Translation efficiency in humans: tissue specificity,global optimization and differences between developmental stages

Various studies in unicellular and multicellular organisms have shown that codon bias plays a significant role in translation efficiency (TE) by co-adaptation to the tRNA pool. Yet, in humans and other mammals the role of codon bias is still an open question, with contradictory results from different studies. Here we address this question, performing a large-scale tissue-specific analysis of TE in humans, using the tRNA Adaptation Index (tAI) as a direct measure for TE. We find tAI to significantly correlate with expression levels both in tissue-specific and in global expression measures, testifying to the TE of human tissues. Interestingly, we find significantly higher correlations in adult tissues as opposed to fetal tissues, suggesting that the tRNA pool is more adjusted to the adult period. Optimization based analysis suggests that the tRNA pool—codon bias co-adaptation is globally (and not tissue-specific) driven. Additionally, we find that tAI correlates with several measures related to the protein functionally importance, including gene essentiality. Using inferred tissue-specific tRNA pools lead to similar results and shows that tissue-specific genes are more adapted to their tRNA pool than other genes and that related sets of functional gene groups are translated efficiently in each tissue. Similar results are obtained for other mammals. Taken together, these results demonstrate the role of codon bias in TE in humans, and pave the way for future studies of tissue-specific TE in multicellular organisms.     

Ants adjust their pheromone deposition to a changing environment and their probability of making errors

Animals must contend with an ever-changing environment. Social animals, especially eusocial insects such as ants and bees, rely heavily on communication for their success. However, in a changing environment, communicated information can become rapidly outdated. This is a particular problem for pheromone trail using ants, as once deposited pheromones cannot be removed. Here, we study the response of ant foragers to an environmental change. Ants were trained to one feeder location, and the feeder was then moved to a different location. We found that ants responded to an environmental change by strongly upregulating pheromone deposition immediately after experiencing the change. This may help maintain the colony''s foraging flexibility, and allow multiple food locations to be exploited simultaneously. Our treatment also caused uncertainty in the foragers, by making their memories less reliable. Ants which had made an error but eventually found the food source upregulated pheromone deposition when returning to the nest. Intriguingly, ants on their way towards the food source downregulated pheromone deposition if they were going to make an error. This may suggest that individual ants can measure the reliability of their own memories and respond appropriately.     

12S,19- and 12S,20-dihydroxyeicosanoids: novel 12S-hydroxy-5,8-cis-10-trans-14-cis-eicosatetraenoic acid metabolites formed by hydroxylation and reduction in murine lymphocytes

Murine spleen cells and purified B lymphocytes oxidized arachidonic acid via the lipoxygenase pathway. The major metabolite of both the whole spleen and enriched B lymphocytes was 12S-hydroxy-5,8-cis-10-trans-14-cis-eicosatetraenoic acid. A novel metabolite was observed that did not have an absorbance from 210 to 400 nm, indicating the absence of a conjugated double bond system. The new metabolite was converted to the methyl ester, reduced by platinum oxide, derivatized to the trimethylsilyl ether, and analyzed by gas chromatography-mass spectrometry. A major and a minor component were observed in the analysis of the new compound. The major component had major diagnostic ions indicating the presence of hydroxyl groups at C-12 and C-19. The minor component had major diagnostic ions indicating the presence of hydroxyl groups at C-12 and C-20. The new metabolites are characterized as a mixture of 12S,19- and 12S,20-dihydroxyeicosanoids presumably formed by hydroxylation and reduction of one or more double bonds of 12S-hydroxy-5,8-cis-10-trans-14-cis-eicosatetraenoic acid. These metabolites were formed predominantly with whole spleen lymphocytes but could be detected at longer incubation times or by using 12S-hydroxy-5,8-cis-10-trans-14-cis-eicosatetraenoic acid as the starting substrate with highly enriched B lymphocytes.     

