Global analysis of mRNA half-lives and de novo transcription in a dinoflagellate, Karenia brevis

Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the roles of differential mRNA stability and de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability and de novo transcription by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed to pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 144 h, with a median of 33 hours. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes. One such family of proteins involved in post-transcriptional regulation in chloroplasts and mitochondria, the pentatricopeptide repeat (PPR) proteins, had dramatically shorter half-lives when compared to the arrayed transcriptome. As transcript abundances for PPR proteins were previously observed to rapidly increase in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of increases in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.

Small RNAs have several important biological functions. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate mRNA stability and translation, and siRNAs cause post-transcriptional gene silencing of transposons, viruses and transgenes and are important in both the establishment and maintenance of cytosine DNA methylation. Here, we study the role of the four Arabidopsis thaliana DICER-LIKE genes (DCL1-DCL4) in these processes. Sequencing of small RNAs from a dcl2 dcl3 dcl4 triple mutant showed markedly reduced tasiRNA and siRNA production and indicated that DCL1, in addition to its role as the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats. DCL2, DCL3 and DCL4 showed functional redundancy in siRNA and tasiRNA production and in the establishment and maintenance of DNA methylation. Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.

Impedance control balances stability with metabolically costly muscle activation.

Humans are able to stabilize their movements in environments with unstable dynamics by selectively modifying arm impedance independently of force and torque. We further investigated adaptation to unstable dynamics to determine whether the CNS maintains a constant overall level of stability as the instability of the environmental dynamics is varied. Subjects performed reaching movements in unstable force fields of varying strength, generated by a robotic manipulator. Although the force fields disrupted the initial movements, subjects were able to adapt to the novel dynamics and learned to produce straight trajectories. After adaptation, the endpoint stiffness of the arm was measured at the midpoint of the movement. The stiffness had been selectively modified in the direction of the instability. The stiffness in the stable direction was relatively unchanged from that measured during movements in a null force field prior to exposure to the unstable force field. This impedance modification was achieved without changes in force and torque. The overall stiffness of the arm and environment in the direction of instability was adapted to the force field strength such that it remained equivalent to that of the null force field. This suggests that the CNS attempts both to maintain a minimum level of stability and minimize energy expenditure.

The water stability of shrimp diets with various polysaccharides as a binding agent

The water stability of shrimp (Penaeus monodon) diets with various polysaccharides as binding agents were tested without steaming. The diet with alginate showed the best water stability and did not completely disintegrate in 24 hours. However, the use of alginate is dependent on cost and availability, so alternate choices may be a combination of sago palm starch and wheat flour or glutinous rice flour.

Breathers and thermal relaxation as a temporal process: A possible way to detect breathers in experimental situations

Breather stability and longevity in thermally relaxing nonlinear arrays is investigated under the scrutiny of the analysis and tools employed for time series and state reconstruction of a dynamical system. We briefly review the methods used in the analysis and characterize a breather in terms of the results obtained with such methods. Our present work focuses on spontaneously appearing breathers in thermal Fermi-Pasta-Ulam arrays but we believe that the conclusions are general enough to describe many other related situations; the particular case described in detail is presented as another example of systems where three incommensurable frequencies dominate their chaotic dynamics (reminiscent of the Ruelle-Takens scenario for the appearance of chaotic behavior in nonlinear systems). This characterization may also be of great help for the discovery of breathers in experimental situations where the temporal evolution of a local variable (like the site energy) is the only available/measured data. © 2005 American Institute of Physics.

Structural and functional properties of the hemoglobin components from the Caspian Sea Acipenser persicus and Acipenser stellatus

