Investigating Patterns for Self-Induced Emotion Recognition from EEG Signals

PubMed Central

Zeng, Ying; Yang, Kai; Tong, Li; Yan, Bin

2018-01-01

Most current approaches to emotion recognition are based on neural signals elicited by affective materials such as images, sounds and videos. However, the application of neural patterns in the recognition of self-induced emotions remains uninvestigated. In this study we inferred the patterns and neural signatures of self-induced emotions from electroencephalogram (EEG) signals. The EEG signals of 30 participants were recorded while they watched 18 Chinese movie clips which were intended to elicit six discrete emotions, including joy, neutrality, sadness, disgust, anger and fear. After watching each movie clip the participants were asked to self-induce emotions by recalling a specific scene from each movie. We analyzed the important features, electrode distribution and average neural patterns of different self-induced emotions. Results demonstrated that features related to high-frequency rhythm of EEG signals from electrodes distributed in the bilateral temporal, prefrontal and occipital lobes have outstanding performance in the discrimination of emotions. Moreover, the six discrete categories of self-induced emotion exhibit specific neural patterns and brain topography distributions. We achieved an average accuracy of 87.36% in the discrimination of positive from negative self-induced emotions and 54.52% in the classification of emotions into six discrete categories. Our research will help promote the development of comprehensive endogenous emotion recognition methods. PMID:29534515

Signal detection with criterion noise: applications to recognition memory.

PubMed

Benjamin, Aaron S; Diaz, Michael; Wee, Serena

2009-01-01

A tacit but fundamental assumption of the theory of signal detection is that criterion placement is a noise-free process. This article challenges that assumption on theoretical and empirical grounds and presents the noisy decision theory of signal detection (ND-TSD). Generalized equations for the isosensitivity function and for measures of discrimination incorporating criterion variability are derived, and the model's relationship with extant models of decision making in discrimination tasks is examined. An experiment evaluating recognition memory for ensembles of word stimuli revealed that criterion noise is not trivial in magnitude and contributes substantially to variance in the slope of the isosensitivity function. The authors discuss how ND-TSD can help explain a number of current and historical puzzles in recognition memory, including the inconsistent relationship between manipulations of learning and the isosensitivity function's slope, the lack of invariance of the slope with manipulations of bias or payoffs, the effects of aging on the decision-making process in recognition, and the nature of responding in remember-know decision tasks. ND-TSD poses novel, theoretically meaningful constraints on theories of recognition and decision making more generally, and provides a mechanism for rapprochement between theories of decision making that employ deterministic response rules and those that postulate probabilistic response rules.

A bacterial tyrosine phosphatase inhibits plant pattern recognition receptor activation

USDA-ARS?s Scientific Manuscript database

Perception of pathogen-associated molecular patterns (PAMPs) by surface-localised pattern-recognition receptors (PRRs) is a key component of plant innate immunity. Most known plant PRRs are receptor kinases and initiation of PAMP-triggered immunity (PTI) signalling requires phosphorylation of the PR...

Signal recognition and parameter estimation of BPSK-LFM combined modulation

NASA Astrophysics Data System (ADS)

Long, Chao; Zhang, Lin; Liu, Yu

2015-07-01

Intra-pulse analysis plays an important role in electronic warfare. Intra-pulse feature abstraction focuses on primary parameters such as instantaneous frequency, modulation, and symbol rate. In this paper, automatic modulation recognition and feature extraction for combined BPSK-LFM modulation signals based on decision theoretic approach is studied. The simulation results show good recognition effect and high estimation precision, and the system is easy to be realized.

Research on the feature extraction and pattern recognition of the distributed optical fiber sensing signal

NASA Astrophysics Data System (ADS)

Wang, Bingjie; Sun, Qi; Pi, Shaohua; Wu, Hongyan

2014-09-01

In this paper, feature extraction and pattern recognition of the distributed optical fiber sensing signal have been studied. We adopt Mel-Frequency Cepstral Coefficient (MFCC) feature extraction, wavelet packet energy feature extraction and wavelet packet Shannon entropy feature extraction methods to obtain sensing signals (such as speak, wind, thunder and rain signals, etc.) characteristic vectors respectively, and then perform pattern recognition via RBF neural network. Performances of these three feature extraction methods are compared according to the results. We choose MFCC characteristic vector to be 12-dimensional. For wavelet packet feature extraction, signals are decomposed into six layers by Daubechies wavelet packet transform, in which 64 frequency constituents as characteristic vector are respectively extracted. In the process of pattern recognition, the value of diffusion coefficient is introduced to increase the recognition accuracy, while keeping the samples for testing algorithm the same. Recognition results show that wavelet packet Shannon entropy feature extraction method yields the best recognition accuracy which is up to 97%; the performance of 12-dimensional MFCC feature extraction method is less satisfactory; the performance of wavelet packet energy feature extraction method is the worst.

Physical signals for protein-DNA recognition

NASA Astrophysics Data System (ADS)

Cao, Xiao-Qin; Zeng, Jia; Yan, Hong

2009-09-01

This paper discovers consensus physical signals around eukaryotic splice sites, transcription start sites, and replication origin start and end sites on a genome-wide scale based on their DNA flexibility profiles calculated by three different flexibility models. These salient physical signals are localized highly rigid and flexible DNAs, which may play important roles in protein-DNA recognition by the sliding search mechanism. The found physical signals lead us to a detailed hypothetical view of the search process in which a DNA-binding protein first finds a genomic region close to the target site from an arbitrary starting location by three-dimensional (3D) hopping and intersegment transfer mechanisms for long distances, and subsequently uses the one-dimensional (1D) sliding mechanism facilitated by the localized highly rigid DNAs to accurately locate the target flexible binding site within 30 bp (base pair) short distances. Guided by these physical signals, DNA-binding proteins rapidly search the entire genome to recognize a specific target site from the 3D to 1D pathway. Our findings also show that current promoter prediction programs (PPPs) based on DNA physical properties may suffer from lots of false positives because other functional sites such as splice sites and replication origins have similar physical signals as promoters do.

Assessment of Homomorphic Analysis for Human Activity Recognition from Acceleration Signals.

PubMed

Vanrell, Sebastian Rodrigo; Milone, Diego Humberto; Rufiner, Hugo Leonardo

2017-07-03

Unobtrusive activity monitoring can provide valuable information for medical and sports applications. In recent years, human activity recognition has moved to wearable sensors to deal with unconstrained scenarios. Accelerometers are the preferred sensors due to their simplicity and availability. Previous studies have examined several \\azul{classic} techniques for extracting features from acceleration signals, including time-domain, time-frequency, frequency-domain, and other heuristic features. Spectral and temporal features are the preferred ones and they are generally computed from acceleration components, leaving the acceleration magnitude potential unexplored. In this study, based on homomorphic analysis, a new type of feature extraction stage is proposed in order to exploit discriminative activity information present in acceleration signals. Homomorphic analysis can isolate the information about whole body dynamics and translate it into a compact representation, called cepstral coefficients. Experiments have explored several configurations of the proposed features, including size of representation, signals to be used, and fusion with other features. Cepstral features computed from acceleration magnitude obtained one of the highest recognition rates. In addition, a beneficial contribution was found when time-domain and moving pace information was included in the feature vector. Overall, the proposed system achieved a recognition rate of 91.21% on the publicly available SCUT-NAA dataset. To the best of our knowledge, this is the highest recognition rate on this dataset.

A two-step recognition of signal sequences determines the translocation efficiency of proteins.

PubMed Central

Belin, D; Bost, S; Vassalli, J D; Strub, K

1996-01-01

The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated derivatives thereof, ovalbumin and preprolactin) were found to have the differential activities in the two events. For example, the mPAI-2 signal sequence first binds SRP with moderate efficiency and secondly promotes the vectorial transport of only a fraction of the SRP-bound nascent chains. Our results provide evidence that the translocation efficiency of proteins can be controlled by the recognition of their signal sequences at two steps: during SRP-mediated targeting and during formation of a committed translocation complex. This second recognition may occur at several time points during the insertion/translocation step. In conclusion, signal sequences have a more complex structure than previously anticipated, allowing for multiple and independent interactions with the translocation machinery. Images PMID:8599930

A two-step recognition of signal sequences determines the translocation efficiency of proteins.

PubMed

Belin, D; Bost, S; Vassalli, J D; Strub, K

1996-02-01

The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated derivatives thereof, ovalbumin and preprolactin) were found to have the differential activities in the two events. For example, the mPAI-2 signal sequence first binds SRP with moderate efficiency and secondly promotes the vectorial transport of only a fraction of the SRP-bound nascent chains. Our results provide evidence that the translocation efficiency of proteins can be controlled by the recognition of their signal sequences at two steps: during SRP-mediated targeting and during formation of a committed translocation complex. This second recognition may occur at several time points during the insertion/translocation step. In conclusion, signal sequences have a more complex structure than previously anticipated, allowing for multiple and independent interactions with the translocation machinery.

S1PR3 Signaling Drives Bacterial Killing and Is Required for Survival in Bacterial Sepsis.

PubMed

Hou, JinChao; Chen, QiXing; Wu, XiaoLiang; Zhao, DongYan; Reuveni, Hadas; Licht, Tamar; Xu, MengLong; Hu, Hu; Hoeft, Andreas; Ben-Sasson, Shmuel A; Shu, Qiang; Fang, XiangMing

2017-12-15

Efficient elimination of pathogenic bacteria is a critical determinant in the outcome of sepsis. Sphingosine-1-phosphate receptor 3 (S1PR3) mediates multiple aspects of the inflammatory response during sepsis, but whether S1PR3 signaling is necessary for eliminating the invading pathogens remains unknown. To investigate the role of S1PR3 in antibacterial immunity during sepsis. Loss- and gain-of-function experiments were performed using cell and murine models. S1PR3 levels were determined in patients with sepsis and healthy volunteers. S1PR3 protein levels were up-regulated in macrophages upon bacterial stimulation. S1pr3 -/- mice showed increased mortality and increased bacterial burden in multiple models of sepsis. The transfer of wild-type bone marrow-derived macrophages rescued S1pr3 -/- mice from lethal sepsis. S1PR3-overexpressing macrophages further ameliorated the mortality rate of sepsis. Loss of S1PR3 led to markedly decreased bacterial killing in macrophages. Enhancing endogenous S1PR3 activity using a peptide agonist potentiated the macrophage bactericidal function and improved survival rates in multiple models of sepsis. Mechanically, the reactive oxygen species levels were decreased and phagosome maturation was delayed in S1pr3 -/- macrophages due to impaired recruitment of vacuolar protein-sorting 34 to the phagosomes. In addition, S1RP3 expression levels were elevated in monocytes from patients with sepsis. Higher levels of monocytic S1PR3 were associated with efficient intracellular bactericidal activity, better immune status, and preferable outcomes. S1PR3 signaling drives bacterial killing and is essential for survival in bacterial sepsis. Interventions targeting S1PR3 signaling could have translational implications for manipulating the innate immune response to combat pathogens.

