Bat-MP: An Ontology-Based Energy Management Platform

This paper presents an Ontology-Based multi-technology platform as part of an open energy management system which also comprises a wireless transducer network for control and monitoring. The platform allows the integration of several building automation protocols, eases the development and implementation of different kinds of services and allows sharing of the data of a building. The system has been implemented and tested in the Energy Efficiency Research Facility at CeDInt-UPM.

Sonar bat for visually impaired people

Visually impaired people have many difficulties when traveling because it is impossible for them to detect obstacles that stand in their way. Bats instead of using the sight to detect these obstacles use a method based on ultrasounds, as their sense of hearing is much more developed than that of sight. The aim of the project is to design and build a device based on the method used by the bats to detect obstacles and transmit this information to people with vision problems to improve their skills. The method involves sending ultrasonic waves and analyzing the echoes produced when these waves collide with an obstacle. The sent signals are pulses and the information needed is the time elapsed from we send a pulse to receive the echo produced. The speed of sound is fixed within the same environment, so measuring the time it takes the wave to make the return trip, we can easily know the distance where the object is located. To build the device we have to design the necessary circuits, fabricate printed circuit boards and mount the components. We also have to design a program that would work within the digital part, which will be responsible for performing distance calculations and generate the signals with the information for the user. The circuits are the emitter and the receiver. The transmitter circuit is responsible for generating the signals that we will use. We use an ultrasonic transmitter which operates at 40 kHz so the sent pulses have to be modulated with this frequency. For this we generate a 40 kHz wave with an astable multivibrator formed by NAND gates and a train of pulses with a timer. The signal is the product of these two signals. The circuit of the receiver is a signal conditioner which transforms the signals received by the ultrasonic receiver in square pulses. The received signals have a 40 kHz carrier, low voltage and very different shapes. In the signal conditioner we will amplify the voltage to appropriate levels, eliminate the component of 40 kHz and make the shape of the pulses square to use them digitally. To simplify the design and manufacturing process in the digital part of the device we will use the Arduino platform. The pulses sent and received echoes enter through input pins with suitable voltage levels. In the Arduino, our program will poll these two signals storing the time when a pulse occurs. These time values are analyzed and used to generate an audible signal with the user information. This information is stored in the frequency of the signal, so that the generated signal frequency varies depending on the distance at which the objects are. RESUMEN Las personas con discapacidad visual tienen muchas dificultades a la hora de desplazarse ya que les es imposible poder detectar los obstáculos que se interpongan en su camino. Los murciélagos en vez de usar la vista para detectar estos obstáculos utilizan un método basado en ultrasonidos, ya que su sentido del oído está mucho más desarrollado que el de la vista. El objetivo del proyecto es diseñar y construir un dispositivo basado en el método usado por los murciélagos para detectar obstáculos y que pueda ser usado por las personas con problemas en la vista para mejorar sus capacidades. El método utilizado consiste en enviar ondas de ultrasonidos y analizar el eco producido cuando estas ondas chocan con algún obstáculo. Las señales enviadas tendrán forma de pulsos y la información necesaria es el tiempo transcurrido entre que enviamos un pulso y recibimos el eco producido. La velocidad del sonido es fija dentro de un mismo entorno, por lo que midiendo el tiempo que tarda la onda en hacer el viaje de ida y vuelta podemos fácilmente conocer la distancia a la que se encuentra el objeto. Para construir el dispositivo tendremos que diseñar los circuitos necesarios, fabricar las placas de circuito impreso y montar los componentes. También deberemos diseñar el programa que funcionara dentro de la parte digital, que será el encargado de realizar los cálculos de la distancia y de generar las señales con la información para el usuario. Los circuitos diseñados corresponden uno al emisor y otro al receptor. El circuito emisor es el encargado de generar las señales que vamos a emitir. Vamos a usar un emisor de ultrasonidos que funciona a 40 kHz por lo que los pulsos que enviemos van a tener que estar modulados con esta frecuencia. Para ello generamos una onda de 40 kHz mediante un multivibrador aestable formado por puertas NAND y un tren de pulsos con un timer. La señal enviada es el producto de estas dos señales. El circuito de la parte del receptor es un acondicionador de señal que transforma las señales recibidas por el receptor de ultrasonidos en pulsos cuadrados. Las señales recibidas tienen una portadora de 40 kHz para poder usarlas con el receptor de ultrasonidos, bajo voltaje y formas muy diversas. En el acondicionador de señal amplificaremos el voltaje a niveles adecuados además de eliminar la componente de 40 kHz y conseguir pulsos cuadrados que podamos usar de forma digital. Para simplificar el proceso de diseño y fabricación en la parte digital del dispositivo usaremos la plataforma Arduino. Las señales correspondientes el envío de los pulsos y a la recepción de los ecos entraran por pines de entrada después de haber adaptado los niveles de voltaje. En el Arduino, nuestro programa sondeara estas dos señales almacenando el tiempo en el que se produce un pulso. Estos valores de tiempo se analizan y se usan para generar una señal audible con la información para el usuario. Esta información ira almacenada en la frecuencia de la señal, por lo que la señal generada variará su frecuencia en función de la distancia a la que se encuentren los objetos.

