Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2

BACKGROUND

Genetic variation in enzymes involved in vitamin metabolism is a candidate for analysis in studies of how nutritional covariates may impact a disease state. The role of folate pathway genes in birth defects and cardiovascular disease in humans has been widely studied. Since incidence rates for these disorders vary by geographic origins, it is useful to know which variants are the best candidates for studies based on genotype and allele frequency, as well as linkage disequilibrium (LD) in founder populations.

METHODS

Six polymorphisms in five folate metabolism‐related genes (MTHFR, MTHFD, MTRR, GCP2, and RFC1) were genotyped on a collection of 1064 DNA samples from populations around the world, which were made available by the Centre d'Étude du Polymorphisme Humain (CEPH) consortium for analysis.

RESULTS

In this study we report the genotype frequencies for variants in the MTHFR, MTHFD, MTRR, GCP2, and RFC1 genes, and the LD for two variants (C677T and A1298C) in MTHFR.

CONCLUSIONS

The rare allele frequency for each of the five genes studied varied widely. LD is strongest in Pakistani and Brazilian populations (D′ = 1.0) and weakest in Mexican populations (D′ = 0.45). These findings will allow the selection of variants that will provide the most power in studies of folate pathway genes involving different ancestral populations, and contribute to our knowledge of the population distribution of selected nutritional gene variants. Birth Defects Research (Part A), 2003. © 2003 Wiley‐Liss, Inc.

     

Our Planet,Our Health

Readers' corner

Our Planet, Our Health Report of the who commission on health and environment     

Using water chemistry to define ecological preferences within the moss genus Scorpidium,from Wales,UK

ABSTRACT

Introduction

Three Scorpidium species: S. scorpioides, S. cossonii and S. revolvens are often associated with habitats of high conservation value. This is the first attempt to define the chemical niches for these Scorpidium species in Wales (UK) and allows us to compare these with earlier European datasets.     

Taxonomy,distribution, and status of gibbons (Hylobates) in Southern China and adjacent areas

Information

Taxonomy, distribution, and status of gibbons (Hylobates) in Southern China and adjacent areas     

Changes in endogenous abscisic acid and stomata of the resurrection fern,Pleopeltis polypodioides,in response to de- and rehydration

Premise

While angiosperms respond uniformly to abscisic acid (ABA) by stomatal closure, the response of ferns to ABA is ambiguous. We evaluated the effect of endogenous ABA, hydrogen peroxide (H₂O₂), nitric oxide (NO), and Ca²⁺, low and high light intensities, and blue light (BL) on stomatal opening of Pleopeltis polypodioides.

Methods

Endogenous ABA was quantified using gas chromatography-mass spectrometry; microscopy results and stomatal responses to light and chemical treatments were analyzed with Image J.

Results

The ABA content increases during initial dehydration, peaks at 15 h and then decreases to one fourth of the ABA content of hydrated fronds. Following rehydration, ABA content increases within 24 h to the level of hydrated tissue. The stomatal aperture opens under BL and remains open even in the presence of ABA. Closure was strongly affected by BL, NO, and Ca²⁺, regardless of ABA, H₂O₂ effect was weak.

Conclusions

The decrease in the ABA content during extended dehydration and insensitivity of the stomata to ABA suggests that the drought tolerance mechanism of Pleopeltis polypodioides is independent of ABA.

     

Farming Eucheuma in Zanzibar,Tanzania

5. Cultivation, tissue culture

Farming Eucheuma in Zanzibar, Tanzania     

Three new species of Euathlus Ausserer, 1875 (Araneae,Theraphosidae) from Argentina

ABSTRACT

Euathlus

Ausserer, 1875 is a South American genus of spiders of the family Theraphosidae known from Chile and Argentina. Three new species from Argentina: Euathlus mauryi sp. n. (from San Juan province), Euathlus grismadoi sp. n. (from La Rioja province), and Euathlus pampa sp. n. (from Salta province) are described here. New records of the previous species Euathlus diamante and Euathlus tenebrarum are contributed. The distribution of these new species expands the geographical distribution of the genus along the Andean hills, with Salta province as the northernmost record of the genus. A key is provided for identification of Euathlus species as well as a map with all the records in Argentina.     