Emotion recognition from multichannel EEG signals using K-nearest neighbor classification.

PubMed

Li, Mi; Xu, Hongpei; Liu, Xingwang; Lu, Shengfu

2018-04-27

Many studies have been done on the emotion recognition based on multi-channel electroencephalogram (EEG) signals. This paper explores the influence of the emotion recognition accuracy of EEG signals in different frequency bands and different number of channels. We classified the emotional states in the valence and arousal dimensions using different combinations of EEG channels. Firstly, DEAP default preprocessed data were normalized. Next, EEG signals were divided into four frequency bands using discrete wavelet transform, and entropy and energy were calculated as features of K-nearest neighbor Classifier. The classification accuracies of the 10, 14, 18 and 32 EEG channels based on the Gamma frequency band were 89.54%, 92.28%, 93.72% and 95.70% in the valence dimension and 89.81%, 92.24%, 93.69% and 95.69% in the arousal dimension. As the number of channels increases, the classification accuracy of emotional states also increases, the classification accuracy of the gamma frequency band is greater than that of the beta frequency band followed by the alpha and theta frequency bands. This paper provided better frequency bands and channels reference for emotion recognition based on EEG.

Dissecting the signaling mechanisms underlying recognition and preference of food odors.

PubMed

Harris, Gareth; Shen, Yu; Ha, Heonick; Donato, Alessandra; Wallis, Samuel; Zhang, Xiaodong; Zhang, Yun

2014-07-09

Food is critical for survival. Many animals, including the nematode Caenorhabditis elegans, use sensorimotor systems to detect and locate preferred food sources. However, the signaling mechanisms underlying food-choice behaviors are poorly understood. Here, we characterize the molecular signaling that regulates recognition and preference between different food odors in C. elegans. We show that the major olfactory sensory neurons, AWB and AWC, play essential roles in this behavior. A canonical Gα-protein, together with guanylate cyclases and cGMP-gated channels, is needed for the recognition of food odors. The food-odor-evoked signal is transmitted via glutamatergic neurotransmission from AWC and through AMPA and kainate-like glutamate receptor subunits. In contrast, peptidergic signaling is required to generate preference between different food odors while being dispensable for the recognition of the odors. We show that this regulation is achieved by the neuropeptide NLP-9 produced in AWB, which acts with its putative receptor NPR-18, and by the neuropeptide NLP-1 produced in AWC. In addition, another set of sensory neurons inhibits food-odor preference. These mechanistic logics, together with a previously mapped neural circuit underlying food-odor preference, provide a functional network linking sensory response, transduction, and downstream receptors to process complex olfactory information and generate the appropriate behavioral decision essential for survival. Copyright © 2014 the authors 0270-6474/14/339389-15$15.00/0.

Dissecting the Signaling Mechanisms Underlying Recognition and Preference of Food Odors

PubMed Central

Harris, Gareth; Shen, Yu; Ha, Heonick; Donato, Alessandra; Wallis, Samuel; Zhang, Xiaodong

2014-01-01

Food is critical for survival. Many animals, including the nematode Caenorhabditis elegans, use sensorimotor systems to detect and locate preferred food sources. However, the signaling mechanisms underlying food-choice behaviors are poorly understood. Here, we characterize the molecular signaling that regulates recognition and preference between different food odors in C. elegans. We show that the major olfactory sensory neurons, AWB and AWC, play essential roles in this behavior. A canonical Gα-protein, together with guanylate cyclases and cGMP-gated channels, is needed for the recognition of food odors. The food-odor-evoked signal is transmitted via glutamatergic neurotransmission from AWC and through AMPA and kainate-like glutamate receptor subunits. In contrast, peptidergic signaling is required to generate preference between different food odors while being dispensable for the recognition of the odors. We show that this regulation is achieved by the neuropeptide NLP-9 produced in AWB, which acts with its putative receptor NPR-18, and by the neuropeptide NLP-1 produced in AWC. In addition, another set of sensory neurons inhibits food-odor preference. These mechanistic logics, together with a previously mapped neural circuit underlying food-odor preference, provide a functional network linking sensory response, transduction, and downstream receptors to process complex olfactory information and generate the appropriate behavioral decision essential for survival. PMID:25009271

A triaxial accelerometer-based physical-activity recognition via augmented-signal features and a hierarchical recognizer.

PubMed

Khan, Adil Mehmood; Lee, Young-Koo; Lee, Sungyoung Y; Kim, Tae-Seong

2010-09-01

Physical-activity recognition via wearable sensors can provide valuable information regarding an individual's degree of functional ability and lifestyle. In this paper, we present an accelerometer sensor-based approach for human-activity recognition. Our proposed recognition method uses a hierarchical scheme. At the lower level, the state to which an activity belongs, i.e., static, transition, or dynamic, is recognized by means of statistical signal features and artificial-neural nets (ANNs). The upper level recognition uses the autoregressive (AR) modeling of the acceleration signals, thus, incorporating the derived AR-coefficients along with the signal-magnitude area and tilt angle to form an augmented-feature vector. The resulting feature vector is further processed by the linear-discriminant analysis and ANNs to recognize a particular human activity. Our proposed activity-recognition method recognizes three states and 15 activities with an average accuracy of 97.9% using only a single triaxial accelerometer attached to the subject's chest.

Real-time mental arithmetic task recognition from EEG signals.

PubMed

Wang, Qiang; Sourina, Olga

2013-03-01

Electroencephalography (EEG)-based monitoring the state of the user's brain functioning and giving her/him the visual/audio/tactile feedback is called neurofeedback technique, and it could allow the user to train the corresponding brain functions. It could provide an alternative way of treatment for some psychological disorders such as attention deficit hyperactivity disorder (ADHD), where concentration function deficit exists, autism spectrum disorder (ASD), or dyscalculia where the difficulty in learning and comprehending the arithmetic exists. In this paper, a novel method for multifractal analysis of EEG signals named generalized Higuchi fractal dimension spectrum (GHFDS) was proposed and applied in mental arithmetic task recognition from EEG signals. Other features such as power spectrum density (PSD), autoregressive model (AR), and statistical features were analyzed as well. The usage of the proposed fractal dimension spectrum of EEG signal in combination with other features improved the mental arithmetic task recognition accuracy in both multi-channel and one-channel subject-dependent algorithms up to 97.87% and 84.15% correspondingly. Based on the channel ranking, four channels were chosen which gave the accuracy up to 97.11%. Reliable real-time neurofeedback system could be implemented based on the algorithms proposed in this paper.

Detection and recognition of targets by using signal polarization properties

NASA Astrophysics Data System (ADS)

Ponomaryov, Volodymyr I.; Peralta-Fabi, Ricardo; Popov, Anatoly V.; Babakov, Mikhail F.

1999-08-01

The quality of radar target recognition can be enhanced by exploiting its polarization signatures. A specialized X-band polarimetric radar was used for target recognition in experimental investigations. The following polarization characteristics connected to the object geometrical properties were investigated: the amplitudes of the polarization matrix elements; an anisotropy coefficient; depolarization coefficient; asymmetry coefficient; the energy of a backscattering signal; object shape factor. A large quantity of polarimetric radar data was measured and processed to form a database of different object and different weather conditions. The histograms of polarization signatures were approximated by a Nakagami distribution, then used for real- time target recognition. The Neyman-Pearson criterion was used for the target detection, and the criterion of the maximum of a posterior probability was used for recognition problem. Some results of experimental verification of pattern recognition and detection of objects with different electrophysical and geometrical characteristics urban in clutter are presented in this paper.

Approximated mutual information training for speech recognition using myoelectric signals.

PubMed

Guo, Hua J; Chan, A D C

2006-01-01

A new training algorithm called the approximated maximum mutual information (AMMI) is proposed to improve the accuracy of myoelectric speech recognition using hidden Markov models (HMMs). Previous studies have demonstrated that automatic speech recognition can be performed using myoelectric signals from articulatory muscles of the face. Classification of facial myoelectric signals can be performed using HMMs that are trained using the maximum likelihood (ML) algorithm; however, this algorithm maximizes the likelihood of the observations in the training sequence, which is not directly associated with optimal classification accuracy. The AMMI training algorithm attempts to maximize the mutual information, thereby training the HMMs to optimize their parameters for discrimination. Our results show that AMMI training consistently reduces the error rates compared to these by the ML training, increasing the accuracy by approximately 3% on average.

Intelligent Automatic Right-Left Sign Lamp Based on Brain Signal Recognition System

NASA Astrophysics Data System (ADS)

Winda, A.; Sofyan; Sthevany; Vincent, R. S.

2017-12-01

Comfort as a part of the human factor, plays important roles in nowadays advanced automotive technology. Many of the current technologies go in the direction of automotive driver assistance features. However, many of the driver assistance features still require physical movement by human to enable the features. In this work, the proposed method is used in order to make certain feature to be functioning without any physical movement, instead human just need to think about it in their mind. In this work, brain signal is recorded and processed in order to be used as input to the recognition system. Right-Left sign lamp based on the brain signal recognition system can potentially replace the button or switch of the specific device in order to make the lamp work. The system then will decide whether the signal is ‘Right’ or ‘Left’. The decision of the Right-Left side of brain signal recognition will be sent to a processing board in order to activate the automotive relay, which will be used to activate the sign lamp. Furthermore, the intelligent system approach is used to develop authorized model based on the brain signal. Particularly Support Vector Machines (SVMs)-based classification system is used in the proposed system to recognize the Left-Right of the brain signal. Experimental results confirm the effectiveness of the proposed intelligent Automatic brain signal-based Right-Left sign lamp access control system. The signal is processed by Linear Prediction Coefficient (LPC) and Support Vector Machines (SVMs), and the resulting experiment shows the training and testing accuracy of 100% and 80%, respectively.

Development of precursors recognition methods in vector signals

NASA Astrophysics Data System (ADS)

Kapralov, V. G.; Elagin, V. V.; Kaveeva, E. G.; Stankevich, L. A.; Dremin, M. M.; Krylov, S. V.; Borovov, A. E.; Harfush, H. A.; Sedov, K. S.

2017-10-01

Precursor recognition methods in vector signals of plasma diagnostics are presented. Their requirements and possible options for their development are considered. In particular, the variants of using symbolic regression for building a plasma disruption prediction system are discussed. The initial data preparation using correlation analysis and symbolic regression is discussed. Special attention is paid to the possibility of using algorithms in real time.

How landmark suitability shapes recognition memory signals for objects in the medial temporal lobes.

