Preconditioning in the reef-building coral Pocillopora damicornis and the potential for trans-generational acclimatization in coral larvae under future climate change conditions

Coral reefs are globally threatened by climate change-related ocean warming and ocean acidification (OA). To date, slow-response mechanisms such as genetic adaptation have been considered the major determinant of coral reef persistence, with little consideration of rapid-response acclimatization mechanisms. These rapid mechanisms such as parental effects that can contribute to trans-generational acclimatization (e.g. epigenetics) have, however, been identified as important contributors to offspring response in other systems. We present the first evidence of parental effects in a cross-generational exposure to temperature and OA in reef-building corals. Here, we exposed adults to high (28.9°C, 805 µatm PCO2) or ambient (26.5°C, 417 µatm PCO2) temperature and OA treatments during the larval brooding period. Exposure to high treatment negatively affected adult performance, but their larvae exhibited size differences and metabolic acclimation when subsequently re-exposed, unlike larvae from parents exposed to ambient conditions. Understanding the innate capacity corals possess to respond to current and future climatic conditions is essential to reef protection and maintenance. Our results identify that parental effects may have an important role through (1) ameliorating the effects of stress through preconditioning and adaptive plasticity, and/or (2) amplifying the negative parental response through latent effects on future life stages. Whether the consequences of parental effects and the potential for trans-generational acclimatization are beneficial or maladaptive, our work identifies a critical need to expand currently proposed climate change outcomes for corals to further assess rapid response mechanisms that include non-genetic inheritance through parental contributions and classical epigenetic mechanisms.

Uniformly reweighted belief propagation for distributed Bayesian hypothesis testing

Belief propagation (BP) is a technique for distributed inference in wireless networks and is often used even when the underlying graphical model contains cycles. In this paper, we propose a uniformly reweighted BP scheme that reduces the impact of cycles by weighting messages by a constant ?edge appearance probability? rho ? 1. We apply this algorithm to distributed binary hypothesis testing problems (e.g., distributed detection) in wireless networks with Markov random field models. We demonstrate that in the considered setting the proposed method outperforms standard BP, while maintaining similar complexity. We then show that the optimal ? can be approximated as a simple function of the average node degree, and can hence be computed in a distributed fashion through a consensus algorithm.

Provision of ecological infrastructures to increase pollinators and other beneficial organisms in rainfed crops in Central Spain

In sustainable intensive agriculture, the biodiversity of monoculture fields can be increased by managing the field margins to provide ecological infrastructures that serve as refuges and resources for beneficial organisms (pollinators and natural enemies). In the present work we summarize two years of field trials following the goal to increase biodiversity of beneficial fauna in a barley field in Central Spain by sowing different herbaceous mixtures in the field margins. The presence of arthropods visiting flowers on plots sown with different types of seed mixtures and unsown natural flora (control plot) was compared by visual sampling every week between April and June. The results showed that a combination of herbaceous big-size seeds was the most successful mixture emerging under our experimental conditions and achieved a higher number of visits of beneficial arthropods than the unsown natural vegetation.

Does the natural "microcosm" created by Tuber aestivum affect soil microarthropods? A new hypothesis based on Collembola in truffle culture

microarthropods play an important role in fungi dispersion, but little is still known about the interaction between truffle and soil microarthropods. The aim of this study was to investigate the ability of the truffle Tuber aestivum to modify soil biogeochemistry (i.e. create a zone of scarce vegetation around the host plant, called a burn or brûlé) and to highlight the effects of the brûlé on the soil fauna community. We compared soil microarthropod communities found in the soil inside versus outside the T. aestivum brûlé with the chemistry of soil collected inside versus outside the brûlé. The study was carried out in three Mediterranean areas, two in Italy and one in Spain. The results confirmed the ability of T. aestivum to modify soil biogeochemistry in the brûlé: pH was higher and total organic carbon tended to be lower inside the brûlé compared to outside. Soil fauna communities showed some interesting differences. Some groups, such as Symphyla and Pauropoda, adapted well to the soil; some Collembolan families, and biodiversity and soil quality indices were generally higher outside the brûlé. Folsomia sp. showed higher abundance in the soil of the brûlé compared to outside. The results suggest that some Collembola groups may be attracted by the fungal metabolites produced by T. aestivum, while other Collembola and other microarthropods may find an unfavourable environment in the soil of the brûlé. The next steps will be to confirm this hypothesis and to extend the study to other keys groups such as nematodes and earthworms and to link fluctuations of soil communities with the biological phases of truffle growth.

