Distributed bees algorithm for task allocation in swarm of robots

In this paper, we propose the distributed bees algorithm (DBA) for task allocation in a swarm of robots. In the proposed scenario, task allocation consists in assigning the robots to the found targets in a 2-D arena. The expected distribution is obtained from the targets' qualities that are represented as scalar values. Decision-making mechanism is distributed and robots autonomously choose their assignments taking into account targets' qualities and distances. We tested the scalability of the proposed DBA algorithm in terms of number of robots and number of targets. For that, the experiments were performed in the simulator for various sets of parameters, including number of robots, number of targets, and targets' utilities. Control parameters inherent to DBA were tuned to test how they affect the final robot distribution. The simulation results show that by increasing the robot swarm size, the distribution error decreased.

Carbon allocation in north-western Amazon forests (Colombia)

Los estudios sobre la asignación del carbono en los ecosistemas forestales proporcionan información esencial para la comprensión de las diferencias espaciales y temporales en el ciclo del carbono de tal forma que pueden aportar información a los modelos y, así predecir las posibles respuestas de los bosques a los cambios en el clima. Dentro de este contexto, los bosques Amazónicos desempeñan un papel particularmente importante en el balance global del carbono; no obstante, existen grandes incertidumbres en cuanto a los controles abióticos en las tasas de la producción primaria neta (PPN), la asignación de los productos de la fotosíntesis a los diferentes componentes o compartimentos del ecosistema (aéreo y subterráneo) y, cómo estos componentes de la asignación del carbono responden a eventos climáticos extremos. El objetivo general de esta tesis es analizar los componentes de la asignación del carbono en bosques tropicales maduros sobre suelos contrastantes, que crecen bajo condiciones climáticas similares en dos sitios ubicados en la Amazonia noroccidental (Colombia): el Parque Natural Nacional Amacayacu y la Estación Biológica Zafire. Con este objetivo, realicé mediciones de los componentes de la asignación del carbono (biomasa, productividad primaria neta, y su fraccionamiento) a nivel ecosistémico y de la dinámica forestal (tasas anuales de mortalidad y reclutamiento), a lo largo de ocho años (20042012) en seis parcelas permanentes de 1 hectárea establecidas en cinco tipos de bosques sobre suelos diferentes (arcilloso, franco-arcilloso, franco-arcilloso-arenoso, franco-arenoso y arena-francosa). Toda esta información me permitió abordar preguntas específicas que detallo a continuación. En el Capítulo 2 evalúe la hipótesis de que a medida que aumenta la fertilidad del suelo disminuye la cantidad del carbono asignado a la producción subterránea (raíces finas con diámetro <2 mm). Y para esto, realicé mediciones de la masa y la producción de raíces finas usando dos métodos: (1) el de los cilindros de crecimiento y, (2) el de los cilindros de extracción secuencial. El monitoreo se realizó durante 2.2 años en los bosques con suelos más contrastantes: arcilla y arena-francosa. Encontré diferencias significativas en la masa de raíces finas y su producción entre los bosques y, también con respecto a la profundidad del suelo (010 y 1020 cm). El bosque sobre arena-francosa asignó más carbono a las raíces finas que el bosque sobre arcillas. La producción de raíces finas en el bosque sobre arena-francosa fue dos veces más alta (media ± error estándar = 2.98 ± 0.36 y 3.33 ± 0.69 Mg C ha1 año1, con el método 1 y 2, respectivamente), que para el bosque sobre arcillas, el suelo más fértil (1.51 ± 0.14, método 1, y desde 1.03 ± 0.31 a 1.36 ± 0.23 Mg C ha1 año1, método 2). Del mismo modo, el promedio de la masa de raíces finas fue tres veces mayor en el bosque sobre arena-francosa (5.47 ± 0.17 Mg C ha1) que en el suelo más fértil (de 1.52 ± 0.08 a 1.82 ± 0.09 Mg C ha1). La masa de las raíces finas también mostró un patrón temporal relacionado con la lluvia, mostrando que la producción de raíces finas disminuyó sustancialmente en el período seco del año 2005. Estos resultados sugieren que los recursos del suelo pueden desempeñar un papel importante en los patrones de la asignación del carbono entre los componentes aéreo y subterráneo de los bosques tropicales; y que el suelo no sólo influye en las diferencias en la masa de raíces finas y su producción, sino que también, en conjunto con la lluvia, sobre la estacionalidad de la producción. En el Capítulo 3 estimé y analicé los tres componentes de la asignación del carbono a nivel del ecosistema: la biomasa, la productividad primaria neta PPN, y su fraccionamiento, en los mismos bosques del Capítulo 2 (el bosque sobre arcillas y el bosque sobre arena-francosa). Encontré diferencias significativas en los patrones de la asignación del carbono entre los bosques; el bosque sobre arcillas presentó una mayor biomasa total y aérea, así como una PPN, que el bosque sobre arena-francosa. Sin embargo, la diferencia entre los dos bosques en términos de la productividad primaria neta total fue menor en comparación con las diferencias entre la biomasa total de los bosques, como consecuencia de las diferentes estrategias en la asignación del carbono a los componentes aéreo y subterráneo del bosque. La proporción o fracción de la PPN asignada a la nueva producción de follaje fue relativamente similar entre los dos bosques. Nuestros resultados de los incrementos de la biomasa aérea sugieren una posible compensación entre la asignación