PubMed

Martin, Chris B; Sullivan, Jacqueline A; Wright, Jessey; Köhler, Stefan

2018-02-01

A role of perirhinal cortex (PrC) in recognition memory for objects has been well established. Contributions of parahippocampal cortex (PhC) to this function, while documented, remain less well understood. Here, we used fMRI to examine whether the organization of item-based recognition memory signals across these two structures is shaped by object category, independent of any difference in representing episodic context. Guided by research suggesting that PhC plays a critical role in processing landmarks, we focused on three categories of objects that differ from each other in their landmark suitability as confirmed with behavioral ratings (buildings > trees > aircraft). Participants made item-based recognition-memory decisions for novel and previously studied objects from these categories, which were matched in accuracy. Multi-voxel pattern classification revealed category-specific item-recognition memory signals along the long axis of PrC and PhC, with no sharp functional boundaries between these structures. Memory signals for buildings were observed in the mid to posterior extent of PhC, signals for trees in anterior to posterior segments of PhC, and signals for aircraft in mid to posterior aspects of PrC and the anterior extent of PhC. Notably, item-based memory signals for the category with highest landmark suitability ratings were observed only in those posterior segments of PhC that also allowed for classification of landmark suitability of objects when memory status was held constant. These findings provide new evidence in support of the notion that item-based memory signals for objects are not limited to PrC, and that the organization of these signals along the longitudinal axis that crosses PrC and PhC can be captured with reference to landmark suitability. Copyright © 2017 Elsevier Inc. All rights reserved.

Intracellular Zn(2+) signaling in the dentate gyrus is required for object recognition memory.

PubMed

Takeda, Atsushi; Tamano, Haruna; Ogawa, Taisuke; Takada, Shunsuke; Nakamura, Masatoshi; Fujii, Hiroaki; Ando, Masaki

2014-11-01

The role of perforant pathway-dentate granule cell synapses in cognitive behavior was examined focusing on synaptic Zn(2+) signaling in the dentate gyrus. Object recognition memory was transiently impaired when extracellular Zn(2+) levels were decreased by injection of clioquinol and N,N,N',N'-tetrakis-(2-pyridylmethyl) ethylendediamine. To pursue the effect of the loss and/or blockade of Zn(2+) signaling in dentate granule cells, ZnAF-2DA (100 pmol, 0.1 mM/1 µl), an intracellular Zn(2+) chelator, was locally injected into the dentate molecular layer of rats. ZnAF-2DA injection, which was estimated to chelate intracellular Zn(2+) signaling only in the dentate gyrus, affected object recognition memory 1 h after training without affecting intracellular Ca(2+) signaling in the dentate molecular layer. In vivo dentate gyrus long-term potentiation (LTP) was affected under the local perfusion of the recording region (the dentate granule cell layer) with 0.1 mM ZnAF-2DA, but not with 1-10 mM CaEDTA, an extracellular Zn(2+) chelator, suggesting that the blockade of intracellular Zn(2+) signaling in dentate granule cells affects dentate gyrus LTP. The present study demonstrates that intracellular Zn(2+) signaling in the dentate gyrus is required for object recognition memory, probably via dentate gyrus LTP expression. Copyright © 2014 Wiley Periodicals, Inc.

Diversity of Innate Immune Recognition Mechanism for Bacterial Polymeric meso-Diaminopimelic Acid-type Peptidoglycan in Insects

PubMed Central

Yu, Yang; Park, Ji-Won; Kwon, Hyun-Mi; Hwang, Hyun-Ok; Jang, In-Hwan; Masuda, Akiko; Kurokawa, Kenji; Nakayama, Hiroshi; Lee, Won-Jae; Dohmae, Naoshi; Zhang, Jinghai; Lee, Bok Luel

2010-01-01

In Drosophila, the synthesis of antimicrobial peptides in response to microbial infections is under the control of the Toll and immune deficiency (Imd) signaling pathway. The Toll signaling pathway responds mainly to the lysine-type peptidoglycan of Gram-positive bacteria and fungal β-1,3-glucan, whereas the Imd pathway responds to the meso-diaminopimelic acid (DAP)-type peptidoglycan of Gram-negative bacteria and certain Gram-positive bacilli. Recently we determined the activation mechanism of a Toll signaling pathway biochemically using a large beetle, Tenebrio molitor. However, DAP-type peptidoglycan recognition mechanism and its signaling pathway are still unclear in the fly and beetle. Here, we show that polymeric DAP-type peptidoglycan, but not its monomeric form, formed a complex with Tenebrio peptidoglycan recognition protein-SA, and this complex activated the three-step proteolytic cascade to produce processed Spätzle, a Toll receptor ligand, and induced Drosophila defensin-like antimicrobial peptide in Tenebrio larvae similarly to polymeric lysine-type peptidoglycan. Monomeric DAP-type peptidoglycan induced Drosophila diptericin-like antimicrobial peptide in Tenebrio hemocytes. In addition, both polymeric and monomeric DAP-type peptidoglycans induced expression of Tenebrio peptidoglycan recognition protein-SC2, which is DAP-type peptidoglycan-selective N-acetylmuramyl-l-alanine amidase that functions as a DAP-type peptidoglycan scavenger, appearing to function as a negative regulator of the DAP-type peptidoglycan signaling by cleaving DAP-type peptidoglycan in Tenebrio larvae. Taken together, these results demonstrate that molecular recognition mechanism for polymeric DAP-type peptidoglycan is different between Tenebrio larvae and Drosophila adults, providing biochemical evidences of biological diversity of innate immune responses in insects. PMID:20702416

Dual-Process Theory and Signal-Detection Theory of Recognition Memory

ERIC Educational Resources Information Center

Wixted, John T.

2007-01-01

Two influential models of recognition memory, the unequal-variance signal-detection model and a dual-process threshold/detection model, accurately describe the receiver operating characteristic, but only the latter model can provide estimates of recollection and familiarity. Such estimates often accord with those provided by the remember-know…

Surface EMG signals based motion intent recognition using multi-layer ELM

NASA Astrophysics Data System (ADS)

Wang, Jianhui; Qi, Lin; Wang, Xiao

2017-11-01

The upper-limb rehabilitation robot is regard as a useful tool to help patients with hemiplegic to do repetitive exercise. The surface electromyography (sEMG) contains motion information as the electric signals are generated and related to nerve-muscle motion. These sEMG signals, representing human's intentions of active motions, are introduced into the rehabilitation robot system to recognize upper-limb movements. Traditionally, the feature extraction is an indispensable part of drawing significant information from original signals, which is a tedious task requiring rich and related experience. This paper employs a deep learning scheme to extract the internal features of the sEMG signals using an advanced Extreme Learning Machine based auto-encoder (ELMAE). The mathematical information contained in the multi-layer structure of the ELM-AE is used as the high-level representation of the internal features of the sEMG signals, and thus a simple ELM can post-process the extracted features, formulating the entire multi-layer ELM (ML-ELM) algorithm. The method is employed for the sEMG based neural intentions recognition afterwards. The case studies show the adopted deep learning algorithm (ELM-AE) is capable of yielding higher classification accuracy compared to the Principle Component Analysis (PCA) scheme in 5 different types of upper-limb motions. This indicates the effectiveness and the learning capability of the ML-ELM in such motion intent recognition applications.

Nasal chemosensory cells use bitter taste signaling to detect irritants and bacterial signals.

PubMed

Tizzano, Marco; Gulbransen, Brian D; Vandenbeuch, Aurelie; Clapp, Tod R; Herman, Jake P; Sibhatu, Hiruy M; Churchill, Mair E A; Silver, Wayne L; Kinnamon, Sue C; Finger, Thomas E

2010-02-16

The upper respiratory tract is continually assaulted with harmful dusts and xenobiotics carried on the incoming airstream. Detection of such irritants by the trigeminal nerve evokes protective reflexes, including sneezing, apnea, and local neurogenic inflammation of the mucosa. Although free intra-epithelial nerve endings can detect certain lipophilic irritants (e.g., mints, ammonia), the epithelium also houses a population of trigeminally innervated solitary chemosensory cells (SCCs) that express T2R bitter taste receptors along with their downstream signaling components. These SCCs have been postulated to enhance the chemoresponsive capabilities of the trigeminal irritant-detection system. Here we show that transduction by the intranasal solitary chemosensory cells is necessary to evoke trigeminally mediated reflex reactions to some irritants including acyl-homoserine lactone bacterial quorum-sensing molecules, which activate the downstream signaling effectors associated with bitter taste transduction. Isolated nasal chemosensory cells respond to the classic bitter ligand denatonium as well as to the bacterial signals by increasing intracellular Ca(2+). Furthermore, these same substances evoke changes in respiration indicative of trigeminal activation. Genetic ablation of either G alpha-gustducin or TrpM5, essential elements of the T2R transduction cascade, eliminates the trigeminal response. Because acyl-homoserine lactones serve as quorum-sensing molecules for gram-negative pathogenic bacteria, detection of these substances by airway chemoreceptors offers a means by which the airway epithelium may trigger an epithelial inflammatory response before the bacteria reach population densities capable of forming destructive biofilms.

Nasal chemosensory cells use bitter taste signaling to detect irritants and bacterial signals

PubMed Central

Tizzano, Marco; Gulbransen, Brian D.; Vandenbeuch, Aurelie; Clapp, Tod R.; Herman, Jake P.; Sibhatu, Hiruy M.; Churchill, Mair E. A.; Silver, Wayne L.; Kinnamon, Sue C.; Finger, Thomas E.

2010-01-01

The upper respiratory tract is continually assaulted with harmful dusts and xenobiotics carried on the incoming airstream. Detection of such irritants by the trigeminal nerve evokes protective reflexes, including sneezing, apnea, and local neurogenic inflammation of the mucosa. Although free intra-epithelial nerve endings can detect certain lipophilic irritants (e.g., mints, ammonia), the epithelium also houses a population of trigeminally innervated solitary chemosensory cells (SCCs) that express T2R bitter taste receptors along with their downstream signaling components. These SCCs have been postulated to enhance the chemoresponsive capabilities of the trigeminal irritant-detection system. Here we show that transduction by the intranasal solitary chemosensory cells is necessary to evoke trigeminally mediated reflex reactions to some irritants including acyl–homoserine lactone bacterial quorum-sensing molecules, which activate the downstream signaling effectors associated with bitter taste transduction. Isolated nasal chemosensory cells respond to the classic bitter ligand denatonium as well as to the bacterial signals by increasing intracellular Ca2+. Furthermore, these same substances evoke changes in respiration indicative of trigeminal activation. Genetic ablation of either Gα-gustducin or TrpM5, essential elements of the T2R transduction cascade, eliminates the trigeminal response. Because acyl–homoserine lactones serve as quorum-sensing molecules for Gram-negative pathogenic bacteria, detection of these substances by airway chemoreceptors offers a means by which the airway epithelium may trigger an epithelial inflammatory response before the bacteria reach population densities capable of forming destructive biofilms. PMID:20133764

Targeting Nrf2 Signaling Improves Bacterial Clearance by Alveolar Macrophages in Patients with COPD and in a Mouse Model

