Microbiota Composition of the Intestinal Mucosa: Association with Fecal Microbiota?

The fecal and mucosal microbiota of infants with rectal bleeding and the fecal microbiota of healthy age-matched controls were investigated by fluorescent in situ hybridization. Bifidobacteria were the main genus in both the feces and mucosa. The other genera tested, Bacteroides, Clostridium, Escherichia coli and lactobacilli/enterococci, represented only minor constituents. No differences in fecal microbiota were observed between patients and controls. In the patients, however, four times greater numbers of bifidobacteria were observed in the feces when compared to the mucosa. Notwithstanding this difference, a strong positive correlation prevailed for bifidobacteria in feces and mucosal samples. The genera assessed accounted for 16% of total bacterial counts on mucosal samples and for 47% of total bacterial counts in feces. This indicates that the unidentified part of the microbiota, especially on the mucosa, deserves more attention.     

The capacity of green oilseeds to utilize photosynthesis to drive biosynthetic processes

Seeds of many plant species are green during embryogenesis. To directly assess the influence of light on the physiological status of green oilseeds in planta, Brassica napus and soybean (Glycine max) seeds were rapidly dissected from plants growing in the light or dark. The activation state of malate dehydrogenase, which reflects reduced thioredoxin and NADP/NADPH ratios, was found to be as high in seeds exposed to light as in leaves and to decrease in the dark. Rubisco was highly activated (carbamylated) in both light and dark, most likely reflecting high seed CO(2) concentrations. Activities of Rubisco and phosphoribulokinase were sufficient to account for significant refixation of CO(2) produced during B. napus oil biosynthesis. To determine the influence of light on oil synthesis in planta, siliques on intact plants in full sunlight or detached siliques fed (3)H(2)O were partly covered with aluminum foil. Seeds from light and dark sections were analyzed, and fatty acid accumulation was found to be higher in seeds exposed to light than seeds from dark sections. The spectrum of light filtering through silique walls and the pigment composition of developing B. napus embryos were determined. In addition to a low chlorophyll a/b ratio, the carotenoid pigments of seeds can provide additional capture of the green light that filters through siliques. Together, these results demonstrate that even the low level of light reaching seeds plays a substantial role in activating light-regulated enzymes, increasing fatty acid synthesis, and potentially powering refixation of CO(2).     

Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates,a study of the distribution of expressed sequence tags in organs,and a web-based database

The genome of Arabidopsis has been searched for sequences of genes involved in acyl lipid metabolism. Over 600 encoded proteins have been identified, cataloged, and classified according to predicted function, subcellular location, and alternative splicing. At least one-third of these proteins were previously annotated as "unknown function" or with functions unrelated to acyl lipid metabolism; therefore, this study has improved the annotation of over 200 genes. In particular, annotation of the lipolytic enzyme group (at least 110 members total) has been improved by the critical examination of the biochemical literature and the sequences of the numerous proteins annotated as "lipases." In addition, expressed sequence tag (EST) data have been surveyed, and more than 3,700 ESTs associated with the genes were cataloged. Statistical analysis of the number of ESTs associated with specific cDNA libraries has allowed calculation of probabilities of differential expression between different organs. More than 130 genes have been identified with a statistical probability > 0.95 of preferential expression in seed, leaf, root, or flower. All the data are available as a Web-based database, the Arabidopsis Lipid Gene database (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). The combination of the data of the Lipid Gene Catalog and the EST analysis can be used to gain insights into differential expression of gene family members and sets of pathway-specific genes, which in turn will guide studies to understand specific functions of individual genes.     

Starch storage in the stems of wheat plants: localization and temporal changes

Background and Aims

Carbohydrate temporarily accumulates in wheat stems during the early reproductive growth phase, predominantly as water soluble carbohydrate (WSC), and is subsequently remobilized during grain filling. Starch has also been reported as a minor storage carbohydrate component in wheat stems, but the details are lacking.

Methods

The accumulation and localization of starch in wheat stem and leaf sheath tissue over a developmental period from 6 d before anthesis to 35 d after anthesis was investigated.

Key Results

The region of the peduncle enclosed by the flag-leaf sheath, and the penultimate internode were the main tissues identified as containing starch, in which the starch grains localized to the storage parenchyma cells. In contrast, the exposed peduncle lacked starch grains. Starch grains were also found in the flag-leaf and second-leaf sheath. Plants grown in low-nitrogen conditions exhibited increased storage of both starch and WSC compared with plants grown in high-nitrogen supply.

Conclusions

The major accumulation and decrease of starch occurred temporally independently to that for WSC, suggesting a different functional role for starch in wheat stems. Starch reutilization concomitant with peduncle growth, and the early development of the reproductive structures, suggested a role in provision of energy and/or carbon scaffolds for these growth processes.Key words: Carbohydrate partitioning, peduncle, starch, wheat stem, storage parenchyma, Triticum aestivum     

Electron flow to oxygen in higher plants and algae: rates and control of direct photoreduction (Mehler reaction) and rubisco oxygenase

