The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Toxicity of organic farming‑compatible products to the coffee leaf miner

The objective of this work was to evaluate the toxicity of organic farming‑compatible products to the coffee leaf miner Leucoptera coffeella. Lime sulphur, enriched Bordeaux mixture (Viça Café Plus), and the "supermagro" biofertilizer were first tested in laboratory. The most promising product was tested afterwards under field conditions. In laboratory, different concentrations of each product were applied on L. coffeella eggs and on infested coffee‑mined leaves. Only lime sulphur had ovicidal effects at an acceptable concentration (1.6%) for field applications, but no significant effect on larvae mortality was found. Enriched Bordeaux mixture and the "supermagro" biofertilizer had no effect on L. coffeella eggs and larvae. In the field trial, biweekly or monthly sprayings of lime sulphur at different concentrations caused population decrease after 30 days; however, this effect was not significant after 60 or 90 days.

Root system distribution and yield of 'Conilon' coffee propagated by seeds or cuttings

The objective of this work was to evaluate the root system distribution and the yield of 'Conilon' coffee (Coffea canephora) propagated by seeds or cuttings. The experiment was carried out with 2x1 m spacing, in an Oxisol with sandy clay loam texture. A randomized complete block design was used, following a 2x9x6 factorial arrangement, with two propagation methods (seeds and cuttings), nine sampling spacings (0.15, 0.30, 0.45, 0.60, 0.75, and 0.90 m between rows, and 0.15, 0.30, and 0.45 between plants within rows), six soil depths (0.10-0.20, 0.20-0.30, 0.30-0.40, 0.40-0.50, and 0.50-0.60 m), and six replicates. Soil cores (27 cm3) with roots were taken from 12 experimental units, 146 months after planting. The surface area of the root system and root diameter, length, and volume were assessed for 13 years and, then, correlated with grain yield. The highest fine root concentration occurred at the superficial soil layers. The variables used to characterize the root system did not differ between propagation methods. Moreover, no differences were observed for net photosynthetic CO2 assimilation rate, stomatal conductance, internal CO2 concentrations, and instantaneous water-use efficiency in the leaves. Cutting-propagated plants were more productive than seed-propagated ones.

Identification of new transformation products during enzymatic treatment of tetracycline and erythromycin antibiotics at laboratory scale by an on-line turbulent flow liquid-chromatography coupled to a high resolution mass spectrometer LTQ-Orbitrap

This work describes the formation of transformation products (TPs) by the enzymatic degradation at laboratory scale of two highly consumed antibiotics: tetracycline (Tc) and erythromycin (ERY). The analysis of the samples was carried out by a fast and simple method based on the novel configuration of the on-line turbulent flow system coupled to a hybrid linear ion trap – high resolution mass spectrometer. The method was optimized and validated for the complete analysis of ERY, Tc and their transformation products within 10 min without any other sample manipulation. Furthermore, the applicability of the on-line procedure was evaluated for 25 additional antibiotics, covering a wide range of chemical classes in different environmental waters with satisfactory quality parameters. Degradation rates obtained for Tc by laccase enzyme and ERY by EreB esterase enzyme without the presence of mediators were ∼78% and ∼50%, respectively. Concerning the identification of TPs, three suspected compounds for Tc and five of ERY have been proposed. In the case of Tc, the tentative molecular formulas with errors mass within 2 ppm have been based on the hypothesis of dehydroxylation, (bi)demethylation and oxidation of the rings A and C as major reactions. In contrast, the major TP detected for ERY has been identified as the “dehydration ERY-A”, with the same molecular formula of its parent compound. In addition, the evaluation of the antibiotic activity of the samples along the enzymatic treatments showed a decrease around 100% in both cases

Identification of metabolites and thermal transformation products of quinolones in raw cow milk by liquid chromatography coupled to high resolution mass spectrometry

The presence of residues of antibiotics, metabolites, and thermal transformation products (TPs), produced during thermal treatment to eliminate pathogenic microorganisms in milk, could represent a risk for people. Cow"s milk samples spiked with enrofloxacin (ENR), ciprofloxacin (CIP), difloxacin (DIF), and sarafloxacin (SAR) and milk samples from cows medicated with ENR were submitted to several thermal treatments. The milk samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to find and identify TPs and metabolites. In this work, 27 TPs of 4 quinolones and 24 metabolites of ENR were found. Some of these compounds had been reported previously, but others were characterized for the first time, including lactose-conjugated CIP, the formamidation reaction for CIP and SAR, and hydroxylation or ketone formation to produce three different isomers for all quinolones studied.

Identification of metabolites and thermal transformation products of quinolones in raw cow milk by liquid chromatography coupled to high resolution mass spectrometry.