Calculation of the spatial distribution of photovoltaic field by arbitrary 2D ilumination patterns en LiNbO3; application to photovoltaic particle trapping.

Patterns of evanescent photovoltaic field induced by illumination on a surface of lithium niobate (LN) have been calculated and compared with the experimental patterns of nano- and microparticles trapped by dielectrophoretic forces. A tool for this calculation has been developed. Calculo de distribución espacial de campo por efecto fotovoltaico con patrones arbitrarios de iluminación, en LiNbO3

Invitación a la Ecología: estrechando lazos con la sociedad Ekologiara hurbiltzeko gonbidapena: gizartearekin bat eginez

Estudio de las incertidumbres de los modelos de distribución de especies validados paleoecológicamente

Technology and characterization of GaN-HEMTs devices: high temperature and trapping effects

Los transistores de alta movilidad electrónica basados en GaN han sido objeto de una extensa investigación ya que tanto el GaN como sus aleaciones presentan unas excelentes propiedades eléctricas (alta movilidad, elevada concentración de portadores y campo eléctrico crítico alto). Aunque recientemente se han incluido en algunas aplicaciones comerciales, su expansión en el mercado está condicionada a la mejora de varios asuntos relacionados con su rendimiento y habilidad. Durante esta tesis se han abordado algunos de estos aspectos relevantes; por ejemplo, la fabricación de enhancement mode HEMTs, su funcionamiento a alta temperatura, el auto calentamiento y el atrapamiento de carga. Los HEMTs normalmente apagado o enhancement mode han atraído la atención de la comunidad científica dedicada al desarrollo de circuitos amplificadores y conmutadores de potencia, ya que su utilización disminuiría significativamente el consumo de potencia; además de requerir solamente una tensión de alimentación negativa, y reducir la complejidad del circuito y su coste. Durante esta tesis se han evaluado varias técnicas utilizadas para la fabricación de estos dispositivos: el ataque húmedo para conseguir el gate-recess en heterostructuras de InAl(Ga)N/GaN; y tratamientos basados en flúor (plasma CF4 e implantación de F) de la zona debajo de la puerta. Se han llevado a cabo ataques húmedos en heteroestructuras de InAl(Ga)N crecidas sobre sustratos de Si, SiC y zafiro. El ataque completo de la barrera se consiguió únicamente en las muestras con sustrato de Si. Por lo tanto, se puede deducir que la velocidad de ataque depende de la densidad de dislocaciones presentes en la estructura, ya que el Si presenta un peor ajuste del parámetro de red con el GaN. En relación a los tratamientos basados en flúor, se ha comprobado que es necesario realizar un recocido térmico después de la fabricación de la puerta para recuperar la heteroestructura de los daños causados durante dichos tratamientos. Además, el estudio de la evolución de la tensión umbral con el tiempo de recocido ha demostrado que en los HEMTs tratados con plasma ésta tiende a valores más negativos al aumentar el tiempo de recocido. Por el contrario, la tensión umbral de los HEMTs implantados se desplaza hacia valores más positivos, lo cual se atribuye a la introducción de iones de flúor a niveles más profundos de la heterostructura. Los transistores fabricados con plasma presentaron mejor funcionamiento en DC a temperatura ambiente que los implantados. Su estudio a alta temperatura ha revelado una reducción del funcionamiento de todos los dispositivos con la temperatura. Los valores iniciales de corriente de drenador y de transconductancia medidos a temperatura ambiente se recuperaron después del ciclo térmico, por lo que se deduce que dichos efectos térmicos son reversibles. Se han estudiado varios aspectos relacionados con el funcionamiento de los HEMTs a diferentes temperaturas. En primer lugar, se han evaluado las prestaciones de dispositivos de AlGaN/GaN sobre sustrato de Si con diferentes caps: GaN, in situ SiN e in situ SiN/GaN, desde 25 K hasta 550 K. Los transistores con in situ SiN presentaron los valores más altos de corriente drenador, transconductancia, y los valores más bajos de resistencia-ON, así como las mejores características en corte. Además, se ha confirmado que dichos dispositivos presentan gran robustez frente al estrés térmico. En segundo lugar, se ha estudiado el funcionamiento de transistores de InAlN/GaN con diferentes diseños y geometrías. Dichos dispositivos presentaron una reducción casi lineal de los parámetros en DC en el rango de temperaturas de 25°C hasta 225°C. Esto se debe principalmente a la dependencia térmica de la movilidad electrónica, y también a la reducción de la drift velocity con la temperatura. Además, los transistores con mayores longitudes de puerta mostraron una mayor reducción de su funcionamiento, lo cual se atribuye a que la drift velocity disminuye más considerablemente con la temperatura cuando