Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Kiwifruit Exchanges for Increased Nutrient Richness with Little Effect on Carbohydrate Intake, Glycaemic Impact, or Insulin Response

Background: Kiwifruit are nutrient-rich and have properties which indicate a low glycaemic impact compared with many cooked cereal foods, suggesting that they may be used for dietary enrichment of vitamin C without glycaemic cost. Aim: To develop tables for equi-carbohydrate and equi-glycaemic partial exchange of kiwifruit for glycaemic carbohydrate foods. Method: The available carbohydrate content of Zespri® Green and Zespri® SunGold kiwifruit was determined as sugars released during in vitro digestive analysis. Glycaemic potency was determined as grams of glucose equivalents (GGEs) in a clinical trial using 200 g (a two-kiwifruit edible portion) of each cultivar, non-diabetic subjects (n = 20), and a glucose reference. GGE values were also estimated for a range of carbohydrate foods in the New Zealand Food Composition Database for which available carbohydrate and glycaemic index values were available. The values allowed exchange tables to be constructed for either equi-carbohydrate or equi-glycaemic partial exchange of kiwifruit for the foods. Results: GGE values of both kiwifruit cultivars were low (“Hayward„, 6.6 glucose equivalents/100 g; “Zesy002„, 6.7 glucose equivalents/100 g). Partial equi-carbohydrate substitution of foods in most carbohydrate food categories substantially increased vitamin C with little change in glycaemic impact, while equi-glycaemic partial substitution by kiwifruit could be achieved with little change in carbohydrate intake. Conclusion: Equi-carbohydrate partial exchange of kiwifruit for starchy staple foods is a means of greatly increasing nutrient richness in a diet without the physiological costs of increased glycaemia and insulin responses or carbohydrate intake

Dietary Fibre and Organic Acids in Kiwifruit Suppress Glycaemic Response Equally by Delaying Absorption—A Randomised Crossover Human Trial with Parallel Analysis of 13C-Acetate Uptake

Non-sugar components of kiwifruit reduce the amplitude of the glycaemic response to co-consumed cereal starch. We determined the relative contribution of different non-sugar kiwifruit components to this anti-glycaemic effect. Healthy participants (n = 9) ingested equal carbohydrate meals containing 20 g starch as wheat biscuit (WB, 30 g), and the sugar equivalent of two kiwifruit (KFsug, 20.4 g), either intrinsic or added as glucose, fructose and sucrose (2:2:1). The meals were WB+KFsug (control, no non-sugar kiwifruit components), WB + whole kiwifruit pulp (WB+KF), WB + neutralised kiwifruit pulp (WB+KFneut), WB + low-fibre kiwifruit juice (WB+KFjuice) and WB+KFsug + kiwifruit organic acids (WB+KFsug+OA). All meals were spiked with 100 mg sodium [1-13C] acetate to measure intestinal absorption. Each participant ingested all meals in random order. Blood glucose and breath 13CO2 were measured at ingestion and at 15 min intervals up to 180 min. Compared with WB+KFsug, whole kiwifruit pulp (WB+KF) almost halved glycaemic response amplitude (p < 0.001), reduced incremental area under the blood glucose response curve (iAUC) at 30 min (peak) by 50% (p < 0.001), and averted late postprandial hypoglycaemia. All other treatments suppressed response amplitude half as much as whole kiwifruit and averted acute hypoglycaemia, with little effect on iAUC. Effects on 13CO2 exhalation paralleled effects on blood glucose (R2 = 0.97). Dietary fibre and organic acids contributed equally to the anti-glycaemic effect of kiwifruit by reducing intestinal absorption rate. Kiwifruit flesh effectively attenuates glycaemic response in carbohydrate exchange, as it contains fructose, dietary fibre and organic acids

The Effects on Immune Function and Digestive Health of Consuming the Skin and Flesh of Zespri® SunGold Kiwifruit (Actinidia Chinensis var. Chinensis ‘Zesy002’) in Healthy and IBS-Constipated Individuals

Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that results in constipation (IBS-C) or diarrhoea with abdominal pain, flatulence, nausea and bloating. Kiwifruit (Actinidia spp.) are nutrient-dense fruit with a number of reported health benefits that include lowering glycaemic response, improving cardiovascular and inflammatory biomarkers, and enhancing gut comfort and laxation. This study investigated the effect of consuming three whole Zespri® SunGold kiwifruit (Actinidia chinensis var. chinensis ‘Zesy002’) with or without skin on cytokine production and immune and gut health in healthy people and those with IBS-C symptoms. This study enrolled thirty-eight participants in a 16 week randomized cross-over study (19 healthy and 19 participants with IBS-C). Participants were randomized to consume either three kiwifruit without eating the skin or three kiwifruit including the skin for 4 weeks each, with a 4 week washout in between each intervention. There was a significant decrease in the pro-inflammatory cytokine, TNF-α, for both the healthy and the IBS-C participants when they consumed whole kiwifruit and skin, and also for the healthy participants when they ate whole kiwifruit without the skin (p < 0.001). The kiwifruit interventions increased bowel frequency and significantly reduced the gastrointestinal symptom rating scale constipation and Birmingham IBS pain scores for both participant groups. We have demonstrated that consuming the skin of SunGold kiwifruit might have beneficial effects on gastrointestinal health that are not produced by consuming the flesh alone

Polyunsaturated fatty acids modify expression of TGF-β in a co-culture model utilising human colorectal cells and human peripheral blood mononuclear cells exposed to Lactobacillus gasseri, Escherichia coli and Staphylococcus aureus

