The pir gene of Erwinia chrysanthemi EC16 regulates hyperinduction of pectate lyase virulence genes in response to plant signals

The plant pathogenic bacterium Erwinia chrysanthemi secretes pectate lyase proteins that are important virulence factors attacking the cell walls of plant hosts. Bacterial production of these enzymes is induced by the substrate polypectate-Na (NaPP) and further stimulated by the presence of plant extracts. The bacterial regulator responsible for induction by plant extracts was identified and purified by using a DNA-binding assay with the promoter region of pelE that encodes a major pectate lyase. A novel bacterial protein, called Pir, was isolated that produced a specific gel shift of the pelE promoter DNA, and the corresponding pir gene was cloned and sequenced. The Pir protein contains 272 amino acids with a molecular mass of 30 kDa and appears to function as a dimer. A homology search indicates that Pir belongs to the IclR family of transcriptional regulators. Pir bound to a 35-bp DNA sequence in the promoter region of pelE. This site overlaps that of a previously described negative regulator, KdgR. Gel shift experiments showed that the binding of either Pir or KdgR interfered with binding of the other protein.

Attenuated T2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution

Fast transverse relaxation of 1H, 15N, and 13C by dipole-dipole coupling (DD) and chemical shift anisotropy (CSA) modulated by rotational molecular motions has a dominant impact on the size limit for biomacromolecular structures that can be studied by NMR spectroscopy in solution. Transverse relaxation-optimized spectroscopy (TROSY) is an approach for suppression of transverse relaxation in multidimensional NMR experiments, which is based on constructive use of interference between DD coupling and CSA. For example, a TROSY-type two-dimensional 1H,15N-correlation experiment with a uniformly 15N-labeled protein in a DNA complex of molecular mass 17 kDa at a 1H frequency of 750 MHz showed that 15N relaxation during 15N chemical shift evolution and 1HN relaxation during signal acquisition both are significantly reduced by mutual compensation of the DD and CSA interactions. The reduction of the linewidths when compared with a conventional two-dimensional 1H,15N-correlation experiment was 60% and 40%, respectively, and the residual linewidths were 5 Hz for 15N and 15 Hz for 1HN at 4°C. Because the ratio of the DD and CSA relaxation rates is nearly independent of the molecular size, a similar percentagewise reduction of the overall transverse relaxation rates is expected for larger proteins. For a 15N-labeled protein of 150 kDa at 750 MHz and 20°C one predicts residual linewidths of 10 Hz for 15N and 45 Hz for 1HN, and for the corresponding uniformly 15N,2H-labeled protein the residual linewidths are predicted to be smaller than 5 Hz and 15 Hz, respectively. The TROSY principle should benefit a variety of multidimensional solution NMR experiments, especially with future use of yet somewhat higher polarizing magnetic fields than are presently available, and thus largely eliminate one of the key factors that limit work with larger molecules.

Circadian rhythms in Neurospora crassa: Lipid deficiencies restore robust rhythmicity to null frequency and white-collar mutants

The conidiation rhythm in the fungus Neurospora crassa is a model system for investigating the genetics of circadian clocks. Null mutants at the frq (frequency) locus (frq9 and frq10) make no functional frq gene products and are arrhythmic under standard conditions. The white-collar strains (wc-1 and wc-2) are insensitive to most effects of light, and are also arrhythmic. All three genes are proposed to be central components of the circadian oscillator. We have been investigating two mutants, cel (chain-elongation) and chol-1 (choline-requirer), which are defective in lipid synthesis and affect the period and temperature compensation of the rhythm. We have constructed the double mutant strains chol-1 frq9, chol-1 frq10, chol-1 wc-1, chol-1 wc-2, cel frq9, cel frq10, and cel wc-2. We find that these double mutant strains are robustly rhythmic when assayed under lipid-deficient conditions, indicating that free-running rhythmicity does not require the frq, wc-1, or wc-2 gene products. The rhythms in the double mutant strains are similar to the cel and chol-1 parents, except that they are less sensitive to light. This suggests that the frq, wc-1, and wc-2 gene products may be components of a pathway that normally supplies input to a core oscillator to transduce light signals and sustain rhythmicity. This pathway can be bypassed when lipid metabolism is altered.