el campo eléctrico es pequeño. De manera similar, al aumentar la distancia entre la puerta y el drenador, el funcionamiento del HEMT presentó una mayor reducción con la temperatura. Por lo tanto, se puede deducir que la degradación del funcionamiento de los HEMTs causada por el aumento de la temperatura depende tanto de la longitud de la puerta como de la distancia entre la puerta y el drenador. Por otra parte, la alta densidad de potencia generada en la región activa de estos transistores conlleva el auto calentamiento de los mismos por efecto Joule, lo cual puede degradar su funcionamiento y Habilidad. Durante esta tesis se ha desarrollado un simple método para la determinación de la temperatura del canal basado en medidas eléctricas. La aplicación de dicha técnica junto con la realización de simulaciones electrotérmicas han posibilitado el estudio de varios aspectos relacionados con el autocalentamiento. Por ejemplo, se han evaluado sus efectos en dispositivos sobre Si, SiC, y zafiro. Los transistores sobre SiC han mostrado menores efectos gracias a la mayor conductividad térmica del SiC, lo cual confirma el papel clave que desempeña el sustrato en el autocalentamiento. Se ha observado que la geometría del dispositivo tiene cierta influencia en dichos efectos, destacando que la distribución del calor generado en la zona del canal depende de la distancia entre la puerta y el drenador. Además, se ha demostrado que la temperatura ambiente tiene un considerable impacto en el autocalentamiento, lo que se atribuye principalmente a la dependencia térmica de la conductividad térmica de las capas y sustrato que forman la heterostructura. Por último, se han realizado numerosas medidas en pulsado para estudiar el atrapamiento de carga en HEMTs sobre sustratos de SiC con barreras de AlGaN y de InAlN. Los resultados obtenidos en los transistores con barrera de AlGaN han presentado una disminución de la corriente de drenador y de la transconductancia sin mostrar un cambio en la tensión umbral. Por lo tanto, se puede deducir que la posible localización de las trampas es la región de acceso entre la puerta y el drenador. Por el contrario, la reducción de la corriente de drenador observada en los dispositivos con barrera de InAlN llevaba asociado un cambio significativo en la tensión umbral, lo que implica la existencia de trampas situadas en la zona debajo de la puerta. Además, el significativo aumento del valor de la resistencia-ON y la degradación de la transconductancia revelan la presencia de trampas en la zona de acceso entre la puerta y el drenador. La evaluación de los efectos del atrapamiento de carga en dispositivos con diferentes geometrías ha demostrado que dichos efectos son menos notables en aquellos transistores con mayor longitud de puerta o mayor distancia entre puerta y drenador. Esta dependencia con la geometría se puede explicar considerando que la longitud y densidad de trampas de la puerta virtual son independientes de las dimensiones del dispositivo. Finalmente se puede deducir que para conseguir el diseño óptimo durante la fase de diseño no sólo hay que tener en cuenta la aplicación final sino también la influencia que tiene la geometría en los diferentes aspectos estudiados (funcionamiento a alta temperatura, autocalentamiento, y atrapamiento de carga). ABSTRACT GaN-based high electron mobility transistors have been under extensive research due to the excellent electrical properties of GaN and its related alloys (high carrier concentration, high mobility, and high critical electric field). Although these devices have been recently included in commercial applications, some performance and reliability issues need to be addressed for their expansion in the market. Some of these relevant aspects have been studied during this thesis; for instance, the fabrication of enhancement mode HEMTs, the device performance at high temperature, the self-heating and the charge trapping. Enhancement mode HEMTs have become more attractive mainly because their use leads to a significant reduction of the power consumption during the stand-by state. Moreover, they enable the fabrication of simpler power amplifier circuits and high-power switches because they allow the elimination of negativepolarity voltage supply, reducing significantly the circuit complexity and system cost. In this thesis, different techniques for the fabrication of these devices have been assessed: wet-etching for achieving the gate-recess in InAl(Ga)N/GaN devices and two different fluorine-based treatments (CF4 plasma and F implantation). Regarding the wet-etching, experiments have been carried out in InAl(Ga)N/GaN grown on different substrates: Si, sapphire, and SiC. The total recess of the barrier was achieved after 3 min of etching in devices grown on Si substrate. This suggests that the etch rate can critically depend on the dislocations present in the structure, since