PubMed Central

Harvey, Christopher J.; Thimmulappa, Rajesh K.; Sethi, Sanjay; Kong, Xiaoni; Yarmus, Lonny; Brown, Robert H.; David, Feller-Kopman; Wise, Robert; Biswal, Shyam

2016-01-01

Patients with chronic obstructive pulmonary disease (COPD) have innate immune dysfunction in the lung largely due to defective macrophage phagocytosis. This deficiency results in periodic bacterial infections that cause acute exacerbations of COPD, a major source of morbidity and mortality. Recent studies indicate that a decrease in Nrf2 (nuclear erythroid–related factor 2) signaling in patients with COPD may hamper their ability to defend against oxidative stress, although the role of Nrf2 in COPD exacerbations has not been determined. Here, we test whether activation of Nrf2 by the phytochemical sulforaphane restores phagocytosis of clinical isolates of nontypeable Haemophilus influenza (NTHI) and Pseudomonas aeruginosa (PA) by alveolar macrophages from patients with COPD. Sulforaphane treatment restored bacteria recognition and phagocytosis in alveolar macrophages from COPD patients. Furthermore, sulforaphane treatment enhanced pulmonary bacterial clearance by alveolar macrophages and reduced inflammation in wild-typemice but not in Nrf2-deficientmice exposed to cigarette smoke for 6 months. Gene expression and promoter analysis revealed that Nrf2 increased phagocytic ability of macrophages by direct transcriptional up-regulation of the scavenger receptor MARCO. Disruption of Nrf2 or MARCO abrogated sulforaphane-mediated bacterial phagocytosis by COPD alveolar macrophages. Our findings demonstrate the importance of Nrf2 and its downstream target MARCO in improving antibacterial defenses and provide a rationale for targeting this pathway, via pharmacological agents such as sulforaphane, to prevent exacerbations of COPD caused by bacterial infection. PMID:21490276

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.

PubMed

Wild, Klemens; Bange, Gert; Motiejunas, Domantas; Kribelbauer, Judith; Hendricks, Astrid; Segnitz, Bernd; Wade, Rebecca C; Sinning, Irmgard

2016-07-17

The signal recognition particle (SRP) is a ribonucleoprotein complex with a key role in targeting and insertion of membrane proteins. The two SRP GTPases, SRP54 (Ffh in bacteria) and FtsY (SRα in eukaryotes), form the core of the targeting complex (TC) regulating the SRP cycle. The architecture of the TC and its stimulation by RNA has been described for the bacterial SRP system while this information is lacking for other domains of life. Here, we present the crystal structures of the GTPase heterodimers of archaeal (Sulfolobus solfataricus), eukaryotic (Homo sapiens), and chloroplast (Arabidopsis thaliana) SRP systems. The comprehensive structural comparison combined with Brownian dynamics simulations of TC formation allows for the description of the general blueprint and of specific adaptations of the quasi-symmetric heterodimer. Our work defines conserved external nucleotide-binding sites for SRP GTPase activation by RNA. Structural analyses of the GDP-bound, post-hydrolysis states reveal a conserved, magnesium-sensitive switch within the I-box. Overall, we provide a general model for SRP cycle regulation by RNA. Copyright © 2016 Elsevier Ltd. All rights reserved.

The time course of individual face recognition: A pattern analysis of ERP signals.

PubMed

Nemrodov, Dan; Niemeier, Matthias; Mok, Jenkin Ngo Yin; Nestor, Adrian

2016-05-15

An extensive body of work documents the time course of neural face processing in the human visual cortex. However, the majority of this work has focused on specific temporal landmarks, such as N170 and N250 components, derived through univariate analyses of EEG data. Here, we take on a broader evaluation of ERP signals related to individual face recognition as we attempt to move beyond the leading theoretical and methodological framework through the application of pattern analysis to ERP data. Specifically, we investigate the spatiotemporal profile of identity recognition across variation in emotional expression. To this end, we apply pattern classification to ERP signals both in time, for any single electrode, and in space, across multiple electrodes. Our results confirm the significance of traditional ERP components in face processing. At the same time though, they support the idea that the temporal profile of face recognition is incompletely described by such components. First, we show that signals associated with different facial identities can be discriminated from each other outside the scope of these components, as early as 70ms following stimulus presentation. Next, electrodes associated with traditional ERP components as well as, critically, those not associated with such components are shown to contribute information to stimulus discriminability. And last, the levels of ERP-based pattern discrimination are found to correlate with recognition accuracy across subjects confirming the relevance of these methods for bridging brain and behavior data. Altogether, the current results shed new light on the fine-grained time course of neural face processing and showcase the value of novel methods for pattern analysis to investigating fundamental aspects of visual recognition. Copyright © 2016 Elsevier Inc. All rights reserved.

Preliminary study on an innovative, simple mast cell-based electrochemical method for detecting foodborne pathogenic bacterial quorum signaling molecules (N-acyl-homoserine-lactones).

PubMed

Jiang, Donglei; Feng, Dongdong; Jiang, Hui; Yuan, Limin; Yongqi, Yin; Xu, Xin; Fang, Weiming

2017-04-15

This paper reports the a novel and simple mast cell-based electrochemical method for detecting of bacterial quorum signaling molecules, N-acylhomoserine lactones (AHLs), which can be utilized to preliminarily evaluate the toxicity of food-borne pathogenic bacteria. Rat basophilic leukemia (RBL-2H3) mast cells encapsulated in alginate/graphene oxide hydrogel were immobilized on a gold electrode, while mast cells as recognition elements were cultured in a 3D cell culture system. Electrochemical impedance spectroscopy (EIS) was utilized to record the cell impedance signal as-influenced by Pseudomonas aeruginosa quorum-sensing molecule, N-3-oxododecanoyl homoserine lactone (3OC 12 -HSL). The results indicated that cellular activities such as cell viability, apoptosis, intracellular calcium, and degranulation were markedly influenced by the AHLs. Importantly, the exposure of 3OC 12 -HSL to mast cells induced a marked decrease in the electrochemical impedance signal in a dose-dependent manner. The detection limit for 3OC 12 -HSL was 0.034μM with a linear range of 0.1-1μM. These results were confirmed via conventional cell assay and transmission electron microscope (TEM) analysis. Altogether, the proposed method appears to be an innovative and effective approach to the quantitative measurement of Gram-negative bacterial quorum signaling molecules; to this effect, it also may serve as a primary evaluation of the cytotoxicity of food-borne pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

The Effect of Asymmetrical Signal Degradation on Binaural Speech Recognition in Children and Adults.

ERIC Educational Resources Information Center

Rothpletz, Ann M.; Tharpe, Anne Marie; Grantham, D. Wesley

2004-01-01

To determine the effect of asymmetrical signal degradation on binaural speech recognition, 28 children and 14 adults were administered a sentence recognition task amidst multitalker babble. There were 3 listening conditions: (a) monaural, with mild degradation in 1 ear; (b) binaural, with mild degradation in both ears (symmetric degradation); and…

Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.

PubMed

Galperin, Michael Y; Higdon, Roger; Kolker, Eugene

2010-04-01

Comparative analysis of the complete genome sequences from a variety of poorly studied organisms aims at predicting ecological and behavioral properties of these organisms and helping in characterizing their habitats. This task requires finding appropriate descriptors that could be correlated with the core traits of each system and would allow meaningful comparisons. Using the relatively simple bacterial models, first attempts have been made to introduce suitable metrics to describe the complexity of organism's signaling machinery, which included introducing the "bacterial IQ" score. Here, we use an updated census of prokaryotic signal transduction systems to improve this parameter and evaluate its consistency within selected bacterial phyla. We also introduce a more elaborate descriptor, a set of profiles of relative abundance of members of each family of signal transduction proteins encoded in each genome. We show that these family profiles are well conserved within each genus and are often consistent within families of bacteria. Thus, they reflect evolutionary relationships between organisms as well as individual adaptations of each organism to its specific ecological niche.

EMD-Based Symbolic Dynamic Analysis for the Recognition of Human and Nonhuman Pyroelectric Infrared Signals.

PubMed

Zhao, Jiaduo; Gong, Weiguo; Tang, Yuzhen; Li, Weihong

2016-01-20

In this paper, we propose an effective human and nonhuman pyroelectric infrared (PIR) signal recognition method to reduce PIR detector false alarms. First, using the mathematical model of the PIR detector, we analyze the physical characteristics of the human and nonhuman PIR signals; second, based on the analysis results, we propose an empirical mode decomposition (EMD)-based symbolic dynamic analysis method for the recognition of human and nonhuman PIR signals. In the proposed method, first, we extract the detailed features of a PIR signal into five symbol sequences using an EMD-based symbolization method, then, we generate five feature descriptors for each PIR signal through constructing five probabilistic finite state automata with the symbol sequences. Finally, we use a weighted voting classification strategy to classify the PIR signals with their feature descriptors. Comparative experiments show that the proposed method can effectively classify the human and nonhuman PIR signals and reduce PIR detector's false alarms.

JAK kinases are required for the bacterial RNA and poly I:C induced tyrosine phosphorylation of PKR

PubMed Central

Bleiblo, Farag; Michael, Paul; Brabant, Danielle; Ramana, Chilakamarti V; Tai, TC; Saleh, Mazen; Parrillo, Joseph E; Kumar, Anand; Kumar, Aseem

2013-01-01

Discriminating the molecular patterns associated with RNA is central to innate immunity. The protein kinase PKR is a cytosolic sensor involved in the recognition of viral dsRNA and triggering interferon-induced signaling. Here, we identified bacterial RNA as a novel distinct pattern recognized by PKR. We show that the tyrosine phosphorylation of PKR induced by either bacterial RNA or poly I:C is impaired in mutant cells lacking TYK2, JAK1, or JAK2 kinases. PKR was found to be a direct substrate for the activated JAKs. Our results indicated that the double-stranded structures of bacterial RNA are required to fully activate PKR. These results suggest that bacterial RNA signaling is analogous in some respects to that of viral RNA and interferons and may have implications in bacterial immunity. PMID:23236554

[A wavelet neural network algorithm of EEG signals data compression and spikes recognition].

PubMed

Zhang, Y; Liu, A; Yu, K

1999-06-01

A novel method of EEG signals compression representation and epileptiform spikes recognition based on wavelet neural network and its algorithm is presented. The wavelet network not only can compress data effectively but also can recover original signal. In addition, the characters of the spikes and the spike-slow rhythm are auto-detected from the time-frequency isoline of EEG signal. This method is well worth using in the field of the electrophysiological signal processing and time-frequency analyzing.

Antimicrobial inflammasomes: unified signalling against diverse bacterial pathogens.