Changes in Osmotic Pressure and Mucilage during Low-Temperature Acclimation of Opuntia ficus-indica

Opuntia ficus-indica, a Crassulacean acid metabolism plant cultivated for its fruits and cladodes, was used to examine chemical and physiological events accompanying low-temperature acclimation. Changes in osmotic pressure, water content, low molecular weight solutes, and extracellular mucilage were monitored in the photosynthetic chlorenchyma and the water-storage parenchyma when plants maintained at day/night air temperatures of 30/20°C were shifted to 10/0°C. An increase in osmotic pressure of 0.13 megapascal occurred after 13 days at 10/0°C. Synthesis of glucose, fructose, and glycerol accounted for most of the observed increase in osmotic pressure during the low-temperature acclimation. Extracellular mucilage and the relative apoplastic water content increased by 24 and 10%, respectively, during exposure to low temperatures. These increases apparently favor the extracellular nucleation of ice closer to the equilibrium freezing temperature for plants at 10/0°C, which could make the cellular dehydration more gradual and less damaging. Nuclear magnetic resonance studies helped elucidate the cellular processes during ice formation, such as those revealed by changes in the relaxation times of two water fractions in the chlorenchyma. The latter results suggested a restricted mobility of intracellular water and an increased mobility of extracellular water for plants at 10/0°C compared with those at 30/20°C. Increased mobility of extracellular water could facilitate extracellular ice growth and thus delay the potentially lethal intracellular freezing during low-temperature acclimation.     

Leaf and Stem CO(2) Uptake in the Three Subfamilies of the Cactaceae

Net CO₂ uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO₂ uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO₂ uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO₂ uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO₂ uptake over 24 hours was by the leaves and some CO₂ uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C₃ plants, whereas nocturnal CO₂ uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C₃ plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways.     

Extreme temperatures and thermal tolerances for seedlings of desert succulents

Summary Extreme temperatures near the soil surface, which can reach 70°C at the main study site in the northwestern Sonoran Desert, markedly affect seedling survival. Computer simulations indicated that for the rather spherical barrel cactus Ferocactus acanthodes (Lem.) Britt. & Rose the maximum surface temperature decreased 8°C and the minimum temperature increased 3°C as the seedling height was increased from 1 mm up to 50 mm. Simulated changes in shortwave and longwave irradiation alone showed that shading could decrease the maximum temperature by about 5°C for the common desert agave, Agave deserti Engelm., and raise the minimum 1°C. Actual field measurements on seedlings of both species, where shading would affect local air temperatures and wind speeds in addition to irradiation, indicated that shading decreased the average maximum surface temperature by 11°C in the summer and raised the minimum temperature by 3°C in winter.Seedlings grown at day/iight air temperatures of 30°C/20°C tolerated low temperatures of about -7°C and high temperatures of about 56°C, as measured by the temperature where stain uptake by chlorenchyma cells was reduced 50%. Seedling tolerance to high temperatures increased slightly with age, and F. acanthodes was more tolerant than A. deserti. Even taking the acclimation of high temperature tolerance into account (2.7°C increase per 10°C increase in temperature), seedlings of A. deserti would not be expected to withstand the high temperatures at exposed sites, consistent with previous observations that these seedlings occur only in protected microhabitats. Based primarily on greater high temperature acclimation (4.3°C per 10°C), seedlings of F. acanthodes have a greater high temperature tolerance and can just barely survive in exposed sites. Wide ranges in photoperiod had little effect on the thermal sensitivities of either species. When drought increased the chlorenchyma osmotic pressure from about 0.5 MPa to 1.3 MPa, seedlings of both species became about 2°C less tolerant of high temperatures, which would be nonadaptive in a desert environment, and 2°C more tolerant of low temperatures, which also occurs for other species.In conclusion, seedlings of A. deserti and F. acanthodes could tolerate tissue temperatures over 60°C when acclimated to high temperatures and below -8°C when acclimated to low temperatures. However, the extreme environment adjacent to desert soil requires sheltered microhabitats to protect the plants from high temperature damage and also to protect them from low temperature damage at their upper elevational limits.     

Productivity of Agave deserti: measurement by dry weight and monthly prediction using physiological responses to environmental parameters

