japanese encephalitis virus (JEV) rapidly and distinguish its genotypes, a TaqMan-based reverse transcriptase quantitative polymerase chain reaction (RT-PCR) detection system was developed. METHODS: By aligning the full-length sequences of JEV (G1-G5), six sets of highly specific TaqMan real-time RT-PCR primers and probes were designed based on the highly conserved NS1, NS2, and M genes of JEV, which included one set for non-specific JEV detection and five sets for the detection of specific JEV genotypes. Twenty batches of mosquito samples were used to evaluate our quantitative PCR assay. RESULTS: With the specific assay, no other flavivirus were detected. The lower limits of detection of the system were 1 pfu/mL for JEV titers and 100 RNA copies/µL. The coefficients of variation of this real-time RT-PCR were all < 2.8%. The amplification efficiency of this method was between 90% and 103%. CONCLUSION: A TaqMan real-time RT-PCR detection system was successfully established to detect and differentiate all five JEV genotypes.

The Relationship between Japanese Encephalitis and Environmental Factors in China Explored Using National Surveillance Data.

Japanese encephalitis (JE) is a serious public health issue. This study was undertaken to better understand the relationship between JE distribution and environmental factors in China. JE data from 2005 to 2010 were retrieved from National Notifiable Disease Report System. ArcGIS, remote sensing techniques, and R software was used to exhibit and explore the relationship between JE distribution and environmental factors. Our results indicated that JE cases were mostly concentrated in warm-temperate, semitropical and tropical zones with annual precipitation > 400 mm; Broad-leaved evergreen forest, shrubs, paddy field, irrigated land, dryland, evergreen coniferous forest, and shrubland were risk factors for JE occurrence, and the former five were risk factors for counties with high JE incidence. These findings will inform the effective allocation of limited health resources such as intensive vaccination, surveillance and training in areas with high environmental risk factors.

From discovery to spread: The evolution and phylogeny of Getah virus.

Getah virus (GETV) was first isolated in Malaysia in 1955. Since then, epidemics in horses and pigs caused by GETV have resulted in huge economic losses. At present, GETV has spread across Eurasia and Southeast Asia, including mainland China, Korea, Japan, Mongolia, and Russia. Data show that the Most Recent Common Ancestor (MRCA) of GETV existed about 145years ago (95% HPD: 75-244) and gradually evolved into four distinct evolutionary populations: Groups I-IV. The MRCA of GETVs in Group III, which includes all GETVs isolated from mosquitoes, pigs, horses, and other animals since the 1960s (from latitude 19°N to 60°N), existed about 51years ago (95% HPD: 51-72). Group III is responsible for most viral epidemics among domestic animals. An analysis of the GETV E2 protein sequence and structure revealed seven common amino acid mutation sites. These sites are responsible for the structural and electrostatic differences detected between widespread Group III isolates and the prototype strain MM2021. These differences may account for the recent geographical radiation of the virus. Considering the economic significance of GETV infection in pigs and horses, we recommend the implementation of strict viral screening and monitoring programs.

Identification of a Newly Isolated Getah Virus in the China-Laos Border, China.

In this study, we isolated a virus strain (YN12031) from specimens of Armigeres subalbatus collected in the China-Laos border. BHK-21 cells infected with YN12031 exhibited an evident cytopathic effect (CPE) 32 h post-infection. The virus particles were spherical, 70 nm in diameter, and enveloped; they also featured surface fibers. Molecular genetic analysis revealed that YN12031 was closely related to alpha viruses such as Chikungunya virus and Sindbis virus, and located in the same clade as MM2021, the prototype of Getahvirus (GETV) isolated in Malaysia in 1955. Phylogenetic analysis of the E2 and capsid genes further revealed that YN12031 was located in the same clade as the Russian isolate LEIV/16275/Mag. Analysis of the homology of nucleotides and amino acids in the coding area and E2 gene demonstrated that the YN12031 isolated from the China-Laos border (tropical region) was related closest to the LEIV/16275/Mag isolate obtained in Russia (North frigid zone area) among other isolates studied. These results suggest that GETV can adapt to different geographical environments to propagate and evolve. Thus, strengthening the detection and monitoring of GETV and its related diseases is very crucial.