Respuesta fisiológica, productiva y cualitativa del cultivar Syrah (Vitis vinifera L) con diferentes frecuencias de riego y densidad de goteros en suelos arcillosos

La disponibilidad hídrica es uno de los principales factores que determinan el rendimiento del viñedo en muchas regiones vitícolas, por lo que sus consecuencias han sido ampliamente estudiadas. Sin embargo, para una cantidad de agua de riego determinada, otros aspectos como la frecuencia de aplicación, o la combinación entre el caudal de los goteros y la distancia entre los mismos (es decir, el patrón de distribución de agua en el suelo), pueden jugar un papel relevante, pero estos factores han sido poco estudiados. El objetivo de este trabajo ha sido evaluar las implicaciones agronómicas y fisiológicas de dos frecuencias de riego (IrrF, cada 2 y 4 días) y dos patrones de distribución de agua (DisP, goteros de 2 L h-1 separados 0,6 m vs. goteros de 4 L h-1 separados 1,2 m). El experimento se llevó a cabo durante cuatro temporadas consecutivas en un viñedo cv. Syrah con un suelo arcilloso en el centro de España, y los dos factores fueron evaluados bajo dos condiciones de disponibilidad hídrica (Baja: 20% de ETo y Media: 40% de ETo). El efecto de la frecuencia de riego y el patrón de distribución de agua en la respuesta agronómica del cv. Syrah se ha estudiado en el capítulo 1. La frecuencia de riego y el patrón de distribución de agua en el suelo afectaron a algunos aspectos de los componentes de rendimiento y desarrollo vegetativo en las dos condiciones de disponibilidad hídrica, aunque los efectos observados no fueron los mismos todos los años. Los efectos fueron más evidentes para IrrF en condiciones de baja disponibilidad hídrica y para DisP en condiciones de disponibilidad hídrica media. Dos de los cuatro años del experimento, el pasar de frecuencia de riego de 2 días a 4 días causó un incremento medio de rendimiento del 20% para la situación de baja disponibilidad hídrica. La textura del suelo, sin duda ha condicionado los resultados obtenidos en los tratamientos regados con el 20% de la ETo, ya que regar cada dos días implicaba la aplicación de pequeñas cantidades de agua y se formaban bulbos de riego superficiales, probablemente favoreciendo las pérdidas por evaporación. En el capítulo 2, se ha analizado el efecto de la frecuencia de riego y del patrón de distribución de agua en el estado hídrico de la planta y el intercambio gaseoso a nivel de hoja con el fin de explicar las diferencias observadas en la respuesta agronómica. En lo que respecta a la frecuencia de riego, en condiciones de baja disponibilidad hídrica, las plantas regadas cada 4 días (plantas 4d), mostraron mayores tasas de asimilación neta y conductancia estomática que las plantas regadas cada 2 días (plantas 2d), lo que es consistente con la hipótesis de que con la frecuencia de riego de 2 días se produjo una pérdida de eficiencia del uso del agua, probablemente debido a una mayor evaporación como consecuencia del hecho de que el volumen de suelo mojado creado era pequeño y cerca de la superficie. En condiciones de disponibilidad hídrica media, las diferencias en el intercambio gaseoso a nivel de hoja fueron mucho más pequeñas. Al comienzo del verano cada frecuencia de riego se comportó mejor uno de los días de medida, compensando al final del ciclo de riego de 4 días. Sin embargo, a medida que avanzó el verano y el déficit de agua se hizo más alto, las diferencias significativas aparecieron sólo en el 'día 4' del ciclo de riego, cuando las plantas 2d se comportaron mejor que las plantas regadas 4d que llevaban tres días sin regarse. Estas diferencias fisiológicas fueron menores que en condiciones de baja disponibilidad hídrica y al parecer no suficientes para afectar el comportamiento agronómico. En cuanto al patrón de distribución de agua, el efecto fue poco significativo, pero la mayor densidad de goteros tendió a presentar un mayor intercambio gaseoso a nivel de hoja, especialmente a media mañana. El efecto fue más importante para las condiciones de disponibilidad hídrica media. En el capítulo 3, se han comparado las relaciones entre el intercambio gaseoso a nivel de hoja, el estado hídrico y la demanda atmosférica, con el fin de explicar los cambios en la intensidad de la respuesta fisiológica observados en el Capítulo 2. No se han encontrado diferencias en dichas relaciones para el patrón de distribución de agua, por lo que sólo se ha analizado el efecto de la frecuencia de riego. El estudio se ha centrado fundamentalmente en si las plantas mostraron una respuesta fisiológica diferente a los cambios en el estado hídrico y en la demanda atmosférica según el tiempo transcurrido desde el último riego. Las diferencias observadas explican los resultados obtenidos en los capítulos anteriores, y sugieren la existencia de procesos de aclimatación vinculados a la frecuencia de riego y a la disponibilidad