PubMed

Eldridge, Matthew J G; Shenoy, Avinash R

2015-02-01

Inflammasomes - molecular platforms for caspase-1 activation - have emerged as common hubs for a number of pathways that detect and respond to bacterial pathogens. Caspase-1 activation results in the secretion of bioactive IL-1β and IL-18 and pyroptosis, and thus launches a systemic immune and inflammatory response. In this review we discuss signal transduction leading to 'canonical' and 'non-canonical' activation of caspase-1 through the involvement of upstream caspases. Recent studies have identified a growing number of regulatory networks involving guanylate binding proteins, protein kinases, ubiquitylation and necroptosis related pathways that modulate inflammasome responses and immunity to bacterial infection. By being able to respond to extracellular, vacuolar and cytosolic bacteria, their cytosolic toxins or ligands for cell surface receptors, inflammasomes have emerged as important sentinels of infection. Copyright © 2014 Elsevier Ltd. All rights reserved.

The recognition signal hypothesis for the adaptive evolution of religion : a phylogenetic test with Christian denominations.

PubMed

Matthews, Luke J

2012-06-01

Recent research on the evolution of religion has focused on whether religion is an unselected by-product of evolutionary processes or if it is instead an adaptation by natural selection. Adaptive hypotheses for religion include direct fitness benefits from improved health and indirect fitness benefits mediated by costly signals and/or cultural group selection. Herein, I propose that religious denominations achieve indirect fitness gains for members through the use of ecologically arbitrary beliefs, rituals, and moral rules that function as recognition markers of cultural inheritance analogous to kin and species recognition of genetic inheritance in biology. This recognition signal hypotheses could act in concert with either costly signaling or cultural group selection to produce evolutionarily altruistic behaviors within denominations. Using a cultural phylogenetic analysis, I show that a large set of religious behaviors among extant Christian denominations supports the prediction of the recognition signal hypothesis that characters change more frequently near historical schisms. By incorporating demographic data into the model, I show that more-distinctive denominations, as measured through dissimilar characteristics, appear to be protected from intrusion by nonmembers in mixed-denomination households, and that they may be experiencing greater biological growth of their populations even in the present day.

Bacterial signaling ecology and potential applications during aquatic biofilm construction.

PubMed

Vega, Leticia M; Alvarez, Pedro J; McLean, Robert J C

2014-07-01

In their natural environment, bacteria and other microorganisms typically grow as surface-adherent biofilm communities. Cell signal processes, including quorum signaling, are now recognized as being intimately involved in the development and function of biofilms. In contrast to their planktonic (unattached) counterparts, bacteria within biofilms are notoriously resistant to many traditional antimicrobial agents and so represent a major challenge in industry and medicine. Although biofilms impact many human activities, they actually represent an ancient mode of bacterial growth as shown in the fossil record. Consequently, many aquatic organisms have evolved strategies involving signal manipulation to control or co-exist with biofilms. Here, we review the chemical ecology of biofilms and propose mechanisms whereby signal manipulation can be used to promote or control biofilms.

Brain angiogenesis inhibitor 1 (BAI1) is a pattern recognition receptor that mediates macrophage binding and engulfment of Gram-negative bacteria

PubMed Central

Das, Soumita; Owen, Katherine A.; Ly, Kim T.; Park, Daeho; Black, Steven G.; Wilson, Jeffrey M.; Sifri, Costi D.; Ravichandran, Kodi S.; Ernst, Peter B.; Casanova, James E.

2011-01-01

Bacterial recognition by host cells is essential for initiation of infection and the host response. Bacteria interact with host cells via multiple pattern recognition receptors that recognize microbial products or pathogen-associated molecular patterns. In response to this interaction, host cell signaling cascades are activated that lead to inflammatory responses and/or phagocytic clearance of attached bacteria. Brain angiogenesis inhibitor 1 (BAI1) is a receptor that recognizes apoptotic cells through its conserved type I thrombospondin repeats and triggers their engulfment through an ELMO1/Dock/Rac1 signaling module. Because thrombospondin repeats in other proteins have been shown to bind bacterial surface components, we hypothesized that BAI1 may also mediate the recognition and clearance of pathogenic bacteria. We found that preincubation of bacteria with recombinant soluble BAI1 ectodomain or knockdown of endogenous BAI1 in primary macrophages significantly reduced binding and internalization of the Gram-negative pathogen Salmonella typhimurium. Conversely, overexpression of BAI1 enhanced attachment and engulfment of Salmonella in macrophages and in heterologous nonphagocytic cells. Bacterial uptake is triggered by the BAI1-mediated activation of Rac through an ELMO/Dock-dependent mechanism, and inhibition of the BAI1/ELMO1 interaction prevents both Rac activation and bacterial uptake. Moreover, inhibition of ELMO1 or Rac function significantly impairs the proinflammatory response to infection. Finally, we show that BAI1 interacts with a variety of Gram-negative, but not Gram-positive, bacteria through recognition of their surface lipopolysaccharide. Together these findings identify BAI1 as a pattern recognition receptor that mediates nonopsonic phagocytosis of Gram-negative bacteria by macrophages and directly affects the host response to infection. PMID:21245295

Problems Associated with Statistical Pattern Recognition of Acoustic Emission Signals in a Compact Tension Fatigue Specimen

NASA Technical Reports Server (NTRS)

Hinton, Yolanda L.

1999-01-01

Acoustic emission (AE) data were acquired during fatigue testing of an aluminum 2024-T4 compact tension specimen using a commercially available AE system. AE signals from crack extension were identified and separated from noise spikes, signals that reflected from the specimen edges, and signals that saturated the instrumentation. A commercially available software package was used to train a statistical pattern recognition system to classify the signals. The software trained a network to recognize signals with a 91-percent accuracy when compared with the researcher's interpretation of the data. Reasons for the discrepancies are examined and it is postulated that additional preprocessing of the AE data to focus on the extensional wave mode and eliminate other effects before training the pattern recognition system will result in increased accuracy.

Analysis of physiological signals for recognition of boredom, pain, and surprise emotions.

PubMed

Jang, Eun-Hye; Park, Byoung-Jun; Park, Mi-Sook; Kim, Sang-Hyeob; Sohn, Jin-Hun

2015-06-18

The aim of the study was to examine the differences of boredom, pain, and surprise. In addition to that, it was conducted to propose approaches for emotion recognition based on physiological signals. Three emotions, boredom, pain, and surprise, are induced through the presentation of emotional stimuli and electrocardiography (ECG), electrodermal activity (EDA), skin temperature (SKT), and photoplethysmography (PPG) as physiological signals are measured to collect a dataset from 217 participants when experiencing the emotions. Twenty-seven physiological features are extracted from the signals to classify the three emotions. The discriminant function analysis (DFA) as a statistical method, and five machine learning algorithms (linear discriminant analysis (LDA), classification and regression trees (CART), self-organizing map (SOM), Naïve Bayes algorithm, and support vector machine (SVM)) are used for classifying the emotions. The result shows that the difference of physiological responses among emotions is significant in heart rate (HR), skin conductance level (SCL), skin conductance response (SCR), mean skin temperature (meanSKT), blood volume pulse (BVP), and pulse transit time (PTT), and the highest recognition accuracy of 84.7% is obtained by using DFA. This study demonstrates the differences of boredom, pain, and surprise and the best emotion recognizer for the classification of the three emotions by using physiological signals.

Development of small molecule biosensors by coupling the recognition of the bacterial allosteric transcription factor with isothermal strand displacement amplification.

PubMed

Yao, Yongpeng; Li, Shanshan; Cao, Jiaqian; Liu, Weiwei; Fan, Keqiang; Xiang, Wensheng; Yang, Keqian; Kong, Deming; Wang, Weishan

2018-05-08

Here, we demonstrate an easy-to-implement and general biosensing strategy by coupling the small-molecule recognition of the bacterial allosteric transcription factor (aTF) with isothermal strand displacement amplification (SDA) in vitro. Based on this strategy, we developed two biosensors for the detection of an antiseptic, p-hydroxybenzoic acid, and a disease marker, uric acid, using bacterial aTF HosA and HucR, respectively, highlighting the great potential of this strategy for the development of small-molecule biosensors.

Electromagnetic signals are produced by aqueous nanostructures derived from bacterial DNA sequences.

PubMed

Montagnier, Luc; Aïssa, Jamal; Ferris, Stéphane; Montagnier, Jean-Luc; Lavallée, Claude

2009-06-01

A novel property of DNA is described: the capacity of some bacterial DNA sequences to induce electromagnetic waves at high aqueous dilutions. It appears to be a resonance phenomenon triggered by the ambient electromagnetic background of very low frequency waves. The genomic DNA of most pathogenic bacteria contains sequences which are able to generate such signals. This opens the way to the development of highly sensitive detection system for chronic bacterial infections in human and animal diseases.

Colocalization recognition-activated cascade signal amplification strategy for ultrasensitive detection of transcription factors.

PubMed

Zhu, Desong; Wang, Lei; Xu, Xiaowen; Jiang, Wei

2017-03-15

Transcription factors (TFs) bind to specific double-stranded DNA (dsDNA) sequences in the regulatory regions of genes to regulate the process of gene transcription. Their expression levels sensitively reflect cell developmental situation and disease state. TFs have become potential diagnostic markers and therapeutic targets of cancers and some other diseases. Hence, high sensitive detection of TFs is of vital importance for early diagnosis of diseases and drugs development. The traditional exonucleases-assisted signal amplification methods suffered from the false positives caused by incomplete digestion of excess recognition probes. Herein, based on a new recognition way-colocalization recognition (CR)-activated dual signal amplification, an ultrasensitive fluorescent detection strategy for TFs was developed. TFs-induced the colocalization of three split recognition components resulted in noticeable increases of local effective concentrations and hybridization of three split components, which activated the subsequent cascade signal amplification including strand displacement amplification (SDA) and exponential rolling circle amplification (ERCA). This strategy eliminated the false positive influence and achieved ultra-high sensitivity towards the purified NF-κB p50 with detection limit of 2.0×10 -13 M. Moreover, NF-κB p50 can be detected in as low as 0.21ngμL -1 HeLa cell nuclear extracts. In addition, this proposed strategy could be used for the screening of NF-κB p50 activity inhibitors and potential anti-NF-κB p50 drugs. Finally, our proposed strategy offered a potential method for reliable detection of TFs in medical diagnosis and treatment research of cancers and other related diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

Testing Signal-Detection Models of Yes/No and Two-Alternative Forced-Choice Recognition Memory

ERIC Educational Resources Information Center

Jang, Yoonhee; Wixted, John T.; Huber, David E.

2009-01-01

The current study compared 3 models of recognition memory in their ability to generalize across yes/no and 2-alternative forced-choice (2AFC) testing. The unequal-variance signal-detection model assumes a continuous memory strength process. The dual-process signal-detection model adds a thresholdlike recollection process to a continuous…

Wavelet-Based Signal and Image Processing for Target Recognition

NASA Astrophysics Data System (ADS)

Sherlock, Barry G.

