The pgip family in soybean and three other legume species: evidence for a birth-and-death model of evolution

Background Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene copies whose evolutionary origin has been poorly investigated. Here we report the complete characterization of the full complement of the pgip family in soybean (Glycine max [L.] Merr.) and the characterization of the genomic region surrounding the pgip family in four legume species. Results BAC clone and genome sequence analyses showed that the soybean genome contains two pgip loci. Each locus is composed of three clustered genes that are induced following infection with the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, and remnant sequences of pgip genes. The analyzed homeologous soybean genomic regions (about 126 Kb) that include the pgip loci are strongly conserved and this conservation extends also to the genomes of the legume species Phaseolus vulgaris L., Medicago truncatula Gaertn. and Cicer arietinum L., each containing a single pgip locus. Maximum likelihood-based gene trees suggest that the genes within the pgip clusters have independently undergone tandem duplication in each species. Conclusions The paleopolyploid soybean genome contains two pgip loci comprised in large and highly conserved duplicated regions, which are also conserved in bean, M. truncatula and C. arietinum. The genomic features of these legume pgip families suggest that the forces driving the evolution of pgip genes follow the birth-and-death model, similar to that proposed for the evolution of resistance (R) genes of NBS-LRR-type.

Selection-mutation balance models with epistatic selection

We present an application of birth-and-death processes on configuration spaces to a generalized mutation4 selection balance model. The model describes the aging of population as a process of accumulation of mu5 tations in a genotype. A rigorous treatment demands that mutations correspond to points in abstract spaces. 6 Our model describes an infinite-population, infinite-sites model in continuum. The dynamical equation which 7 describes the system, is of Kimura-Maruyama type. The problem can be posed in terms of evolution of states 8 (differential equation) or, equivalently, represented in terms of Feynman-Kac formula. The questions of interest 9 are the existence of a solution, its asymptotic behavior, and properties of the limiting state. In the non-epistatic 10 case the problem was posed and solved in [Steinsaltz D., Evans S.N., Wachter K.W., Adv. Appl. Math., 2005, 11 35(1)]. In our model we consider a topological space X as the space of positions of mutations and the influence of epistatic potentials

A case study of boundary layer ventilation by convection and coastal processes

It is often assumed that ventilation of the atmospheric boundary layer is weak in the absence of fronts, but is this always true? In this paper we investigate the processes responsible for ventilation of the atmospheric boundary layer during a nonfrontal day that occurred on 9 May 2005 using the UK Met Office Unified Model. Pollution sources are represented by the constant emission of a passive tracer everywhere over land. The ventilation processes observed include shallow convection, turbulent mixing followed by large-scale ascent, a sea breeze circulation and coastal outflow. Vertical distributions of tracer are validated qualitatively with AMPEP (Aircraft Measurement of chemical Processing Export fluxes of Pollutants over the UK) CO aircraft measurements and are shown to agree impressively well. Budget calculations of tracers are performed in order to determine the relative importance of these ventilation processes. Coastal outflow and the sea breeze circulation were found to ventilate 26% of the boundary layer tracer by sunset of which 2% was above 2 km. A combination of coastal outflow, the sea breeze circulation, turbulent mixing and large-scale ascent ventilated 46% of the boundary layer tracer, of which 10% was above 2 km. Finally, coastal outflow, the sea breeze circulation, turbulent mixing, large-scale ascent and shallow convection together ventilated 52% of the tracer into the free troposphere, of which 26% was above 2 km. Hence this study shows that significant ventilation of the boundary layer can occur in the absence of fronts (and thus during high-pressure events). Turbulent mixing and convection processes can double the amount of pollution ventilated from the boundary layer.

Gender stereotyping and decision processes: extending and reversing the gender bias in fame judgements

M. R. Banaji and A. G. Greenwald (1995) demonstrated a gender bias in fame judgments—that is, an increase in judged fame due to prior processing that was larger for male than for female names. They suggested that participants shift criteria between judging men and women, using the more liberal criterion for judging men. This "criterion-shift" account appeared problematic for a number of reasons. In this article, 3 experiments are reported that were designed to evaluate the criterion-shift account of the gender bias in the false-fame effect against a distribution-shift account. The results were consistent with the criterion-shift account, and they helped to define more precisely the situations in which people may be ready to shift their response criterion on an item-by-item basis. In addition, the results were incompatible with an interpretation of the criterion shift as an artifact of the experimental situation in the experiments reported by M. R. Banaji and A. G. Greenwald. (PsycINFO Database Record (c) 2010 APA, all rights reserved)

Implicit and explicit processes in a second-language learning task

Two experiments examined the learning of a set of Greek pronunciation rules through explicit and implicit modes of rule presentation. Experiment 1 compared the effectiveness of implicit and explicit modes of presentation in two modalities, visual and auditory. Subjects in the explicit or rule group were presented with the rule set, and those in the implicit or natural group were shown a set of Greek words, composed of letters from the rule set, linked to their pronunciations. Subjects learned the Greek words to criterion and were then given a series of tests which aimed to tap different types of knowledge. The results showed an advantage of explicit study of the rules. In addition, an interaction was found between mode of presentation and modality. Explicit instruction was more effective in the visual than in the auditory modality, whereas there was no modality effect for implicit instruction. Experiment 2 examined a possible reason for the advantage of the rule groups by comparing different combinations of explicit and implicit presentation in the study and learning phases. The results suggested that explicit presentation of the rules is only beneficial when it is followed by practice at applying them.