hídrica. Las plantas bajo condiciones de baja disponibilidad hídrica se mostraron más aclimatadas al estrés hídrico que aquellas en condiciones de disponibilidad hídrica media. La frecuencia de riego afectó claramente la relación entre los parámetros de intercambio gaseoso a nivel de hoja, el estado hídrico de la planta y las condiciones atmosféricas, y junto con la cantidad de agua aplicada tuvo implicaciones en el desarrollo de mecanismos de aclimatación que afectaron a la respuesta fisiológica de la planta, afectando a la eficiencia del riego. ABSTRACT Water availability is one of the major factors that determine vineyard performance in many grape growing regions, so its implications have been widely studied before. However, for a given irrigation water amount, other aspects such as application frequency, or emitter spacing and flow rate (i.e., distribution pattern), may play a relevant role, but these factors have been scarcely studied. The aim of this work was to evaluate the agronomic and physiological implications of two irrigation frequencies (IrrF, every 2 and 4 days) and two water distribution patterns (DisP, 2 L h−1 emitters every 0.6 m vs. 4 L h−1 emitters every 1.2 m). The experiment was carried out during four consecutive seasons in a cv. Syrah vineyard with a clay soil in central Spain, and the two factors were evaluated under two water availability conditions (LOW WA: 20% of ETo and MEDIUM WA: 40% of ETo). The effect of irrigation frequency and water distribution pattern on the agronomical response of cv. Syrah was studied in Chapter 1. IrrF and DisP affected some aspects of vegetative development and yield components under both water availability conditions, although the effects observed were not the same every year. The effects were more evident for IrrF under low water availability and for DisP under medium water availability. Two out of the four years of the experiment, the change of irrigation frequency from 2 days to 4 days promoted an average yield increase of 20% for the LOW WA situation. Soil texture certainly conditioned the results obtained under LOW WA conditions, since high frequency irrigation implied applying small amounts of water that resulted in limited superficial water bulbs, which probably favored water evaporation. In Chapter 2, the effect of irrigation frequency and water distribution pattern on plant water status and leaf gas exchange was analyzed to explain the differences observed in the agronomical response. Concerning irrigation frequency, under LOW WA conditions, applying irrigation every 4 days, resulted in higher net assimilation rates and stomatal conductance than doing it every 2 days, supporting the hypothesis that the latter frequency resulted in a water use efficiency loss, probably due to higher evaporation as a consequence of the fact the wetted soil volume created was small and close to the surface. Under MEDIUM WA conditions, differences in leaf gas exchange were much smaller. At the beginning of the summer each irrigation frequency behaved better one of the measurements days, compensating at the end of the 4-day irrigation cycle. However, as the summer progressed and water deficit became higher, significant differences appeared only on ‘day 4’ of the irrigation cycle, when 2d plants behaved better than 4d plants. These physiological differences were smaller than under LOW WA conditions and apparently not sufficient to affect agronomical performance. Regarding water distribution pattern, the effect was less significant but the closest emitter spacing resulted in general terms in a higher leaf gas exchange, especially at midmorning. The effect was more noticeable for MEDIUM WA conditions. In Chapter 3, the relationships between leaf gas exchange and leaf water status and atmospheric demand were compared to explain the changes in the intensity of the physiological response observed in Chapter 2. No differences were found in the relationships for water distribution pattern, so only the effect of irrigation frequency was analyzed focusing on whether the plants have a different physiological response to changes in water status and atmospheric demand according to the time elapsed since the last irrigation. Differences observed in the relationships explained the results obtained in the previous chapters, and point at the occurrence of acclimation processes linked to irrigation frequency and to water availability. Plants under LOW WATER AVAILABILITY conditions seemed to be more acclimated to water stress than those under MEDIUM WATER AVAILABILITY conditions. Irrigation frequency clearly affected the relationship between leaf gas exchange parameters, plant water status and atmospheric conditions, and together with the amount of water applied had implications in the development of acclimation mechanisms that affected plant physiological response, thus affecting irrigation efficiency.

