Genetic identification of human remains from the Korean War.

The genetic identification of skeletal remains from Chinese People's Volunteers (CPVs) of the Korean War has been challenging because of the degraded DNA samples and the lack of living close relatives. This study established a workflow for identifying CPVs by combining Y-chromosome short tandem repeats (Y-STRs), mitochondrial DNA (mtDNA) hypervariable regions I and II, autosomal STRs (aSTRs), and identity-informative SNPs (iiSNPs). A total of 20 skeletal remains of CPVs and 46 samples from their alleged relatives were collected. The success rate of DNA extraction from human remains was 100%. Based on Y-STRs, six remains shared the same male lineages with their alleged relatives. Meanwhile, mtDNA genotyping supports two remains sharing the same maternal lineages with their alleged relatives. Likelihood ratios (LRs) were further obtained from 27 aSTRs and 94 iiSNPs or 1936 iiSNPs to confirm their relationship. All joint pedigree LRs were >100. Finally, six remains were successfully identified. This pilot study for the systematic genetic identification of CPVs from the Korean War can be applied for the large-scale identification of CPVs in the future.

The Large Nonstructural Protein (NS1) of Human Bocavirus 1 Directly Interacts with Ku70, Which Plays an Important Role in Virus Replication in Human Airway Epithelia.

Human bocavirus 1 (HBoV1), an autonomous human parvovirus, causes acute respiratory tract infections in young children. HBoV1 infects well-differentiated (polarized) human airway epithelium cultured at an air-liquid interface (HAE-ALI). HBoV1 expresses a large nonstructural protein, NS1, that is essential for viral DNA replication. HBoV1 infection of polarized human airway epithelial cells induces a DNA damage response (DDR) that is critical to viral DNA replication involving DNA repair with error-free Y-family DNA polymerases. HBoV1 NS1 or the isoform NS1-70 per se induces a DDR. In this study, using the second-generation proximity-dependent biotin identification (BioID2) approach, we identified that Ku70 is associated with the NS1-BioID2 pulldown complex through a direct interaction with NS1. Biolayer interferometry (BLI) assay determined a high binding affinity of NS1 with Ku70, which has an equilibrium dissociation constant (KD) value of 0.16 µM and processes the strongest interaction at the C-terminal domain. The association of Ku70 with NS1 was also revealed during HBoV1 infection of HAE-ALI. Knockdown of Ku70 and overexpression of the C-terminal domain of Ku70 significantly decreased HBoV1 replication in HAE-ALI. Thus, our study provides, for the first time, a direct interaction of parvovirus large nonstructural protein NS1 with Ku70. IMPORTANCE Parvovirus infection induces a DNA damage response (DDR) that plays a pivotal role in viral DNA replication. The DDR includes activation of ATM (ataxia telangiectasia mutated), ATR (ATM- and RAD3-related), and DNA-PKcs (DNA-dependent protein kinase catalytic subunit). The large nonstructural protein (NS1) often plays a role in the induction of DDR; however, how the DDR is induced during parvovirus infection or simply by the NS1 is not well studied. Activation of DNA-PKcs has been shown as one of the key DDR pathways in DNA replication of HBoV1. We identified that HBoV1 NS1 directly interacts with Ku70, but not Ku80, of the Ku70/Ku80 heterodimer at high affinity. This interaction is also important for HBoV1 replication in HAE-ALI. We propose that the interaction of NS1 with Ku70 recruits the Ku70/Ku80 complex to the viral DNA replication center, which activates DNA-PKcs and facilitates viral DNA replication.

Rapid identification and antibiotic susceptibility test of pathogens in blood based on magnetic separation and surface-enhanced Raman scattering.

An effective surface-enhanced Raman scattering (SERS) method is presented for the rapid identification and drug sensitivity analysis of pathogens in blood. In a first step, polyethyleneimine-modified magnetic microspheres (Fe3O4@PEI) were used to enrich bacteria from blood samples. Next, the Fe3O4@PEI@bacteria complex was cultured on both ordinary and drug-sensitive plates. Lastly, the SERS spectra of single colonies were acquired in order to identify different pathogens and their resistant strains by comparison with established standardized bacterial SERS spectras and orthogonal partial least squares discriminant analysis (OPLS-DA) method. Staphylococcus aureus, Acinetobacter baumannii, Pseudomonas aeruginosa and their resistant strains were used to evaluate the performance of the SERS method. The results demonstrate that the method can accurately detect and identify all the tested sensitive and drug-resistant strains of bacteria, including 77 clinical blood infection samples. The method provides a way for rapid identification and susceptibility test of pathogens, and has great potential to replace currently used time-consuming methods. Graphical abstract Schematic presentation of a method for the rapid identification and drug sensitivity analysis of pathogens in blood. It is based on a combination of magnetic separation, SERS fingerprint analysis and orthogonal partial least squares discriminant analysis (OPLS-DA).