2002-11-01

The PI visited NSWC Dahlgren, VA, for six weeks in May-June 2002 and collaborated with scientists in the G33 TEAMS facility, and with Marilyn Rudzinsky of T44 Technology and Photonic Systems Branch. During this visit the PI also presented six educational seminars to NSWC scientists on various aspects of signal processing. Several items from the grant proposal were completed, including (1) wavelet-based algorithms for interpolation of 1-d signals and 2-d images; (2) Discrete Wavelet Transform domain based algorithms for filtering of image data; (3) wavelet-based smoothing of image sequence data originally obtained for the CRITTIR (Clutter Rejection Involving Temporal Techniques in the Infra-Red) project. The PI visited the University of Stellenbosch, South Africa to collaborate with colleagues Prof. B.M. Herbst and Prof. J. du Preez on the use of wavelet image processing in conjunction with pattern recognition techniques. The University of Stellenbosch has offered the PI partial funding to support a sabbatical visit in Fall 2003, the primary purpose of which is to enable the PI to develop and enhance his expertise in Pattern Recognition. During the first year, the grant supported publication of 3 referred papers, presentation of 9 seminars and an intensive two-day course on wavelet theory. The grant supported the work of two students who functioned as research assistants.

Escherichia coli twin arginine (Tat) mutant translocases possessing relaxed signal peptide recognition specificities.

PubMed

Kreutzenbeck, Peter; Kröger, Carsten; Lausberg, Frank; Blaudeck, Natascha; Sprenger, Georg A; Freudl, Roland

2007-03-16

The twin arginine (Tat) secretion pathway allows the translocation of folded proteins across the cytoplasmic membrane of bacteria. Tat-specific signal peptides contain a characteristic amino acid motif ((S/T)RRXFLK) including two highly conserved consecutive arginine residues that are thought to be involved in the recognition of the signal peptides by the Tat translocase. Here, we have analyzed the specificity of Tat signal peptide recognition by using a genetic approach. Replacement of the two arginine residues in a Tat-specific precursor protein by lysine-glutamine resulted in an export-defective mutant precursor that was no longer accepted by the wild-type translocase. Selection for restored export allowed for the isolation of Tat translocases possessing single mutations in either the amino-terminal domain of TatB or the first cytosolic domain of TatC. The mutant Tat translocases still efficiently accepted the unaltered precursor protein, indicating that the substrate specificity of the translocases was not strictly changed; rather, the translocases showed an increased tolerance toward variations of the amino acids occupying the positions of the twin arginine residues in the consensus motif of a Tat signal peptide.

Emotion Recognition from EEG Signals Using Multidimensional Information in EMD Domain.

PubMed

Zhuang, Ning; Zeng, Ying; Tong, Li; Zhang, Chi; Zhang, Hanming; Yan, Bin

2017-01-01

This paper introduces a method for feature extraction and emotion recognition based on empirical mode decomposition (EMD). By using EMD, EEG signals are decomposed into Intrinsic Mode Functions (IMFs) automatically. Multidimensional information of IMF is utilized as features, the first difference of time series, the first difference of phase, and the normalized energy. The performance of the proposed method is verified on a publicly available emotional database. The results show that the three features are effective for emotion recognition. The role of each IMF is inquired and we find that high frequency component IMF1 has significant effect on different emotional states detection. The informative electrodes based on EMD strategy are analyzed. In addition, the classification accuracy of the proposed method is compared with several classical techniques, including fractal dimension (FD), sample entropy, differential entropy, and discrete wavelet transform (DWT). Experiment results on DEAP datasets demonstrate that our method can improve emotion recognition performance.

Linearmycins Activate a Two-Component Signaling System Involved in Bacterial Competition and Biofilm Morphology

PubMed Central

2017-01-01

ABSTRACT Bacteria use two-component signaling systems to adapt and respond to their competitors and changing environments. For instance, competitor bacteria may produce antibiotics and other bioactive metabolites and sequester nutrients. To survive, some species of bacteria escape competition through antibiotic production, biofilm formation, or motility. Specialized metabolite production and biofilm formation are relatively well understood for bacterial species in isolation. How bacteria control these functions when competitors are present is not well studied. To address fundamental questions relating to the competitive mechanisms of different species, we have developed a model system using two species of soil bacteria, Bacillus subtilis and Streptomyces sp. strain Mg1. Using this model, we previously found that linearmycins produced by Streptomyces sp. strain Mg1 cause lysis of B. subtilis cells and degradation of colony matrix. We identified strains of B. subtilis with mutations in the two-component signaling system yfiJK operon that confer dual phenotypes of specific linearmycin resistance and biofilm morphology. We determined that expression of the ATP-binding cassette (ABC) transporter yfiLMN operon, particularly yfiM and yfiN, is necessary for biofilm morphology. Using transposon mutagenesis, we identified genes that are required for YfiLMN-mediated biofilm morphology, including several chaperones. Using transcriptional fusions, we found that YfiJ signaling is activated by linearmycins and other polyene metabolites. Finally, using a truncated YfiJ, we show that YfiJ requires its transmembrane domain to activate downstream signaling. Taken together, these results suggest coordinated dual antibiotic resistance and biofilm morphology by a single multifunctional ABC transporter promotes competitive fitness of B. subtilis. IMPORTANCE DNA sequencing approaches have revealed hitherto unexplored diversity of bacterial species in a wide variety of environments that

Molecular Pathways for Immune Recognition of Preproinsulin Signal Peptide in Type 1 Diabetes.

PubMed

Kronenberg-Versteeg, Deborah; Eichmann, Martin; Russell, Mark A; de Ru, Arnoud; Hehn, Beate; Yusuf, Norkhairin; van Veelen, Peter A; Richardson, Sarah J; Morgan, Noel G; Lemberg, Marius K; Peakman, Mark

2018-04-01

The signal peptide region of preproinsulin (PPI) contains epitopes targeted by HLA-A-restricted (HLA-A0201, A2402) cytotoxic T cells as part of the pathogenesis of β-cell destruction in type 1 diabetes. We extended the discovery of the PPI epitope to disease-associated HLA-B*1801 and HLA-B*3906 (risk) and HLA-A*1101 and HLA-B*3801 (protective) alleles, revealing that four of six alleles present epitopes derived from the signal peptide region. During cotranslational translocation of PPI, its signal peptide is cleaved and retained within the endoplasmic reticulum (ER) membrane, implying it is processed for immune recognition outside of the canonical proteasome-directed pathway. Using in vitro translocation assays with specific inhibitors and gene knockout in PPI-expressing target cells, we show that PPI signal peptide antigen processing requires signal peptide peptidase (SPP). The intramembrane protease SPP generates cytoplasm-proximal epitopes, which are transporter associated with antigen processing (TAP), ER-luminal epitopes, which are TAP independent, each presented by different HLA class I molecules and N-terminal trimmed by ER aminopeptidase 1 for optimal presentation. In vivo, TAP expression is significantly upregulated and correlated with HLA class I hyperexpression in insulin-containing islets of patients with type 1 diabetes. Thus, PPI signal peptide epitopes are processed by SPP and loaded for HLA-guided immune recognition via pathways that are enhanced during disease pathogenesis. © 2018 by the American Diabetes Association.

The DSF Family of Cell–Cell Signals: An Expanding Class of Bacterial Virulence Regulators

PubMed Central

Ryan, Robert P.; An, Shi-qi; Allan, John H.; McCarthy, Yvonne; Dow, J. Maxwell

2015-01-01

Many pathogenic bacteria use cell–cell signaling systems involving the synthesis and perception of diffusible signal molecules to control virulence as a response to cell density or confinement to niches. Bacteria produce signals of diverse structural classes. Signal molecules of the diffusible signal factor (DSF) family are cis-2-unsaturated fatty acids. The paradigm is cis-11-methyl-2-dodecenoic acid from Xanthomonas campestris pv. campestris (Xcc), which controls virulence in this plant pathogen. Although DSF synthesis was thought to be restricted to the xanthomonads, it is now known that structurally related molecules are produced by the unrelated bacteria Burkholderia cenocepacia and Pseudomonas aeruginosa. Furthermore, signaling involving these DSF family members contributes to bacterial virulence, formation of biofilms and antibiotic tolerance in these important human pathogens. Here we review the recent advances in understanding DSF signaling and its regulatory role in different bacteria. These advances include the description of the pathway/mechanism of DSF biosynthesis, identification of novel DSF synthases and new members of the DSF family, the demonstration of a diversity of DSF sensors to include proteins with a Per-Arnt-Sim (PAS) domain and the description of some of the signal transduction mechanisms that impinge on virulence factor expression. In addition, we address the role of DSF family signals in interspecies signaling that modulates the behavior of other microorganisms. Finally, we consider a number of recently reported approaches for the control of bacterial virulence through the modulation of DSF signaling. PMID:26181439

Signal recognition efficiencies of artificial neural-network pulse-shape discrimination in HPGe -decay searches

NASA Astrophysics Data System (ADS)

Caldwell, A.; Cossavella, F.; Majorovits, B.; Palioselitis, D.; Volynets, O.

2015-07-01

A pulse-shape discrimination method based on artificial neural networks was applied to pulses simulated for different background, signal and signal-like interactions inside a germanium detector. The simulated pulses were used to investigate variations of efficiencies as a function of used training set. It is verified that neural networks are well-suited to identify background pulses in true-coaxial high-purity germanium detectors. The systematic uncertainty on the signal recognition efficiency derived using signal-like evaluation samples from calibration measurements is estimated to be 5 %. This uncertainty is due to differences between signal and calibration samples.

Molecular cloning and characterization of a short peptidoglycan recognition protein from silkworm Bombyx mori.

PubMed

Yang, P-J; Zhan, M-Y; Ye, C; Yu, X-Q; Rao, X-J

2017-12-01

Peptidoglycan is the major bacterial component recognized by the insect immune system. Peptidoglycan recognition proteins (PGRPs) are a family of pattern-recognition receptors that recognize peptidoglycans and modulate innate immune responses. Some PGRPs retain N-acetylmuramoyl-L-alanine amidase (Enzyme Commission number: 3.5.1.28) activity to hydrolyse bacterial peptidoglycans. Others have lost the enzymatic activity and work only as immune receptors. They are all important modulators for innate immunity. Here, we report the cloning and functional analysis of PGRP-S4, a short-form PGRP from the domesticated silkworm, Bombyx mori. The PGRP-S4 gene encodes a protein of 199 amino acids with a signal peptide and a PGRP domain. PGRP-S4 was expressed in the fat body, haemocytes and midgut. Its expression level was significantly induced by bacterial challenges in the midgut. The recombinant PGRP-S4 bound bacteria and different peptidoglycans. In addition, it inhibited bacterial growth and hydrolysed an Escherichia coli peptidoglycan in the presence of Zn 2+ . Scanning electron microscopy showed that PGRP-S4 disrupted the bacterial cell surface. PGRP-S4 further increased prophenoloxidase activation caused by peptidoglycans. Taken together, our data suggest that B. mori PGRP-S4 has multiple functions in immunity. © 2017 The Royal Entomological Society.