Hemoglobin (Hb) variability is a commonly used index of phylogenetic differentiation and molecular adaptation in fish. In the current study, the structural and functional characteristics of Hbs from two Sturgeon species of the Southern Caspian Sea Basin were investigated. After extraction and separation of hemoglobin from whole blood , the polyacrylamide gel electrophoresis (SDSPAGE), native-PAGE and isoelectric focusing (IEF) were used to confirm Hb variability in these fishes. Ion-exchange on CM-cellulose chromatography was used for purification of the dominant Hbs from these fishes. The accuracy of the methods was confirmed by IEF and SDS-PAGE. Spectral studies using fluorescence spectrophotometery, circular dichroism spectropolarimetry (CD) analysis and UV–vis spectrophotometery. Oxygen affinities of these Hbs were compared using Hb-oxygen dissociation curves. Also, the dominant Hbs from these blood fishes were utilized for further experiments. The behavior of Hbs during the denaturation process by n-dodecyl trimethylammonium bromide (DTAB) is investigated by UV–vis spectrophotometer and circular dichroism spectropolarimetry. The thermal denaturation properties of the Hbs wereinvestigated by differential scanning calorimetry (DSC) and Hbs aggregation performed chemically in the presence of dithiotreitol (DTT) by UV–vis spectrophotometer and chemometric study. The results demonstrate a significant relationship between stability of fish hemoglobins and the ability of fish for entering to deeper depths. The UV–Vis absorption spectra identified species of hemoglobin and showed the concentration of oxyHb and metHb decreases and deoxyHb increases upon interaction with DTAB. Besides the UV–vis spectrophotometry, the interaction of DTAB with hemoglobins has been studied using circular dichroism spectropolarimetry analysis. This experiment was utilized to measure the unfolding mechanism and compared alpha-helix secondary structure under different conditions for Hbs. The results reveal that the Acipenser stellatus Hb in comparison with Acipenser persicus Hb has more stability and more structural compactness. Besides, the results confirm the hypothesis that there is a meaningful relation between average habitat depth, partial oxygen pressure, oxygen affinity, structural compactness of Hb, and its stability.

Enhancing the stability of subsonic compressors using casing grooves

Casing grooves are known to increase the stable operating range of axial compressors. The mechanism by which this stability enhancement occurs is poorly understood. This paper develops a better understanding of the behavior of casing grooves through analysis of new data. An experimental parametric study is used to demonstrate the effect of varying the axial location of a single casing groove on the stability and efficiency of the compressor. The effect that the groove has on rotor outflow blockage, blade loading, and the near-casing flow field is then investigated using both experimental and computational methods. It is found that the interaction of the groove with the flow field is different when the groove is positioned forward or aft relative to the blade. The interaction of the groove with the flow in the tip region in both of these positions is presented in detail. Finally, the implications of these findings for the design of casing grooves of different depths are discussed. © 2011 American Society of Mechanical Engineers.

Enhancing the stability of subsonic compressors using casing grooves

Casing grooves are known to increase the stable operating range of axial compressors. The mechanism by which this stability enhancement occurs is poorly understood. This paper develops a better understanding of the behaviour of grooves through analysis of new data. An experimental parametric study is used to demonstrate the effect of varying the axial location of a single casing groove on the stability and efficiency of the compressor. The effect that the groove has on rotor outflow blockage, blade loading and the near-casing flow field is then studied using both experimental and computational methods. It is found that the interaction of the groove with the flow field is different when the groove is positioned forward or aft relative to the blade. The interaction of the groove with the flow in the tip region in both of these positions is presented in detail. Finally, the implications of these findings for the design of casing grooves of different depths are discussed. Copyright © 2009 Rolls-Royce plc.

A critical review of Glucose biosensors based on Carbon nanomaterials: Carbon nanotubes and graphene

There has been an explosion of research into the physical and chemical properties of carbon-based nanomaterials, since the discovery of carbon nanotubes (CNTs) by Iijima in 1991. Carbon nanomaterials offer unique advantages in several areas, like high surface-volume ratio, high electrical conductivity, chemical stability and strong mechanical strength, and are thus frequently being incorporated into sensing elements. Carbon nanomaterial-based sensors generally have higher sensitivities and a lower detection limit than conventional ones. In this review, a brief history of glucose biosensors is firstly presented. The carbon nanotube and grapheme-based biosensors, are introduced in Sections 3 and 4, respectively, which cover synthesis methods, up-to-date sensing approaches and nonenzymatic hybrid sensors. Finally, we briefly outline the current status and future direction for carbon nanomaterials to be used in the sensing area. © 2012 by the authors; licensee MDPI, Basel, Switzerland.

