Impact of intercropping on the photosynthetic activity of coffee / Impacto do cultivo consorciado na atividade fotossintética do café

Conducting studies that assist in the evaluation of agroecosystems is essential for advancing biodiverse and sustainable agriculture. This study aimed to assess the impact of intercropping on the photosynthetic activity of Arabica coffee plants. The experiment was conducted in the municipality of Alegre, Espírito Santo, southeastern Brazil. Three coffee cropping systems were studied: Arabica coffee monoculture; Arabica coffee intercropped with Nanicon variety banana; and Arabica coffee intercropped with Nanicon variety banana and Juçara palm. The Arabica coffee variety used was Catuaí Vermelho IAC 44, planted in 1991, with a spacing of 3.0 m between rows and 2.0 m between holes, accommodating two plants per hole. In 2010, coffee trees underwent mid-height pruning (low-cutting pruning), and the Nanicon bananas were planted between rows with a spacing of 5.0 x 3.0 m. Three years later, palm seedlings were planted in the same rows as the banana plants, with a spacing of 5 x 3 m. Five experimental units were randomly selected for each cropping system. The evaluated variables included chlorophyll indexes (chlorophyll a, chlorophyll b, total chlorophyll, and chlorophyll a/b ratio) and gas exchange parameters (net CO2 assimilation rate, stomatal conductance, intercellular CO2 concentration, transpiration, intrinsic water use efficiency, instantaneous water use efficiency, and carboxylation efficiency). Regarding chlorophyll indexes, differences were observed only in chlorophyll b, with monoculture coffee displaying the highest values. In terms of gas exchange, intercropped coffee exhibited lower values of intrinsic and instantaneous water use efficiency, and higher values of stomatal conductance and transpiration. The highest net assimilation rate values were observed in coffee with banana intercropping, while the highest water use efficiency was found in coffee in monoculture. In summary, monoculture coffee showed the highest values for most of the variables related to photosynthetic activity, followed by Arabica coffee intercropped with banana, which stood out for achieving the highest net assimilation rate.(AU)

Realizar estudos que auxiliem na avaliação de agroecossistemas são de vital importância para avançar no desenvolvimento de uma agricultura biodiversa e sustentável. Desta forma, o objetivo da pesquisa foi avaliar o impacto do consórcio na atividade fotossintética de plantas de cafeeiro arábica. O experimento foi desenvolvido no município de Alegre, Espírito Santo, sudeste do Brasil. O estudo foi realizado em plantações de café sob três sistemas de cultivo: café Arábica em monocultura; café Arábica consorciado com banana variedade Nanicon; e café Arábica consorciado com banana variedade Nanicon e palmito Juçara. A variedade de café Arábica usada nos sistemas de cultivo foi o Catuaí Vermelho IAC 44, plantada em 1991, com espaçamento de 3,0 m entre linhas e 2,0 m entre covas, com duas plantas por cova. Em 2010, as árvores de café foram podadas na altura média (poda de baixo corte) e as bananas da variedade Nanicon foram plantadas entre as fileiras a 5,0 x 3,0 m de espaçamento. Três anos depois, as mudas de palmito foram plantadas na mesma linha que a banana a 5 x 3 m de espaçamento. Em cada sistema foram estabelecidas cinco unidades experimentais, selecionadas aleatoriamente. As variáveis avaliadas foram índices de clorofila (clorofila a, clorofila b, clorofila total e razão clorofila a/b) e trocas gasosas (taxa de assimilação líquida de CO2, condutância estomática, concentração subestomática de CO2, transpiração, eficiência intrínseca do uso da água, eficiência instantânea do uso da água e eficiência da carboxilação). Para os índices de clorofila, as diferenças são observadas apenas na clorofila b, onde o café em monocultura obteve os maiores índices. No caso das trocas gasosas, os menores valores de eficiência intrínseca e instantânea do uso da água, e os maiores valores de condutância estomática e transpiração, foram encontrados no café com consórcio, em que os maiores valores líquidos taxa de assimilação correspondeu ao café consorciado com banana, enquanto maior eficiência no uso da água, ao café em monocultura. Desta forma, observou-se que o café em monocultivo obteve os maiores valores para a maioria das variáveis envolvidas na atividade fotossintética, seguido pelo consórcio de café Arábica com banana, que se destacou por obter a maior taxa de assimilação líquida.(AU)