Horizontal gene transfer among genomes: The complexity hypothesis

Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes. Extensive horizontal transfer has occurred for operational genes (those involved in housekeeping), whereas informational genes (those involved in transcription, translation, and related processes) are seldomly horizontally transferred. Through phylogenetic analysis of six complete prokaryotic genomes and the identification of 312 sets of orthologous genes present in all six genomes, we tested two theories describing the temporal flow of horizontal transfer. We show that operational genes have been horizontally transferred continuously since the divergence of the prokaryotes, rather than having been exchanged in one, or a few, massive events that occurred early in the evolution of prokaryotes. In agreement with earlier studies, we found that differences in rates of evolution between operational and informational genes are minimal, suggesting that factors other than rate of evolution are responsible for the observed differences in horizontal transfer. We propose that a major factor in the more frequent horizontal transfer of operational genes is that informational genes are typically members of large, complex systems, whereas operational genes are not, thereby making horizontal transfer of informational gene products less probable (the complexity hypothesis).

When defense backfires: Detrimental effect of a plant’s protective trichomes on an insect beneficial to the plant

The plant Mentzelia pumila (family Loasaceae) has leaves and stems densely covered with tiny hooked trichomes. The structures entrap and kill insects and therefore are most probably protective. But they are also maladaptive in that they incapacitate a coccinellid beetle (Hippodamia convergens) that preys upon an aphid enemy (Macrosiphum mentzeliae) of the plant. The adaptive benefit provided by the trichomes is evidently offset by a cost.

Testing the Cambrian explosion hypothesis by using a molecular dating technique

Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account adequately for variation in rate of evolution. A method of dating divergence times from molecular data addresses the criticisms of earlier studies and provides more realistic, but wider, confidence intervals. The data are not compatible with the Cambrian explosion hypothesis as an explanation for the origin of metazoan phyla, and provide additional support for an extended period of Precambrian metazoan diversification.

