Factors influencing oral microbiome analysis: from saliva sampling methods to next-generation sequencing platforms

The exploration of oral microbiome has been increasing due to its relatedness with various systemic diseases, but standardization of saliva sampling for microbiome analysis has not been established, contributing to the lack of data comparability. Here, we evaluated the factors that influence the microbiome data. Saliva samples were collected by the two collection methods (passive drooling and mouthwash) using three saliva-preservation methods (OMNIgene, DNA/RNA shield, and simple collection). A total of 18 samples were sequenced by both Illumina short-read and Nanopore long-read next-generation sequencing (NGS). The component of the oral microbiome in each sample was compared with alpha and beta diversity and the taxonomic abundances, to find out the effects of factors on oral microbiome data. The alpha diversity indices of the mouthwash sample were significantly higher than that of the drooling group with both short-read and long-read NGS, while no significant differences in microbial diversities were found between the three saliva-preservation methods. Our study shows mouthwash and simple collection are not inferior to other sample collection and saliva-preservation methods, respectively. This result is promising since the convenience and cost-effectiveness of mouthwash and simple collection can simplify the saliva sample preparation, which would greatly help clinical operators and lab workers.

Development of diagnostic tests for pathogen identification and detection of antimicrobial resistance on WHO global priority pathogens using modular real-time nucleic acid amplification test

BACKGROUND

Concerns regarding antimicrobial resistance (AMR) have resulted in the World Health Organization (WHO) designating so-called global priority pathogens (GPPs). However, little discussion has focused on the diagnosis of GPPs. To enable the simultaneous identification of pathogens and AMR, we developed a modular real-time nucleic acid amplification test (MRT-NAAT).

METHODS

Sequence-specific primers for each modular unit for MRT-NAAT pathogen identification and AMR sets were designed. The composition of the reaction mixture and the real-time PCR program were unified irrespective of primer type so to give MRT-NAAT modularity. Standard strains and clinical isolates were used to evaluate the performance of MRT-NAAT by real-time PCR and melting curve analysis. Probit analysis for the MRT-NAAT pathogen identification set was used to assess the limit of detection (LoD).

RESULTS

The MRT-NAAT pathogen identification set was made up of 15 modular units 109-199 bp in product size and with a T_ms of 75.5-87.5 °C. The LoD was < 15.548 fg/μL, and nine modular units successfully detected the target pathogens. The MRT-NAAT AMR set included 24 modular units 65-785 bp in product size with a T_ms of 75.5-87.5 °C; it showed high performance for detecting GPP target genes and variants.

CONCLUSIONS

MRT-NAAT enables pathogen identification and AMR gene detection and is time-effective. By unifying the reaction settings of each modular unit, the modularity where combinations of primers can be used according to need could be achieved. This would greatly help in reflecting the researcher's need and the AMR status of a certain region while successfully detecting pathogens and AMR genes.

Zika Virus Infection During Research Vaccine Development: Investigation of the Laboratory-Acquired Infection via Nanopore Whole-Genome Sequencing

Zika virus (ZIKV) emerged as a serious public health problem since the first major outbreak in 2007. Current ZIKV diagnostic methods can successfully identify known ZIKV but are impossible to track the origin of viruses and pathogens other than known ZIKV strains. We planned to determine the ability of Whole Genome Sequencing (WGS) in clinical epidemiology by evaluating whether it can successfully detect the origin of ZIKV in a suspected case of laboratory-acquired infection (LAI). ZIKV found in the patient sample was sequenced with nanopore sequencing technology, followed by the production of the phylogenetic tree, based on the alignment of 38 known ZIKV strains with the consensus sequence. The closest viral strain with the consensus sequence was the strain used in the laboratory, with a percent identity of 99.27%. We think WGS showed its time-effectiveness and ability to detect the difference between strains to the level of a single base. Additionally, to determine the global number of LAIs, a literature review of articles published in the last 10 years was performed, and 53 reports of 338 LAIs were found. The lack of a universal reporting system was worrisome, as in the majority of cases (81.1%), the exposure route was unknown.