The presence of residues of antibiotics, metabolites, and thermal transformation products (TPs), produced during thermal treatment to eliminate pathogenic microorganisms in milk, could represent a risk for people. Cow"s milk samples spiked with enrofloxacin (ENR), ciprofloxacin (CIP), difloxacin (DIF), and sarafloxacin (SAR) and milk samples from cows medicated with ENR were submitted to several thermal treatments. The milk samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to find and identify TPs and metabolites. In this work, 27 TPs of 4 quinolones and 24 metabolites of ENR were found. Some of these compounds had been reported previously, but others were characterized for the first time, including lactose-conjugated CIP, the formamidation reaction for CIP and SAR, and hydroxylation or ketone formation to produce three different isomers for all quinolones studied.

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.

Seasonality of net radiation in two sub-basins of Paracatu by the use of modis sensor products

The net radiation (Rn) represents the main source of energy for physical and chemical processes that occur in the surface-atmosphere interface, and it is used for air and soil heating, water transfer, in the form of vapor from the surface to the atmosphere, and for the metabolism of plants, especially photosynthesis. If there is no record of net radiation in certain areas, the use of information is important to help determine it. Among them we can highlight those provided by remote sensing. In this context, this work aims to estimate the net radiation, with the use of products of MODIS sensor, in the sub-basins of Entre Ribeiros creek and Preto River, located between the Brazilian states of Goiás and Minas Gerais. The SEBAL (Surface Energy Balance Algorithm for Land) was used to obtain the Rn in four different days in the period of July to October, 2007. The Rn results obtained were consistent with others cited in the literature and are important because the orbital information can help determine the Rn in areas where there are not automatic weather stations to record the net radiation.

Soil water potential during different phenological phases of coffee irrigated by center pivot

Irrigation management can be established, considering the soil water potential, as the limiting factor for plant growth, assuming the soil water content between the field capacity and the permanent wilting point as available water for crops. Thus, the aim of this study was to establish the soil water potential interval during four different phenological phases of coffee irrigated by center pivot. The experiment was set at the experimental area of the Engineering Department at the Federal University of Lavras, in Brazil. The coffee variety planted is designated as Rubi, planted 0.8 meters apart, with rows spaced 3.5 meters apart. The treatments corresponded to the water depths applied based on different percentages of Kc and reference evapotranspiration (ET0) values. Sensors were used to measure the soil water potential interval, installed 25 centimeters depth. In order to compare the results, it was considered as the best matric potential the one that was balanced with the soil water content that resulted in the largest coffee productivity. Based on the obtained results, we verified that in the phases of fruit expansion and ripening, the best results were obtained, before the irrigations, when the soil water potential values reached -35 and -38 kPa, respectively. And in the flowering, small green and fruit expansion phases, when the values reached -31 and -32 kPa, respectively.

Start-up of horizontal anaerobic reactors with sludge blanket and fixed bed for wastewater treatment from coffee processing by wet method

In this study it was evaluated the start-up procedures of anaerobic treatment system with three horizontal anaerobic reactors (R1, R2 and R3), installed in series, with volume of 1.2 L each. R1 had sludge blanket, and R2 and R3 had half supporter of bamboo and coconut fiber, respectively. As an affluent, it was synthesized wastewater from mechanical pulping of the coffee fruit by wet method, with a mean value of total chemical oxygen demand (CODtotal) of 16,003 mg L-1. The hydraulic retention time (HRT) in each reactor was 30 h. The volumetric organic loading (VOL) applied in R1 varied from 8.9 to 25.0 g of CODtotal (L d)-1. The mean removal efficiencies of CODtotal varied from 43 to 97% in the treatment system (R1+R2+R3), stabilizing above 80% after 30 days of operation. The mean content of methane in the biogas were of 70 to 76%, the mean volumetric production was 1.7 L CH4 (L reactor d)-1 in the system, and the higher conversions were around at 0.20 L CH4 (g CODremoved)-1 in R1 and R2. The mean values of pH in the effluents ranged from 6.8 to 8.3 and the mean values of total volatile acids remained below 200 mg L-1 in the effluent of R3. The concentrations of total phenols of the affluent ranged from 45 to 278 mg L-1, and the mean removal efficiency was of 52%. The start-up of the anaerobic treatment system occurred after 30 days of operation as a result of inoculation with anaerobic sludge with active microbiota.

Performance of UASB reactors in two stages followed by post-treatment with activated sludge in wastewater batch of wet-processed coffee

In this study it was evaluated the efficiency of the treatment of wet-processed coffee wastewater in upflow anaerobic sludge blanket (UASB) reactors in two stages, in bench scale, followed by post-treatment with activated sludge in batch. The first UASB reactor was submitted to an hydraulic retention time (HRT) of 6.2 d and organic loading rates (OLR) of 2.3 and 4.5g CODtotal (L d)-1, and the second UASB reactor to HRT of 3.1 d with OLR of 0.4 and 1.4g CODtotal (L d)-1. The average values of the affluent CODtotal increased from 13,891 to 27,926mg L-1 and the average efficiencies of removal of the CODtotal decreased from 95 to 91%, respectively, in the UASB reactors in two stages. The volumetric methane production increased from 0.274 to 0.323L CH4 (L reactor d)-1 with increment in the OLR. The average concentrations of total phenols in the affluent were of 48 and 163mg L-1, and the removal efficiencies in the UASB reactors in two stages of 92 and 90%, respectively, and increased to 97% with post-treatment. The average values of the removal efficiencies of total nitrogen and phosphorus were of 57 to 80% and 44 to 60%, respectively, in the UASB reactors in two stages and increased to 91 and 84% with the post-treatment.