Plasticity of the cochleotopic (frequency) map in specialized and nonspecialized auditory cortices

Auditory conditioning (associative learning) causes reorganization of the cochleotopic (frequency) maps of the primary auditory cortex (AI) and the inferior colliculus. Focal electric stimulation of the AI also evokes basically the same cortical and collicular reorganization as that caused by conditioning. Therefore, part of the neural mechanism for the plasticity of the central auditory system caused by conditioning can be explored by focal electric stimulation of the AI. The reorganization is due to shifts in best frequencies (BFs) together with shifts in frequency-tuning curves of single neurons. In the AI of the Mongolian gerbil (Meriones unguiculatus) and the posterior division of the AI of the mustached bat (Pteronotus parnellii), focal electric stimulation evokes BF shifts of cortical auditory neurons located within a 0.7-mm distance along the frequency axis. The amount and direction of BF shift differ depending on the relationship in BF between stimulated and recorded neurons, and between the gerbil and mustached bat. Comparison in BF shift between different mammalian species and between different cortical areas of a single species indicates that BF shift toward the BF of electrically stimulated cortical neurons (centripetal BF shift) is common in the AI, whereas BF shift away from the BF of electrically stimulated cortical neurons (centrifugal BF shift) is special. Therefore, we propose a hypothesis that reorganization, and accordingly organization, of cortical auditory areas caused by associative learning can be quite different between specialized and nonspecialized (ordinary) areas of the auditory cortex.

Maternal effects and the evolution of aposematic signals

Aposematic signals that warn predators of the noxious qualities of prey gain their greatest selective advantage when predators have already experienced similar signals. Existing theory explains how such signals can spread through selective advantage after they are present at some critical frequency, but is unclear about how warning signals can be selectively advantageous when the trait is initially rare (i.e., when it first arises through mutation) and predators are naive. When aposematism is controlled by a maternal effect gene, the difficulty of initial rarity may be overcome. Unlike a zygotically expressed gene, a maternally expressed aposematism gene will be hidden from selection because it is not phenotypically expressed in the first individual with the mutation. Furthermore, the first individual carrying the new mutation will produce an entire family of aposematic offspring, thereby providing an immediate fitness advantage to this gene.

Shift Work and the United States Female Workforce: The Relationship Between Shift-Work and Ill-Health Effects

The present study was designed to determine the magnitude of the relationship between amount, frequency, and length of shift work completed by female transportation employees and the number, degree, and extent of problems related to physical, menstrual and psychological health including depression. It was hypothesized that workers that are employed in areas such as transportation who are working shift work on a regular basis place themselves at higher risk for developing health or psychosocial related effects. These health related outcomes can have a profound impact on an employee’s job performance, daily functioning, and personal life. The present study sought to understand the potential relationship between working shift work and higher disturbances to the bodies’ natural functioning. The present study has the potential for explaining new ways to decrease the risk factors for those working shift work by contributing to the overall understanding of this multifaceted relationship. This study has many important findings and implications. This study has implications for explaining that the effects of disturbances to the circadian rhythm as a result of certain shift work schedules can result in ill-related health effects. Additionally, this study sought to challenge limitations to current research that has been conducted on the topic as the majority of studies have been performed on men. The overall purpose of the study was to gain a better understanding of the negative effects of shift work on females working within the transportation industry. This study sought to explain the health implications specifically for female workers as fewer studies have been conducted with gender as a main effect in the analysis. The present study suggests that due to the circadian rhythm controlling hormone secretion within the body, disturbances to its natural rhythm can have additional effects on female cycles such as menstruation. Overall, this study offers implications for further research on females working shift work and highlights the continued importance for further exploration into recent developments. These implications have the potential to further our current understanding of the relationship between shift work and ill-health effects, particularly the factors that women face.

Mid-to Late Holocene flood frequency in the northeastern Alps as recorded in varved sediments of Lake Mondsee