Análises fisiológicas e de crescimento e produtividade da mandioca sob níveis de irrigação / Physiological and growth analysis and productivity of cassava under irrigation levels

O objetivo dessa pesquisa foi avaliaro crescimento,produtividade easrespostas fisiológicas da mandioca sob níveis de irrigação na Zona da Mata de Alagoas. O delineamento estatístico utilizado foi blocos casualizados, em esquema de parcelas subdivididas, com quatro repetições. Os tratamentos foram seis níveis de irrigação, em função da evapotranspiração da cultura ­ETC(L0= 0% (sequeiro), L1= 40%, L2= 80%, L3= 120%, L4= 160% e L5= 200% da ETC). As variáveis foram divididas em grupos: crescimento e produção (avaliadas em seis períodosbimestrais ­1 ano) e as fisiológicas (taxa fotossintética líquida e transpiratória, temperatura foliar, condutância estomática, eficiência instantânea do uso de água, rendimento quântico potencial, eficiência quântica efetiva do fotossistema II (ΦPSII) eíndice SPADforam avaliadas em cinco períodos bimestrais ­10 meses).Obalanço hídrico dos níveis de irrigação, foi realizado em escala decendial. A evapotranspiração anual da cultura da mandiocaestimada foi1.030 mm, e nas áreas de sequeiro, a chuva efetiva somouapenas 522 mm, o que geroudéficit hídrico de 508 mm, e isso torna evidente a importância de utilização da irrigação em cultivos na região. De maneira geral, crescimento, produtividade e as respostas fisiológicas da mandioca são superiores em áreas irrigadas quando comparadas com cultivos de sequeiro e a irrigação proporciona as produtividades de raízes e biomassa total de 97 e 155 t ha-1, sob os níveis de irrigação de 129 e 136% da ETC, respectivamente, na região estudada.(AU)

The objective of this research was to evaluate the growth, productivity and the physiological responses of cassava under irrigation levels in the Alagoas Forest Zone. The statistical design used was randomized blocks, in a split-plot scheme, with four replications. The treatments were six levels of irrigation, depending on the evapotranspiration of the crop ­ETC(L0=0% (Rainfed), L1= 40%, L2= 80%, L3= 120%, L4= 160% and L5= 200% of the ETC). The variables were divided into groups: growth and production (evaluated in six bimonthly periods -1 year) and the physiological (net photosynthetic rate and transpiratory,leaf temperature, stomatal conductance, instantaneous water use efficiency, potential quantum yield, effective quantum efficiency of photosystem II and SPAD indexwere evaluated in five bimonthly periods ­10 months). The water balance of the irrigation levels was carried out, on a decendial scale. The annual evapotranspiration of cassava addedaround 1,030 mm, and in dryland areas, the effective rainfall is only 522 mm, which generates a water deficit of 508 mm, and this makes the importance evident of use of irrigation in crops in the region. In general, cassava growth, yield andthephysiological responses are superior in irrigated areas when compared with therainfed crops, and irrigation providestheroot and total biomass yields of 97 and 155 Mg ha-1,under the irrigation levels of 129 and 136% of the ETC, respectively, in the studied region.(AU)

Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria.

