Video-based observation research: A systematic review of studies in outpatient health care settings.

OBJECTIVE: To examine the use of video-based observation research in outpatient health care encounter research. METHODS: We conducted a systematic search of MEDLINE, Scopus, Cochrane and other databases from database inception to October 2020 for reports of studies that used video recording to investigate ambulatory patient-clinician interactions. Two authors independently reviewed all studies for eligibility and extracted information related to study setting and purpose, participant recruitment and consent processes, data collection procedures, method of analysis, and participant sample characteristics. RESULTS: 175 articles were included. Most studies (65%) took place in a primary care or family practice setting. Study objectives were overwhelmingly focused on patient-clinician communication (81%). Reporting of key study elements was inconsistent across included studies. CONCLUSION: Video recording has been used as a research method in outpatient health care in a limited number and scope of clinical contexts and research domains. In addition, reporting of study design, methodological characteristics, and ethical considerations needs improvement. PRACTICE IMPLICATIONS: Video recording as a method has been relatively underutilized within many clinical and research contexts. This review will serve as a practical resource for health care researchers as they plan and execute future video-based studies.

Single molecule sequencing of the M13 virus genome without amplification.

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe.

Transposable elements (TEs) constitute a substantial fraction of the eukaryotic genome and, as a result, have a complex relationship with their host that is both adversarial and dependent. To minimize damage to cellular genes, TEs possess mechanisms that target integration to sequences of low importance. However, the retrotransposon Tf1 of Schizosaccharomyces pombe integrates with a surprising bias for promoter sequences of stress-response genes. The clustering of integration in specific promoters suggests that Tf1 possesses a targeting mechanism that is important for evolutionary adaptation to changes in environment. We report here that Sap1, an essential DNA-binding protein, plays an important role in Tf1 integration. A mutation in Sap1 resulted in a 10-fold drop in Tf1 transposition, and measures of transposon intermediates support the argument that the defect occurred in the process of integration. Published ChIP-Seq data on Sap1 binding combined with high-density maps of Tf1 integration that measure independent insertions at single-nucleotide positions show that 73.4% of all integration occurs at genomic sequences bound by Sap1. This represents high selectivity because Sap1 binds just 6.8% of the genome. A genome-wide analysis of promoter sequences revealed that Sap1 binding and amounts of integration correlate strongly. More important, an alignment of the DNA-binding motif of Sap1 revealed integration clustered on both sides of the motif and showed high levels specifically at positions +19 and -9. These data indicate that Sap1 contributes to the efficiency and position of Tf1 integration.