Tim Keighley

Background: The laparoscopic sleeve gastrectomy (LSG) and the incisionless endoscopic sleeve gastroplasty (ESG) weight loss procedures require further investigation of their efficacy, safety and patient-centered outcomes in the Australian setting. Methods: The aim was to examine the 6- and 12-month weight loss efficacy, safety, and weight-related quality of life (QoL) of adults with obesity who received the ESG or LSG bariatric procedure with 12+ months of adjuvant multidisciplinary pre- and postprocedural support. Data were from a two-arm prospective cohort study that followed patients from baseline to 12-months postprocedure from a medical center in Queensland. Percent excess weight loss (%EWL) was the primary outcome. Secondary outcomes were body composition (fat mass, fat-free mass, android:gynoid ratio, bone mineral content) via dual energy X-ray absorptiometry, weight-related QoL, lipid, glycemic, and hepatic biochemistry, and adverse events. Results: 16 ESG (19% attrition; 81.2% female; aged:41.4 (SD: 10.4) years; BMI: 35.5 (SD: 5.2) kg/m²) and 45 LSG (9% attrition; 84.4% female; aged:40.4 (SD: 9.0) years; BMI: 40.7 (SD: 5.6) kg/m²) participants were recruited. At 12-months postprocedure, ESG %EWL was 57% (SD: 32%; p < 0.01) and LSG %EWL was 79% (SD: 24%; p < 0.001). ESG and LSG cohorts improved QoL (19.8% in ESG [p > 0.05]; 48.1% in LSG [p < 0.05]), liver function (AST: − 4.4 U/L in ESG [p < 0.05]; − 2.7 U/L in LSG [p < 0.05]), HbA1c (− 0.5% in ESG [p < 0.05]; − 0.1% in LSG [p < 0.05]) and triglycerides (− 0.6 mmol/L in ESG [p > 0.05]; − 0.4 mmol/L in LSG [P < 0.05]) at 12-months. Both cohorts reduced fat mass (p < 0.05). The ESG maintained but LSG decreased fat-free mass at 6-months (p < 0.05); and both cohorts lost fat-free mass at 12-months (p < 0.05). There were no adverse events directly related to the procedure. The ESG reported 25% mild-moderate adverse events possibly related to the procedure, and the LSG reported 27% mild-severe adverse events possibly related to the procedure. Conclusions: In this setting, the ESG and LSG were safe and effective weight loss treatments for obese adults alongside multidisciplinary support. Patients who elected the ESG maintained fat-free mass at 6-months but both cohorts lost fat-free mass at 12-months postprocedure. Patients who elected the LSG had large and significant improvements to weight-related quality of life. Further well-powered studies are required to confirm these findings. Trial registration: This study was registered prospectively at the Australia New Zealand Clinical Trials Registry on 06/03/2018, Registration Number ACTRN12618000337279.

The high prevalence of non-communicable disease in New Zealand (NZ) is driven in part by unhealthy diet selections, with food costs contributing to an increased risk for vulnerable population groups. This study aimed to: (i) identify the nutrient density-to-cost ratio of NZ foods; (ii) model the impact of substituting foods with a lower nutrient density-to-cost ratio with those with a higher nutrient density-to-cost ratio on diet quality and affordability in representative NZ population samples for low and medium socioeconomic status (SES) households by ethnicity; and (iii) evaluate food processing level. Foods were categorized, coded for processing level and discretionary status, analyzed for nutrient density and cost, and ranked by nutrient density-to-cost ratio. The top quartile of nutrient dense, low-cost foods were 56% unprocessed (vegetables, fruit, porridge, pasta, rice, nuts/seeds), 31% ultra-processed (vegetable dishes, fortified bread, breakfast cereals unfortified <15 g sugars/100 g and fortified 15–30 g sugars/100 g), 6% processed (fruit juice), and 6% culinary processed (oils). Using substitution modeling, diet quality improved by 59% and 71% for adults and children, respectively, and affordability increased by 20–24%, depending on ethnicity and SES. The NZ diet can be made healthier and more affordable when nutritious, low-cost foods are selected. Processing levels in the healthier, modeled diet suggest that some non-discretionary ultra-processed foods may provide a valuable source of low-cost nutrition for food insecure populations.

Food costs are a barrier to healthier diet selections, particularly for low socioeconomic households who regularly choose processed foods containing refined grains, added sugars, and added fats. In this study, the objectives were to: (i) identify the nutrient density-to-cost ratio of Australian foods; (ii) model the impact of substituting foods with lower nutrient density-to-cost ratio with those with the highest nutrient density-to-cost ratio for diet quality and affordability in low and medium socioeconomic households; and (iii) evaluate food processing levels. Foods were categorized, coded for processing level, analysed for nutrient density and cost, and ranked by nutrient density-to-cost ratio. The top quartile of nutrient dense, low-cost foods included 54% unprocessed (vegetables and reduced fat dairy), 33% ultra-processed (fortified wholegrain bread and breakfast cereals <20 g sugars/100 g), and 13% processed (fruit juice and canned legumes). Using substitution modelling, diet quality improved by 52% for adults and 71% for children across all households, while diet affordability improved by 25% and 27% for low and medium socioeconomic households, respectively. The results indicate that the quality and affordability of the Australian diet can be improved when nutritious, low-cost foods are selected. Processing levels in the healthier modelled diets suggest that some ultra-processed foods may provide a beneficial source of nutrition when consumed within national food group recommendations.