The missense variation landscape of FTO,MC4R,and TMEM18 in obese children of African Ancestry

Objective:

Common variation at the loci harboring fat mass and obesity (FTO), melanocortin receptor 4 (MC4R), and transmembrane protein 18 (TMEM18) is consistently reported as being statistically most strongly associated with obesity. Investigations if these loci also harbor rarer missense variants that confer substantially higher risk of common childhood obesity in African American (AA) children were conducted.

Design and Methods:

The exons of FTO, MC4R, and TMEM18 in an initial subset of our cohort were sequenced, that is, 200 obese (BMI≥95th percentile) and 200 lean AA children (BMI≤5th percentile). Any missense exonic variants that were uncovered went on to be further genotyped in a further 768 obese and 768 lean (BMI≤50th percentile) children of the same ethnicity.

Results:

A number of exonic variants were observed from our sequencing effort: seven in FTO, of which four were non‐synonymous (A163T, G182A, M400V, and A405V), thirteen in MC4R, of which six were non‐synonymous (V103I, N123S, S136A, F202L, N240S, and I251L), and four in TMEM18, of which two were non‐synonymous (P2S and V113L). Follow‐up genotyping of these missense variants revealed only one significant difference in allele frequency between cases and controls, namely with N240S in MC4R (Fisher's exact P = 0.0001).

Conclusion:

In summary, moderately rare missense variants within the FTO, MC4R, and TMEM18 genes observed in our study did not confer risk of common childhood obesity in African Americans except for a degree of evidence for one known loss‐of‐function variant in MC4R.     

Analysing Betula litwinowii encroachment and reforestation in the Kazbegi region,Greater Caucasus,Georgia

Aims

The encroachment of tree and shrub species in high mountains is an increasing worldwide phenomenon, which is expected to dramatically alter high‐mountain ecosystems and their functioning. Moreover it indicates in some cases a reforestation process, which will result in important ecological and social benefits, including carbon sequestration and protection against landslides. We therefore examined the spatial extent of forest growth and shrub encroachment mainly of birch (Betula litwinowii) in the sub‐alpine belt of the Central Greater Caucasus between 1987 and 2010 and its relation to topographic site conditions.

Location

Kazbegi district, Central Greater Caucasus, Georgia.

Methods

We analysed 155 vegetation relevés sampled in 2009, 2011 and 2015, mainly derived from the Caucasus Vegetation Database, to obtain information about topographic site conditions and structure of B. litwinowii stands. B. litwinowii forest growth was assessed by digitizing the forest outlines from aerial and space‐borne imagery (1987, 2005 and 2010). To identify areas of B. litwinowii encroachment as an indicator for different encroachment stages, we modelled the tree and shrub cover using the Random Forest algorithm.

Results

We found four types of B. litwinowii stands, characterized by different tree and shrub coverage (initial Bromus variegatus–Betula litwinowii encroachment indicating the first stage of succession, Aconitum nasutum–Betula litwinowii forest, Rubus idaeus–Betula litwinowii forest and Rhododendron caucasicum–Betula litwinowii tree line scrubs). B. litwinowii forest increased 25% compared to 1987 mainly in an uphill direction. Furthermore the modelled tree and shrub cover (R² = .69) could be related to the four vegetation types.

Conclusions

Our results indicate a recent trend towards shrub encroachment and consequently reforestation in the Kazbegi region.     

The microbiology of Bandji,palm wine of Borassus akeassii from Burkina Faso: identification and genotypic diversity of yeasts,lactic acid and acetic acid bacteria

Aim

To investigate physicochemical characteristics and especially genotypic diversity of the main culturable micro‐organisms involved in fermentation of sap from Borassus akeassii, a newly identified palm tree from West Africa.