del carbono al crecimiento de las raíces finas versus el de la madera, a diferencia de la compensación comúnmente asumida entre la parte aérea y la subterránea en general. A pesar de estas diferencias entre los bosques en términos de los componentes de la asignación del carbono, el índice de área foliar fue relativamente similar entre ellos, lo que sugiere que el índice de área foliar es más un indicador de la PPN total que de la asignación de carbono entre componentes. En el Capítulo 4 evalué la variación espacial y temporal de los componentes de la asignación del carbono y la dinámica forestal de cinco tipos e bosques amazónicos y sus respuestas a fluctuaciones en la precipitación, lo cual es completamente relevante en el ciclo global del carbono y los procesos biogeoquímicos en general. Estas variaciones son así mismo importantes para evaluar los efectos de la sequía o eventos extremos sobre la dinámica natural de los bosques amazónicos. Evalué la variación interanual y la estacionalidad de los componentes de la asignación del carbono y la dinámica forestal durante el periodo 2004−2012, en cinco bosques maduros sobre diferentes suelos (arcilloso, franco-arcilloso, franco-arcilloso-arenoso, franco-arenoso y arena-francosa), todos bajo el mismo régimen local de precipitación en la Amazonia noroccidental (Colombia). Quería examinar sí estos bosques responden de forma similar a las fluctuaciones en la precipitación, tal y como pronostican muchos modelos. Consideré las siguientes preguntas: (i) ¿Existe una correlación entre los componentes de la asignación del carbono y la dinámica forestal con la precipitación? (ii) ¿Existe correlación entre los bosques? (iii) ¿Es el índice de área foliar (LAI) un indicador de las variaciones en la producción aérea o es un reflejo de los cambios en los patrones de la asignación del carbono entre bosques?. En general, la correlación entre los componentes aéreo y subterráneo de la asignación del carbono con la precipitación sugiere que los suelos juegan un papel importante en las diferencias espaciales y temporales de las respuestas de estos bosques a las variaciones en la precipitación. Por un lado, la mayoría de los bosques mostraron que los componentes aéreos de la asignación del carbono son susceptibles a las fluctuaciones en la precipitación; sin embargo, el bosque sobre arena-francosa solamente presentó correlación con la lluvia con el componente subterráneo (raíces finas). Por otra parte, a pesar de que el noroeste Amazónico es considerado sin una estación seca propiamente (definida como <100 mm meses −1), la hojarasca y la masa de raíces finas mostraron una alta variabilidad y estacionalidad, especialmente marcada durante la sequía del 2005. Además, los bosques del grupo de suelos francos mostraron que la hojarasca responde a retrasos en la precipitación, al igual que la masa de raíces finas del bosque sobre arena-francosa. En cuanto a la dinámica forestal, sólo la tasa de mortalidad del bosque sobre arena-francosa estuvo correlacionada con la precipitación (ρ = 0.77, P <0.1). La variabilidad interanual en los incrementos en el tallo y la biomasa de los individuos resalta la importancia de la mortalidad en la variación de los incrementos en la biomasa aérea. Sin embargo, las tasas de mortalidad y las proporciones de individuos muertos por categoría de muerte (en pie, caído de raíz, partido y desaparecido), no mostraron tendencias claras relacionadas con la sequía. Curiosamente, la hojarasca, el incremento en la biomasa aérea y las tasas de reclutamiento mostraron una alta correlación entre los bosques, en particular dentro del grupo de los bosques con suelos francos. Sin embargo, el índice de área foliar estimado para los bosques con suelos más contrastantes (arcilla y arena-francosa), no presentó correlación significativa con la lluvia; no obstante, estuvo muy correlacionado entre bosques; índice de área foliar no reflejó las diferencias en la asignación de los componentes del carbono, y su respuesta a la precipitación en estos bosques. Por último, los bosques estudiados muestran que el noroeste amazónico es susceptible a fenómenos climáticos, contrario a lo propuesto anteriormente debido a la ausencia de una estación seca propiamente dicha. ABSTRACT Studies of carbon allocation in forests provide essential information for understanding spatial and temporal differences in carbon cycling that can inform models and predict possible responses to changes in climate. Amazon forests play a particularly significant role in the global carbon balance, but there are still large uncertainties regarding abiotic controls on the rates of net primary production (NPP) and the allocation of photosynthetic products to different ecosystem components; and how the carbon allocation components of Amazon forests respond to extreme climate events. The overall objective of this thesis is to examine the carbon allocation components in old-growth tropical forests on contrasting soils, and under similar climatic conditions in two sites at the Amacayacu National Natural Park and the Zafire Biological Station, located in the north-western Amazon (Colombia). Measurements of above- and below-ground carbon allocation components (biomass, net primary production, and its partitioning) at the ecosystem level, and dynamics of tree mortality and recruitment were done along eight years (20042012) in six 1-ha plots established in five Amazon forest types on different soils (clay, clay-loam, sandy-clay-loam, sandy-loam and loamy-sand) to address specific questions detailed in the next paragraphs. In Chapter 2, I evaluated the hypothesis that as soil fertility increases the amount of carbon