Linear electron transport in chloroplasts produces a number of reduced components associated with photosystem I (PS I) that may subsequently participate in reactions that reduce O2. The two primary reactions that have been extensively studied are: first, the direct reduction of O2 to superoxide by reduced donors associated with PS I (the Mehler reaction), and second, the rubisco oxygenase (ribulose 1,5-bisphosphate carboxylase oxygenase EC 4.1.1.39) reaction and associated peroxisomal and mitochondrial reactions of the photorespiratory pathway. This paper reviews a number of recent and past studies with higher plants, algae and cyanobacteria that have attempted to quantify O2 fluxes under various conditions and their contributions to a number of roles, including photon energy dissipation. In C3 and Crassulacean acid metabolism (CAM) plants, a Mehler O2 uptake reaction is unlikely to support a significant flow of electron transport (probably less than 10%). In addition, if it were present it would appear to scale with photosynthetic carbon oxidation cycle (PCO) and photosynthetic carbon reduction cycle (PCR) activity This is supported by studies with antisense tobacco plants with reduced rubisco at low and high temperatures and high light, as well as studies with potatoes, grapes and madrone during water stress. The lack of significant Mehler in these plants directly argues for a strong control of Mehler reaction in the absence of ATP consumption by the PCR and PCO cycles. The difference between C3 and C4 plants is primarily that the level of light-dependent O2 uptake is generally much lower in C4 plants and is relatively insensitive to the external CO2 concentration. Such a major difference is readily attributed to the operation of the C4 CO2 concentrating mechanism. Algae show a range of light-dependent O2 uptake rates, similar to C4 plants. As in C4 plants, the O2 uptake appears to be largely insensitive to CO2, even in species that lack a CO2 concentrating mechanism and under conditions that are clearly limiting with respect to inorganic carbon supply. A part explanation for this could be that many algal rubsicos have considerably different oxygenase kinetic properties and exhibit far less oxygenase activity in air. This would lead to the conclusion that perhaps a greater proportion of the observed O2 uptake may be due to a Mehler reaction and less to rubisco, compared with C3 plants. In contrast to algae and higher plants, cyanobacteria appear to have a high capacity for Mehler O2 uptake, which appears to be not well coupled or limited by ATP consumption. It is likely that in all higher plants and algae, which have a well-developed non-photochemical quenching mechanism, non-radiative energy dissipation is the major mechanism for dissipating excess photons absorbed by the light-harvesting complexes under stressful conditions. However, for cyanobacteria, with a lack of significant non-photochemical quenching, the situation may well be different.     

Reactions of birch leaves to changes in light during early ontogeny: comparison between in vivo and in vitro techniques to measure carbon uptake

Trends in several photosynthetic parameters and their responseto changed growth light were followed for 15 d in leaves ofyoung birch saplings using a rapid-response gas exchange measuringequipment. These in vivo measurements were compared to biochemicalassays that were made from the same leaves after the gas exchangestudies. The measurements were made on leaves that were selectedprior to the study and were at that time of similar age. Forthe first 7 d the photosynthetic parameters were followed fromthe growth conditions of moderate light (200 µmol m^–2s^–1; referred to as controls later in the text). On day7 some of the saplings were transferred to grow either underhigh (450 µmol m^–2 s^–1; referred to as highlight plants) or low (75 µmol m^–2 s^–1; referredto as low light plants) light and the capability of the preselectedleaves for acclimation was followed for 6 d. For comparison,at the end of the experiment the measurements were made on bothcontrols and on young leaves that had developed under high andlow light. Generally the in vivo measured rate of CO₂ uptake (gross photosynthesis)both at 310 ppm CO₂ and 2000 ppm CO₂ corresponded very wellto the biochemically determined CO₂ fixation capacity in vitroafter rapid extraction (measured as the initial and total activityof Rubisco, respectively). However, if the flux of CO₂ intothe chloroplasts was limited by the closure of the stomata,as was the case of the high light plants, then the in vitromeasured Rubisco activity was greater than the in vivo measuredCO₂ uptake. V_max, calculated from the mesophyll conductanceat 1% O₂, exceeded the initial activity of Rubisco (assayedat saturating RuBP and CO₂) constantly by 60%. The catalyticactivity of Rubisco in birch leaves was overall very low, evenwhen calculated from the total activity of Rubisco (K_cat 0.63–1.18 s^–1), when compared to herbaceous C₃ species. Signs of light acclimation were not observed in most of thephotosynthetic parameters and in chloroplast structure whenmature birch leaves were subjected to changes in growth lightfor 6 d. However, the change of the growth light either to highor low light caused day-to-day fluctuations in most of the measuredphotosynthetic parameters and in the case of the high lightplants signs of photoinhibition and photodestruction were alsoobserved (decrease in the amount of chlorophyll and increasein chlorophyll a/b ratio). As a result of these fluctuationsthese plants achieved a new and lower steady-state conditionbetween the light and dark reactions, as judged from the molarratio of RuBP to Rubisco binding site. Key words: Acclimation, photosynthesis, light, Rubisco, birch     

Contrapuntal networks of gene expression during Arabidopsis seed filling

We have used cDNA microarrays to examine changes in gene expression during Arabidopsis seed development and to compare wild-type and mutant wrinkled1 (wri1) seeds that have an 80% reduction in oil. Between 5 and 13 days after flowering, a period preceding and including the major accumulation of storage oils and proteins, approximately 35% of the genes represented on the array changed at least twofold, but a larger fraction (65%) showed little or no change in expression. Genes whose expression changed most tended to be expressed more in seeds than in other tissues. Genes related to the biosynthesis of storage components showed several distinct temporal expression patterns. For example, a number of genes encoding core fatty acid synthesis enzymes displayed a bell-shaped pattern of expression between 5 and 13 days after flowering. By contrast, the expression of storage proteins, oleosins, and other known abscisic acid-regulated genes increased later and remained high. Genes for photosynthetic proteins followed a pattern very similar to that of fatty acid synthesis proteins, implicating a role in CO(2) refixation and the supply of cofactors for oil synthesis. Expression profiles of key carbon transporters and glycolytic enzymes reflected shifts in flux from cytosolic to plastid metabolism. Despite major changes in metabolism between wri1 and wild-type seeds, <1% of genes differed by more than twofold, and most of these were involved in central lipid and carbohydrate metabolism. Thus, these data define in part the downstream responses to disruption of the WRI1 gene.