Omega images at the active zone may be endocytotic rather than exocytotic: Implications for the vesicle hypothesis of transmitter release

A Ca2+-dependent synaptic vesicle-recycling pathway emanating from the plasma membrane adjacent to the dense body at the active zone has been demonstrated by blocking pinch-off of recycling membrane by using the Drosophila mutant, shibire. Exposure of wild-type Drosophila synapses to low Ca2+/high Mg2+ saline is shown here to block this active zone recycling pathway at the stage in which invaginations of the plasma membrane develop adjacent to the dense body. These observations, in combination with our previous demonstration that exposure to high Ca2+ causes “docked” vesicles to accumulate in the identical location where active zone endocytosis occurs, suggest the possibility that a vesicle-recycling pathway emanating from the active zone may exist that is stimulated by exposure to elevated Ca2+, thereby causing an increase in vesicle recycling, and is suppressed by exposure to low Ca2+ saline, thereby blocking newly forming vesicles at the invagination stage. The presence of a Ca2+-dependent endocytotic pathway at the active zone opens up the following possibilities: (i) electron microscopic omega-shaped images (and their equivalent, freeze fracture dimples) observed at the active zone adjacent to the dense body could represent endocytotic images (newly forming vesicles) rather than exocytotic images; (ii) vesicles observed attached to the plasma membrane adjacent to the dense body could represent newly formed vesicles rather than vesicles “docked” for release of transmitter.

Sex-specific quantitative trait loci affecting longevity in Drosophila melanogaster

Senescence, the decline in survivorship and fertility with increasing age, is a near-universal property of organisms. Senescence and limited lifespan are thought to arise because weak natural selection late in life allows the accumulation of mutations with deleterious late-age effects that are either neutral (the mutation accumulation hypothesis) or beneficial (the antagonistic pleiotropy hypothesis) early in life. Analyses of Drosophila spontaneous mutations, patterns of segregating variation and covariation, and lines selected for late-age fertility have implicated both classes of mutation in the evolution of aging, but neither their relative contributions nor the properties of individual loci that cause aging in nature are known. To begin to dissect the multiple genetic causes of quantitative variation in lifespan, we have conducted a genome-wide screen for quantitative trait loci (QTLs) affecting lifespan that segregate among a panel of recombinant inbred lines using a dense molecular marker map. Five autosomal QTLs were mapped by composite interval mapping and by sequential multiple marker analysis. The QTLs had large sex-specific effects on lifespan and age-specific effects on survivorship and mortality and mapped to the same regions as candidate genes with fertility, cellular aging, stress resistance and male-specific effects. Late age-of-onset QTL effects are consistent with the mutation accumulation hypothesis for the evolution of senescence, and sex-specific QTL effects suggest a novel mechanism for maintaining genetic variation for lifespan.

Constitutive expression of the cold-regulated Arabidopsis thaliana COR15a gene affects both chloroplast and protoplast freezing tolerance

Cold acclimation in plants is associated with the expression of COR (cold-regulated) genes that encode polypeptides of unknown function. It has been widely speculated that products of these genes might have roles in freezing tolerance. Here we provide direct evidence in support of this hypothesis. We show that constitutive expression of COR15a, a cold-regulated gene of Arabidopsis thaliana that encodes a chloroplast-targeted polypeptide, enhances the in vivo freezing tolerance of chloroplasts in nonacclimated plants by almost 2°C, nearly one-third of the increase that occurs upon cold acclimation of wild-type plants. Significantly, constitutive expression of COR15a also affects the in vitro freezing tolerance of protoplasts. At temperatures between −5 and −8°C, the survival of protoplasts isolated from leaves of nonacclimated transgenic plants expressing COR15a was greater than that of protoplasts isolated from leaves of nonacclimated wild-type plants. At temperatures between −2 and −4°C, constitutive expression of COR15a had a slight negative effect on survival. The implications of these data regarding possible modes of COR15a action are discussed.

