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.     

Structure of maltoheptaose by difference Fourier methods and a model for glycogen

The structure of the glucose heptamer, maltoheptaose, has been determined by difference Fourier analysis at 0.25 nm resolution through its binding to phosphorylase a. It is a left-handed helical structure, with 6.5 glucose residues per turn and a rise per residue of 2.4 Å. The molecule shows short-range order when no protein is present to stabilize its conformation in solution. With one exception, the individual torsion angles between sugar residues vary over a narrow range and preserve a good O₍₂₎O_(3′) hydrogen bond. The length of an individual chain for glycogen can be extrapolated from the maltoheptaose data and agrees well with the size for glycogen predicted by the Whelan model.     

Plasma prolactin concentrations in breeding pied flycatchers (Ficedula hypoleuca) with an experimentally prolonged brooding period

This experiment explored the stimulatory effect of brooding newly hatched young on plasma prolactin concentration in male and female pied flycatchers, Ficedula hypoleuca. By exchanging offspring between nestboxes, one group of parents was exposed to 1- to 3-day-old nestlings for 12 days. Females in this group continued night-time brooding during these 12 days. The females, but not the males (who do not participate in brooding nestlings), after 6 days had higher plasma prolactin concentrations than control birds which had shown a 50% reduction in night-time brooding at this stage. By Day 12, however, prolactin concentration had decreased to the same level as in control birds, even though these females were still brooding 3-day-old nestlings. Female flycatchers given 3-day-old nestlings on the day their own eggs hatched showed an earlier reduction in night-time brooding and an earlier decrease in plasma prolactin than did control birds. An early decrease in prolactin was also seen in the males of this experimental group.     

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.     

The three-dimensional structure of acarbose bound to glycogen phosphorylase

Acarbose, a pseudotetrasaccharide with a conduritol ring at the nonreducing terminus, is a naturally occurring inhibitor of amylases. It is shown here to be an inhibitor of glycogen phosphorylase and to bind more tightly to the enzyme than the equivalent malto-oligosaccharide substrate. X-ray crystallographic studies of the acarbose-phosphorylase a complex in the presence of glucose and caffeine reveal the structure of acarbose as bound to the storage site of phosphorylase. The acarbose binds in an orientation such that the conduritol ring makes no protein contacts. As with malto-oligosaccharides bound at this site, the observed conformation of acarbose is stabilized by O-2-O-3' hydrogen bonding and is similar to, but not identical with, that predicted by hard-sphere exo-anomeric effect calculations and justified by 1H nuclear magnetic resonance studies (Bock, K., and Pedersen, H. (1984) Carbohydr. Res. 132, 142-149). Intramolecular O2-O3' hydrogen bonds appear to play an important role in stabilizing the conformation observed in these studies, even for those residues closely associated with the protein.     

Response of a human head/neck/upper-torso replica to dynamic loading--I. Physical model

A human head/neck/upper-torso replica was constructed and instrumented and its response to impact and dynamic loading was studied. The model consists of a water-filled cadaver skull; plastic vertebrae, sternum and ribs; silicon rubber disks and ligaments; and fabric muscles. The static behavior of the system under sagittal plane and lateral loading was adjusted so as to correspond to that of cadaver behavior under similar loading. The structure was loaded impulsively by the sudden arrest of a supporting sled running on a track and by direct head impact with a suspended steel ball. The measured response included the head acceleration, the disk pressures, the muscle strains, the intracranial pressures and the skull strains; the sled motion was also monitored. These data were recorded with a microcomputer and oscilloscopes; the overall system deformation was observed by high-speed cameras. The muscle contraction effects were determined with the aid of microcomputer-controlled devices including a vacuum system, solenoid valves and plastic syringes.     

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.     

Thyroxine treatment prevents the development of photosensitivity in european starlings (Sturnus vulgaris)

Summary In starlings, the breeding season is terminated by a state of photorefractoriness. Birds remain completely reproductively inactive as long as long days are maintained, and only exposure to short days restores photosensitivity. Two experiments investigated the role of different doses of thyroxine in the development of photosensitivity in castrated starlings. First, photorefractory castrated male starlings were moved from long (18L:6D) to short (8L:16D) days, and received in the drinking water either 1 or 10 mg · 1^-1 thyroxine for the first 7 weeks of a 14-week observation period. Control birds regained photosensitivity after 5 weeks of short days, as signaled by a spontaneous increase in plasma LH, whereas the return to photosensitivity was delayed until weeks 7 and 9 in the 1- and 10-mg · 1^-1 thyroxine-treated birds, respectively. In the second experiment, the effect of different doses of thyroxine was explored at the level of the hypothalamic Gn-RH neurosecretory neurones. The acquisition of photosensitivity in control birds transferred from long to short days was characterized by a marked increase in hypothalamic Gn-RH content (while long-day controls maintained low Gn-RH content). Doses of 10 and 20 mg · 1^-1 of thyroxine completely prevented the return to photosensitivity, as seen through changes in either plasma LH concentrations or hypothalamic Gn-RH content, while a dose of 1 mg · 1^-1 allowed a partial recovery of photosensitivity, as hypothalamic Gn-RH content increased to an intermediate level and the spontaneous rise in plasma LH occurred slowly but steadily.Abbreviations Gn-RH gonadotrophin-releasing hormone - LH luteinizing hormone - LHRH-I luteinizing hormone releasing hormone