Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to 91 462 coffee consumers of European ancestry with top single-nucleotide polymorphisms (SNPs) followed-up in ~30 062 and 7964 coffee consumers of European and African-American ancestry, respectively. Studies from both stages were combined in a trans-ethnic meta-analysis. Confirmed loci were examined for putative functional and biological relevance. Eight loci, including six novel loci, met GW significance (log10Bayes factor (BF)>5.64) with per-allele effect sizes of 0.03-0.14 cups per day. Six are located in or near genes potentially involved in pharmacokinetics (ABCG2, AHR, POR and CYP1A2) and pharmacodynamics (BDNF and SLC6A4) of caffeine. Two map to GCKR and MLXIPL genes related to metabolic traits but lacking known roles in coffee consumption. Enhancer and promoter histone marks populate the regions of many confirmed loci and several potential regulatory SNPs are highly correlated with the lead SNP of each. SNP alleles near GCKR, MLXIPL, BDNF and CYP1A2 that were associated with higher coffee consumption have previously been associated with smoking initiation, higher adiposity and fasting insulin and glucose but lower blood pressure and favorable lipid, inflammatory and liver enzyme profiles (P<5 × 10-8).Our genetic findings among European and African-American adults reinforce the role of caffeine in mediating habitual coffee consumption and may point to molecular mechanisms underlying inter-individual variability in pharmacological and health effects of coffee.

Coffee polyphenols change the expression of STAT5b and ATF-2 modifying cyclin D1 levels in cancer cells

Background: Epidemiological studies suggest that coffee consumption reduces the risk of cancer, but the molecular mechanisms of its chemopreventive effects remain unknown. Objective: To identify differentially expressed genes upon incubation of HT29 colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using whole genome microarrays. Results: ICC incubation of HT29 cells caused the overexpression of 57 genes and the underexpression of 161, while CA incubation induced the overexpression of 12 genes and the underexpression of 32. Using Venn-Diagrams, we built a list of five overexpressed genes and twelve underexpressed genes in common between the two experimental conditions. This list was used to generate a biological association network in which STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2, were dowregulated by CA in colon cancer cells and by ICC and CA in breast cancer cells. Conclusions: Coffee polyphenols are able to affect cyclin D1 expression in cancer cells through the modulation of STAT5B and ATF-2.

Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.

Supercritical CO2 recovery of caffeine from green coffee oil: new experimental solubility data and modeling

The caffeine solubility in supercritical CO2 was studied by assessing the effects of pressure and temperature on the extraction of green coffee oil (GCO). The Peng-Robinson¹ equation of state was used to correlate the solubility of caffeine with a thermodynamic model and two mixing rules were evaluated: the classical mixing rule of van der Waals with two adjustable parameters (PR-VDW) and a density dependent one, proposed by Mohamed and Holder² with two (PR-MH, two parameters adjusted to the attractive term) and three (PR-MH3 two parameters adjusted to the attractive and one to the repulsive term) adjustable parameters. The best results were obtained with the mixing rule of Mohamed and Holder² with three parameters.

Development and validation of a method for the analysis of Ochratoxin A in roasted coffee by liquid chromatography/electrospray-mass spectrometry in Tandem (LC/ESI-MS/MS)

A method using LC/ESI-MS/MS for the quantitative analysis of Ochratoxin A in roasted coffee was described. Linearity was demonstrated (r = 0.9175). The limits of detection and quantification were 1.0 and 3.0 ng g-1, respectively. Trueness, repeatability and intermediate precision values were 89.0-108.8%; 2.4-13.7%; 12.5-17.8%, respectively. To the best of our knowledge, this is the first report in which Ochratoxin A in roasted coffee is analysed by LC/ESI-MS/MS, contributing to the field of mycotoxin analysis, and it will be used for future production of Certified Reference Material.

Description of epidemics of coffee rust with neural networks

The objective of this paper was to evaluate the potential of neural networks (NN) as an alternative method to the basic epidemiological approach to describe epidemics of coffee rust. The NN was developed from the intensities of coffee (Coffea arabica) rust along with the climatic variables collected in Lavras-MG between 13 February 1998 and 20 April 2001. The NN was built with climatic variables that were either selected in a stepwise regression analysis or by the Braincel® system, software for NN building. Fifty-nine networks and 26 regression models were tested. The best models were selected based on small values of the mean square deviation (MSD) and of the mean prediction error (MPE). For the regression models, the highest coefficients of determination (R²) were used. The best model developed with neural networks had an MSD of 4.36 and an MPE of 2.43%. This model used the variables of minimum temperature, production, relative humidity of the air, and irradiance 30 days before the evaluation of disease. The best regression model was developed from 29 selected climatic variables in the network. The summary statistics for this model were: MPE=6.58%, MSE=4.36, and R²=0.80. The elaborated neural networks from a time series also were evaluated to describe the epidemic. The incidence of coffee rust at four previous fortnights resulted in a model with MPE=4.72% and an MSD=3.95.

