Extracellular RNA: A new perspective on the human pre-implantation embryos.

It is currently a challenge to perform noninvasive molecular biological analysis of in vitro fertilized embryos. In this issue of Cell Genomics, Wu et al.1 developed a non-invasive method to evaluate human pre-implantation embryos by characterizing the extracellular RNAs in spent media from the culture of in vitro fertilization embryos.

The Mechanism of Overflow Amplitude in Nanopore Experiments and Its Application in Molecule Detection.

The investigation of abnormal experimental phenomena observed in nanopore research improves our understanding of nanopores. In this article, we report and explore the unusual phenomenon that the amplitude of current blockage decreases beyond zero baseline (overflow amplitudes), which was observed in the translocation behavior of 100 bp double-stranded DNA molecules through SiNx nanopores. In our experiments, the overflow amplitude decreases with the increase of salt concentration and also decreases when the dwell time is shortened as the normalized amplitude of the overflow current showed a reduction with the increase of voltage. Upon analyzing the electric double layer meanwhile, the overflow amplitudes were shown to be positively correlated with the depth of the electric double layer and the duration of interaction between biological molecules. The formation of overflow amplitude can be attributed to the double electric layer ionic perturbation and reconfiguration, which are the results of the interaction between the biomolecule and the electric bilayer. The validation of the assumption using biomolecules containing different charges demonstrated that the overflow amplitude increased with the increase of the charge. It was concluded that proteins that pass through the nanopore with different orientation were differentiated based on their different overflow amplitude patterns. The investigation of overflow amplitude helps to enhance the understanding and the performance of nanopores.

Solid-state nanopore analysis on the conformation change of DNA polymerase I induced by a DNA substrate.

Proteins with a changeable conformation, such as polymerases, play a very important role in various life activities. Their conformational changes can be reflected in their structural size and flexibility, which may influence their transport kinetics. Recently, solid-state nanopore sensors have been widely applied to characterize the conformation of proteins and other complex structures as sensitive and high throughput single-molecule detectors. In this work, we used a SiN nanopore sensor to study the conformational changes between the Klenow fragment (KF) and its monomer complex with a DNA substrate (KF-DNA). By calculating their hydrodynamic radii, pore volume, the duration of translocation events, drift velocity, and molecular dynamics simulations, we found that the KF-DNA monomer complex has a tighter structure and transports slower. The study performed here can be potentially used to identify single polymerases in real time and may ultimately reveal conformation changes and the interaction between polymerases and their substrates.

[Transmission chains of clusters of COVID-19 associated with a market in Beijing].

Objective: To investigate the clusters of COVID-19 associated with a market (market Y) in Haidian District, Beijing, and analyze the chain of transmission and provide reference for effective prevention and control of COVID-19. Methods: The investigation of field epidemiology and cluster epidemic was used to describe the distributions of all COVID-19 cases. The time sequence diagram of the cases, disease onset was drawn and transmission chains were analyzed. Real-time RT-PCR assay was conducted for SARS-CoV-2 nucleic acid test by using the respiratory samples of the cases. Results: The COVID-19 epidemic, originated from a wholesale farm produce market (market X) in Fengtai District, Beijing, was introduced by a marketer in the market Y who had exposed to market X, causing 8 clusters of 20 confirmed cases of COVID-19 and one asymptomatic case, including 8 men and 13 women, in market Y, surrounding communities, food plaza, companies,families and other places. The incidence peaked during June 10-14, 2020; the median age of the cases was 45 years, ranging from 5 years to 87 years. The initial symptoms of the cases included fever (10/20) and pharynx discomfort (7/20). The median of incubation period was 5 days (IQR:3-8). The median of serial interval between primary case and secondary cases was 5 days with a secondary attack rate of 3.7%(20/538), and the secondary attack rate in household close-contacts was 14.0% (7/50). Conclusions: The clusters of COVID-19 associated with market Y were caused by several modes of transmission, including human-to-human, contaminated material-to-human, etc. The combined public-health response measures were effective to control the COVID-19 epidemic in Haidian district of Beijing.