Annually laminated (varved) lake sediments with intercalated detrital layers resulting from sedimentary input by runoff events are ideal archives to establish precisely dated records of past extreme runoff events. In this study, the mid- to late Holocene varved sediments of Lake Mondsee (Upper Austria) were analysed by combining sedimentological, geophysical and geochemical methods. This approach allows to distinguish two types of detrital layers related to different types of extreme runoff events (floods and debris flows) and to detect changes in flood activity during the last 7100 years. In total, 271 flood and 47 debris flow layers, deposited during spring and summer, were identified, which cluster in 18 main flood episodes (FE 1-18) with durations of 30-50 years each. These main flood periods occurred during the Late Neolithic (7100-7050 vyr BP and 6470-4450 vyr BP), the late Bronze Age and the early Iron Age (3300-3250 and 2800-2750 vyr BP), the late Iron Age (2050-2000 vyr BP), throughout the Dark Ages Cold Period (1500-1200 vyr BP), and at the end of the Medieval Warm Period and the Little Ice Age (810-430 vyr BP). Summer flood episodes in Lake Mondsee are generally more abundant during the last 1500 years, often coinciding with major advances of alpine glaciers. Prior to 1500 vyr BP, spring/summer floods and debris flows are generally less frequent, indicating a lower number of intense rainfall events that triggered erosion. In comparison with the increase of late Holocene flood activity in western and northwestern (NW) Europe, commencing already as early as 2800 yr BP, the hydro-meteorological shift in the Lake Mondsee region occurred much later. These time lags in the onset of increased hydrological activity might be either due to regional differences in atmospheric circulation pattern or to the sensitivity of the individual flood archives. The Lake Mondsee sediments represent the first precisely dated and several millennia long summer flood record for the northeastern (NE) Alps, a key region at the climatic boundary of Atlantic, Mediterranean and East European air masses aiding a better understanding of regional and seasonal peculiarities of flood occurrence under changing climate conditions.

Frequency, Form, and Distribution of Illocutionary Speech Acts in Swedish Parent-Child Interaction

In this study, young children’s development of speech acts was examined. Interaction between six Swedish-speaking parents and their children was observed. The frequency, form and distribution of speech acts in the output from the parents were compared with the frequency, form and distribution of the children’s speech acts. The frequency was measured by occurrences per analysed session. The aim of the analysis was to examine if the parent’s behaviour could be treated as a baseline for the child’s development. Both the parents’ and the children’s illocutionary speech acts were classified. Each parent-child dyad was observed at four different occasions, when the children were 1;0, 1;6, 2;0, and 2;6 years of age. Similar studies have previously shown that parents keep a consistent frequency of speech acts within a given time span of interaction, though the distribution of different types of speech acts may shift, depending on contextual factors. The form, in terms of Mean Length of Speech Act in Words (MLSAw), were correlated with the longitudinal result of the children’s MLSAw. The distribution of the parents’ speech acts showed extensive individual differences. The result showed that the children’s MLSAw move significantly closer the MLSAw of their parents. Since the parent’s MLSAw showed a wide distribution, these results indicate that the parent’s speech acts can be treated as a baseline for certain aspects of the children’s development, though further studies are needed.

Non-invasive Detection of Cortical Control Signals for Brain-Computer Interfaces

Thesis (Ph.D.)--University of Washington, 2016-05

The High Frequency Component of Heart Rate Variability and Delta EEG Power during Sleep in Healthy Women and Women with Irritable Bowel Syndrome

Thesis (Ph.D.)--University of Washington, 2016-06

Suitability of acoustic perturbation measures in analysing periodic and nearly periodic voice signals

In recent years, acoustic perturbation measurement has gained clinical and research popularity due to the ease of availability of commercial acoustic analysing software packages in the market. However, because the measurement itself depends critically on the accuracy of frequency tracking from the voice signal, researchers argue that perturbation measures are not suitable for analysing dysphonic voice samples, which are aperiodic in nature. This study compares the fundamental frequency, relative amplitude perturbation, shimmer percent and noise-to-harmonic ratio between a group of dysphonic and non-dysphonic subjects. One hundred and twelve dysphonic subjects ( 93 females and 19 males) and 41 non-dysphonic subjects ( 35 females and 6 males) participated in the study. All the 153 voice samples were categorized into type I ( periodic or nearly periodic), type II ( signals with subharmonic frequencies that approach the fundamental frequency) and type III ( aperiodic) signals. Only the type I ( periodic and nearly periodic) voice signals were acoustically analysed for perturbation measures. Results revealed that the dysphonic female group presented significantly lower fundamental frequency, significantly higher relative amplitude perturbation and shimmer percent values than the non-dysphonic female group. However, none of these three perturbation measures were able to differentiate between male dysphonic and male non-dysphonic subjects. The noise-to-harmonic ratio failed to differentiate between the dysphonic and non-dysphonic voices for both gender groups. These results question the sensitivity of acoustic perturbation measures in detecting dysphonia and suggest that contemporary acoustic perturbation measures are not suitable for analysing dysphonic voice signals, which are even nearly periodic. Copyright (C) 2005 S. Karger AG, Basel.

