The effect of roasting on boron isotope ratio in coffee beans: Implications for provenance studies of roasted coffee.

We determined δ11B values of green and roasted coffee beans from 20 locations worldwide and conducted laboratory experiments with the aim to investigate boron isotope fractionation during roasting. Authentic single origin roasted coffees were found to be isotopically lighter than their green bean counterparts, with an average difference of 1.5‰. This isotope fractionation can be explained as arising from partial dissociation of boric acid in capillary water of green beans, where 11B isotopes are preferentially partitioned into molecules of undissociated boric acid and are then volatised during roasting. However, boron isotope fractionation induced by roasting was significantly smaller than between-origin variations in δ11B values of green coffee beans that had the range of ∼54‰. This implies that δ11B isotopic composition of roasted coffee retains the geographical origin information within δ11B values of green beans when regional differences in boron isotopic composition of coffee are considered.

Investigation of Mitochondrial Related Variants in a Cerebral Small Vessel Disease Cohort.

Monogenic forms of cerebral small vessel disease (CSVD) can be caused by both variants in nuclear DNA and mitochondrial DNA (mtDNA). Mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is known to have a phenotype similar to Cerebral Autosomal Dominant Arteriopathy with Sub-cortical Infarcts and Leukoencephalopathy (CADASIL), and can be caused by variants in the mitochondrial genome and in several nuclear-encoded mitochondrial protein (NEMP) genes. The aim of this study was to screen for variants in the mitochondrial genome and NEMP genes in a NOTCH3-negative CADASIL cohort, to identify a potential link between mitochondrial dysfunction and CSVD pathology. Whole exome sequencing was performed for 50 patients with CADASIL-like symptomology on the Ion Torrent system. Mitochondrial sequencing was performed using an in-house designed protocol with sequencing run on the Ion GeneStudio S5 Plus (S5 +). NEMP genes and mitochondrial sequencing data were examined for rare (MAF < 0.001), non-synonymous variants that were predicted to have a deleterious effect on the protein. We identified 29 candidate NEMP variants that had links to either MELAS-, encephalopathy-, or Alzheimer's disease-related phenotypes. Based on these changes, variants affecting POLG, MTO1, LONP1, NDUFAF6, NDUFB3, and TCIRG1 were thought to play a potential role in CSVD pathology in this cohort. Overall, the exploration of the mitochondrial genome identified a potential role for mitochondrial related proteins and mtDNA variants contributing to CSVD pathologies.

Genetic variants associated with exercise performance in both moderately trained and highly trained individuals.

Adaptation to exercise training is a complex trait that may be influenced by genetic variants. We identified 36 single nucleotide polymorphisms (SNPs) that had been previously associated with endurance or strength performance, exercise-related phenotypes or exercise intolerant disorders. A MassARRAY multiplex genotyping assay was designed to identify associations with these SNPs against collected endurance fitness phenotype parameters obtained from two exercise cohorts (Gene SMART study; n = 58 and Hawaiian Ironman Triathlon 2008; n = 115). These parameters included peak power output (PP), a time trial (TT), lactate threshold (LT), maximal oxygen uptake (VO2 max) in recreationally active individuals and a triathlon time-to-completion (Hawaiian Ironman Triathlon cohort only). A nominal significance threshold of α < 0.05 was used to identify 17 variants (11 in the Gene SMART population and six in the Hawaiian Ironman Triathlon cohort) which were significantly associated with performance gains in highly trained individuals. The variant rs1474347 located in Interleukin 6 (IL6) was the only variant with a false discovery rate < 0.05 and was found to be associated with gains in VO2 max (additional 4.016 mL/(kg min) for each G allele inherited) after training in the Gene SMART cohort. In summary, this study found further evidence to suggest that genetic variance can influence training response in a moderately trained cohort and provides an example of the potential application of genomic research in the assessment of exercise trait response.

Investigating diagnostic sequencing techniques for CADASIL diagnosis.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease caused by mutations in the NOTCH3 gene. Our laboratory has been undertaking genetic diagnostic testing for CADASIL since 1997. Work originally utilised Sanger sequencing methods targeting specific NOTCH3 exons. More recently, next-generation sequencing (NGS)-based technologies such as a targeted gene panel and whole exome sequencing (WES) have been used for improved genetic diagnostic testing. In this study, data from 680 patient samples was analysed for 764 tests utilising 3 different sequencing technologies. Sanger sequencing was performed for 407 tests, a targeted NGS gene panel which includes NOTCH3 exonic regions accounted for 354 tests, and WES with targeted analysis was performed for 3 tests. In total, 14.7% of patient samples (n = 100/680) were determined to have a mutation. Testing efficacy varied by method, with 10.8% (n = 44/407) of tests using Sanger sequencing able to identify mutations, with 15.8% (n = 56/354) of tests performed using the NGS custom panel successfully identifying mutations and a likely non-NOTCH3 pathogenic variant (n = 1/3) identified through WES. Further analysis was then performed through stratification of the number of mutations detected at our facility based on the number of exons, level of pathogenicity and the classification of mutations as known or novel. A systematic review of NOTCH3 mutation testing data from 1997 to 2017 determined the diagnostic rate of pathogenic findings and found the NGS-customised panel increases our ability to identify disease-causing mutations in NOTCH3.

A novel route to substituted 4-methylene-4,5-dihydroisoxazoles mediated by hafnium(IV) chloride.

Heating alkyl vinyl ketones and N-tert-butylarylmethylideneamine N-oxides in the presence of HfCl4 results in the formation of 4-methylene-4,5-dihydroisoxazoles in good yield.