The tree bark environment is an important microbial habitat distributed worldwide on thrillions of trees. However, the microbial communities of tree bark are largely unknown, with most studies on plant aerial surfaces focused on the leaves. Recently, we presented a metagenomic study of bark microbial communities from avocado. In these communities, oxygenic and anoxygenic photosynthesis genes were very abundant, especially when compared to rhizospheric soil from the same trees. In this work, Evolutionary Placement Algorithm analysis was performed on metagenomic reads orthologous to the PufLM gene cluster, encoding for the bacterial type II photosynthetic reaction center. These photosynthetic genes were found affiliated to different groups of bacteria, mostly aerobic anoxygenic photosynthetic Alphaproteobacteria, including Sphingomonas, Methylobacterium and several Rhodospirillales. These results suggest that anoxygenic photosynthesis in avocado bark microbial communities functions primarily as additional energy source for heterotrophic growth. Together with our previous results, showing a large abundance of cyanobacteria in these communities, a picture emerges of the tree holobiont, where light penetrating the tree canopies and reaching the inner stems, including the trunk, is probably utilized by cyanobacteria for oxygenic photosynthesis, and the far-red light aids the growth of aerobic anoxygenic photosynthetic bacteria.

Microalgae: Cultivation Aspects and Bioactive Compounds

Abstract Microalgae are aquatic unicellular microorganisms that can be found both in freshwater and marine systems; are capable of photosynthesis; and can grow as individual cells or associated in chains or small colonies. Microalgae cultivation has gained large momentum among researchers in the past decades due to their ability to produce value metabolites, remarkable photosynthetic efficiency, and versatile nature. The wide technological potential, and thus increasing amount of scattered knowledge, may become the very first barrier that a post graduating student, or any non-specialist reader, will face when introduced to the subject. In this review paper, we access the core aspects of microalgae technology, covering their main characteristics, and comprehensively presenting the main features of their various cultivation modes and biological activity from metabolites.

Copper-induced increased expression of genes involved in photosynthesis, carotenoid synthesis and C assimilation in the marine alga Ulva compressa.

BACKGROUND: The marine alga Ulva compressa is the dominant species in coastal areas receiving effluents from copper mines. The alga can accumulate high amounts of copper and possesses a strong antioxidant system. Here, we performed short-term transcriptomic analyses using total RNA of the alga cultivated with 10 µM of copper for 0, 3, 6, 12 and 24 h by RNA-seq. RESULTS: De novo transcriptomes were assembled using the Trinity software, putative proteins were annotated and classified using Blast2GO. Differentially expressed transcripts were identified using edgeR. Transcript levels were compared by paired times 0 vs 3, 0 vs 6, 0 vs 12 and 0 vs 24 h at an FDR < 0.01 and Log2 Fold Change > 2. Up-regulated transcripts encode proteins belonging to photosystem II (PSII), Light Harvesting II Complex (LHCII), PSI and LHCI, proteins involved in assembly and repair of PSII, and assembly and protection of PSI. In addition, transcripts encoding enzymes leading to ß-carotene synthesis and enzymes belonging to the Calvin-Benson cycle were also increased. We further analyzed photosynthesis and carotenoid levels in the alga cultivated with 10 µM of copper for 0 to 24 h. Photosynthesis was increased from 3 to 24 h as well as the level of total carotenoids. The increase in transcripts encoding enzymes of the Calvin-Benson cycle suggests that C assimilation may also be increased. CONCLUSIONS: Thus, U. compressa displays a short-term response to copper stress enhancing the expression of genes encoding proteins involved in photosynthesis, enzymes involved carotenoids synthesis, as well as those belonging to the Calvin-Benson cycle, which may result in an increase in C assimilation.

Taraxerol 4-Methoxybenzoate, an in vitro Inhibitor of Photosynthesis Isolated from Pavonia multiflora A. St-Hil. (Malvaceae).

A phytochemical study of Pavonia multiflora A. St-Hil. (Malvaceae) led to the isolation through chromatographic techniques of 10 secondary metabolites: vanillic acid (1), ferulic acid (2), p-hydroxybenzoic acid (3), p-coumaric acid (4), loliolide (5), vomifoliol (6), 4,5-dihydroblumenol A (7), 3-oxo-α-ionol (9), blumenol C (10), and taraxerol 4-methoxybenzoate (8), the latter being a novel metabolite. Their structures were identified by (1) H- and (13) C-NMR, using one- and two-dimensional techniques, and X-ray crystallography. In this work, we report the effect of compounds 5 and 8 on several photosynthetic activities in an attempt to search for new compounds as potential herbicide agents that affect photosynthesis. Both compounds inhibited the electron flow from H2 O to methyl viologen; therefore, they act as Hill reaction inhibitors. Using polarographic techniques and studies of the fluorescence of chlorophyll a, the interaction sites of these compounds were located at photosystem II.