Methods and Results

Physicochemical characterization was performed using conventional methods. Identification of micro‐organisms included phenotyping and sequencing of: 26S rRNA gene for yeasts, 16S rRNA and gyrB genes for lactic acid bacteria (LAB) and acetic acid bacteria (AAB). Interspecies and intraspecies genotypic diversities of the micro‐organisms were screened respectively by amplification of the ITS1‐5.8S rDNA‐ITS2/16S‐23S rDNA ITS regions and repetitive sequence‐based PCR (rep‐PCR). The physicochemical characteristics of samples were: pH: 3·48–4·12, titratable acidity: 1·67–3·50 mg KOH g^?1, acetic acid: 0·16–0·37%, alcohol content: 0·30–2·73%, sugars (degrees Brix): 2·70–8·50. Yeast included mainly Saccharomyces cerevisiae and species of the genera Arthroascus, Issatchenkia, Candida, Trichosporon, Hanseniaspora, Kodamaea, Schizosaccharomyces, Trigonopsis and Galactomyces. Lactobacillus plantarum was the predominant LAB species. Three other species of Lactobacillus were also identified as well as isolates of Leuconostoc mesenteroides, Fructobacillus durionis and Streptococcus mitis. Acetic acid bacteria included nine species of the genus Acetobacter with Acetobacter indonesiensis as predominant species. In addition, isolates of Gluconobacter oxydans and Gluconacetobacter saccharivorans were also identified. Intraspecies diversity was observed for some species of micro‐organisms including four genotypes for Acet. indonesiensis, three for Candida tropicalis and Lactobacillus fermentum and two each for S. cerevisiae, Trichosporon asahii, Candida pararugosa and Acetobacter tropicalis.

Conclusion

fermentation of palm sap from B. akeassii involved multi‐yeast‐LAB‐AAB cultures at genus, species and intraspecies level.

Significance and Impact of the Study

First study describing microbiological and physicochemical characteristics of palm wine from B. akeassii. Genotypic diversity of palm wine LAB and AAB not reported before is demonstrated and this constitutes valuable information for better understanding of the fermentation which can be used to improve the product quality and develop added value by‐products.     

Placement,survival and predator identity of Eurasian Curlew Numenius arquata nests on lowland grass-heath

ABSTRACT

Capsule

Within the UK’s largest lowland Eurasian Curlew Numenius arquata population, curlew preferentially nested on physically disturbed (treated) than undisturbed (control) grassland, and low nest survival rates were primarily attributable to predation by Red Fox Vulpes vulpes.     

Induction of 3'-O-beta-D-ribofuranosyl adenosine during compatible, but not during incompatible, interactions of Arabidopsis thaliana or Lycopersicon esculentum with Pseudomonas syringae pathovar tomato

All hitherto identified aromatic compounds accumulating in leaves of Arabidopsis thaliana (L.) Heynh. upon infection with virulent or avirulent strains of Pseudomonas syringae pathovar tomato (Pst) were indolic metabolites. We now report the strong accumulation of a novel type of natural product, 3-O--d-ribofuranosyl adenosine (3RA), exclusively during compatible interactions. In contrast to the various indolic metabolites, 3RA was undetectable in incompatible interactions of A. thaliana leaves with an avirulent Pst strain, as well as in uninfected control leaves. A similar, strong induction of 3RA was observed in compatible but, again, not in incompatible interactions of Pst with its natural host, Lycopersicon esculentum. The strength of the effect and its confinement to compatible interactions suggests that it may be applicable as a diagnostic tool.Abbreviations Pst Pseudomonas syringae pathovar tomato - 3RA 3-O--d-ribofuranosyl adenosine     

Index to new names, combinations and emendation appearing in Mycoscience 51 (4)

Index

Index to new names, combinations and emendation appearing in Mycoscience 51 (4)     

Piper regnellii extract biopolymer‐based microparticles: production,characterization and antifungal activity

Aims

This study aims to improve characteristics of Piper regnellii extract to make it applicable in formulations to treat dermatophytosis, also known as ringworm.

Methods and Results

Microparticles (MPs) were produced by spray drying with gelatin, alginate and chitosan as encapsulating agents; characterized by scanning electron microscopy, encapsulation efficiency, thermal analyses and X‐ray diffraction; and tested against Trichophyton rubrum by broth microdilution. Produced MPs had a mean diameter less than 2 μm, an increase in stability and release of the extract and good results for encapsulation efficiency, being 85·6% to gelatin MP, 71·3% to chitosan MP and 60·6% to alginate. MPs preserved the antifungal activity of P. regnellii extract T. rubrum.

Conclusion

Microencapsulation provided a significant improvement in the stability of the P. regnellii extract and better solubilization of chemical compounds, maintaining the antifungal effect against T. rubrum.

Significance and Impact of the Study

These results are useful for developing a formulation to treat fungal infections caused by dermatophyte species.     