A whole-genome assembly of Drosophila.

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

Genomic strategies for defining and dissecting developmental and physiological pathways.

A major challenge in genetics research is defining and dissecting the diversity of developmental and physiological pathways that lie between genes and traits. New functional genomics methods are transforming these studies by providing comprehensive and systematic approaches that complement traditional methods of formal genetics, biochemistry, and cell biology. Together, these complementary approaches will test whether reductionism can account for the complex web of interactions that lead from genetic variation to morphological, physiological, and behavioral traits in health and disease.

Current state of metabolic control achieved in a New Zealand diabetes clinic.

AIMS: To report on current degree of metabolic control achieved in diabetic patients in a New Zealand diabetes clinic. METHODS: All metabolic data were reviewed for patients attending the Waikato diabetes clinic from 1 January 1992 to 1 January 1995. Values were obtained from 409 insulin treated patients (IDDM), with a mean age of 39 (SD 15 yr); 200 patients who transferred from diet or pills to insulin (NIDDM-I) with a mean age of 59 (SD 12 yr); and 290 noninsulin dependent patients (NIDDM), mean age 54 (SD 13 yr). Results. Percentage of fructosamine values in the normal range: IDDM 10%, NIDDM-I 12.5% and NIDDM 37.9%. Mean values (SD). IDDM group: fructosamine 376 (78) mmol/L, cholesterol 5.24 (1.1) mmol/L, HDL cholesterol 1.47 (0.45) mmol/L, triglycerides 1.71 (1.35) mmol/L. NIDDM-I group: fructosamine 359 (67) mmol/L, cholesterol 5.82 (1.1) mmol/L, HDL cholesterol 1.21 (0.45) mmol/L, triglycerides 2.92 (3.8) mmol/L. NIDDM group: fructosamine, 312 (73) mmol/L, cholesterol 5.83 (1.24) mmol/L, HDL cholesterol 1.1 (0.33) mmol/L, triglycerides 3.11 (3.59) mmol/L. Percentage of smokers in each group: IDDM 24%, NIDDM-I 8.5%, NIDDM 17.2%. CONCLUSIONS: the majority of patients fail to achieve normal fructosamine values. Lipid control is poor, other than in the IDDM group. A significant number of patients continue to smoke. Considerable scope for improvement is noted.

The prognostic significance of urinary albumin in Polynesians with non-insulin-dependent diabetes.

Polynesian (59 Maori and 30 Pacific Island) patients were identified from two diabetes clinic registers and followed for a mean of 4.8 years, in order to determine the prognostic significance of urinary albumin excretion. Events were defined as death or entry onto a renal replacement programme. Fourteen events occurred during the period of follow-up. Urinary albumin/creatinine ratio was treated as a continuous variable in a proportional hazards analysis. A 10-fold increase in albumin/creatinine ratio was associated with a 5-fold increase in the risk of an event (95% C.I. = 2.05-12.09). In conclusion, elevated urinary albumin/creatinine predicted mortality and renal morbidity in Maori and Pacific Island patients with non-insulin-dependent diabetes.

Discover diabetes: a community based screening programme for diabetic eye disease.

AIM: To evaluate a diabetic retinopathy screening programme for rural people with diabetes. METHOD: A retinal camera was transported to rural Waikato communities. Colour slide photographs were taken of the retina and lens of diabetic patients who had not had a previous review of their eyes by an ophthalmologist. The photographs were reviewed by an ophthalmologist, and those patients with an abnormality were referred back to their general practitioner who arranged further specialist assessment. RESULTS: Three hundred and ninety six patients have been screened and 116 patients have been referred on for specialist review. Fifty two of these patients had evidence of diabetic retinopathy, eight have been treated with laser treatment and one patient has had retinal surgery. No patients had to be recalled for repeat photographs. CONCLUSION: Retinal photography is an effective method of screening for sight threatening pathology in rural people with diabetes. Transportation of the retinal camera by station wagon is a practical way of making the service accessible.

Discover diabetes: screening for diabetes mellitus in the Waikato.

AIMS: Free screening for diabetes mellitus was offered, in three rural communities as part of an initiative of the Waikato Area Health Board to improve the detection and management of type 2 diabetes. METHOD: An organised campaign promoted glucose testing as an important preventative health measure for 'at risk' members of the community. At risk was defined as being either Maori over 20 years of age, European over 40 years of age, obese or having a family history of diabetes. The testing method was a random capillary glucose test followed by an oral glucose tolerance test for those with a result > or = 8 mmol/L. RESULTS: Five thousand five hundred and eighty nine people voluntarily attended screening at various sites. Sixty of these people were already known to have diabetes and were subsequently excluded. One thousand and four people had no recognised risk factors. Four thousand five hundred and twenty one people with risk factors for type 2 diabetes had a capillary blood glucose test and 162 were found to have a capillary glucose greater than 8 mmol/L. Four patients did not have their glucose result recorded. One hundred and forty one oral glucose tolerance tests were performed and 56 new patients with diabetes were identified based on WHO criteria for diabetes. The prevalence of previously undiagnosed diabetes was higher in those over 50 years of age, particularly if they were Maori. It was also higher in obese Maori in the 30-49 year age group. CONCLUSIONS: Although over 5000 patients attended screening, this testing included only 34% of the at risk age group. Thus voluntary testing, despite a major investment in promotion, proved ineffective as a population screening tool. A random capillary glucose test proved to be a simple and sensitive method of helping to identify previously undiagnosed disease. This could be effectively used by general practitioners, targeting all adults over 50 years of age, and all adult Maori with obesity as defined by a BMI > or = 30.