Statistical tests of load-unload response ratio signals by lattice solid model: Implication to tidal triggering and earthquake prediction

Statistical tests of Load-Unload Response Ratio (LURR) signals are carried in order to verify statistical robustness of the previous studies using the Lattice Solid Model (MORA et al., 2002b). In each case 24 groups of samples with the same macroscopic parameters (tidal perturbation amplitude A, period T and tectonic loading rate k) but different particle arrangements are employed. Results of uni-axial compression experiments show that before the normalized time of catastrophic failure, the ensemble average LURR value rises significantly, in agreement with the observations of high LURR prior to the large earthquakes. In shearing tests, two parameters are found to control the correlation between earthquake occurrence and tidal stress. One is, A/(kT) controlling the phase shift between the peak seismicity rate and the peak amplitude of the perturbation stress. With an increase of this parameter, the phase shift is found to decrease. Another parameter, AT/k, controls the height of the probability density function (Pdf) of modeled seismicity. As this parameter increases, the Pdf becomes sharper and narrower, indicating a strong triggering. Statistical studies of LURR signals in shearing tests also suggest that except in strong triggering cases, where LURR cannot be calculated due to poor data in unloading cycles, the larger events are more likely to occur in higher LURR periods than the smaller ones, supporting the LURR hypothesis.

Detecting finite bandwidth periodic signals in stationary noise using the signal coherence spectrum

All signals that appear to be periodic have some sort of variability from period to period regardless of how stable they appear to be in a data plot. A true sinusoidal time series is a deterministic function of time that never changes and thus has zero bandwidth around the sinusoid's frequency. A zero bandwidth is impossible in nature since all signals have some intrinsic variability over time. Deterministic sinusoids are used to model cycles as a mathematical convenience. Hinich [IEEE J. Oceanic Eng. 25 (2) (2000) 256-261] introduced a parametric statistical model, called the randomly modulated periodicity (RMP) that allows one to capture the intrinsic variability of a cycle. As with a deterministic periodic signal the RMP can have a number of harmonics. The likelihood ratio test for this model when the amplitudes and phases are known is given in [M.J. Hinich, Signal Processing 83 (2003) 1349-13521. A method for detecting a RMP whose amplitudes and phases are unknown random process plus a stationary noise process is addressed in this paper. The only assumption on the additive noise is that it has finite dependence and finite moments. Using simulations based on a simple RMP model we show a case where the new method can detect the signal when the signal is not detectable in a standard waterfall spectrograrn display. (c) 2005 Elsevier B.V. All rights reserved.

Electrical impedance tomography in extremely prematurely born infants and during high frequency oscillatory ventilation analyzed in the frequency domain

Functional electrical impedance tomography (EIT) measures relative impedance change that occurs in the chest during a distinct observation period and an EIT image describing regional relative impedance change is generated. Analysis of such an EIT image may be erroneous because it is based on an impedance signal that has several components. Most of the change in relative impedance in the chest is caused by air movement but other physiological events such as cardiac activity change in end expiratory level or pressure swings originating from a ventilator circuit can influence the impedance signal. We obtained EIT images and signals in spontaneously breathing healthy adults, in extremely prematurely born infants on continuous positive airway pressure and in ventilated sheep on conventional mechanical or high frequency oscillatory ventilation (HFOV). Data were analyzed in the frequency domain and results presented after band pass filtering within the frequency range of the physiological event of interest. Band pass filtering of EIT data is necessary in premature infants and on HFOV to differentiate and eliminate relative impedance changes caused by physiological events other than the one of interest.

Frequency band selection of radars for buried object detection

Choice of the operational frequency is one of the most responsible parts of any radar design process. Parameters of radars for buried object detection (BOD) are very sensitive to both carrier frequency and ranging signal bandwidth. Such radars have a specific propagation environment with a strong frequency-dependent attenuation and, as a result, short operational range. This fact dictates some features of the radar's parameters: wideband signal-to provide a high range resolution (fractions of a meter) and a low carrier frequency (tens or hundreds megahertz) for deeper penetration. The requirement to have a wideband ranging signal and low carrier frequency are partly in contradiction. As a result, low-frequency (LF) ultrawide-band (UWB) signals are used. The major goal of this paper is to examine the influence of the frequency band choice on the radar performance and develop relevant methodologies for BOD radar design and optimization. In this article, high-efficient continuous wave (CW) signals with most advanced stepped frequency (SF) modulation are considered; however, the main conclusions can be applied to any kind of ranging signals.