Life and death in a civitas capital: metabolic disease and trauma in the children from late Roman Dorchester, Dorset

The impact that “Romanization” and the development of urban centers had on the health of the Romano-British population is little understood. A re-examination of the skeletal remains of 364 nonadults from the civitas capital at Roman Dorchester (Durnovaria) in Dorset was carried out to measure the health of the children living in this small urban area. The cemetery population was divided into two groups; the first buried their dead organized within an east–west alignment with possible Christian-style graves, and the second with more varied “pagan” graves, aligned north–south. A higher prevalence of malnutrition and trauma was evident in the children from Dorchester than in any other published Romano-British group, with levels similar to those seen in postmedieval industrial communities. Cribra orbitalia was present in 38.5% of the children, with rickets and/or scurvy at 11.2%. Twelve children displayed fractures of the ribs, with 50% of cases associated with rickets and/or scurvy, suggesting that rib fractures should be considered during the diagnosis of these conditions. The high prevalence of anemia, rickets, and scurvy in the Poundbury children, and especially the infants, indicates that this community may have adopted child-rearing practices that involved fasting the newborn, a poor quality weaning diet, and swaddling, leading to general malnutrition and inadequate exposure to sunlight. The Pagan group showed no evidence of scurvy or rib fractures, indicating difference in religious and child-rearing practices but that both burial groups were equally susceptible to rickets and anemia suggests a shared poor standard of living in this urban environment.

Flavor characterization of sugar-added pennywort (Centella asiatica L.) juices treated with ultra-high pressure and thermal processes

The flavor characteristics of pennywort juices with added sugar treated by ultra-high pressure, pasteurization, and sterilization were investigated using solid phase microextraction combined with gas chromatography-mass spectrometry. It was found that sesquiterpene hydrocarbons comprised the major class of volatile components present and the juices had a characteristic aroma due to the presence of volatiles including beta-caryophyllene and humulene and alpha-copaene. In comparison with heated juices, HPP-treated samples could retain more volatile compounds such as linalool and geraniol similar to those present in fresh juice, whereas some volatiles such as alpha-terpinene and ketone class were apparently formed by thermal treatment. All processing operations produced juice that was not significantly different in the concentration of total volatiles. Practical Application: Pennywort juice is considered a nutraceutical drink for health benefits. Therefore, to preserve all aroma and active components in this juice, a nonthermal process such as ultra-high pressure should be a more appropriate technique for retention of its nutritive values than pasteurization and sterilization.

Vertical and horizontal processes in the global atmosphere and the maximum entropy production conjecture

The objective of this paper is to reconsider the Maximum Entropy Production conjecture (MEP) in the context of a very simple two-dimensional zonal-vertical climate model able to represent the total material entropy production due at the same time to both horizontal and vertical heat fluxes. MEP is applied first to a simple four-box model of climate which accounts for both horizontal and vertical material heat fluxes. It is shown that, under condition of fixed insolation, a MEP solution is found with reasonably realistic temperature and heat fluxes, thus generalising results from independent two-box horizontal or vertical models. It is also shown that the meridional and the vertical entropy production terms are independently involved in the maximisation and thus MEP can be applied to each subsystem with fixed boundary conditions. We then extend the four-box model by increasing its resolution, and compare it with GCM output. A MEP solution is found which is fairly realistic as far as the horizontal large scale organisation of the climate is concerned whereas the vertical structure looks to be unrealistic and presents seriously unstable features. This study suggest that the thermal meridional structure of the atmosphere is predicted fairly well by MEP once the insolation is given but the vertical structure of the atmosphere cannot be predicted satisfactorily by MEP unless constraints are imposed to represent the determination of longwave absorption by water vapour and clouds as a function of the state of the climate. Furthermore an order-of-magnitude estimate of contributions to the material entropy production due to horizontal and vertical processes within the climate system is provided by using two different methods. In both cases we found that approximately 40 mW m−2 K−1 of material entropy production is due to vertical heat transport and 5–7 mW m−2 K−1 to horizontal heat transport

Ethylene and senescence processes

Senescence is a vitally important sequence of events in the latter phase of the life cycle of a plant that determines yield and reproductive success. In many species, and in different plant organs, ethylene is a key regulator of senescence and an increased understanding of the way the hormone functions will enable the timing and location of senescence to be manipulated in order to improve yield, quality and longevity. This chapter examines the physiological and molecular regulation of senescence in different plant organs and introduces the concept of the ‘senescence window’ in which plant organs are receptive to ethylene-mediated senescence cues. Several studies have attempted to elucidate global patterns of the regulation of senescence, which have enabled the function of ethylene to be placed in the context of the involvement of other, often antagonistic, hormones in the execution of senescence and downstream processes. Finally, we examine the consequences of senescence for post-harvest biology, an area where the control of ethylene action has been actively sought in order to control precisely the timing of senescence and ripening processes so that crop quality can be enhanced and maintained.