the Si exhibits the highest mismatch to GaN. Concerning the fluorine-based treatments, a post-gate thermal annealing was required to recover the damages caused to the structure during the fluorine-treatments. The study of the threshold voltage as a function of this annealing time has revealed that in the case of the plasma-treated devices it become more negative with the time increase. On the contrary, the threshold voltage of implanted HEMTs showed a positive shift when the annealing time was increased, which is attributed to the deep F implantation profile. Plasma-treated HEMTs have exhibited better DC performance at room temperature than the implanted devices. Their study at high temperature has revealed that their performance decreases with temperature. The initial performance measured at room temperature was recovered after the thermal cycle regardless of the fluorine treatment; therefore, the thermal effects were reversible. Thermal issues related to the device performance at different temperature have been addressed. Firstly, AlGaN/GaN HEMTs grown on Si substrate with different cap layers: GaN, in situ SiN, or in situ SiN/GaN, have been assessed from 25 K to 550 K. In situ SiN cap layer has been demonstrated to improve the device performance since HEMTs with this cap layer have exhibited the highest drain current and transconductance values, the lowest on-resistance, as well as the best off-state characteristics. Moreover, the evaluation of thermal stress impact on the device performance has confirmed the robustness of devices with in situ cap. Secondly, the high temperature performance of InAlN/GaN HEMTs with different layouts and geometries have been assessed. The devices under study have exhibited an almost linear reduction of the main DC parameters operating in a temperature range from room temperature to 225°C. This was mainly due to the thermal dependence of the electron mobility, and secondly to the drift velocity decrease with temperature. Moreover, HEMTs with large gate length values have exhibited a great reduction of the device performance. This was attributed to the greater decrease of the drift velocity for low electric fields. Similarly, the increase of the gate-to-drain distance led to a greater reduction of drain current and transconductance values. Therefore, this thermal performance degradation has been found to be dependent on both the gate length and the gate-to-drain distance. It was observed that the very high power density in the active region of these transistors leads to Joule self-heating, resulting in an increase of the device temperature, which can degrade the device performance and reliability. A simple electrical method have been developed during this work to determine the channel temperature. Furthermore, the application of this technique together with the performance of electro-thermal simulations have enabled the evaluation of different aspects related to the self-heating. For instance, the influence of the substrate have been confirmed by the study of devices grown on Si, SiC, and Sapphire. HEMTs grown on SiC substrate have been confirmed to exhibit the lowest self-heating effects thanks to its highest thermal conductivity. In addition to this, the distribution of the generated heat in the channel has been demonstrated to be dependent on the gate-to-drain distance. Besides the substrate and the geometry of the device, the ambient temperature has also been found to be relevant for the self-heating effects, mainly due to the temperature-dependent thermal conductivity of the layers and the substrate. Trapping effects have been evaluated by means of pulsed measurements in AlGaN and InAIN barrier devices. AlGaN barrier HEMTs have exhibited a de crease in drain current and transconductance without measurable threshold voltage change, suggesting the location of the traps in the gate-to-drain access region. On the contrary, InAIN barrier devices have showed a drain current associated with a positive shift of threshold voltage, which indicated that the traps were possibly located under the gate region. Moreover, a significant increase of the ON-resistance as well as a transconductance reduction were observed, revealing the presence of traps on the gate-drain access region. On the other hand, the assessment of devices with different geometries have demonstrated that the trapping effects are more noticeable in devices with either short gate length or the gate-to-drain distance. This can be attributed to the fact that the length and the trap density of the virtual gate are independent on the device geometry. Finally, it can be deduced that besides the final application requirements, the influence of the device geometry on the performance at high temperature, on the self-heating, as well as on the trapping effects need to be taken into account during the device design stage to achieve the optimal layout.