Nyanhanda, T ORCiD: 0000-0001-6502-5645Commensal bacteria and polyunsaturated fatty acids (PUFAs) have both been shown independently to modulate immune responses. This study tested the hypothesis that the different colonic immunomodulatory responses to commensal (Lactobacillus gasseri) and pathogenic bacteria (Escherichia coli and Staphylococcus aureus) may be modified by PUFAs. Experiments used a Transwell system combining the colorectal cell line HT29, or its mucous secreting sub-clone HT29-MTX, with peripheral blood mononuclear cells to analyse immunomodulatory signalling in response to bacteria, with and without prior treatment with arachidonic acid, eicosapentaenoic acid or docosahexaenoic acid. L. gasseri increased transforming growth factor β1 (TGF-β1) mRNA and protein secretion in colonic cell lines when compared with controls, an effect that was enhanced by pre-treatment with eicosapentaenoic acid. In contrast, the Gram-negative pathogen E. coli LF82 had no significant effect on TGF-β1 protein. L. gasseri also increased IL-8 mRNA but not protein while E. coli increased both; although differences between PUFA treatments were detected, none were significantly different to controls. Colonic epithelial cells show different immunomodulatory signalling patterns in response to the commensal L. gasseri compared to E. coli and S. aureus and pre-treatment of these cells with PUFAs can modify responses. Practical applications: We have demonstrated an interaction between dietary PUFAs and epithelial cell response to both commensal and pathogenic bacteria found in the gastrointestinal tract by utilising in vitro co-culture models. The data suggest that n-3 PUFAs may provide some protection against the potentially damaging effects of pathogens. Furthermore, the beneficial effects of combining n-3 PUFAs and the commensal bacteria, and potential probiotic, L. gasseri are illustrated by the increased expression of immunoregulatory TGF-β1. © 2014 The Authors

Polyunsaturated fatty acids modify colorectal epithelial cell cytokine expression in a leucocyte co-culture model in response to probiotic bacteria

Nyanhanda, T ORCiD: 0000-0001-6502-5645Diets high in n–3 polyunsaturated fatty acids (PUFAs) have been linked to improved colorectal health(1). One possible mechanism underlying this observation is that different PUFAs affect the immune response of epithelial cells to beneficial bacteria such as probiotics. The aim of this study was therefore to test whether pre-incubation of cells with different PUFAs would modify the epithelial cell response to probiotic bacteria

Polyunsaturated fatty acids modify expression of TGF‐β in a co‐culture model ultilising human colorectal cells and human peripheral blood mononuclear cells exposed to Lactobacillus gasseri

Commensal bacteria and polyunsaturated fatty acids (PUFAs) have both been shown independently to modulate immune responses. This study tested the hypothesis that the different colonic immunomodulatory responses to commensal (Lactobacillus gasseri) and pathogenic bacteria (Escherichia coli and Staphylococcus aureus) may be modified by PUFAs. Experiments used a Transwell system combining the colorectal cell line HT29, or its mucous secreting sub‐clone HT29‐MTX, with peripheral blood mononuclear cells to analyse immunomodulatory signalling in response to bacteria, with and without prior treatment with arachidonic acid, eicosapentaenoic acid or docosahexaenoic acid. L. gasseri increased transforming growth factor β1 (TGF‐β1) mRNA and protein secretion in colonic cell lines when compared with controls, an effect that was enhanced by pre‐treatment with eicosapentaenoic acid. In contrast, the Gram‐negative pathogen E. coli LF82 had no significant effect on TGF‐β1 protein. L. gasseri also increased IL‐8 mRNA but not protein while E. coli increased both; although differences between PUFA treatments were detected, none were significantly different to controls. Colonic epithelial cells show different immunomodulatory signalling patterns in response to the commensal L. gasseri compared to E. coli and S. aureus and pre‐treatment of these cells with PUFAs can modify responses. Practical applications: We have demonstrated an interaction between dietary PUFAs and epithelial cell response to both commensal and pathogenic bacteria found in the gastrointestinal tract by utilising in vitro co‐culture models. The data suggest that n‐3 PUFAs may provide some protection against the potentially damaging effects of pathogens. Furthermore, the beneficial effects of combining n‐3 PUFAs and the commensal bacteria, and potential probiotic, L. gasseri are illustrated by the increased expression of immunoregulatory TGF‐β1

Mechanisms of Selenium Enrichment and Measurement in Brassicaceous Vegetables, and Their Application to Human Health

Selenium (Se) is an essential micronutrient for human health. Se deficiency affects hundreds of millions of people worldwide, particularly in developing countries, and there is increasing awareness that suboptimal supply of Se can also negatively affect human health. Selenium enters the diet primarily through the ingestion of plant and animal products. Although, plants are not dependent on Se they take it up from the soil through the sulphur (S) uptake and assimilation pathways. Therefore, geographic differences in the availability of soil Se and agricultural practices have a profound influence on the Se content of many foods, and there are increasing efforts to biofortify crop plants with Se. Plants from the Brassicales are of particular interest as they accumulate and synthesize Se into forms with additional health benefits, such as methylselenocysteine (MeSeCys). The Brassicaceae are also well-known to produce the glucosinolates; S-containing compounds with demonstrated human health value. Furthermore, the recent discovery of the selenoglucosinolates in the Brassicaceae raises questions regarding their potential bioefficacy. In this review we focus on Se uptake and metabolism in the Brassicaceae in the context of human health, particularly cancer prevention and immunity. We investigate the close relationship between Se and S metabolism in this plant family, with particular emphasis on the selenoglucosinolates, and consider the methodologies available for identifying and quantifying further novel Se-containing compounds in plants. Finally, we summarize the research of multiple groups investigating biofortification of the Brassicaceae and discuss which approaches might be most successful for supplying Se deficient populations in the future