Effect of extracts from citric biomass, rusted coffee leaves and coffee berry husks on Phoma costarricencis of coffee plants

Phoma leaf spot, caused by Phoma costarricensis poses a serious threat to coffee (Coffea arabica) production, especially in the highlands of the state of Minas Gerais, Brazil. Extracts of citric biomass, coffee berry husks and coffee leaves severely affected by rust caused by Hemileia vastatrix, were evaluated against P. costarricensis. In an in vitro assay, aqueous extracts of rusted leaves and berry husks plus the commercial extracts based on citric biomass named Ecolife® and Agromil® were tested at various dilutions on the mycelial growth inhibition of P. costarricensis. In vivo, coffee seedlings maintained in glasshouse, were sprayed with these extracts seven days before inoculation of P. costarricensis. Only extracts from citric biomass had inhibitory effects on the fungus. In vivo, Ecolife® (5 ml/l), Agromil® (5 g/l) and the aqueous extract of rusted coffee leaves (dilution 1:6) reduced Phoma leaf spot. Both, Ecolife® and the extract of rusted coffee leaves were significantly more effective in reducing the area under the lesion progress curve when applied at lower doses, indicating a possible effect on the induction of resistance.

Virulence pattern of Pyricularia grisea isolates from farmers' fields on newly released upland rice cultivars

The virulence pattern of the isolates of Pyricularia grisea from commercial fields of the upland rice (Oryza sativa) cultivars 'Primavera' and 'BRS Bonança' was analyzed. A hundred and seventy monoconidial isolates of the pathogen virulent to 'Primavera' and 139 to 'BRS Bonança' collected from eight fields, during two years (2001-2003) were tested, under greenhouse conditions, on six newly released rice cultivars. Differences in virulence pattern were observed in pathogenic populations of 'Primavera' and 'BRS Bonança'. Isolates with virulence to improved cultivars were common in samples from farmers' fields in the absence of aloinfection. The virulence frequency of P. grisea isolates collected from 'Primavera'' to cultivars 'BRS Vencedora', 'BRS Colosso', 'BRS Liderança', 'BRS Soberana', 'BRS Curinga' and 'BRS Talento', was high in descending order. On the other hand, in the fungus population of 'BRS BRS Bonança' virulence frequency was high in 'BRS Talento', followed by 'BRS Curinga', 'BRS Vencedora', 'BRS Liderança', 'BRS Colosso' and 'BRS Soberana'. While virulence to 'BRS Talento' was rare among isolates from 'Primavera', it was most frequent in isolates of 'BRS Bonança'. The six improved rice cultivars permitted to differentiating agriculturally important virulences in the pathogen population which can be utilized in selecting breeding lines for specific resistance, in rice blast improvement program.

Vírus da mancha anular do cafeeiro (Coffee ringspot virus - CoRSV): influência na qualidade da bebida e na produção de grãos de café

A mancha anular do cafeeiro, causada pelo Coffee ringspot virus (CoRSV) que é transmitido pelo ácaro Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae), tem sido observada em altas incidências em várias regiões cafeeiras do Estado de Minas Gerais. O CoRSV causa manchas cloróticas arrendondadas ou irregulares nas folhas, caules e frutos. Foi feita uma avaliação do efeito da infecção de frutos do cafeeiro pelo CoRSV na qualidade da bebida por meio de teste bioquímico e de degustação, e também na eventual perda de peso nos grãos. Testes revelaram que grãos provenientes de frutos de café infectados pelo CoRSV apresentavam menor teor de açúcares redutores e maior condutividade elétrica. Houve também depreciação na qualidade de bebida gerada pelos frutos infectados por meio do teste de degustação (teste de xícara). O peso médio dos grãos provenientes de frutos manchados foi cerca de 5% menor do que dos grãos de frutos sem sintomas.

Incubation period of Hemileia vastatrix in coffee plants in Brazil simulated under climate change

Risk analysis of climate change on plant diseases has great importance for agriculture since it allows the evaluation of management strategies to minimize future damages. This work aimed to simulate future scenarios of coffee rust (Hemileia vastatrix) epidemics by elaborating geographic distribution maps using a model that estimates the pathogen incubation period and the output from three General Circulation Models (CSIRO-Mk3.0, INM-CM3.0, and MIROC3.2.medres). The climatological normal from 1961-1990 was compared with that of the decades 2020s, 2050s and 2080s using scenarios A2 and B1 from the IPCC. Maps were prepared with a spatial resolution of 0.5 × 0.5 degrees of latitude and longitude for ten producing states in Brazil. The climate variables used were maximum and minimum monthly temperatures. The maps obtained in scenario A2 showed a tendency towards a reduction in the incubation period when future scenarios are compared with the climatological normal from 1961-1990. A reduction in the period was also observed in scenario B1, although smaller than that in scenario A2.