Evaluation of the performance of Illumina's ForenSeq™ system on serially degraded samples.

The use of next generation sequencing is increasing in the field of forensic genomics. This study assesses the performance of Illumina's MiSeq FGx System in the recovery of forensic genomic sequencing information from degraded and low-template DNA. The analysis involved a sensitivity study where a range of 1 ng to 5 pg of 2800M DNA was utilized. DNA was artificially and systematically degraded by incubating 2800 M DNA at 98°C for 10, 20, 30, 40, 50, 60, 70, 120 and 180 min (resulting in degradation index values ranging from 0.837 to 232.247). The results revealed the detected allele call frequencies were greater than 80% when the DNA input was > = 50 pg or the degradation index was lower than 72.28. The allele balance was lower than 0.6 when the samples were heated for more than 120 min or the input quantity was less than 25 pg. Our data also indicated that the stutter type and ratio depend on the specific locus, while the sequencing run was the most significant factor in noise occurrence. The results of this study will help laboratories to develop workflows for the analysis of challenging samples using the ForenSeq FGx system.

Fast and non-invasive serum detection technology based on surface-enhanced Raman spectroscopy and multivariate statistical analysis for liver disease.

This study explored a rapid and nondestructive liver disease detection technique based on surface-enhanced Raman spectroscopy (SERS) to realize the early diagnosis, prevention, and treatment of liver disease. SERS signals of serum were obtained from 304 normal individuals, 333 patients with hepatopathy, and 99 patients with esophageal cancer. The Raman spectra of different diseases were compared and diagnostic models of liver disease were established using orthogonal partial least squares discriminant analysis (OPLS-DA). The classification efficiencies of the different models were comprehensively evaluated through the receiver operating characteristic (ROC) curve and ten-fold cross validation. Area under the ROC curve is of greater than 0.97, indicating excellent classification of the groups. The accuracy rate of the test set reached 95.33%, and the lowest was 81.76% using the ten-fold cross validation. Thus, OPLS-DA combined with serum SERS is a rapid and non-invasive technique for the diagnosis of liver disease.

Characteristics of mucin hypersecretion in different inflammatory patterns based on endotypes of chronic rhinosinusitis.

BACKGROUND: Chronic rhinosinusitis (CRS) is usually accompanied by mucin hypersecretion that can lead to mucus accumulation and impair nasal mucociliary clearance, thus exacerbating airway inflammation. Abnormal mucin hypersecretion is regulated by different T helper (Th) cytokines, which are associated with different endotype-driven inflammatory responses. Therefore, it is of great significance to understand how these factors regulate mucin hypersecretion to provide precise treatment strategies for different endotypes of CRS. BODY: Thus far, the most common endotypes of CRS are classified as type 1, type 2, or type 3 immune responses based on innate and adaptive cell-mediated effector immunity, and the representative Th cytokines in these immune responses, such as IFN-γ, TNF-α, IL-4, IL-5, IL-13, IL-10, IL-17, and IL-22, play an important regulatory role in mucin secretion. We reviewed all the related literature in the PubMed database to determine the expression of these Th cytokines in CRS and the role they play in the regulation of mucin secretion. CONCLUSION: We believe that the main Th cytokines involved in specific endotypes of CRS play a key role in regulating abnormal mucin secretion, which contributes to better understanding of the pathogenesis of CRS and provides therapeutic targets for airway inflammatory diseases associated with mucin hypersecretion.

In-situ Raman spectroscopic insight into charge delocalization-improved electrical conductivity in metal-cyanide frameworks.

Porous crystalline materials (PCMs) have attracted widespread attention due to their high porosity and chemical tunability. To solve the problem of the low electrical conductivity of traditional PCMs, a guest-promoted approach has been developed to impart electrical conductivity, whereas microscopic understanding of this process from experiments is largely lacking. Here we use in-situ electrochemical surface-enhanced Raman spectroscopy (EC-SERS) to investigate the microscopic mechanism of the enhanced electrical conductivity in metal-cyanide frameworks, in Prussian Blue (PB), induced by alkali metal ions. The EC-SERS result demonstrates that the charge is localized around the iron atom in PB and becomes delocalized on the CN bond after insertion of the alkali metal ions, verified by density functional theory (DFT) calculations. The enhanced electrical conductivity of PCMs promoted by the guest via the through-bond mechanism instead of the through-space hopping mechanism in pristine PB, offers a new approach to develop conductive PCMs.

Recent Advances in Molecular Biology of Human Bocavirus 1 and Its Applications.