Photosynthetic Light Responses May Explain Vertical Distribution of Hymenophyllaceae Species in a Temperate Rainforest of Southern Chile.

Some epiphytic Hymenophyllaceae are restricted to lower parts of the host (< 60 cm; 10-100 µmol photons m(-2) s(-1)) in a secondary forest of Southern Chile; other species occupy the whole host height (≥ 10 m; max PPFD > 1000 µmol photons m(-2) s(-1)). Our aim was to study the photosynthetic light responses of two Hymenophyllaceae species in relation to their contrasting distribution. We determined light tolerance of Hymenoglossum cruentum and Hymenophyllum dentatum by measuring gas exchange, PSI and PSII light energy partitioning, NPQ components, and pigment contents. H. dentatum showed lower maximum photosynthesis rates (A max) than H. cruentum, but the former species kept its net rates (An) near Amax across a wide light range. In contrast, in the latter one, An declined at PPFDs > 60 µmol photons m(-2) s(-1). H. cruentum, the shadiest plant, showed higher chlorophyll contents than H. dentatum. Differences in energy partitioning at PSI and PSII were consistent with gas exchange results. H. dentatum exhibited a higher light compensation point of the partitioning of absorbed energy between photochemical Y(PSII) and non-photochemical Y(NPQ) processes. Hence, both species allocated energy mainly toward photochemistry instead of heat dissipation at their light saturation points. Above saturation, H. cruentum had higher heat dissipation than H. dentatum. PSI yield (YPSI) remained higher in H. dentatum than H. cruentum in a wider light range. In both species, the main cause of heat dissipation at PSI was a donor side limitation. An early dynamic photo-inhibition of PSII may have caused an over reduction of the Qa+ pool decreasing the efficiency of electron donation to PSI. In H. dentatum, a slight increase in heat dissipation due to acceptor side limitation of PSI was observed above 300 µmol photons m(-2)s(-1). Differences in photosynthetic responses to light suggest that light tolerance and species plasticity could explain their contrasting vertical distribution.

Role of protein fluctuation correlations in electron transfer in photosynthetic complexes.

We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron (exciton) sites. The fluctuations of the protein environment are modeled by random telegraph processes, which act either collectively (correlated) or independently (uncorrelated) on the electron sites. We derived an exact closed system of first-order linear differential equations with constant coefficients, for the average density matrix elements and for their first moments. Under some conditions, we obtained analytic expressions for the electron transfer rates and found the range of parameters for their applicability by comparing with the exact numerical simulations. We also compared the correlated and uncorrelated regimes and demonstrated numerically that the uncorrelated fluctuations of the protein environment can, under some conditions, either increase or decrease the electron transfer rates.

Influences of cadmium on fine structure and metabolism of Hypnea musciformis (Rhodophyta, Gigartinales) cultivated in vitro.

The in vitro effect of cadmium on apical segments of Hypnea musciformis was examined. Over a period of 7 days, the segments were cultivated with different concentrations of cadmium, ranging from 50 to 300 µM. The samples were processed for microscopic and histochemical analysis of growth rates, content of photosynthetic pigments, and photosynthetic performance. Cadmium treatments increased cell wall thickness and the accumulation of plastoglobuli. Destruction of chloroplast internal organization was observed. Compared to controls, algae exposed to cadmium showed growth rate reduction, depigmentation, and blending in the lateral branches. The content of photosynthetic pigments, including chlorophyll a and phycobiliproteins, decreased after exposure to different concentrations of cadmium. These results agree with the decreased photosynthetic performance and relative electron transport rate observed after exposure of algae to cadmium. Taken together, these findings strongly indicate that cadmium negatively affects the architecture and metabolism of the carragenophyte H. musciformis, thus posing a threat to the economic vitality of this red macroalgae.

