Sequentially Rationalizable Choice Manzini, Paola; Mariotti, Marco
The American economic review,
12/2007, Volume:
97, Issue:
5
Journal Article
Peer reviewed
Open access
A sequentially rationalizable choice function is a choice function that can be retrieved by applying sequentially to each choice problem the same fixed set of asymmetric binary relations (rationales) ...to remove inferior alternatives. These concepts translate into economic language some human choice heuristics studied in psychology and explain cyclical patterns of choice observed in experiments. We study some properties of sequential rationalizability and provide a full characterization of choice functions rationalizable by two and three rationales.
Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In ...selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat.
Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat ...genomes for 24.
We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian (25 proteins) selenoproteomes, and describe how they evolved along lineages through gene duplication (20 events), gene loss (10 events) and replacement of Sec with cysteine (12 events). We show that an intronless selenophosphate synthetase 2 gene evolved in early mammals and replaced functionally the original multiexon gene in placental mammals, whereas both genes remain in marsupials. Mammalian thioredoxin reductase 1 and thioredoxin-glutathione reductase evolved from an ancestral glutaredoxin-domain containing enzyme, still present in fish. Selenoprotein V and GPx6 evolved specifically in placental mammals from duplications of SelW and GPx3, respectively, and GPx6 lost Sec several times independently. Bony fishes were characterized by duplications of several selenoprotein families (GPx1, GPx3, GPx4, Dio3, MsrB1, SelJ, SelO, SelT, SelU1, and SelW2). Finally, we report identification of new isoforms for several selenoproteins and describe unusually conserved selenoprotein pseudogenes.
This analysis represents the first comprehensive survey of the vertebrate and mammal selenoproteomes, and depicts their evolution along lineages. It also provides a wealth of information on these selenoproteins and their forms.
In nitrate vulnerable zones (NVZs), site-specific techniques are needed to match N availability with durum wheat (Triticum turgidum subsp. durum Desf.) requirements. Enhanced-efficiency fertilizers ...can improve efficient N supply and reduce leaching, contributing to sustainable agriculture. Two-year field experiments were carried out at two Mediterranean nitrate vulnerable zones in Central Italy (Pisa and Arezzo) to study the effects of nitrogen sources, timings, and application rates. The trial compared: (i) three N sources for the first topdressing application (urea, methylene urea, and urea with the nitrification inhibitor DMPP); (ii) two stages for the first topdressing N application (1st tiller visible—BBCH21 and 1st node detectable—BBCH31); (iii) two N rates: one based on the crop N requirements (Optimal—NO), the other based on action programme prescriptions of the two NVZs (Action Programme—NAP). Grain yield and yield components were determined, together with N uptake. The results showed that: (i) grain and biomass production were reduced with NAP at both locations; (ii) urea performed better than slow-release fertilizers; (iii) the best application time depended on the N source and location: in Pisa, enhanced-efficiency fertilizers achieved higher yields when applied earliest, while for urea the opposite was true; in Arezzo different N fertilizers showed similar performances between the two application timings. Different behaviors of topdressing fertilizers at the two localities could be related to the diverse patterns of temperatures and rainfall. Thus, optimal fertilization strategies would seem to vary according to environmental conditions.
Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at ...the 3' UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.
We model a boundedly rational agent who suffers from limited attention. The agent considers each feasible alternative with a given (unobservable) probability, the attention parameter, and then ...chooses the alternative that maximizes a preference relation within the set of considered alternatives. We show that this random choice rule is the only one for which the impact of removing an alternative on the choice probability of any other alternative is asymmetric and menu independent. Both the preference relation and the attention parameters are identified uniquely by stochastic choice data.
Summary
Lifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, ...NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life‐history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer‐lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing. Interestingly, these gene expression patterns resembled those of flies under dietary restriction and several other lifespan‐extending interventions, although on the individual gene level, there was no significant overlap with genes previously reported to have lifespan‐extension effects. We experimentally tested the lifespan regulation potential of several candidate genes and found no consistent effects, suggesting that individual genes generally do not explain the observed longevity patterns. Instead, it appears that lifespan regulation across species is modulated by complex relationships at the system level represented by global gene expression.