Human bocavirus 1 (HBoV1) was discovered in human nasopharyngeal specimens in 2005. It is an autonomous human parvovirus and causes acute respiratory tract infections in young children. HBoV1 infects well differentiated or polarized human airway epithelial cells in vitro. Unique among all parvoviruses, HBoV1 expresses 6 non-structural proteins, NS1, NS1-70, NS2, NS3, NS4, and NP1, and a viral non-coding RNA (BocaSR), and three structural proteins VP1, VP2, and VP3. The BocaSR is the first identified RNA polymerase III (Pol III) transcribed viral non-coding RNA in small DNA viruses. It plays an important role in regulation of viral gene expression and a direct role in viral DNA replication in the nucleus. HBoV1 genome replication in the polarized/non-dividing airway epithelial cells depends on the DNA damage and DNA repair pathways and involves error-free Y-family DNA repair DNA polymerase (Pol) η and Pol κ. Importantly, HBoV1 is a helper virus for the replication of dependoparvovirus, adeno-associated virus (AAV), in polarized human airway epithelial cells, and HBoV1 gene products support wild-type AAV replication and recombinant AAV (rAAV) production in human embryonic kidney (HEK) 293 cells. More importantly, the HBoV1 capsid is able to pseudopackage an rAAV2 or rHBoV1 genome, producing the rAAV2/HBoV1 or rHBoV1 vector. The HBoV1 capsid based rAAV vector has a high tropism for human airway epithelia. A deeper understanding in HBoV1 replication and gene expression will help find a better way to produce the rAAV vector and to increase the efficacy of gene delivery using the rAAV2/HBoV1 or rHBoV1 vector, in particular, to human airways. This review summarizes the recent advances in gene expression and replication of HBoV1, as well as the use of HBoV1 as a parvoviral vector for gene delivery.

Label-free identification carbapenem-resistant Escherichia coli based on surface-enhanced resonance Raman scattering.

In this study, a surface-enhanced resonance Raman scattering (SERRS) method has been developed for the accurate detection and identification of carbapenem-resistant and carbapenem-sensitive Escherichia coli. A total of 89 human isolates of Enterobacteriaceae, comprising 41 strains of carbapenem-sensitive E. coli (CSEC) and 48 strains of carbapenem-resistant E. coli (CREC), were tested to assess the feasibility of our proposed SERRS method as a clinical tool, and the results showed almost 100% accuracy.

A Simple and Efficient Method of Extracting DNA from Aged Bones and Teeth.

DNA is often difficult to extract from old bones and teeth due to low levels of DNA and high levels of degradation. This study established a simple yet efficient method for extracting DNA from 20 aged bones and teeth (approximately 60 years old). Based on the concentration and STR typing results, the new method of DNA extraction (OM) developed in this study was compared with the PrepFiler™ BTA Forensic DNA Extraction Kit (BM). The total amount of DNA extracted using the OM method was not significantly different from that extracted using the commercial kit (p > 0.05). However, the number of STR loci detected was significantly higher in the samples processed using the OM method than using the BM method (p < 0.05). This study aimed to establish a DNA extraction method for aged bones and teeth to improve the detection rate of STR typing and reduce costs compared to the BM technique.

Vancomycin-modified Fe3O4@SiO2@Ag microflowers as effective antimicrobial agents.

Nanomaterials combined with antibiotics exhibit synergistic effects and have gained increasing interest as promising antimicrobial agents. In this study, vancomycin-modified magnetic-based silver microflowers (Van/Fe3O4@SiO2@Ag microflowers) were rationally designed and prepared to achieve strong bactericidal ability, a wide antimicrobial spectrum, and good recyclability. High-performance Fe3O4@SiO2@Ag microflowers served as a multifunction-supporting matrix and exhibited sufficient magnetic response property due to their 200 nm Fe3O4 core. The microflowers also possessed a highly branched flower-like Ag shell that provided a large surface area for effective Ag ion release and bacterial contact. The modified-vancomycin layer was effectively bound to the cell wall of bacteria to increase the permeability of the cell membrane and facilitate the entry of the Ag ions into the bacterium, resulting in cell death. As such, the fabricated Van/Fe3O4@SiO2@Ag microflowers were predicted to be an effective and environment-friendly antibacterial agent. This hypothesis was verified through sterilization of Gram-negative Escherichia coli and Gram-positive methicillin-resistant Staphylococcus aureus, with minimum inhibitory concentrations of 10 and 20 µg mL-1, respectively. The microflowers also showed enhanced effect compared with bare Fe3O4@SiO2@Ag microflowers and free-form vancomycin, confirming the synergistic effects of the combination of the two components. Moreover, the antimicrobial effect was maintained at more than 90% after five cycling assays, indicating the high stability of the product. These findings reveal that Van/Fe3O4@SiO2@Ag microflowers exhibit promising applications in the antibacterial fields.