EasyNanopore: A Ready-to-Use Processing Software for Translocation Events in Nanopore Translocation Experiments.

We developed EasyNanopore which is a ready-to-use software to select the events of a nanopore molecular translocation experiment. The software is released as an executable file with a graphical user interface and provides several versions suitable for different operating systems without installing any running environment to execute it. We use the adaptive threshold which adapts to the low-frequency variation of the baseline to detect events and uses a multiprocess method to accelerate the process of event detection. After the event is identified, its duration and amplitude information will be extracted and a resulting txt file will be generated for further analysis. Our software runs fast and can effectively extract the data from data of large-scale nanopore molecular translocation experiments.

Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores.

As a type of biological macromolecule, the conformation of proteins dynamically changes in a solution, which often results in a change in their function. However, traditional biological assays have significant drawbacks in detecting the conformation properties of proteins. Alternatively, nanopores have potential advantages in this area, which can detect protein in high throughput and without labelling. Herein, we investigated the translocation of calmodulins through silicon nitride nanopores using molecular dynamics (MD) simulation. Initially, the calmodulins were fixed in the nanopore. Distinguished blocked ionic currents were obtained between the two forms of calmodulin. Next, in the translocation simulations, a prominent difference in time resolution was easily found between the two states of calmodulin by using the appropriate voltage and comparable size of pore to protein, rp/rg→ 1, 4.5 nm (where rp is the protein radius and rg is the gyration radius). These simulations on the nanoscale are helpful for developing Ca2+-sensitive ion channels and nanodevices.

Microfluidic Systems Applied in Solid-State Nanopore Sensors.

Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.

Advanced transferring of large-area freestanding graphene films by using fullerenes.

Freestanding graphene films are desired to be widely applied in biosensor fabrication due to their distinctive physical properties and improved performance. Chemical vapor deposition has been developed to efficiently fabricate large-area graphene. However, some of the fabricated graphene films might break or be contaminated in the current transferring step using polymers. A stable and high-quality transfer method is needed. Herein, we report on an advanced transfer method of large-area graphene film which uses fullerene as a supporting substrate. Unlike polymers, which are commonly eliminated by being dissolved in an organic solution, fullerene can be easily removed by evaporation in a vacuum because it has a different heat stability to graphene. By using the improved transferring method, the percentage of integrated freestanding films after transferring was increased from 60.7% to 93.4%. The vacuum is beneficial in terms of keeping the brittle freestanding films intact. Graphene films transferred using fullerene showed an advanced flatness and a simplicial elementary composition in comparison to those transferred using polymers. Even through there is trace residue, this stable allotrope of graphene is considered to have almost no impact on biomolecule sensing. These advantages make the fullerene transferring method an attractive candidate for fabricating large-area freestanding graphene films, especially for using in the field of biochemistry analysis and biosensors.

A hospital-associated measles outbreak in health workers in Beijing: Implications for measles elimination in China, 2018.

BACKGROUND: Since the National Action Plan for Measles Elimination 2006-2012 was released in 2006, China has entered into an era of accelerated measles elimination. Despite substantial decline, measles outbreak continued to occur mainly in a non-targeted population, in particular health workers due to occupational exposure. We investigated a measles outbreak in a Chinese medicine hospital, Beijing, in March 2018. METHODS: Descriptive analysis was performed on epidemiology of the outbreak, clinical and laboratory evaluations, vaccination status of cases, and public health response. A case-control study was also conducted to identify the associated risk factors for measles. RESULTS: From March 13, 2018, through March 27, 2018, a total of 11 measles cases in health workers were reported in Hospital X, Beijing. The median age of cases was 26 years (range, 21-53) and 4 (36.4%) were male. Of the 11 cases, ten had not been vaccinated or had unknown vaccination status; two occurred in emergency departments. No inpatients became infected, 141 (83.9%) of whom in affected departments were 55 years of age or older. The outbreak was confirmed by laboratory testing; the virus strain was genotype H1. The response activities included isolation of cases, and enhanced health surveillance of health workers and inpatients, particularly in affected departments. A total of 2234 doses of measles-containing vaccines (MCVs) were administered, covering 93.3% of susceptible health workers, in addition to 973 doses to the susceptible individuals in household and community. Lack of documentation of MCV vaccination before the outbreak was identified as a risk factor for measles (odd ratio: 3.333, 95% confidence interval: 1.295-8.621). CONCLUSIONS: High coverage of outbreak response immunization activities contributed largely to limit the spread of measles and might provide an indirect protection for inpatients. 2-Dose measles-containing vaccination of personnel in healthcare settings is warranted to prevent potential nosocomial transmission of measles.