Summary An environmental productivity index based on physiological responses to three environmental variables was used to predict the net productivity of a common succulent perennial of the Sonoran Desert, Agave deserti, on a monthly basis. Productivity was also independently measured in the field from dry weight changes. The index was based on soil water availability, day/night air temperatures, and photosynthetically active radiation (PAR), which were individually varied in the laboratory and the effect on net CO₂ uptake by the leaves determined. From monthly precipitation, temperature, and PAR at the field site together with the responses measured in the laboratory, an index (maximum value of unity) was assigned to each of these three environmental variables and their product was termed the environmental productivity index. This index indicates the fraction of maximal CO₂ uptake expected in the field for each month (well-watered A. deserti assimilated 285 mmol CO₂ m^-2 leaf area day^-1 at PAR saturation and optimal day/night temperatures of 25° C/15° C). The dry weight analysis was based on the monthly unfolding of new leaves from the central spike of the rosette and their seasonal increase in dry weight, which were determined in the field. The production of new leaves was highly correlated with the environmental productivity index (r²=0.93), which in turn was highly correlated with the water status index (r²=0.97). After correction for respiration by folded leaves, stem, and roots, plant productivity predicted by the average environmental productivity index (0.36) over a wet June-to-October period agreed within 4% with the productivity based on the conventional dry weight analysis. The net productivity of A. deserti over this 5-month period was 0.57 kg m^-2 ground area (5.7 Mg ha^-1), a large value for a desert CAM plant. The environmental productivity index proposed here may provide a reliable means for predicting net productivity on a monthly basis, which may be particularly useful for species in relatively variable environments such as deserts.     

Water Relations, Diurnal Acidity Changes, and Productivity of a Cultivated Cactus, Opuntia ficus-indica

Physiological responses of the Crassulacean acid metabolism (CAM) plant Opuntia ficus-indica (Cactaceae) were studied on a commercial plantation in central Chile. Young cladodes (flattened stems) and flower buds exhibited daytime stomatal opening, whereas mature cladodes and fruit exhibited the nocturnal stomatal opening characteristic of CAM plants. Severe water stress suppressed the nocturnal stomatal opening by mature cladodes, but their high water vapor conductance occurring near dawn was not affected. Nocturnal acidity increases were not as sensitive to water stress as was the nocturnal stomatal opening. The magnitude of the nocturnal acidity increases depended on the total daily photosynthetically active radiation (PAR), being 90% PAR-saturated at 27 moles per square meter per day for a mean nighttime air temperature of 5°C and at 20 moles per square meter per day for 18°C. Inasmuch as the PAR received on unshaded vertical surfaces averaged about 21 moles per square meter per day, nocturnal acidity increases by the cladodes were on the verge of being PAR-limited in the field. The net assimilation rate, which was positive throughout the year, annually averaged 3.4 grams per square meter per day for 1.0- and 2.0-year-old plants. Plants that were 5.4 years old had 7.2 square meters of cladode surface area (both sides) and an annual dry weight productivity of 13 megagrams (metric tons) per hectare per year when their ground cover was 32%. This substantial productivity for a CAM plant was accompanied by the highest nocturnal acidity increase so far observed in the field, 0.78 mole H⁺ per square meter.     

Relationships between Photosynthetically Active Radiation, Nocturnal Acid Accumulation, and CO(2) Uptake for a Crassulacean Acid Metabolism Plant, Opuntia ficus-indica

The influences of photosynthetically active radiation (PAR) and water status on nocturnal Crassulacean acid metabolism (CAM) were quantitatively examined for a widely cultivated cactus, Opuntia ficus-indica (L.) Miller. When the total daily PAR was maintained at 10 moles photons per square meter per day but the instantaneous PAR level varied, the rate of nocturnal H⁺ accumulation (tissue acidification) became 90% saturated near 700 micromoles per square meter per second, a PAR level typical for similar light saturation of C₃ photosynthesis. The total nocturnal H⁺ accumulation and CO₂ uptake reached 90% of maximum for a total daily PAR of about 22 moles per square meter per day. Light compensation occurred near 0 moles per square meter per day for nocturnal H⁺ accumulation and 4 moles per square meter per day for CO₂ uptake. Above a total daily PAR of 36 moles per square meter per day or for an instantaneous PAR of 1150 micromoles per square meter per second for more than 6 hours, the nocturnal H⁺ accumulation actually decreased. This inhibition, which occurred at PAR levels just above those occurring in the field, was accompanied by a substantial decrease in chlorophyll content over a 1-week period.

A minimum ratio of H⁺ accumulated to CO₂ taken up of 2.5 averaged over the night occurred for a total daily PAR of 31 moles per square meter per day under wet conditions. About 2 to 6 hours into the night under such conditions, a minimum H⁺-to-CO₂ ratio of 2.0 was observed. Under progressively drier conditions, both nocturnal H⁺ accumulation and CO₂ uptake decreased, but the H⁺-to-CO₂ ratio increased. A ratio of two H⁺ per CO₂ is consistent with the H⁺ production accompanying the conversion of starch to malic acid, and it apparently occurs for O. ficus-indica when CAM CO₂ uptake is strongly favored over respiratory activity.