allocated to below-ground production (fine-roots) should decrease. To address this hypothesis the standing crop mass and production of fine-roots (<2 mm) were estimated by two methods: (1) ingrowth cores and, (2) sequential soil coring, during 2.2 years in the most contrasting forests: the clay-soil forest and the loamy-sand forest. We found that the standing crop fine-root mass and its production were significantly different between forests and also between soil depths (0–10 and 10–20 cm). The loamysand forest allocated more carbon to fine-roots than the clay-soil forest, with fine-root production in the loamy-sand forest twice (mean ± standard error = 2.98 ± 0.36 and 3.33 ± 0.69 Mg C ha −1 yr −1, method 1 and 2, respectively) as much as for the more fertile claysoil forest (1.51 ± 0.14, method 1, and from 1.03 ± 0.31 to 1.36 ± 0.23 Mg C ha −1 yr −1, method 2). Similarly, the average of standing crop fine-root mass was three times higher in the loamy-sand forest (5.47 ± 0.17 Mg C ha1) than in the more fertile soil (from 1.52 ± 0.08 a 1.82 ± 0.09 Mg C ha1). The standing crop fine-root mass also showed a temporal pattern related to rainfall, with the production of fine-roots decreasing substantially in the dry period of the year 2005. These results suggest that soil resources may play an important role in patterns of carbon allocation of below-ground components, not only driven the differences in the biomass and its production, but also in the time when it is produced. In Chapter 3, I assessed the three components of stand-level carbon allocation (biomass, NPP, and its partitioning) for the same forests evaluated in Chapter 2 (clay-soil forest and loamy-sand forest). We found differences in carbon allocation patterns between these two forests, showing that the forest on clay-soil had a higher aboveground and total biomass as well as a higher above-ground NPP than the loamy-sand forest. However, differences between the two types of forests in terms of stand-level NPP were smaller, as a consequence of different strategies in the carbon allocation of above- and below-ground components. The proportional allocation of NPP to new foliage production was relatively similar between the two forests. Our results of aboveground biomass increments and fine-root production suggest a possible trade-off between carbon allocation to fine-roots versus wood growth (as it has been reported by other authors), as opposed to the most commonly assumed trade-off between total above- and below-ground production. Despite these differences among forests in terms of carbon allocation components, the leaf area index showed differences between forests like total NPP, suggesting that the leaf area index is more indicative of total NPP than carbon allocation. In Chapter 4, I evaluated the spatial and temporal variation of carbon allocation components and forest dynamics of Amazon forests as well as their responses to climatic fluctuations. I evaluated the intra- and inter-annual variation of carbon allocation components and forest dynamics during the period 2004−2012 in five forests on different soils (clay, clay-loam, sandy-clay-loam, sandy-loam and loamy-sand), but growing under the same local precipitation regime in north-western Amazonia (Colombia). We were interested in examining if these forests respond similarly to rainfall fluctuations as many models predict, considering the following questions: (i) Is there a correlation in carbon allocation components and forest dynamics with precipitation? (ii) Is there a correlation among forests? (iii) Are temporal responses in leaf area index (LAI) indicative of variations of above-ground production or a reflection of changes in carbon allocation patterns among forests?. Overall, the correlation of above- and below-ground carbon allocation components with rainfall suggests that soils play an important role in the spatial and temporal differences of responses of these forests to rainfall fluctuations. On the one hand, most forests showed that the above-ground components are susceptible to rainfall fluctuations; however, there was a forest on loamy-sand that only showed a correlation with the below-ground component (fine-roots). On the other hand, despite the fact that north-western Amazonia is considered without a conspicuous dry season (defined as <100 mm month−1), litterfall and fine-root mass showed high seasonality and variability, particularly marked during the drought of 2005. Additionally, forests of the loam-soil group showed that litterfall respond to time-lags in rainfall as well as and the fine-root mass of the loamy-sand forest. With regard to forest dynamics, only the mortality rate of the loamy-sand forest was significantly correlated with rainfall (77%). The observed inter-annual variability of stem and biomass increments of individuals highlighted the importance of the mortality in the above-ground biomass increment. However, mortality rates and death type proportion did not show clear trends related to droughts. Interestingly, litterfall, above-ground biomass increment and recruitment rates of forests showed high correlation among forests, particularly within the loam-soil forests group. Nonetheless, LAI measured in the most contrasting forests (clay-soil and loamysand) was poorly correlated with rainfall but highly correlated between forests; LAI did not reflect the differences in the carbon allocation components, and their response to rainfall on these forests. Finally, the forests studied highlight that north-western Amazon forests are also susceptible to climate fluctuations, contrary to what has been proposed previously due to their lack of a pronounced dry season.