Energetic sustainability of three arabica coffee growing systems used by family farming units in Espírito Santo state

Three growing systems of Arabica coffee were evaluated under the energy perspective, in the state of Espírito Santo in Brazil. The systems are conventional cultivation (CC), cultivation with good agricultural practices (CGP) and organic farming (OF). It was made a comparison of the energy flows within these three systems to show sustainable levels of each one based on production average data of several family-farming units. Therefore, we analyzed crop yield, total energy efficiency reverse (TEER), energy efficiency of ripe coffee (EERC) and non-renewable energy efficiency (NREE). OF system had values for TEER, EERC and NREE of 3.3 4.7 and 7.9 respectively. Yet CC showed values of 1.8, 1.9 and 1.6 for TEER, EERC and NREE respectively. Furthermore, CGP presented values for TEER, EERC and NREE of 0.7, 1.3 and 1.4 respectively. The highest yield was observed in CGP, reaching an amount of 1794 kg ha-1(17,455 MJ); however, this system expends more energy than it converts. Thus, over those points, OF is the most sustainable system.

Brazilian roasted coffee oil obtained by mechanical expelling: compositional analysis by GC-MS

A preliminary analysis by GC-MS comparing the mass spectrum of the compounds with the Wiley 275 L mass spectral data base was used to identify the fatty acids and mainly, some volatile compounds responsible for the flavor of the roasted coffee oil. The oil was obtained by mechanical expelling of Brazilian beans (Coffea arabica) roasted at 238ºC for 10 minutes. Different sample preparation methodologies such as headspace, adsorbent suction trapping and esterification were used. It was possible to identify pyrazines, pyridines, furan derivatives and other compounds not reported in the literature.

Detection of enterotoxins produced by B. cereus through PCR analysis of ground and roasted coffee samples in Rio de Janeiro, Brazil

Coffee is one of the most appreciated drinks in the world. Coffee ground is obtained from the fruit of a small plant that belongs to the genus Coffea. Coffea arabica and Coffea canephora robusta are the two most commercially important species. They are more commonly known as arabica and robusta, respectively. Two-thirds of Coffea arabica plants are grown in South and Central America, and Eastern Africa - the place of origin for this coffee species. Contamination by microorganisms has been a major matter affecting coffee quality in Brazil, mainly due to the harvesting method adopted. Brazilian harvests are based on fruits collected from the ground mixed with those that fall on collection cloths. As the Bacillus cereus bacterium frequently uses the soil as its environmental reservoir, it is easily capable of becoming a contaminant. This study aimed to evaluate the contamination and potential of B. cereus enterotoxin genes encoding the HBL and NHE complexes, which were observed in strains of ground and roasted coffee samples sold in Rio de Janeiro. The PCR (Polymerase Chain Reaction) results revealed high potential of enterotoxin production in the samples. The method described by Speck (1984) was used for the isolation of contaminants. The investigation of the potential production of enterotoxins through isolates of the microorganism was performed using the B. cereus enterotoxin Reverse Passive Latex Agglutination test-kit (BCET-RPLA, Oxoid), according to the manufacturer's instructions. The potential of enterotoxin production was investigated using polymerase chain reaction (PCR) methods for hblA, hblD and hblC genes (encoding hemolysin HBL) and for nheA, nheB and nheC genes (encoding non-hemolytic enterotoxin - NHE). Of all the 17 strains, 100% were positive for at least 1 enterotoxin gene; 52.9% (9/17) were positive for the 3 genes encoding the HBL complex; 35.3% (6/17) were positive for the three NHE encoding genes; and 29.4% (5/17) were positive for all enterotoxic genes.

Partial chemical and functional characterization of milk whey products obtained by different processes

Whey protein samples (S-1 to S-5) were tested in vivo and in vitro for nutritional properties and selected bioactivities. Weanling male Wistar rats fed modified AIN-93G (12 g protein.100 g-1) diets for 21 days were used the in vivo studies. The nutritional parameters did not differ among the protein diets tested. Erythrocyte glutathione content was considered high and was higher for S-3, but liver glutathione was the same for all dietary groups. For S-3, cytokine secretion (IL-10 and TNF-α) by human peripheral blood mononuclear cells (in RPMI-1640 medium) was higher in the absence of antigen than in the presence of BCG antigen. Interleukin-4 secretion was repressed in all treatments. The IC50, whey protein concentration required to inhibit 50% of the melanoma cell proliferation, was 2.68 mg.mL-1 of culture medium for the S-3 sample and 3.66 mg.mL-1 for the S-2 sample. Based on these results, it was concluded that S-3 (whey protein concentrate enriched with TGF-β and lactoferrin) produced better nutritional and immunological responses than the other products tested.