Tree size and light availability increase photochemical instead of non-photochemical capacities of Nothofagus nitida trees growing in an evergreen temperate rain forest.

Nothofagus nitida (Phil.) Krasser (Nothofagaceae) regenerates under the canopy in microsites protected from high light. Nonetheless, it is common to find older saplings in clear areas and adults as emergent trees of the Chilean evergreen forest. We hypothesized that this shade to sun transition in N. nitida is supported by an increase in photochemical and non-photochemical energy dissipation capacities of both photosystems in parallel with the increase in plant size and light availability. To dissect the relative contribution of light environment and plant developmental stage to these physiological responses, the photosynthetic performance of both photosystems was studied from the morpho-anatomical to the biochemical level in current-year leaves of N. nitida plants of different heights (ranging from 0.1 to 7 m) growing under contrasting light environments (integrated quantum flux (IQF) 5-40 mol m(-2). Tree height (TH) and light environment (IQF) independently increased the saturated electron transport rates of both photosystems, as well as leaf and palisade thickness, but non-photochemical energy flux, photoinhibition susceptibility, state transition capacity, and the contents of D1 and PsbS proteins were not affected by IQF and TH. Spongy mesophyll thickness and palisade cell diameter decreased with IQF and TH. A(max), light compensation and saturation points, Rubisco and nitrogen content (area basis) only increased with light environment (IQF), whereas dark respiration (R(d)) decreased slightly and relative chlorophyll content was higher in taller trees. Overall, the independent effects of more illuminated environment and tree height mainly increased the photochemical instead of the non-photochemical energy flux. Regardless of the photochemical increase with TH, carbon assimilation only significantly improved with higher IQF. Therefore it seems that mainly acclimation to the light environment supports the phenotypic transition of N. nitida from shade to sun.

Unique communities of anoxygenic phototrophic bacteria in saline lakes of Salar de Atacama (Chile): evidence for a new phylogenetic lineage of phototrophic Gammaproteobacteria from pufLM gene analyses.

Phototrophic bacteria are important primary producers of salt lakes in the Salar de Atacama and at times form visible mass developments within and on top of the lake sediments. The communities of phototrophic bacteria from two of these lakes were characterized by molecular genetic approaches using key genes for the biosynthesis of the photosynthetic apparatus in phototrophic purple bacteria (pufLM) and in green sulfur bacteria (fmoA). Terminal restriction fragment length polymorphism of the pufLM genes indicated high variability of the community composition between the two lakes and subsamples thereof. The communities were characterized by the dominance of a novel, so far undescribed lineage of pufLM containing bacteria and the presence of representatives related to known halophilic Chromatiaceae and Ectothiorhodospiraceae. In addition, the presence of BChl b-containing anoxygenic phototrophic bacteria and of aerobic anoxygenic bacteria was indicated. Green sulfur bacteria were not detected in the environmental samples, although a bacterium related to Prosthecochloris indicum was identified in an enrichment culture. This is the first comprehensive description of phototrophic bacterial communities in a salt lake of South America made possible only due to the application of the functional pufLM genes.

Theoretic, experimental, clinical bases of the water oscillator hypothesis in near-infrared photobiomodulation.

The objective of this review is to propose and document a role for the water oscillator in near-infrared (NIR) photobiomodulation. Greater understanding of the role of the water oscillator may add to a more-coherent description of central effects of NIR light on redox centers and key transmembrane enzymes such as cytochrome c oxidase (CcO). In addition, water provides a complementary pathway for absorption and transportation of NIR energy in photobiomodulation. Because of its unexpected potential, we propose terming it the "water oscillator paradox." Photobiologic mechanisms involved in the treatment of complex diseases are discussed in light of the present state of the art.

Senescence-associated degradation of chloroplast proteins inside and outside the organelle.