The interaction of elasticity and rocking in flexible structures allowed to uplift

Numerous structures uplift under the influence of strong ground motion. Although many researchers have investigated the effects of base uplift on very stiff (ideally rigid) structures, the rocking response of flexible structures has received less attention. Related practical analysis methods treat these structures with simplified 'equivalent' oscillators without directly addressing the interaction between elasticity and rocking. This paper addresses the fundamental dynamics of flexible rocking structures. The nonlinear equations of motion, derived using a Lagrangian formulation for large rotations, are presented for an idealized structural model. Particular attention is devoted to the transition between successive phases; a physically consistent classical impact framework is utilized alongside an energy approach. The fundamental dynamic properties of the flexible rocking system are compared with those of similar linear elastic oscillators and rigid rocking structures, revealing the distinct characteristics of flexible rocking structures. In particular, parametric analysis is performed to quantify the effect of elasticity on uplift, overturning instability, and harmonic response, from which an uplifted resonance emerges. The contribution of stability and strength to the collapse of flexible rocking structures is discussed. © 2012 John Wiley & Sons, Ltd.

Gasoline fuelled partially premixed compression ignition in a light duty multi cylinder engine: A study of low load and low speed operation

The objective of this study was to examine the operating characteristics of a light duty multi cylinder compression ignition engine with regular gasoline fuel at low engine speed and load. The effects of fuel stratification by means of multiple injections as well as the sensitivity of auto-ignition and burn rate to intake pressure and temperature are presented. The measurements used in this study included gaseous emissions, filter smoke opacity and in-cylinder indicated information. It was found that stable, low emission operation was possible with raised intake manifold pressure and temperature, and that fuel stratification can lead to an increase in stability and a reduced reliance on increased temperature and pressure. It was also found that the auto-ignition delay sensitivity of gasoline to intake temperature and pressure was low within the operating window considered in this study. Nevertheless, the requirement for an increase of pressure, temperature and stratification in order to achieve auto-ignition time scales small enough for combustion in the engine was clear, using pump gasoline. Copyright © 2009 SAE International.

Contraction and observer design on cones

We consider the problem of positive observer design for positive systems defined on solid cones in Banach spaces. The design is based on the Hilbert metric and convergence properties are analyzed in the light of the Birkhoff theorem. Two main applications are discussed: positive observers for systems defined in the positive orthant, and positive observers on the cone of positive semi-definite matrices with a view on quantum systems. © 2011 IEEE.

Rhythmic feedback control of a blind planar juggler

The paper considers the feedback stabilization of periodic orbits in a planar juggler. The juggler is "blind," i.e, he has no other sensing capabilities than the detection of impact times. The robustness analysis of the proposed control suggests that the arms acceleration at impact is a crucial design parameter even though it plays no role in the stability analysis. Analytical results and convergence proofs are provided for a simplified model of the juggler. The control law is then adapted to a more accurate model and validated in an experimental setup. © 2007 IEEE.

Stabilization of planar collective motion: All-to-all communication

This paper proposes a design methodology to stabilize isolated relative equilibria in a model of all-to-all coupled identical particles moving in the plane at unit speed. Isolated relative equilibria correspond to either parallel motion of all particles with fixed relative spacing or to circular motion of all particles with fixed relative phases. The stabilizing feedbacks derive from Lyapunov functions that prove exponential stability and suggest almost global convergence properties. The results of the paper provide a low-order parametric family of stabilizable collectives that offer a set of primitives for the design of higher-level tasks at the group level. © 2007 IEEE.

Advanced carbon nanotubes and carbon nanotube fibers for biosensing applications

Since the discovery of Carbon Nanotubes (CNTs) by Iijima in 1991[1, 2], there has been an explosion of research into the physical and chemical properties of this novel material. CNT based biosensors can play an important role in amperometric, immunosensor and nucleic-acid sensing devices, e.g. for detection of life threatening biological agents in time of war or in terrorist attacks, saving life and money for the NHS. CNTs offer unique advantages in several areas, like high surfacevolume ratio, high electrical conductivity, chemical stability and strong mechanical strength, and CNT based sensors generally have higher sensitivities and lower detection limit than conventional ones. In this review, recent advances in biosensors utilising carbon nanotubes and carbon nanotube fibres will be discussed. The synthesis methods, nanostructure approaches and current developments in biosensors using CNTs will be introduced in the first part. In the second part, the synthesis methods and up-to-date progress in CNT fibre biosensors will be reviewed. Finally, we briefly outline some exciting applications for CNT and CNT fibres which are being targeted. By harnessing the continual advancements in micro and nano- technology, the functionality and capability of CNT-based biosensors will be enhanced, thus expanding and enriching the possible applications that can be delivered by these devices. © 2012 Bentham Science Publishers. All rights reserved.