Optimal water allocation in shortage situations as applied to an irrigation community.

This work studies the most beneficial way of allocating water in an irrigation community in water shortage situations. Therefore, it proposes that the irrigation surface area be divided into homogeneous zones, each with a beneficial relationship with respect to the water applied. The mathematical formula that enables one to obtain the optimal quota for the users or irrigation community as a whole has been found for individual relations of a quadratic or power type, and these have yielded different and complementary characteristics. Dimensionless variables have been used to display the results, and to compare with other alternative allocation rules such as the proportional rule, referencing the situation without water restrictions. As a result, for each water shortage situation, the water that is allocated to each user is obtained, together with the losses in individual income and the losses for the community as a whole. Furthermore, a proposal is put forth for establishing the marginal benefit from the water available, which could be of interest in enabling each community to analyze whether it is in its best interest to invest in increasing the resource, or to sell the resource to other users. Finally, an example is given to demonstrate how the method works and to show that, when the differences between the production schemes are considered, the differences in benefit reduction between the proportional allocation and the optimal allocation are also sizeable. Read More: http://ascelibrary.org/doi/abs/10.1061/(ASCE)IR.1943-4774.0000667

Temporal task allocation in periodic environments. An approach based on synchronization

In this paper, we study a robot swarm that has to perform task allocation in an environment that features periodic properties. In this environment, tasks appear in different areas following periodic temporal patterns. The swarm has to reallocate its workforce periodically, performing a temporal task allocation that must be synchronized with the environment to be effective. We tackle temporal task allocation using methods and concepts that we borrow from the signal processing literature. In particular, we propose a distributed temporal task allocation algorithm that synchronizes robots of the swarm with the environment and with each other. In this algorithm, robots use only local information and a simple visual communication protocol based on light blinking. Our results show that a robot swarm that uses the proposed temporal task allocation algorithm performs considerably more tasks than a swarm that uses a greedy algorithm.

High isolation series-shunt photoconductive microwave switch

This article presents a wide band compact high isolation photoconductive switch, which is based on the series-shunt switch design with three photoconductive switches made of diced high-resistivity silicon wafer placed over a microstrip gap and activated by 808-nm near-infrared laser diodes. The switch shows an insertion loss of 1.2 dB and an isolation of 44.8 dB at 2 GHz. It is easy to operate and control by light, high-speed, electromagnetically transparent and it does not require any biasing circuits.