Leaf proteins, and in particular the photosynthetic proteins of plastids, are extensively degraded during senescence. Although this involves massive amounts of protein, the mechanisms responsible for chloroplast protein degradation are largely unknown. Degradation within the plastid itself is supported by the observation that chloroplasts contain active proteases, and that chloroplasts isolated from senescing leaves can cleave Rubisco to release partially digested fragments. It is less clear whether chloroplasts can complete Rubisco degradation. Chloroplastic proteases are likely involved in the breakdown of the D1 and LHCII proteins of photosystem II. Small senescence-associated vacuoles (SAVs) with high-proteolytic activity develop in senescing leaf cells, and there is evidence that SAVs contain chloroplast proteins. Thus, an extra-plastidic pathway involving SAVs might participate in the degradation of some chloroplast proteins. Plastidic and extra-plastidic pathways might cooperate in the degradation of chloroplast proteins, or they might represent alternative, redundant pathways for photosynthetic protein degradation.

Singlet oxygen generation in the reaction centers of Rhodobacter sphaeroides.

Singlet oxygen (1O2) generation in the reaction centers (RCs) of Rhodobacter sphaeroides wild type was characterized by luminescent emission in the near infrared region (time resolved transients and emission spectra) and quantified to have quantum yield of 0.03 +/- 0.005. 1O2 emission was measured as a function of temperature, ascorbate, urea and potassium ferricyanide concentrations and as a function of incubation time in H2O:D2O mixtures. 1O2 was shown to be affected by the RC dynamics and to originate from the reaction of molecular oxygen with two sources of triplets: photoactive dimer formed by singlet-triplet mixing and bacteriopheophytin formed by direct photoexcitation and intersystem crossing.

Cooperative interaction of high-potential hemes in the cytochrome subunit of the photosynthetic reaction center of bacterium Ectothiorhodospira shaposhnikovii.

Cooperative interaction of the high-potential hemes (C(h)) in the cytochrome subunit of the photosynthesizing bacterium Ectothiorhodospira shaposhnikovii was studied by comparing redox titration curves of the hemes under the conditions of pulse photoactivation inducing single turnover of electron-transport chain and steady-state photoactivation, as well as by analysis of the kinetics of laser-induced oxidation of cytochromes by reaction center (RC). A mathematical model of the processes of electron transfer in cytochrome-containing RC was considered. Theoretical analysis revealed that the reduction of one heme C(h) facilitated the reduction of the other heme, which was equivalent to a 60 mV positive shift of the midpoint potential. In addition, reduction of the second heme C(h) caused a three- to four-fold acceleration of the electron transfer from the cytochrome subunit to RC.

Regulation of two photosynthetic pigment-related genes during stress-induced pigment formation in the green alga, Dunaliella salina.

The expression of mRNAs coding for 1-deoxyxylulose-5-phosphate synthase (DXS) and phytoene synthase (PSY) were studied in Dunaliella salina grown under nitrogen-sufficient (NS) and nitrogen-limited (NL) conditions. Under NS conditions growth was 2.5 times higher than under NL conditions. No differences were found in chlorophyll a content per cell, and total carotenoid content per cell was 5.33 pg 1(-1) for the NS treatment and 7.76 pg 1(-1) for the NL. DXS transcripts exhibited diminished expression under NL conditions, peaking at day 15 of cultivation in both treatments. Simultaneously, PSY transcripts exhibited constant expression under both conditions. These results suggest that these genes play an important role in the balance of photosynthetic pigments during pigment accumulation.

Oxygen and light effects on the expression of the photosynthetic apparatus in Bradyrhizobium sp. C7T1 strain.