Accurate and sensitive single-cell-level detection of copy number variations by micro-channel multiple displacement amplification (µcMDA).

Whole genome amplification (WGA) has laid the foundation for investigating complex genomic alteration with single-cell or even single-molecule resolution. Coupled with sequencing-based copy number variation (CNV) analysis, it promotes understanding of the nature of commonly existing genetic heterogeneity by constructing the sequencing profiles for every single cell. However, prevailing methods only provide insights into limited aspects due to their intrinsic technical challenges. Their output data, as a result, fails to render comprehensive information (which is) concerned. Here, we describe the CNV detection analysis based on micro-channel multiple displacement amplification (µcMDA), a protocol able to provide optimized amplification uniformity while inheriting the advantages of MDA chemistry. We demonstrate the analysis of both the normal diploid YH-1 cell line and the aneuploid K562 cancer cell line. In the detection of simulated CNVs ranging from 300 kb to 2 Mb, µcMDA can respectively increase the detection rates of copy number loss and gain by 28.8% and 40.2% on average, using only 0.2× sequencing data. When detecting the inherent CNVs in tumor cells, the resolution of CNV recognition can be improved to 250 kb. Starting from either superabundant template copies or minute single-cell-level input, this easily accessible approach is capable of providing quantitatively reliable coverage as well as more robust GC-content regression for CNV detection.

To establish a talent pool for global health in China: from political will to action.

Recently, China has played a more and more important role in global health, mainly by improving health outcomes of its own population nationwide and participating international health activities. In addition, China has participated in a dozen of international organizations, which all contained health domains, particularly the Belt and Road Initiative with an ambitious goal to improve health of the people in the countries alongside closely partnered with the World Health Organization. All these highlight the need of human resource for global health at the national level. The National Health and Family Planning Commission translated this political will into action - that a talent pool candidate for global health will be established in China. The establishment of the talent pool would be of great significance for China's engagement in global health activities. However, much work, such as training, collaboration, and innovation, etc., remains to be done in the future. Based on the successful practice, China can share lessons learned to other countries.

An efficient strategy for a controllable droplet merging system for digital analysis.

Droplet merging is an important part of droplet manipulation approaches. Droplet merging methods with expansions inside channels can merge droplets in pairs through simple structures. However, they have a low success rate of merging under unstable fluidic conditions since the one-to-one pairing strategy is sensitive to fluctuation. This study presents a one-to-a-cluster pairing strategy to improve the success rate of merging under fluctuation. The one-to-a-cluster method was suitable for digital analysis and droplet MDA was performed in merged droplets successfully.

Epidemiology of varicella in Haidian district, Beijing, China-2007-2015.

