Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features.

Single cells are the building blocks of tissue systems that determine organ phenotypes, behaviors, and functions. Understanding the differences between cell types and their activities might provide us with insights into normal tissue physiology, development of disease, and new therapeutic strategies. Although -omic level single-cell technologies are a relatively recent development that have been used only in research settings, these approaches might eventually be used in the clinic. We review the prospects of applying single-cell genome, transcriptome, epigenome, proteome, and metabolome analyses to gastroenterology and hepatology research. Combining data from multi-omic platforms coupled to rapid technological development could lead to new diagnostic, prognostic, and therapeutic approaches.

Quantitative assessment of cell population diversity in single-cell landscapes.

Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for the systematic investigation of cellular diversity. As a number of computational tools have been developed to identify and visualize cell populations within a single scRNA-seq dataset, there is a need for methods to quantitatively and statistically define proportional shifts in cell population structures across datasets, such as expansion or shrinkage or emergence or disappearance of cell populations. Here we present sc-UniFrac, a framework to statistically quantify compositional diversity in cell populations between single-cell transcriptome landscapes. sc-UniFrac enables sensitive and robust quantification in simulated and experimental datasets in terms of both population identity and quantity. We have demonstrated the utility of sc-UniFrac in multiple applications, including assessment of biological and technical replicates, classification of tissue phenotypes and regional specification, identification and definition of altered cell infiltrates in tumorigenesis, and benchmarking batch-correction tools. sc-UniFrac provides a framework for quantifying diversity or alterations in cell populations across conditions and has broad utility for gaining insight into tissue-level perturbations at the single-cell resolution.

A survey of respiratory and sleep services in New Zealand undertaken by the Thoracic Society of Australia and New Zealand (TSANZ).

AIMS: In 2004, the NZ Branch of the TSANZ published "Standards for Adult Respiratory and Sleep Services" on the Ministry of Health's (MoH) website.1 The aim of this survey was to evaluate each of the 21 District Health Boards' (DHBs) performance against the published standards, concentrating particularly on staffing, infrastructure, clinical support services, implementation of guidelines, quality assurance activity, and basic services (sleep, lung function, and oxygen). METHODS: Postal questionnaire survey of all DHBs in late 2006. RESULTS: All 21 DHBs responded. Only 10 of 21 DHBs were complying with the minimum standards of care. Main deficiencies in care related to: inadequate medical staffing rates, lack of quality assurance measures and insufficient laboratory testing (sleep and lung function). The lack of monitoring of such basic activities as outpatient clinic attendances, oxygen and sleep services, and the non implementation of treatment guidelines were of particular concern. Seven-fold variations in prescription of assisted ventilation equipment and oxygen therapy exist across the country. CONCLUSIONS: When evaluated against minimum standards of care published in 2004, major gaps in service provision exist in New Zealand. Access to services is variable. There is a lack of national leadership and insufficient regional organisation leading to large gaps in service provision of even basic respiratory services. Immediate changes to the current service provision structures are required.