Edaphic controls on ecosystem-level carbon allocation in two contrasting Amazon forests

Three components of carbon allocation, biomass, flux, and partitioning, were measured in two contrasting Amazon forests growing under similar climatic conditions. Allocation to aboveground compartments was highest in a high-stature forest growing on clay soils, while allocation to fine roots was higher in a short-stature forest growing on white sands. Differences in carbon allocation components where not proportional between the two forests, with soils controlling a trade-off between allocation to fine roots versus aboveground parts.

The optimal allocation rule and the water market as the most effective tools of managing water shortage in an irrigation district

The conference program will cover all areas of environmental and resource economics, ranging from topics prevailing in the general debate, such as climate change, energy sources, water management and ecosystem services evaluation, to more specialized subjects such as biodiversity conservation or persistent organic pollutants. The congress will be held on the Faculty of Economics of the University of Girona, located in Montilivi, a city quarter situated just few minutes from the city center, conveniently connected by bus lines L8 and L11.

Iterative bit- and power allocation in correlated MIMO systems

In this contribution a novel iterative bit- and power allocation (IBPA) approach has been developed when transmitting a given bit/s/Hz data rate over a correlated frequency non-selective (4× 4) Multiple-Input MultipleOutput (MIMO) channel. The iterative resources allocation algorithm developed in this investigation is aimed at the achievement of the minimum bit-error rate (BER) in a correlated MIMO communication system. In order to achieve this goal, the available bits are iteratively allocated in the MIMO active layers which present the minimum transmit power requirement per time slot.

Resource allocation in GMD and SVD-based MIMO System

Singular-value decomposition (SVD)-based multiple-input multiple output (MIMO) systems, where the whole MIMO channel is decomposed into a number of unequally weighted single-input single-output (SISO) channels, have attracted a lot of attention in the wireless community. The unequal weighting of the SISO channels has led to intensive research on bit- and power allocation even in MIMO channel situation with poor scattering conditions identified as the antennas correlation effect. In this situation, the unequal weighting of the SISO channels becomes even much stronger. In comparison to the SVD-assisted MIMO transmission, geometric mean decomposition (GMD)-based MIMO systems are able to compensate the drawback of weighted SISO channels when using SVD, where the decomposition result is nearly independent of the antennas correlation effect. The remaining interferences after the GMD-based signal processing can be easily removed by using dirty paper precoding as demonstrated in this work. Our results show that GMD-based MIMO transmission has the potential to significantly simplify the bit and power loading processes and outperforms the SVD-based MIMO transmission as long as the same QAM-constellation size is used on all equally-weighted SISO channels.

Mobilization of the A-kinase N-myristate through an isoform-specific intermolecular switch

Although the catalytic (C) subunit of cAMP-dependent protein kinase is N-myristylated, it is a soluble protein, and no physiological role has been identified for its myristyl moiety. To determine whether the interaction of the two regulatory (R) subunit isoforms (RI and RII) with the N-myristylated C subunit affects its ability to target membranes, the effect of N-myristylation and the RI and RII subunit isoforms on C subunit binding to phosphatidylcholine/phosphatidylserine liposomes was examined. Only the combination of N-myristylation and RII subunit interaction produced a dramatic increase in the rate of liposomal binding. To assess whether the RII subunit also increased the conformational flexibility of the C subunit N terminus, the effect of N-myristylation and the RI and RII subunits on the rotational freedom of the C subunit N terminus was measured. Specifically, fluorescein maleimide was conjugated to Cys-16 in the N-terminal domain of a K16C mutant of the C subunit, and the time-resolved emission anisotropy was determined. The interaction of the RII subunit, but not the RI subunit, significantly increased the backbone flexibility around the site of mutation and labeling, strongly suggesting that RII subunit binding to the myristylated C subunit induced a unique conformation of the C subunit that is associated with an increase in both the N-terminal flexibility and the exposure of the N-myristate. RII subunit thus appears to serve as an intermolecular switch that disrupts of the link between the N-terminal and core catalytic domains of the C subunit to expose the N-myristate and poise the holoenzyme for interaction with membranes.