BACKGROUND: 1-Dose varicella vaccination was recommended for children in Beijing before November 2012. To further control school-based outbreaks and decrease incidence, a 2-dose vaccination was implemented in 2013. We described the varicella epidemiology and assessed impact of the 2-dose vaccination in Haidian district, Beijing, 2007-2015. METHODS: We examined the estimated incidence and disease characteristics of varicella during 2007-2015 and obtained the 1-dose vaccination coverage for children born during 2005-2013. Number of vaccine doses given was used to indirectly reflect the second-dose vaccination coverage. Overall and age-specific estimated incidences were compared between 2007-2012 and 2013-2015. RESULTS: A total of 23,497 cases were reported during 2007-2015. Of the 23,497 cases, 13,440 (57.20%) were male, and 68.40% were <20years of age and 70.02% were students and children in kindergarten. The estimated incidence increased from 82 cases per 100,000 population in 2007 to 104 in 2011, before substantially decreasing from 86 in 2012 to 56 in 2015. The median age increased from 14years in 2007 to 18years in 2015. The 1-dose varicella coverage for children at ≥2years of age gradually increased from 74.21% in 2007 to 90.06% in 2015. Compared with 2007-2012, two-fold average vaccine doses were given during 2013-2015, and the overall estimated incidence declined by 34.4%, particularly in children aged 5-9years, with a significantly declined trend in children aged 1-9years and older adolescents aged 15-19years and non-significantly declined trend in adults aged ≥20years, but a significant increasing trend in infants. CONCLUSIONS: The overall incidence of varicella has decreased substantially in Haidian district since 2013, with largest decline in children aged 5-9years. The 2-dose varicella vaccination might not lead to increase in incidence in adults. Long-term surveillance is needed to fully evaluate the long-term impact of the 2-dose varicella vaccination.

Outbreak of varicella in a highly vaccinated preschool population.

BACKGROUND: Varicella vaccine is available for private purchase in Beijing, with single dose recommended for children aged ≥12 months before 2013. Despite the success achieved in reducing varicella incidence, varicella outbreaks continued to occur, including in schools and kindergartens among highly vaccinated children. We investigated a varicella outbreak in a preschool with high varicella vaccination coverage in Haidian district, Beijing. METHODS: Through questionnaires, data including children's medical and vaccination history were collected from their parents. A case of varicella was defined as an acute, generalized, maculopapulovesicular rash without other apparent cause in a child in the preschool from March 10 through March 29, 2010. Attack rates in vaccinated and unvaccinated children were calculated, and the analyses of vaccine effectiveness (VE) and of risk factors for breakthrough disease (varicella occurring >42 days after vaccination) were conducted. RESULTS: A total of 12 cases occurred during the outbreak, and ten of them (83.3%) had breakthrough varicella. The index case with mild varicella occurred in a child who had been vaccinated four years previously. Questionnaires were returned for all of 150 children in the preschool. Of all the 150 children, 144 (96.0%) had no prior history of varicella disease. Among these children, 135(93.7%) had received single-dose varicella vaccine before the outbreak. VE was 84.5% [95% confidence interval (CI): 62.8%∼93.5%] in preventing varicella of any severity, and VE was 92.2% (95% CI: 81.4%∼96.8%) against moderate to severe varicella. Age at vaccination (<15 months vs. ≥15 months) and time since vaccination before the outbreak (<3 years vs. ≥3 years) were not associated with the increased risk of breakthrough varicella(P=0.124 and 1, respectively). All the varicella cases with vaccination history verified through immunization records had received varicella vaccine and measles-mumps-rubella vaccine >30 days apart. CONCLUSIONS: Breakthrough infection with fever in vaccinated person may be as infectious as varicella in unvaccinated persons. High single-dose varicella vaccination coverage is effective in reducing varicella incidence, but not sufficient to prevent outbreak. To control varicella outbreak a second dose may deserve additional consideration.

[Investigation on measles cases of new genotype D8 in Beijing, 2013].

OBJECTIVE: To investigate the epidemiological characteristics of measles cases of new genotype D8 in Beijing from January to June, 2013. METHODS: Epidemiological survey and descriptive analysis was conducted. RESULTS: 661 suspected measles were reported from January to June, 2013. 416 were confirmed measles cases by serology and etiology detection. 28 measles cases were caused by genotype D8 measles virus by genotype identification. There were 2 measles outbreak including 14 cases and 14 sporadic cases. The incidence peak was during April and May. 25 cases (89.3%, 25/28) occurred in downtown and suburban districts. 22 cases (78.5%, 22/28) were adults aged 15-39 years and 19 cases (67.9%, 19/28) were migrant population. 12 cases (85.7%, 12/14) in outbreak were migrant population working in clothing sales. There was epidemiological association between 2 outbreaks. CONCLUSION: Measles cases of genotype D8 were found for the first time in Beijing. Genotype D8 virus mainly infected migrant adults and caused local outbreak and endemic.