Somatostatin Signaling in Neuronal Cilia Is Criticalfor Object Recognition Memory

PubMed Central

Einstein, Emily B.; Patterson, Carlyn A.; Hon, Beverly J.; Regan, Kathleen A.; Reddi, Jyoti; Melnikoff, David E.; Mateer, Marcus J.; Schulz, Stefan; Johnson, Brian N.

2010-01-01

Most neurons possess a single, nonmotile cilium that projects out from the cell surface. These microtubule-based organelles are important in brain development and neurogenesis; however, their function in mature neurons is unknown. Cilia express a complement of proteins distinct from other neuronal compartments, one of which is the somatostatin receptor subtype SST3. We show here that SST3 is critical for object recognition memory in mice. sst3 knock-out mice are severely impaired in discriminating novel objects, whereas they retain normal memory for object location. Further, systemic injection of an SST3 antagonist (ACQ090) disrupts recall of familiar objects in wild-type mice. To examine mechanisms of SST3, we tested synaptic plasticity in CA1 hippocampus. Electrically evoked long-term potentiation (LTP) was normal in sst3 knock-out mice, while adenylyl cyclase/cAMP-mediated LTP was impaired. The SST3 antagonist also disrupted cAMP-mediated LTP. Basal cAMP levels in hippocampal lysate were reduced in sst3 knock-out mice compared with wild-type mice, while the forskolin-induced increase in cAMP levels was normal. The SST3 antagonist inhibited forskolin-stimulated cAMP increases, whereas the SST3 agonist L-796,778 increased basal cAMP levels in hippocampal slices but not hippocampal lysate. Our results show that somatostatin signaling in neuronal cilia is critical for recognition memory and suggest that the cAMP pathway is a conserved signaling motif in cilia. Neuronal cilia therefore represent a novel nonsynaptic compartment crucial for signaling involved in a specific form of synaptic plasticity and in novelty detection. PMID:20335466

An intelligent signal processing and pattern recognition technique for defect identification using an active sensor network

NASA Astrophysics Data System (ADS)

Su, Zhongqing; Ye, Lin

2004-08-01

The practical utilization of elastic waves, e.g. Rayleigh-Lamb waves, in high-performance structural health monitoring techniques is somewhat impeded due to the complicated wave dispersion phenomena, the existence of multiple wave modes, the high susceptibility to diverse interferences, the bulky sampled data and the difficulty in signal interpretation. An intelligent signal processing and pattern recognition (ISPPR) approach using the wavelet transform and artificial neural network algorithms was developed; this was actualized in a signal processing package (SPP). The ISPPR technique comprehensively functions as signal filtration, data compression, characteristic extraction, information mapping and pattern recognition, capable of extracting essential yet concise features from acquired raw wave signals and further assisting in structural health evaluation. For validation, the SPP was applied to the prediction of crack growth in an alloy structural beam and construction of a damage parameter database for defect identification in CF/EP composite structures. It was clearly apparent that the elastic wave propagation-based damage assessment could be dramatically streamlined by introduction of the ISPPR technique.

A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors

NASA Astrophysics Data System (ADS)

Ortega, Davi R.; Yang, Chen; Ames, Peter; Baudry, Jerome; Parkinson, John S.; Zhulin, Igor B.

2013-12-01

Bacterial chemoreceptors are widely used as a model system for elucidating the molecular mechanisms of transmembrane signalling and have provided a detailed understanding of how ligand binding by the receptor modulates the activity of its associated kinase CheA. However, the mechanisms by which conformational signals move between signalling elements within a receptor dimer and how they control kinase activity remain unknown. Here, using long molecular dynamics simulations, we show that the kinase-activating cytoplasmic tip of the chemoreceptor fluctuates between two stable conformations in a signal-dependent manner. A highly conserved residue, Phe396, appears to serve as the conformational switch, because flipping of the stacked aromatic rings of an interacting F396-F396‧ pair in the receptor homodimer takes place concomitantly with the signal-related conformational changes. We suggest that interacting aromatic residues, which are common stabilizers of protein tertiary structure, might serve as rotameric molecular switches in other biological processes as well.

[An Extraction and Recognition Method of the Distributed Optical Fiber Vibration Signal Based on EMD-AWPP and HOSA-SVM Algorithm].

PubMed

Zhang, Yanjun; Liu, Wen-zhe; Fu, Xing-hu; Bi, Wei-hong

2016-02-01

Given that the traditional signal processing methods can not effectively distinguish the different vibration intrusion signal, a feature extraction and recognition method of the vibration information is proposed based on EMD-AWPP and HOSA-SVM, using for high precision signal recognition of distributed fiber optic intrusion detection system. When dealing with different types of vibration, the method firstly utilizes the adaptive wavelet processing algorithm based on empirical mode decomposition effect to reduce the abnormal value influence of sensing signal and improve the accuracy of signal feature extraction. Not only the low frequency part of the signal is decomposed, but also the high frequency part the details of the signal disposed better by time-frequency localization process. Secondly, it uses the bispectrum and bicoherence spectrum to accurately extract the feature vector which contains different types of intrusion vibration. Finally, based on the BPNN reference model, the recognition parameters of SVM after the implementation of the particle swarm optimization can distinguish signals of different intrusion vibration, which endows the identification model stronger adaptive and self-learning ability. It overcomes the shortcomings, such as easy to fall into local optimum. The simulation experiment results showed that this new method can effectively extract the feature vector of sensing information, eliminate the influence of random noise and reduce the effects of outliers for different types of invasion source. The predicted category identifies with the output category and the accurate rate of vibration identification can reach above 95%. So it is better than BPNN recognition algorithm and improves the accuracy of the information analysis effectively.

Bacterial effectors target the common signaling partner BAK1 to disrupt multiple MAMP receptor-signaling complexes and impede plant immunity.

PubMed

Shan, Libo; He, Ping; Li, Jianming; Heese, Antje; Peck, Scott C; Nürnberger, Thorsten; Martin, Gregory B; Sheen, Jen

2008-07-17

Successful pathogens have evolved strategies to interfere with host immune systems. For example, the ubiquitous plant pathogen Pseudomonas syringae injects two sequence-distinct effectors, AvrPto and AvrPtoB, to intercept convergent innate immune responses stimulated by multiple microbe-associated molecular patterns (MAMPs). However, the direct host targets and precise molecular mechanisms of bacterial effectors remain largely obscure. We show that AvrPto and AvrPtoB bind the Arabidopsis receptor-like kinase BAK1, a shared signaling partner of both the flagellin receptor FLS2 and the brassinosteroid receptor BRI1. This targeting interferes with ligand-dependent association of FLS2 with BAK1 during infection. It also impedes BAK1-dependent host immune responses to diverse other MAMPs and brassinosteroid signaling. Significantly, the structural basis of AvrPto-BAK1 interaction appears to be distinct from AvrPto-Pto association required for effector-triggered immunity. These findings uncover a unique strategy of bacterial pathogenesis where virulence effectors block signal transmission through a key common component of multiple MAMP-receptor complexes.

Involvement of Pacific oyster CgPGRP-S1S in bacterial recognition, agglutination and granulocyte degranulation.

PubMed

Iizuka, Masao; Nagasaki, Toshihiro; Takahashi, Keisuke G; Osada, Makoto; Itoh, Naoki

2014-03-01

Peptidoglycan recognition protein (PGRP) recognizes invading bacteria through their peptidoglycans (PGN), a component of the bacterial cell wall. Insect PGRPs contribute to effective immune systems as inducers of other host defense responses, while this function has not been reported from PGRP of bivalves. In this study, recombinant CgPGRP-S1S (rCgPGRP-S1S), produced in the mantle and the gill, was synthesized and used to elucidate the immunological function of CgPGRP-S1S. rCgPGRP-S1S bound specifically to DAP-type PGN and to Escherichia coli cells, but not to other DAP-type PGN-containing bacterial species, Vibrio anguillarum, or Bacillus subtilis. Antibacterial activity was not detected, but E. coli cells were agglutinated. Moreover, in addition to these direct interactions with bacterial cells, rCgPGRP-S1S induced secretion of granular contents by hemocyte degranulation. Taken together, these results suggest for the first time that a PGRP of bivalves is, just as in insects, involved in host defense, not only by direct interaction with bacteria, but also by triggering other defense pathways. Copyright © 2013 Elsevier Ltd. All rights reserved.

Recognition of anaerobic bacterial isolates in vitro using electronic nose technology.

PubMed

Pavlou, A; Turner, A P F; Magan, N

2002-01-01

Use of an electronic nose (e.nose) system to differentiation between anaerobic bacteria grown in vitro on agar media. Cultures of Clostridium spp. (14 strains) and Bacteroides fragilis (12 strains) were grown on blood agar plates and incubated in sampling bags for 30 min before head space analysis of the volatiles. Qualitative analyses of the volatile production patterns was carried out using an e.nose system with 14 conducting polymer sensors. Using data analysis techniques such as principal components analysis (PCA), genetic algorithms and neural networks it was possible to differentiate between agar blanks and individual species which accounted for all the data. A total of eight unknowns were correctly discriminated into the bacterial groups. This is the first report of in vitro complex volatile pattern recognition and differentiation of anaerobic pathogens. These results suggest the potential for application of e.nose technology in early diagnosis of microbial pathogens of medical importance.

An Individual Finger Gesture Recognition System Based on Motion-Intent Analysis Using Mechanomyogram Signal

PubMed Central

Ding, Huijun; He, Qing; Zhou, Yongjin; Dan, Guo; Cui, Song

2017-01-01

Motion-intent-based finger gesture recognition systems are crucial for many applications such as prosthesis control, sign language recognition, wearable rehabilitation system, and human–computer interaction. In this article, a motion-intent-based finger gesture recognition system is designed to correctly identify the tapping of every finger for the first time. Two auto-event annotation algorithms are firstly applied and evaluated for detecting the finger tapping frame. Based on the truncated signals, the Wavelet packet transform (WPT) coefficients are calculated and compressed as the features, followed by a feature selection method that is able to improve the performance by optimizing the feature set. Finally, three popular classifiers including naive Bayes (NBC), K-nearest neighbor (KNN), and support vector machine (SVM) are applied and evaluated. The recognition accuracy can be achieved up to 94%. The design and the architecture of the system are presented with full system characterization results. PMID:29167655

Low-shear modeled microgravity: a global environmental regulatory signal affecting bacterial gene expression, physiology, and pathogenesis

NASA Technical Reports Server (NTRS)

Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; LeBlanc, Carly L.; Honer zu Bentrup, Kerstin; Hammond, Timothy; Pierson, Duane L.