Photosynthetic bradyrhizobia are nitrogen-fixing symbionts colonizing the stem and roots of some leguminous plants like Aeschynomene. The effect of oxygen and light on the formation of the photosynthetic apparatus of Bradyrhizobium sp. C7T1 strain is described here. Oxygen is required for growth, but at high concentration inhibits the synthesis of bacteriochlorophyll (BChl) and of the photosynthetic apparatus. However, we show that in vitro, aerobic photosynthetic electron transport occurred leading to ADP photophosphorylation. The expression of the photosynthetic apparatus was regulated by oxygen in a manner which did not agree with earlier results in other photosynthetic bradyrhizobia since BChl accumulation was the highest under microaerobic conditions. This strain produces photosynthetic pigments when grown under cyclic illumination or darkness. However, under continuous white light illumination, a Northern blot analysis of the puf operon showed that, the expression of the photosynthetic genes of the antenna was considerable. Under latter conditions BChl accumulation in the cells was dependent on the oxygen concentration. It was not detectable at high oxygen tensions but became accumulated under low oxygen (microaerobiosis). It is known that in photosynthetic bradyrhizobia bacteriophytochrome photoreceptor (BphP) partially controls the synthesis of the photosystem in response to light. In C7T1 strain far-red light illumination did not stimulate the synthesis of the photosynthetic apparatus suggesting the presence of a non-functional BphP-mediated light regulatory mechanism.

A new amphipathy scale I. Determination of the scale from molecular dynamics data.

Two new amphipathy scales elaborated from molecular dynamics data are presented. Their applications contribute for the identification of the hydrophobic or hydrophilic regions in proteins solely from the primary structure. The new amphipathy coefficients (AC) reflect the side chain/solvent molecules configurational energies. A polar (water) and an apolar solvent, CCl4, were used resulting in the two ACwater and ACCCl4 scales. These solvents were chosen to simulate the aqueous phases and the transmembrane ambients of cellular membranes where the membrane proteins act. The new amphipathy scales were compared with some previous scales determined by different methods, which were also compared between them, indicating more than 90% of the correlation coefficients are less than 0.9: the scales are strictly dependent on the methodologies used in their determination. The ACCCl4 scale is related with the size of side chain amino acids while ACwater is related with the hydrophobicity of side chain amino acids. The quality of the scales was confirmed by an example of application where ACwater was able to identify correctly the transmembrane, hydrophobic regions of a membrane protein. These results also indicate that water is an important factor responsible for the tertiary structure of membrane proteins.

Finding unexpected patterns in microarray data.

We describe the performance of a protocol based on the sequential application of unsupervised and supervised methods to analyze microarray samples defined by a combination of factors. Correspondence analysis is used to visualize the emerging patterns of three set of novel or previously published data: photoreceptor mutants of Arabidopsis grown under different light/dark conditions, Arabidopsis exposed to different types of biotic and abiotic stress, and human acute leukemia. We find, for instance, that light has a dramatic effect on plants despite the absence of the four major photoreceptors, that bacterial-, fungal-, and viral-induced responses converge at later stages of attack, and that sample preparation procedures used in different hospitals have large effects on transcriptome patterns. We use canonical discriminant analysis to identify the genes associated with these patters and hierarchical clustering to find groups of coregulated genes that are easily visualized in a second round of correspondence analysis and ordered tables. The unconventional combination of standard descriptive multivariate methods offers a previously unrecognized tool to uncover unexpected information.

Limitations to photosynthesis under light and heat stress in three high-yielding wheat genotypes.

Three high-yielding wheat genotypes (T. aestivum L., c.v. Siete Cerros, Seri and Bacanora, released in 1966, 1982 and 1988, respectively) were grown under irrigation in two high radiation, low relative humidity environments (Tlaltizapan and Ciudad Obregon CIMMYT experimental stations, Mexico). Gas exchange and fluorescence parameters were assessed on the flag leaf during the day. Carbon isotope discrimination (delta) was analysed in flag leaf at anthesis and in grain at maturity. In both environments, gas exchange and fluorescence parameters varied markedly with irradiance and temperature. Analysis of their respective variation indicated the occurrence of photo-respiration and photo-inhibition, particularly in Tlaltizapan, the warmest environment, and in Siete Cerros. In Ciudad Obregon (high-yielding environment) lower Ci (internal CO2 concentration) and delta La (carbon isotope discrimination of the leaf) suggested a higher intrinsic photosynthetic capacity in the variety Bacanora. Higher yield of this genotype was also associated with higher Fv'/Fo' (ratio of photochemical and non photochemical rate constants in the light) and Fm'/Fm (ratio of the non photochemical rate constants in the dark and light adapted state).