In this chapter we describe the workflow used in our laboratory for label-free quantitative shotgun proteomics based on spectral counting. The main tools used are a series of R modules known collectively as the Scrappy program. We describe how to go from peptide to spectrum matching in a shotgun proteomics experiment using the XTandem algorithm, to simultaneous quantification of up to thousands of proteins, using normalized spectral abundance factors. The outputs of the software are described in detail, with illustrative examples provided for some of the graphical images generated. While it is not strictly within the scope of this chapter, some consideration is given to how best to extract meaningful biological information from quantitative shotgun proteomics data outputs.

Cabernet Sauvignon grapevines were exposed to a progressive, increasing water defict over 16 days. Shoot elongation and photosynthesis were measured for physiological responses to water deficit. The effect of water deficit over time on the abundance of individual proteins in growing shoot tips (including four immature leaves) was analyzed using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS).

We describe the PloGO R package, a simple open‐source tool for plotting gene ontology (GO) annotation and abundance information, which was developed to aid with the bioinformatics analysis of multi‐condition label‐free proteomics experiments using quantitation based on spectral counting. PloGO can incorporate abundance (raw spectral counts) or normalized spectral abundance factors (NSAF) data in addition to the GO annotation, as well as handle multiple files and allow for a targeted collection of GO categories of interest. Our main aims were to help identify interesting subsets of proteins for further analysis such as those arising from a protein data set partition based on the presence and absence or multiple pair‐wise comparisons, as well as provide GO summaries that can be easily used in subsequent analyses. Though developed with label‐free proteomics experiments in mind it is not specific to that approach and can be used for any multi‐condition experiment for which GO information has been generated.

Rice (Oryza sativa L. cv. IR64) was grown in split-root systems to analyze long-distance drought signaling within root systems. This in turn underpins how root systems in heterogeneous soils adapt to drought. The approach was to compare four root tissues: (1) fully watered; (2) fully droughted and split-root systems where (3) one-half was watered and (4) the other half was droughted. This was specifically aimed at identifying how droughted root tissues altered the proteome of adjacent wet roots by hormone signals and how wet roots reciprocally affected dry roots hydraulically. Quantitative label-free shotgun proteomic analysis of four different root tissues resulted in identification of 1487 nonredundant proteins, with nearly 900 proteins present in triplicate in each treatment. Drought caused surprising changes in expression, most notably in partially droughted roots where 38% of proteins were altered in level compared to adjacent watered roots. Specific functional groups changed consistently in drought. Pathogenesis-related proteins were generally up-regulated in response to drought and heat-shock proteins were totally absent in roots of fully watered plants. Proteins involved in transport and oxidation–reduction reactions were also highly dependent upon drought signals, with the former largely absent in roots receiving a drought signal while oxidation–reduction proteins were strongly present during drought. Finally, two functionally contrasting protein families were compared to validate our approach, showing that nine tubulins were strongly reduced in droughted roots while six chitinases were up-regulated, even when the signal arrived remotely from adjacent droughted roots.

The genus Pachycladon consists of ten species of alpine plants, nine of which are endemic to New Zealand. The species are closely related to the model plant Arabidopsis thaliana with respect to their sequence divergence and chromosome synteny, occupy distinct geographical habitats in terms of both latitude and altitude, and display a range of morphologies. We have performed label‐free quantitative shotgun proteomic analysis of five different species of Pachycladon, namely P. cheesemanii (CH), P. exile (EX), P. fastigiatum (FA), P. enysii (EN) and P. novae‐zelandiae (NZ). The total non‐redundant data set for all five species contained 1489 proteins. The numbers of proteins identified reproducibly in each species ranged from 629 for CH to 987 for NZ, with 681 for EN, 741 for EX and 934 for FA. Previous metabolite‐based studies have shown that FA hydrolyzes glucosinolates completely to isothiocyanates while EN converts glucosinolates to nitriles. In this study, we observed high expression of ESP (At1g54040, epithiospecifying senescence regulator protein) and myrosinase 2 (At5g25980, glycosyl hydrolase family protein), which result in production of nitriles and epithionitriles, in EN and NZ, and we also observed higher expression of ESM1 (At3g14210, GDSL esterase/lipase), which mediates the formation of isothiocyanate, in FA.