Calculation of dielectrophoretic potential generated under illumination patterns on x- and z-cut LiNbO3 : application to photovoltaic particle trapping

The dielectrophoretic potential generated near the surface of a z-cut LiNbO3 by photovoltaic charge transport has been calculated for first time. The procedure and results are compared with the ones corresponding to x-cut. Diferences in the position, sharpness and time evolution are reported, and their implication on particle trapping are discussed.

Echo-delay resolution in sonar images of the big brown bat, Eptesicus fuscus

Echolocating big brown bats (Eptesicus fuscus) broadcast ultrasonic frequency-modulated (FM) biosonar sounds (20–100 kHz frequencies; 10–50 μs periods) and perceive target range from echo delay. Knowing the acuity for delay resolution is essential to understand how bats process echoes because they perceive target shape and texture from the delay separation of multiple reflections. Bats can separately perceive the delays of two concurrent electronically generated echoes arriving as little as 2 μs apart, thus resolving reflecting points as close together as 0.3 mm in range (two-point threshold). This two-point resolution is roughly five times smaller than the shortest periods in the bat’s sounds. Because the bat’s broadcasts are 2,000–4,500 μs long, the echoes themselves overlap and interfere with each other, to merge together into a single sound whose spectrum is shaped by their mutual interference depending on the size of the time separation. To separately perceive the delays of overlapping echoes, the bat has to recover information about their very small delay separation that was transferred into the spectrum when the two echoes interfered with each other, thus explicitly reconstructing the range profile of targets from the echo spectrum. However, the bat’s 2-μs resolution limit is so short that the available spectral cues are extremely limited. Resolution of delay seems overly sharp just for interception of flying insects, which suggests that the bat’s biosonar images are of higher quality to suit a wider variety of orientation tasks, and that biosonar echo processing is correspondingly more sophisticated than has been suspected.

Experience-dependent corticofugal adjustment of midbrain frequency map in bat auditory system

Recent studies of corticofugal modulation of auditory information processing indicate that cortical neurons mediate both a highly focused positive feedback to subcortical neurons “matched” in tuning to a particular acoustic parameter and a widespread lateral inhibition to “unmatched” subcortical neurons. This cortical function for the adjustment and improvement of subcortical information processing is called egocentric selection. Egocentric selection enhances the neural representation of frequently occurring signals in the central auditory system. For our present studies performed with the big brown bat (Eptesicus fuscus), we hypothesized that egocentric selection adjusts the frequency map of the inferior colliculus (IC) according to auditory experience based on associative learning. To test this hypothesis, we delivered acoustic stimuli paired with electric leg stimulation to the bat, because such paired stimuli allowed the animal to learn that the acoustic stimulus was behaviorally important and to make behavioral and neural adjustments based on the acquired importance of the acoustic stimulus. We found that acoustic stimulation alone evokes a change in the frequency map of the IC; that this change in the IC becomes greater when the acoustic stimulation is made behaviorally relevant by pairing it with electrical stimulation; that the collicular change is mediated by the corticofugal system; and that the IC itself can sustain the change evoked by the corticofugal system for some time. Our data support the hypothesis.