Coherence properties of individual femtosecond pulses of an x-ray free-electron laser

Measurements of the spatial and temporal coherence of single, femtosecond x-ray pulses generated by the first hard x-ray free-electron laser, the Linac Coherent Light Source, are presented. Single-shot measurements were performed at 780 eV x-ray photon energy using apertures containing double pinholes in "diffract-and-destroy" mode. We determined a coherence length of 17  μm in the vertical direction, which is approximately the size of the focused Linac Coherent Light Source beam in the same direction. The analysis of the diffraction patterns produced by the pinholes with the largest separation yields an estimate of the temporal coherence time of 0.55 fs. We find that the total degree of transverse coherence is 56% and that the x-ray pulses are adequately described by two transverse coherent modes in each direction. This leads us to the conclusion that 78% of the total power is contained in the dominant mode.

Solution structures of the N-terminal domain of histone H4

Histones, nuclear proteins that interact with DNA to form nucleosomes, are essential for both the regulation of transcription and the packaging of DNA within chromosomes. The N-terminal domain of histone H4 contains four acetylation sites at lysine residues and may play a separate role in chromatin structure from the remainder of the H4 chain. We performed circular dichroism and NMR characterization of both native (H4NTP) and acetylated (Ace-H4NTP) peptides containing N-terminal acetylation domain of histone H4 for various pH environments. Data from CD and NMR suggested that H4NTP exhibited a pH-dependent conformational change, whereas the Ace-H4NTP is insensitive to pH change. However, both peptides showed a defined structural form at acidic pH environments. The solution structure for Ace-H4NTP shows two structurally independent regions comprising residues of Leu10-Gly13 and Arg19-Leu22, demonstrating relatively well-defined turn-type structures. Our results suggest that N-terminal acetylated region of H4 prefers an extended backbone conformation at neutral pH, however, upon acetylation, the regions containing lysine residues induce structural transition, having defined structural form for its optimum function.

Solution structure of a new hypothalamic neuropeptide, human hypocretin-2/orexin-B

Orexin-A and orexin-B (also called hypocretin-1 and hypocretin-2, respectively) are novel hypothalamic neuropeptides encoded by a single mRNA transcript; they stimulate food intake. We have determined the three-dimensional solution structure of human hypocretin-2/orexin-B using two-dimensional 1H-NMR data and dynamical simulated annealing calculations. On the basis of NOEs, 3JHNalpha coupling constants and hydrogen-deuterium exchange rates together with chemical shift indices, human hypocretin-2/orexin-B was deduced to consist of two alpha-helices connected with a short linker in both H2O and 30% trifluoroethanol solutions. The helical axis of helix I is oriented about 60-80 degrees relative to helix II. Hybrid distance geometry and simulated-annealing protocols were used to generate an ensemble of 30 structures with no constraint violations greater than 0.03 nm for distances and 3 degrees for angles. In addition, human hypocretin-2/orexin-B shares a similar secondary-structural motif with human neuropeptide Y. This result can form the basis for further study on ligand-receptor recognition of human orexin receptors.

Etiologic aspects and orthodontic treatment of unilateral localized arrested tooth-development combined with hearing loss

In this study a case has been presented involving localized, arrested maxillary tooth development, asymmetric maxillary development, and unilateral loss of hearing. No similar case seems to have been described before. The orthodontic treatment comprised extraction of four permanent tooth germs in the maxilla and autotransplantation of mandibular teeth, followed by the use of fixed orthodontic appliances and a one-unit bridge restoration. Etiologic aspects are discussed. It is suggested that a severe attack of mumps that involved massive swelling of the parotid glands immediately after chicken pox and measles at the age of 4 to 5 years, may have resulted in a neurologic reduction of hearing and arrested tooth development. The teeth in which root development in relation to mumps does not appear to have been reported previously, whereas hearing loss after mumps has been reported. In the search for verification of this possible connection, children with arrested tooth development should be examined for reduction of hearing, and children with hearing loss after mumps ought to have their dental development checked.

A survey of urban and rural participants in the Otago-Southland pilot breast cancer screening programme

AIMS

By surveying participants in a pilot breast cancer screening programme, to measure satisfaction with the screening service, to provide feedback for programme staff, to obtain an indication of future participation, and to collect information about costs to women.

METHODS

A self administered questionnaire was posted to representative samples of urban and rural women (total 474) who had participated in the Otago-Southland pilot breast cancer screening programme in its first year of operation.

RESULTS

There was a 93% response rate to the survey, after one reminder letter. Although some demographic characteristics of urban and rural women differed, their opinions about the screening programme were similar. Satisfaction with the service is extremely high, with 94% of respondents planning to participate again in two years.

CONCLUSIONS

The Otago-Southland pilot programme provides a service which is regarded as satisfactory by the great majority of participants.