Oxidation of cysteine thiols by physiological reactive oxygen species (ROS) initiates thermogenesis in brown and beige adipose tissues. Cellular selenocysteines, where sulfur is replaced with ...selenium, exhibit enhanced reactivity with ROS. Despite their critical roles in physiology, methods for broad and direct detection of proteogenic selenocysteines are limited. Here we developed a mass spectrometric method to interrogate incorporation of selenium into proteins. Unexpectedly, this approach revealed facultative incorporation of selenium as selenocysteine or selenomethionine into proteins that lack canonical encoding for selenocysteine. Selenium was selectively incorporated into regulatory sites on key metabolic proteins, including as selenocysteine-replacing cysteine at position 253 in uncoupling protein 1 (UCP1). This facultative utilization of selenium was initiated by increasing cellular levels of organic, but not inorganic, forms of selenium. Remarkably, dietary selenium supplementation elevated facultative incorporation into UCP1, elevated energy expenditure through thermogenic adipose tissue, and protected against obesity. Together, these findings reveal the existence of facultative protein selenation, which correlates with impacts on thermogenic adipocyte function and presumably other biological processes as well.
Naked mole rats (NMRs) are the longest‐lived rodents yet their stem cell characteristics remain enigmatic. Here, we comprehensively mapped the NMR hematopoietic landscape and identified unique ...features likely contributing to longevity. Adult NMRs form red blood cells in spleen and marrow, which comprise a myeloid bias toward granulopoiesis together with decreased B‐lymphopoiesis. Remarkably, youthful blood and marrow single‐cell transcriptomes and cell compositions are largely maintained until at least middle age. Similar to primates, the primitive stem and progenitor cell (HSPC) compartment is marked by CD34 and THY1. Stem cell polarity is seen for Tubulin but not CDC42, and is not lost until 12 years of age. HSPC respiration rates are as low as in purified human stem cells, in concert with a strong expression signature for fatty acid metabolism. The pool of quiescent stem cells is higher than in mice, and the cell cycle of hematopoietic cells is prolonged. By characterizing the NMR hematopoietic landscape, we identified resilience phenotypes such as an increased quiescent HSPC compartment, absence of age‐related decline, and neotenic traits likely geared toward longevity.
Synopsis
Naked mole‐rats are the longest‐lived rodents but their hematopoietic system and contained self‐renewing stem cell populations remain poorly characterized. Combining surface marker and sequencing analysis, this resource reports the first comprehensive map of the naked mole‐rat blood system, uncovering similarities to their human counterpart during ageing.
A cross‐reactive FACS antibody panel allows for purification of naked mole‐rat stem, progenitor and effector cells from blood, spleen and bone marrow.
Red blood cells are produced in both bone marrow and spleen, exemplifying a neotenic trait.
Enlargement of the myeloid compartment and concomitantly reduced B‐lymphopoiesis in the bone marrow resemble fetal stages of white blood cell production.
CD34 marks the primitive stem and progenitor compartment, similar as in humans.
An enlarged quiescent stem cell pool preserves hematopoiesis during an extended lifespan.
Stem and progenitor cells feature a prolonged cell cycle in vivo, with a low metabolic profile and elevated lipid metabolism.
In‐depth profiling of the naked mole‐rat hematopoietic system by surface marker analysis and single‐cell sequencing uncovers resilience phenotypes and unexpected similarities with humans.
Optimizing the productivity and efficiency of cereal–legume intercropping through exploiting differences in nitrogen (N) acquisition of the two crops is crucial in Mediterranean areas. A two-year ...field study was conducted in Central Italy to determine how N fertilization rate affected forage and grain production as well as intercropping efficiency in a barley (Hordeum vulgare L.) and field bean (Vicia faba L. var minor) intercrop. Crops were grown as monocrops or intercropped in alternate rows in an additive design and fertilized with five N rates from 0 to 200 kg ha−1. Forage production was determined both at heading and early dough, while grain yield was assessed at full ripening. Besides, land equivalent ratio, competitive ratio, and aggressivity index were calculated. Consistently between years, results highlighted that intercropping of barley with field bean can be a sustainable cropping system because both forage production and efficiency indices improved. Anyway, with 150 and 200 kg N ha−1, the grain yield was lower in intercropping than in sole crops, due to higher interspecific competition. We concluded that the optimal N fertilization depends on the farmer’s objective in terms of forage or grain production and the targeted proportion between the cereal and the legume at harvest.
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