Optical trapping and manipulation of neutral particles using lasers

The techniques of optical trapping and manipulation of neutral particles by lasers provide unique means to control the dynamics of small particles. These new experimental methods have played a revolutionary role in areas of the physical and biological sciences. This paper reviews the early developments in the field leading to the demonstration of cooling and trapping of neutral atoms in atomic physics and to the first use of optical tweezers traps in biology. Some further major achievements of these rapidly developing methods also are considered.

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[a]- pyrene diol epoxide adducts at the 6-amino group of adenine

DNA topoisomerase I (top1) is the target of potent anticancer agents, including camptothecins and DNA intercalators, which reversibly stabilize (trap) top1 catalytic intermediates (cleavage complexes). The aim of the present study was to define the structural relationship between the site(s) of covalently bound intercalating agents, whose solution conformations in DNA are known, and the site(s) of top1 cleavage. Two diastereomeric pairs of oligonucleotide 22-mers, derived from a sequence used to determine the crystal structure of top1–DNA complexes, were synthesized. One pair contained either a trans-opened 10R- or 10S-benzo[a]pyrene 7,8-diol 9,10-epoxide adduct at the N6-amino group of a central 2′-deoxyadenosine residue in the scissile strand, and the other pair contained the same two adducts in the nonscissile strand. These adducts were derived from the (+)-(7R,8S,9S,10R)- and (−)-(7S,8R,9R,10S)-7,8-diol 9,10-epoxides in which the benzylic 7-hydroxyl group and the epoxide oxygen are trans. On the basis of analogy with known solution conformations of duplex oligonucleotides containing these adducts, we conclude that top1 cleavage complexes are trapped when the hydrocarbon adduct is intercalated between the base pairs flanking a preexisting top1 cleavage site, or between the base pairs immediately downstream (3′ relative to the scissile strand) from this site. We propose a model with the +1 base rotated out of the duplex, and in which the intercalated adduct prevents religation of the corresponding nucleotide at the 5′ end of the cleaved DNA. These results suggest mechanisms whereby intercalating agents interfere with the normal function of human top1.

Syntax processing by auditory cortical neurons in the FM–FM area of the mustached bat Pteronotus parnellii

Syntax denotes a rule system that allows one to predict the sequencing of communication signals. Despite its significance for both human speech processing and animal acoustic communication, the representation of syntactic structure in the mammalian brain has not been studied electrophysiologically at the single-unit level. In the search for a neuronal correlate for syntax, we used playback of natural and temporally destructured complex species-specific communication calls—so-called composites—while recording extracellularly from neurons in a physiologically well defined area (the FM–FM area) of the mustached bat’s auditory cortex. Even though this area is known to be involved in the processing of target distance information for echolocation, we found that units in the FM–FM area were highly responsive to composites. The finding that neuronal responses were strongly affected by manipulation in the time domain of the natural composite structure lends support to the hypothesis that syntax processing in mammals occurs at least at the level of the nonprimary auditory cortex.

Trapping the transition state of an ATP-binding cassette transporter: Evidence for a concerted mechanism of maltose transport

High-affinity uptake into bacterial cells is mediated by a large class of periplasmic binding protein-dependent transport systems, members of the ATP-binding cassette superfamily. In the maltose transport system of Escherichia coli, the periplasmic maltose-binding protein binds its substrate maltose with high affinity and, in addition, stimulates the ATPase activity of the membrane-associated transporter when maltose is present. Vanadate inhibits maltose transport by trapping ADP in one of the two nucleotide-binding sites of the membrane transporter immediately after ATP hydrolysis, consistent with its ability to mimic the transition state of the γ-phosphate of ATP during hydrolysis. Here we report that the maltose-binding protein becomes tightly associated with the membrane transporter in the presence of vanadate and simultaneously loses its high affinity for maltose. These results suggest a general model explaining how ATP hydrolysis is coupled to substrate transport in which a binding protein stimulates the ATPase activity of its cognate transporter by stabilizing the transition state.