Possible ecological risks of transgenic organism release when transgenes affect mating success: Sexual selection and the Trojan gene hypothesis

Widespread interest in producing transgenic organisms is balanced by concern over ecological hazards, such as species extinction if such organisms were to be released into nature. An ecological risk associated with the introduction of a transgenic organism is that the transgene, though rare, can spread in a natural population. An increase in transgene frequency is often assumed to be unlikely because transgenic organisms typically have some viability disadvantage. Reduced viability is assumed to be common because transgenic individuals are best viewed as macromutants that lack any history of selection that could reduce negative fitness effects. However, these arguments ignore the potential advantageous effects of transgenes on some aspect of fitness such as mating success. Here, we examine the risk to a natural population after release of a few transgenic individuals when the transgene trait simultaneously increases transgenic male mating success and lowers the viability of transgenic offspring. We obtained relevant life history data by using the small cyprinodont fish, Japanese medaka (Oryzias latipes) as a model. Our deterministic equations predict that a transgene introduced into a natural population by a small number of transgenic fish will spread as a result of enhanced mating advantage, but the reduced viability of offspring will cause eventual local extinction of both populations. Such risks should be evaluated with each new transgenic animal before release.

Further examination of the Xist promoter-switch hypothesis in X inactivation: Evidence against the existence and function of a P0 promoter

The onset of X inactivation coincides with accumulation of Xist RNA along the future inactive X chromosome. A recent hypothesis proposed that accumulation is initiated by a promoter switch within Xist. In this hypothesis, an upstream promoter (P0) produces an unstable transcript, while the known downstream promoter (P1) produces a stable RNA. To test this hypothesis, we examined expression and half-life of Xist RNA produced from an Xist transgene lacking P0 but retaining P1. We confirm the previous finding that P0 is dispensable for Xist expression in undifferentiated cells and that P1 can be used in both undifferentiated and differentiated cells. Herein, we show that Xist RNA initiated at P1 is unstable and does not accumulate. Further analysis indicates that the transcriptional boundary at P0 does not represent the 5′ end of a distinct Xist isoform. Instead, P0 is an artifact of cross-amplification caused by a pseudogene of the highly expressed ribosomal protein S12 gene Rps12. Using strand-specific techniques, we find that transcription upstream of P1 originates from the DNA strand opposite Xist and represents the 3′ end of the antisense Tsix RNA. Thus, these data do not support the existence of a P0 promoter and suggest that mechanisms other than switching of functionally distinct promoters control the up-regulation of Xist.

Heterothermal acclimation: An experimental paradigm for studying the control of thermal acclimation in crabs

A method for the study of the control of the attainment of thermal acclimation has been applied to the crabs, Cancer pagurus and Carcinus maenas. Crabs were heterothermally acclimated by using an anterior–posterior partition between two compartments, one at 8°C and the other at 22°C. One compartment held a three-quarter section of the crab including the central nervous system (CNS), eye stalks, and ipsilateral legs; the other held a quarter section including the contralateral legs. Criteria used to assess the acclimation responses were comparisons of muscle plasma membrane fatty acid composition and “fluidity.” In both species, the major fatty acids of phosphatidylcholine were 16:0, 18:1, 20:5, and 22:6, whereas phosphatidylethanolamine contained significantly less 16:0 but more 18:0; these fatty acids comprised 80% of the total. Differences in fatty acid composition were demonstrated between fractions obtained from the ipsilateral and contralateral legs from the same heterothermally acclimated individual. In all acclimation states (except 22CNS, phosphatidylcholine fraction), membrane lipid saturation was significantly increased with acclimation at 22° as compared with 8°C. Membrane fluidity was determined by using 1,3-diphenyl-1,3,5 hexatriene (DPH) fluorescence polarization. In both species, membranes from legs held at 8° were more fluid than from legs held at 22°C irrespective of the acclimation temperature of the CNS. Heterothermal acclimation demonstrated that leg muscle membrane composition and fluidity respond primarily to local temperature and were not predominately under central direction. The responses between 8°C- and 22°C-acclimated legs were more pronounced when the CNS was cold-acclimated, so a central influence cannot be excluded.