Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model

<p>Abstract</p> <p>Background</p> <p>Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to evaluate dynamical changes in data are therefore important to filter experimental noise and to enable extraction of unexpected, biologically important information.</p> <p>Results</p> <p>Here we demonstrate the effectiveness of a Markov model, named the Linear Dynamical System, to simulate the dynamics of a transcript or metabolite time series, and propose a probabilistic index that enables detection of time-sensitive changes. This method was applied to time series datasets from <it>Bacillus subtilis </it>and <it>Arabidopsis thaliana </it>grown under stress conditions; in the former, only gene expression was studied, whereas in the latter, both gene expression and metabolite accumulation. Our method not only identified well-known changes in gene expression and metabolite accumulation, but also detected novel changes that are likely to be responsible for each stress response condition.</p> <p>Conclusion</p> <p>This general approach can be applied to any time-series data profile from which one wishes to identify elements responsible for state transitions, such as rapid environmental adaptation by an organism.</p

The arginine transporter Can1 negatively regulates biofilm formation in yeasts

The arginine transporter Can1 is a multifunctional protein of the conventional yeast Saccharomyces cerevisiae. Apart from facilitating arginine uptake, Can1 plays a pivotal role in regulating proline metabolism and maintaining cellular redox balance. Here, we report a novel function of Can1 in the control of yeast biofilm formation. First, the S. cerevisiae CAN1 gene knockout strain displayed a significant growth delay compared to the wild-type strain. Our genetic screening revealed that the slow growth of the CAN1 knockout strain is rescued by a functional deficiency of the FLO8 gene, which encodes the master transcription factor associated with biofilm formation, indicating that Can1 is involved in biofilm formation. Intriguingly, the CAN1 knockout strain promoted the Flo11-dependent aggregation, leading to higher biofilm formation. Furthermore, the CAN1 knockout strain of the pathogenic yeast Candida glabrata exhibited slower growth and higher biofilm formation, similar to S. cerevisiae. More importantly, the C. glabrata CAN1 gene knockout strain showed severe toxicity to macrophage-like cells and nematodes. The present results could help to elucidate both the molecular mechanism underlying yeast biofilm formation and the role it plays. Future investigations may offer insights that contribute to development of antibiofilm agents

Changes in intentional binding effect during a novel perceptual-motor task

Perceptual-motor learning describes the process of improving the smoothness and accuracy of movements. Intentional binding (IB) is a phenomenon whereby the length of time between performing a voluntary action and the production of a sensory outcome during perceptual-motor control is perceived as being shorter than the reality. How IB may change over the course of perceptual-motor learning, however, has not been explicitly investigated. Here, we developed a set of IB tasks during perceptual-motor learning. Participants were instructed to stop a circular moving object by key press when it reached the center of a target circle on the display screen. The distance between the center of the target circle and the center of the moving object was measured, and the error was used to approximate the perceptual-motor performance index. This task also included an additional exercise that was unrelated to the perceptual-motor task: after pressing the key, a sound was presented after a randomly chosen delay of 200, 500, or 700 ms and the participant had to estimate the delay interval. The difference between the estimated and actual delay was used as the IB value. A cluster analysis was then performed using the error values from the first and last task to group the participants based on their perceptual-motor performance. Participants showing a very small change in error value, and thus demonstrating a small effect of perceptual-motor learning, were classified into cluster 1. Those who exhibited a large decrease in error value from the first to the last set, and thus demonstrated a strong improvement in perceptual-motor performance, were classified into cluster 2. Those who exhibited perceptual-motor learning also showed improvements in the IB value. Our data suggest that IB is elevated when perceptual-motor learning occurs

Kinematic Structure of Molecular Gas around High-mass Star YSO, Papillon Nebula, in N159 East in the Large Magellanic Cloud

We present the ALMA Band 3 and Band 6 results of 12CO(2-1), 13$CO(2-1), H30alpha recombination line, free-free emission around 98 GHz, and the dust thermal emission around 230 GHz toward the N159 East Giant Molecular Cloud (N159E) in the Large Magellanic Cloud (LMC). LMC is the nearest active high-mass star forming face-on galaxy at a distance of 50 kpc and is the best target for studing high-mass star formation. ALMA observations show that N159E is the complex of filamentary clouds with the width and length of ~1 pc and 5 pc - 10 pc, respectively. The total molecular mass is 0.92 x 10^5 Msun from the 13CO(2-1) intensity. N159E harbors the well-known Papillon Nebula, a compact high-excitation HII region. We found that a YSO associated with the Papillon Nebula has the mass of 35 Msun and is located at the intersection of three filamentary clouds. It indicates that the formation of the high-mass YSO was induced by the collision of filamentary clouds. Fukui et al. 2015 reported a similar kinematic structure toward a YSO in the N159 West region which is another YSO that has the mass larger than 35 Msun in these two regions. This suggests that the collision of filamentary clouds is a primary mechanism of high-mass star formation. We found a small molecular hole around the YSO in Papillon Nebula with sub-pc scale. It is filled by free-free and H30alpha emission. Temperature of the molecular gas around the hole reaches ~ 80 K. It indicates that this YSO has just started the distruction of parental molecular cloud.Comment: 28 pages, 7 figures. Submitted to Ap