Diagnosing lactic acid fermentation based on specific rates of growth,substrate consumption and product formation

The on-line calculated specific rates of growth, substrate consumption and product formation were used to diagnose microbial activities during a lactic acid fermentation. The specific rates were calculated from on-line measured cell mass, and substrate and product concentrations. The specific rates were more sensitive indicators of slight changes in fermentation conditions than such monitored data as cell mass or product concentrations.List of Symbols 1/h specific rate of cell growth - 1/h specific rate of substrate consumption - 1/h specific rate of product formation - ^* dimensionless specific rate of cell growth - ^* dimensionless specific rate of substrate consumption - ^* dimensionless specific rate of product formation - _max 1/h maximum specific rate of cell growth - _max 1/h maximum specific rate of substrate consumption - _max 1/h maximum specific rate of product formation - X g/l cell mass concentration - S g/l substrate concentration - S ^* dimensionless substrate concentration - S ₀ g/l initial substrate concentration - P g/l product concentration     

Cortisol,obesity, and the metabolic syndrome: A cross‐sectional study of obese subjects and review of the literature

Objective:

Circulating cortisol and psychosocial stress may contribute to the pathogenesis of obesity and metabolic syndrome (MS). To evaluate these relationships, a cross‐sectional study of 369 overweight and obese subjects and 60 healthy volunteers was performed and reviewed the previous literature.

Design and Methods:

Overweight and obese subjects had at least two other features of Cushing's syndrome. They underwent measurements representing cortisol dynamics (24 h urine cortisol excretion (UFC), bedtime salivary cortisol, 1 mg dexamethasone suppression test) and metabolic parameters (BMI, blood pressure (BP); fasting serum triglycerides, HDL, insulin, and glucose). Subjects also completed the Perceived Stress Scale (PSS). UFC, salivary cortisol, and weight from 60 healthy volunteers were analyzed.

Results:

No subject had Cushing's syndrome. UFC and dexamethasone responses were not associated with BMI or weight. However, salivary cortisol showed a trend to increase as BMI increased (P < 0.0001), and correlated with waist circumference (WC) in men (r_s = 0.28, P = 0.02) and systolic BP in women (r_s = 0.24, P = 0.0008). Post‐dexamethasone cortisol levels were weak to moderately correlated with fasting insulin (r_s = ?0.31, P = 0.01) and HOMA‐IR (r_s = ?0.31, P = 0.01) in men and systolic (r_s = 0.18, P = 0.02) and diastolic BP (r_s = 0.20, P = 0.009) in women. PSS results were higher in obese subjects than controls, but were not associated with cortisol or metabolic parameters. As expected, WC correlated with fasting insulin, HOMA‐IR, and systolic BP (adjusted for BMI and gender; P < 0.01). Literature showed inconsistent relationships between cortisol and metabolic parameters.

Conclusion:

Taken together, these data do not support a strong relationship between systemic cortisol or stress and obesity or MS.

     

Objectively measured sedentary behavior,physical activity,and plasma lipids in overweight and obese children

Objective:

This study examines the associations between objectively measured sedentary behavior, light physical activity (LPA), and moderate‐to‐vigorous physical activity (MVPA), and plasma lipids in overweight and obese children.

Design and Methods:

Cross‐sectional analyses were conducted among 126 children aged 5.5‐9.9 years. Sedentary behavior, LPA, and MVPA were assessed using accelerometry. Fasting blood samples were analyzed for plasma lipids (high‐density lipoprotein cholesterol [HDL‐C], low‐density lipoprotein cholesterol [LDL‐C], total cholesterol [TC], and triglycerides [TG]).

Results:

MVPA was not related to plasma lipids (P > 0.05). Independent of age, sex, energy intake, and waist circumference z‐score, sedentary behavior and LPA were associated with HDL‐C (β = ?0.23, 95% CI ?0.42 to ?0.04, P = 0.020; β = 0.20, 95% CI 0.14 to 0.39, P = 0.036, respectively). The strength of the associations remained after additionally adjusting for MVPA (sedentary behavior: β = ?0.22, 95% CI ?0.44 to 0.006, P = 0.056; LPA: β = 0.19, 95% CI ?0.005 to 0.38, P = 0.056, respectively).

Conclusion:

Substituting at least LPA for sedentary time may contribute to the development of healthy HDL‐C levels among overweight and obese children, independent of their adiposity. Comprehensive prevention and treatment strategies to improve plasma HDL‐C among overweight and obese children should target reductions in total sedentary time and promote the benefits of LPA, in addition to promoting healthy levels of adiposity, healthy dietary behaviors, and MVPA.