Integrated fossil and molecular data reconstruct bat echolocation

Molecular and morphological data have important roles in illuminating evolutionary history. DNA data often yield well resolved phylogenies for living taxa, but are generally unattainable for fossils. A distinct advantage of morphology is that some types of morphological data may be collected for extinct and extant taxa. Fossils provide a unique window on evolutionary history and may preserve combinations of primitive and derived characters that are not found in extant taxa. Given their unique character complexes, fossils are critical in documenting sequences of character transformation over geologic time and may elucidate otherwise ambiguous patterns of evolution that are not revealed by molecular data alone. Here, we employ a methodological approach that allows for the integration of molecular and paleontological data in deciphering one of the most innovative features in the evolutionary history of mammals—laryngeal echolocation in bats. Molecular data alone, including an expanded data set that includes new sequences for the A2AB gene, suggest that microbats are paraphyletic but do not resolve whether laryngeal echolocation evolved independently in different microbat lineages or evolved in the common ancestor of bats and was subsequently lost in megabats. When scaffolds from molecular phylogenies are incorporated into parsimony analyses of morphological characters, including morphological characters for the Eocene taxa Icaronycteris, Archaeonycteris, Hassianycteris, and Palaeochiropteryx, the resulting trees suggest that laryngeal echolocation evolved in the common ancestor of fossil and extant bats and was subsequently lost in megabats. Molecular dating suggests that crown-group bats last shared a common ancestor 52 to 54 million years ago.

Identification of GIT1/Cat-1 as a substrate molecule of protein tyrosine phosphatase ζ/β by the yeast substrate-trapping system

We used a genetic method, the yeast substrate-trapping system, to identify substrates for protein tyrosine phosphatases ζ (PTPζ/RPTPβ). This method is based on the yeast two-hybrid system, with two essential modifications: conditional expression of protein tyrosine kinase v-src (active src) to tyrosine-phosphorylate the prey proteins and screening by using a substrate-trap mutant of PTPζ (PTPζ-D1902A) as bait. By using this system, several substrate candidates for PTPζ were isolated. Among them, GIT1/Cat-1 (G protein-coupled receptor kinase-interactor 1/Cool-associated, tyrosine-phosphorylated 1) was examined further. GIT1/Cat-1 bound to PTPζ-D1902A dependent on the substrate tyrosine phosphorylation. Tyrosine-phosphorylated GIT1/Cat-1 was dephosphorylated by PTPζ in vitro. Immunoprecipitation experiments indicated that PTPζ-D1902A and GIT1/Cat-1 form a stable complex also in mammalian cells. Immunohistochemical analyses revealed that PTPζ and GIT1/Cat-1 were colocalized in the processes of pyramidal cells in the hippocampus and neocortex in rat brain. Subcellular colocalization was further verified in the growth cones of mossy fibers from pontine explants and in the ruffling membranes and processes of B103 neuroblastoma cells. Moreover, pleiotrophin, a ligand for PTPζ, increased tyrosine phosphorylation of GIT1/Cat-1 in B103 cells. All these results indicate that GIT1/Cat-1 is a substrate molecule of PTPζ.

Conformational trapping in a membrane environment: a regulatory mechanism for protein activity?

Functional regulation of proteins is central to living organisms. Here it is shown that a nonfunctional conformational state of a polypeptide can be kinetically trapped in a lipid bilayer environment. This state is a metastable structure that is stable for weeks just above the phase transition temperature of the lipid. When the samples are incubated for several days at 68 degrees C, 50% of the trapped conformation converts to the minimum-energy functional state. This result suggests the possibility that another mechanism for functional regulation of protein activity may be available for membrane proteins: that cells may insert proteins into membranes in inactive states pending the biological demand for protein function.