抗ヒスタミン薬ケトチフェンの連日投与による体内時計位相調節

富山大学・富生命博甲第90号・AHMAD ALSAWAF・2017/03/23Sleep and Biological Rhythms,2016.1,14(1),117-120,doi: 10.1007/s41105-015-0021-yに掲載。富山大学201

Incidence of endophthalmitis after intravitreal injection of an anti-VEGF agent with or without topical antibiotics

Intravitreal injection (IVI) of anti-vascular endothelial growth factor (VEGF) is the standard treatment modality in various types of retinal diseases. However, endophthalmitis remains the most serious complication. Despite the lack of evidence that antibiotics prevent endophthalmitis, topical antibiotics are still used routinely in Japan. We conducted a retrospective multicenter study by analyzing records from patients who underwent IVI of anti-VEGF agents with or without antibiotic treatment. In the analysis of a total of 147,440 eyes, the incidence of endophthalmitis was 0.007%: 0.005% with no use of antibiotics, 0.009% with antibiotic pretreatment, 0.012% with posttreatment, and 0.005% with pre- and posttreatment. There was no statistically significant difference among the four groups (chi-square test, p = 0.57). Most facilities used masks, sterilized gloves, and drapes. Nine of the 10 eyes that developed endophthalmitis received topical antibiotics, and all infected eyes underwent IVI with aflibercept, not the prefilled syringe delivery system. In four patients who received multiple IVI, the detection of causative bacteria revealed resistance to used antibiotics. Data from this large population, treated with or without antibiotics, suggests that antibiotic prophylaxis does not reduce the rate of endophthalmitis after IVI

High-mass star formation triggered by collision between CO filaments in N159 West in the Large Magellanic Cloud

We have carried out 13CO(J=2-1) observations of the active star-forming region N159 West in the LMC with ALMA. We have found that the CO distribution at a sub-pc scale is highly elongated with a small width. These elongated clouds called "filaments" show straight or curved distributions with a typical width of 0.5-1.0pc and a length of 5-10pc. All the known infrared YSOs are located toward the filaments. We have found broad CO wings of two molecular outflows toward young high-mass stars in N159W-N and N159W-S, whose dynamical timescale is ~10^4 yrs. This is the first discovery of protostellar outflow in external galaxies. For N159W-S which is located toward an intersection of two filaments we set up a hypothesis that the two filaments collided with each other ~10^5 yrs ago and triggered formation of the high-mass star having ~37 Mo. The colliding clouds show significant enhancement in linewidth in the intersection, suggesting excitation of turbulence in the shocked interface layer between them as is consistent with the magneto-hydro-dynamical numerical simulations (Inoue & Fukui 2013). This turbulence increases the mass accretion rate to ~6x10^-4 Mo yr^-1, which is required to overcome the stellar feedback to form the high-mass star.Comment: 20 pages, 3 figures, accepted for publication in ApJ

Philosophy and Meaning in Life Vol.4

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Brain activity associated with the illusion of motion evoked by different vibration stimulation devices: an fNIRS study

[Purpose] A number of different stimulation devices are used in basic and clinical research studies, and their frequencies of use vary. However, whether or not they are equally effective has not been investigated. The purpose of the present study was to investigate neural activity in the brain during the illusion of motion evoked by stimulating the tendons of the wrist extensor muscles using various vibration devices. [Subjects] Twelve righthanded university students with no history of nervous system disorder or orthopedic disease participated in the study. [Methods] The wrist extensor tendon was stimulated using 3 different devices: 1) a vibration stimulation device (SL-0105 LP; Asahi Seisakusho Co., Ltd., Saitama, Japan), frequency 80 Hz; 2) a handy massager (YCM-20; Yamazen Corporation, Osaka, Japan), frequency 70 Hz; and 3) a handy massager (Thrive MD-01; Thrive Co., Ltd., Osaka, Japan), frequency 91.7 Hz. Brain activity was recorded during stimulation by using functional near-infrared spectroscopy. [Results] Increased neural activity was observed in both the premotor cortices and the parietal region in both hemispheres in all 3 cases. The level and localization of neural activity was comparable for all 3 stimulation devices used. [Conclusion] This suggests that subjects experience the illusion of motion while the tendon is being stimulated using any vibration device