In vivo kinetics of a redox-regulated transcriptional switch

SoxR is a transcription activator governing a cellular response to superoxide and nitric oxide in Escherichia coli. SoxR protein is a homodimer, and each monomer has a redox-active [2Fe–2S] cluster. Oxidation and reduction of the [2Fe–2S] clusters can reversibly activate and inactivate SoxR transcriptional activity. Here, we use electron paramagnetic resonance spectroscopy to follow the redox-switching process of SoxR protein in vivo. SoxR [2Fe–2S] clusters were in the fully reduced state during normal aerobic growth, but were completely oxidized after only 2-min aerobic exposure of the cells to superoxide-generating agents such as paraquat. The oxidized SoxR [2Fe–2S] clusters were rapidly re-reduced in vivo once the oxidative stress was removed. The in vivo kinetics of SoxR [2Fe–2S] cluster oxidation and reduction exactly paralleled the increase and decrease of transcription of soxS, the target gene for SoxR. The kinetic analysis also revealed that an oxidative stress-linked decrease in soxS mRNA stability contributes to the rapid attainment of a new steady state after SoxR activation. Such a redox stress-related change in soxS mRNA stability may represent a new level of biological control.

Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21

Conformational changes in ras p21 triggered by the hydrolysis of GTP play an essential role in the signal transduction pathway. The path for the conformational change is determined by molecular dynamics simulation with a holonomic constraint directing the system from the known GTP-bound structure (with the γ-phosphate removed) to the GDP-bound structure. The simulation is done with a shell of water molecules surrounding the protein. In the switch I region, the side chain of Tyr-32, which undergoes a large displacement, moves through the space between loop 2 and the rest of the protein, rather than on the outside of the protein. As a result, the charged residues Glu-31 and Asp-33, which interact with Raf in the homologous RafRBD–Raps complex, remain exposed during the transition. In the switch II region, the conformational changes of α2 and loop 4 are strongly coupled. A transient hydrogen bonding complex between Arg-68 and Tyr-71 in the switch II region and Glu-37 in switch I region stabilizes the intermediate conformation of α2 and facilitates the unwinding of a helical turn of α2 (residues 66–69), which in turn permits the larger scale motion of loop 4. Hydrogen bond exchange between the protein and solvent molecules is found to be important in the transition. Possible functional implications of the results are discussed.

“Switch I” mutant forms of the bacterial enhancer-binding protein NtrC that perturb the response to DNA

NtrC (nitrogen regulatory protein C) is a bacterial enhancer-binding protein of 469 residues that activates transcription by σ54-holoenzyme. A region of its transcriptional activation (central) domain that is highly conserved among homologous activators of σ54-holoenzyme—residues 206–220—is essential for interaction with this RNA polymerase: it is required for contact with the polymerase and/or for coupling the energy from ATP hydrolysis to a change in the conformation of the polymerase that allows it to form transcriptionally productive open complexes. Several mutant NtrC proteins with amino acid substitutions in this region, including NtrCA216V and NtrCG219K, have normal ATPase activity but fail in transcriptional activation. We now report that other mutant forms carrying amino acid substitutions at these same positions, NtrCA216C and NtrCG219C, are capable of activating transcription when they are not bound to a DNA template (non-DNA-binding derivatives with an altered helix–turn–helix DNA-binding motif at the C terminus of the protein) but are unable to do so when they are bound to a DNA template, whether or not it carries a specific enhancer. Enhancer DNA remains a positive allosteric effector of ATP hydrolysis, as it is for wild-type NtrC but, surprisingly, appears to have become a negative allosteric effector for some aspect of interaction with σ54-holoenzyme. The conserved region in which these amino acid substitutions occur (206–220) is equivalent to the Switch I region of a large group of purine nucleotide-binding proteins. Interesting analogies can be drawn between the Switch I region of NtrC and that of p21ras.

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.

Novel mechanism for carbamoyl-phosphate synthetase: A nucleotide switch for functionally equivalent domains

Carbamoyl-phosphate synthetases (CPSs) utilize two molecules of ATP at two internally duplicated domains, B and C. Domains B and C have recently been shown to be structurally [Thoden, J. B., Holden, H. M., Wesenberg, G., Raushel, F. M. & Rayment, I. (1997) Biochemistry 36, 6305–6316] and functionally [Guy, H. I. & Evans, D. R. (1996) J. Biol. Chem. 271, 13762–13769] equivalent. We have carried out a site-directed mutagenic analysis that is consistent with ATP binding to a palmate motif rather than to a Walker A/B motif in domains B and C. To accommodate our present findings, as well as the other recent findings of structural and functional equivalence, we are proposing a novel mechanism for CPS. In this mechanism utilization of ATP bound to domain C is coupled to carbamoyl-phosphate synthesis at domain B via a nucleotide switch, with the energy of ATP hydrolysis at domain C allowing domain B to cycle between two alternative conformations.