GFP-fluorescent protein on the study of blister spot in coffee plants

In Brazil, Colletotrichum gloeosporioides is associated with a complex of symptoms in coffee culture. Although this pathogen had its pathogenesis observed and identified, its importance has still been questioned due to its several endophytic forms, raising doubts as to the real importance of the pathosystem. The aim of this study was to demonstrate, by using an isolate transformed with the gene gfp, the infection and colonization capability of C. gloeosporioides in coffee seedlings. After the fourth day of inoculation, manifestation of symptoms as punctual necrosis could be observed, which progressed during the evaluation period, culminating in the death of seedlings. Epifluorescence microscopy confirmed the presence of the pathogen in the seedlings, as well as the visualization of internal colonization of tissues, acervulus formation and conidium production, confirming that it was responsible for the observed symptoms.

Anatomical changes on coffee leaves infected by Pseudomonas syringae pv. garcae

ABSTRACTAlthough poorly studied, the bacterial halo blight is an important disease in the major coffee-producing states of Brazil. External damage and anatomical changes on leaves were measured in seedlings of Coffea arabica cv. Mundo Novo, susceptible to Pseudomonas syringae pv. garcae, by using histological sections obtained at 10 and 20 days after inoculation (DAI). The changes on the epidermis were smaller than the lesions measured in the mesophyll, irrespective of the evaluated colonization period, showing that the internal damage caused by the bacterium represent twice the damage observed externally. From the inoculation site, lysis occurred on the epidermal cells and on the palisade and spongy parenchyma cells, with strong staining of their cellular contents, as well as abnormal intercellular spaces in the palisade parenchyma, hypertrophy and hyperplasia of mesophyll cells and partial destruction of chloroplasts. Additionally, this study revealed the presence of inclusion bodies in epidermal and mesophyll cells. Bacterial masses were found in the apoplast between and within mesophyll cells. Bacteria were also observed in the bundle sheath and vascular bundles and were more pronounced at 20 DAI, not only near the inoculation site but also in distant areas, suggesting displacement through the vascular system. These results can be useful to understand this plant-pathogen interaction.

Measurement and simulation of solar radiation availability in relation to the growth of coffee plants in an agroforestry system with rubber trees

Solar radiation is an important factor for plant growth, being its availability to understory crops strongly modified by trees in an Agroforestry System (AFS). Coffee trees (Coffea arabica - cv. Obatã IAC 1669-20) were planted at a 3.4 x 0.9 m spacing inside and aside rows of monocrops of 12 year-old rubber trees (Hevea spp.), in Piracicaba-SP, Brazil (22º42'30" S, 47º38'00" W - altitude: 546m). One-year-old coffee plants exposed to 25; 30; 35; 40; 45; 80; 90; 95 and 100% of the total solar radiation were evaluated according to its biophysical parameters of solar radiation interception and capture. The Goudriaan (1977) adapted by Bernardes et al. (1998) model for radiation attenuation fit well to the measured data. Coffee plants tolerate a decrease in solar radiation availability to 50% without undergoing a reduction on growth and LAI, which was approximately 2m².m-2 under this condition. Further reductions on the availability of solar radiation caused a reduction in LAI (1.5m².m-2), thus poor land cover and solar radiation interception, resulting in growth reduction.

Coffee water use in agroforestry system with rubber trees

Water uptake and use by plants are essentially energy processes that can be largely modified by percentage of soil cover, plant type; foliage area and its distribution; phenological stage and several environmental factors. Coffee trees (Coffea arabica - cv. Obatã IAC 1669-20) in Agrforestry System (AFS) spaced 3.4x0.9m apart, were planted inside and along rows of 12- year-old rubber trees (Hevea spp.) in Piracicaba-SP, Brazil (22 42'30" S, 47 38'00" W - altitude: 546m). Sap flow of one-year-old coffee plants exposed to 35; 45; 80; 95 and 100% of total solar radiation was estimated by the heat balance technique (Dynamax Inc.). Coffee plants under shade showed greater water loss per unit of incident irradiance. On the other hand, plants in monocrop (full sun) had the least water loss per unit of incident irradiance. For the evaluated positions average water use was (gH2O.m-2Leaf area.MJ-1): 64.71; 67.75; 25.89; 33.54; 27.11 in Dec./2002 and 97.14; 72.50; 40.70; 32.78; 26.13 in Feb./2003. This fact may be attributed to the higher stomata sensitivity of the coffee plants under more illuminated conditions, thus plants under full sun presented the highest water use efficiency. Express transpiration by leaf mass can be a means to access plant adaptation to the various environments, which is inaccessible when the approach is made by leaf area.