2003-01-01

Bacteria inhabit an impressive variety of ecological niches and must adapt constantly to changing environmental conditions. While numerous environmental signals have been examined for their effect on bacteria, the effects of mechanical forces such as shear stress and gravity have only been investigated to a limited extent. However, several important studies have demonstrated a key role for the environmental signals of low shear and/or microgravity in the regulation of bacterial gene expression, physiology, and pathogenesis [Chem. Rec. 1 (2001) 333; Appl. Microbiol. Biotechnol. 54 (2000) 33; Appl. Environ. Microbiol. 63 (1997) 4090; J. Ind. Microbiol. 18 (1997) 22; Curr. Microbiol. 34(4) (1997) 199; Appl. Microbiol. Biotechnol. 56(3-4) (2001) 384; Infect Immun. 68(6) (2000) 3147; Cell 109(7) (2002) 913; Appl. Environ. Microbiol. 68(11) (2002) 5408; Proc. Natl. Acad. Sci. U. S. A. 99(21) (2002) 13807]. The response of bacteria to these environmental signals, which are similar to those encountered during prokaryotic life cycles, may provide insight into bacterial adaptations to physiologically relevant conditions. This review focuses on the current and potential future research trends aimed at understanding the effect of the mechanical forces of low shear and microgravity analogues on different bacterial parameters. In addition, this review also discusses the use of microgravity technology to generate physiologically relevant human tissue models for research in bacterial pathogenesis.

An approach to emotion recognition in single-channel EEG signals: a mother child interaction

NASA Astrophysics Data System (ADS)

Gómez, A.; Quintero, L.; López, N.; Castro, J.

2016-04-01

In this work, we perform a first approach to emotion recognition from EEG single channel signals extracted in four (4) mother-child dyads experiment in developmental psychology. Single channel EEG signals are analyzed and processed using several window sizes by performing a statistical analysis over features in the time and frequency domains. Finally, a neural network obtained an average accuracy rate of 99% of classification in two emotional states such as happiness and sadness.

Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat.

PubMed

Schoonbeek, Henk-Jan; Wang, Hsi-Hua; Stefanato, Francesca L; Craze, Melanie; Bowden, Sarah; Wallington, Emma; Zipfel, Cyril; Ridout, Christopher J

2015-04-01

Perception of pathogen (or microbe)-associated molecular patterns (PAMPs/MAMPs) by pattern recognition receptors (PRRs) is a key component of plant innate immunity. The Arabidopsis PRR EF-Tu receptor (EFR) recognizes the bacterial PAMP elongation factor Tu (EF-Tu) and its derived peptide elf18. Previous work revealed that transgenic expression of AtEFR in Solanaceae confers elf18 responsiveness and broad-spectrum bacterial disease resistance. In this study, we developed a set of bioassays to study the activation of PAMP-triggered immunity (PTI) in wheat. We generated transgenic wheat (Triticum aestivum) plants expressing AtEFR driven by the constitutive rice actin promoter and tested their response to elf18. We show that transgenic expression of AtEFR in wheat confers recognition of elf18, as measured by the induction of immune marker genes and callose deposition. When challenged with the cereal bacterial pathogen Pseudomonas syringae pv. oryzae, transgenic EFR wheat lines had reduced lesion size and bacterial multiplication. These results demonstrate that AtEFR can be transferred successfully from dicot to monocot species, further revealing that immune signalling pathways are conserved across these distant phyla. As novel PRRs are identified, their transfer between plant families represents a useful strategy for enhancing resistance to pathogens in crops. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

The role of multimodal signals in species recognition between tree-killing bark beetles in a narrow sympatric zone.

Treesearch

Deepa S. Pureswaran; Richard W. Hofstetter; Brian Sullivan; Kristen A. Potter

2016-01-01

When related species coexist, selection pressure should favor evolution of species recognition mechanisms to prevent interspecific pairing and wasteful reproductive encounters. We investigated the potential role of pheromone and acoustic signals in species recognition between two species of tree-killing bark beetles, the southern pine beetle, Dendroctonus frontalis...

A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts.

PubMed

Galperin, Michael Y

2005-06-14

Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. This paper presents results of a comprehensive census of signal transduction proteins--histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases--encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others. The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set) can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the highest IQ, including the current leader Wolinella succinogenes

Estradiol-induced object recognition memory consolidation is dependent on activation of mTOR signaling in the dorsal hippocampus

PubMed Central

Fortress, Ashley M.; Fan, Lu; Orr, Patrick T.; Zhao, Zaorui; Frick, Karyn M.

2013-01-01

The mammalian target of rapamycin (mTOR) signaling pathway is an important regulator of protein synthesis and is essential for various forms of hippocampal memory. Here, we asked whether the enhancement of object recognition memory consolidation produced by dorsal hippocampal infusion of 17β-estradiol (E2) is dependent on mTOR signaling in the dorsal hippocampus, and whether E2-induced mTOR signaling is dependent on dorsal hippocampal phosphatidylinositol 3-kinase (PI3K) and extracellular signal-regulated kinase (ERK) activation. We first demonstrated that the enhancement of object recognition induced by E2 was blocked by dorsal hippocampal inhibition of ERK, PI3K, or mTOR activation. We then showed that an increase in dorsal hippocampal ERK phosphorylation 5 min after intracerebroventricular (ICV) E2 infusion was also blocked by dorsal hippocampal infusion of the three cell signaling inhibitors. Next, we found that ICV infusion of E2 increased phosphorylation of the downstream mTOR targets S6K (Thr-421) and 4E-BP1 in the dorsal hippocampus 5 min after infusion, and that this phosphorylation was blocked by dorsal hippocampal infusion of inhibitors of ERK, PI3K, and mTOR. Collectively, these data demonstrate for the first time that activation of the dorsal hippocampal mTOR signaling pathway is necessary for E2 to enhance object recognition memory consolidation and that E2-induced mTOR activation is dependent on upstream activation of ERK and PI3K signaling. PMID:23422279

Bacterial chemoreceptors: high-performance signaling in networked arrays.

PubMed

Hazelbauer, Gerald L; Falke, Joseph J; Parkinson, John S

2008-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on-off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device.

Bacterial chemoreceptors: high-performance signaling in networked arrays

PubMed Central

Hazelbauer, Gerald L.; Falke, Joseph J.; Parkinson, John S.

2010-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on–off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device. PMID:18165013

Investigating Strength and Frequency Effects in Recognition Memory Using Type-2 Signal Detection Theory

ERIC Educational Resources Information Center

Higham, Philip A.; Perfect, Timothy J.; Bruno, Davide

2009-01-01

Criterion- versus distribution-shift accounts of frequency and strength effects in recognition memory were investigated with Type-2 signal detection receiver operating characteristic (ROC) analysis, which provides a measure of metacognitive monitoring. Experiment 1 demonstrated a frequency-based mirror effect, with a higher hit rate and lower…

Assembly of the Human Signal Recognition Particle

NASA Astrophysics Data System (ADS)

Menichelli, Elena; Nagai, Kiyoshi

Large RNA-protein complexes (ribonucleoprotein particles or RNPs) control fundamental biological processes. Their correct assembly is essential for function and occurs by the ordered addition of proteins to the RNA. A good model system for studying RNP assembly is provided by the Signal Recognition Particle (SRP), an RNP conserved from bacteria to humans, with different degrees of complexity. Human SRP, composed of a single RNA molecule and six pro teins, is responsible for the co-translational targeting of secretory and membrane proteins to the endoplasmic reticulum membrane. In vitro studies reveal that the SRP proteins need to be added to the RNA sequentially. If the order of addition is altered, non-native particles are formed. The sequential association of proteins causes conformational changes in the RNA, allowing binding of other proteins. The in vivo assembly is regulated by the translocation of precursors between different cellular compartments. In this chapter we review the current understanding of the human SRP assembly mechanism.

A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts

PubMed Central

Galperin, Michael Y

2005-01-01

Background Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. Results This paper presents results of a comprehensive census of signal transduction proteins – histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases – encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others. Conclusion The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set) can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the highest IQ, including the

Emerging Bordetella pertussis Strains Induce Enhanced Signaling of Human Pattern Recognition Receptors TLR2, NOD2 and Secretion of IL-10 by Dendritic Cells

PubMed Central

Hovingh, Elise S.; van Gent, Marjolein; Hamstra, Hendrik-Jan; Demkes, Marc; Mooi, Frits R.; Pinelli, Elena

2017-01-01

Vaccines against pertussis have been available for more than 60 years. Nonetheless, this highly contagious disease is reemerging even in countries with high vaccination coverage. Genetic changes of Bordetella pertussis over time have been suggested to contribute to the resurgence of pertussis, as these changes may favor escape from vaccine-induced immunity. Nonetheless, studies on the effects of these bacterial changes on the immune response are limited. Here, we characterize innate immune recognition and activation by a collection of genetically diverse B. pertussis strains isolated from Dutch pertussis patients before and after the introduction of the pertussis vaccines. For this purpose, we used HEK-Blue cells transfected with human pattern recognition receptors TLR2, TLR4, NOD2 and NOD1 as a high throughput system for screening innate immune recognition of more than 90 bacterial strains. Physiologically relevant human monocyte derived dendritic cells (moDC), purified from peripheral blood of healthy donors were also used. Findings indicate that, in addition to inducing TLR2 and TLR4 signaling, all B. pertussis strains activate the NOD-like receptor NOD2 but not NOD1. Furthermore, we observed a significant increase in TLR2 and NOD2, but not TLR4, activation by strains circulating after the introduction of pertussis vaccines. When using moDC, we observed that the recently circulating strains induced increased activation of these cells with a dominant IL-10 production. In addition, we observed an increased expression of surface markers including the regulatory molecule PD-L1. Expression of PD-L1 was decreased upon blocking TLR2. These in vitro findings suggest that emerging B. pertussis strains have evolved to dampen the vaccine-induced inflammatory response, which would benefit survival and transmission of this pathogen. Understanding how this disease has resurged in a highly vaccinated population is crucial for the design of improved vaccines against pertussis

Electromyography (EMG) signal recognition using combined discrete wavelet transform based adaptive neuro-fuzzy inference systems (ANFIS)

NASA Astrophysics Data System (ADS)

Arozi, Moh; Putri, Farika T.; Ariyanto, Mochammad; Khusnul Ari, M.; Munadi, Setiawan, Joga D.

2017-01-01

People with disabilities are increasing from year to year either due to congenital factors, sickness, accident factors and war. One form of disability is the case of interruptions of hand function. The condition requires and encourages the search for solutions in the form of creating an artificial hand with the ability as a human hand. The development of science in the field of neuroscience currently allows the use of electromyography (EMG) to control the motion of artificial prosthetic hand into the necessary use of EMG as an input signal to control artificial prosthetic hand. This study is the beginning of a significant research planned in the development of artificial prosthetic hand with EMG signal input. This initial research focused on the study of EMG signal recognition. Preliminary results show that the EMG signal recognition using combined discrete wavelet transform and Adaptive Neuro-Fuzzy Inference System (ANFIS) produces accuracy 98.3 % for training and 98.51% for testing. Thus the results can be used as an input signal for Simulink block diagram of a prosthetic hand that will be developed on next study. The research will proceed with the construction of artificial prosthetic hand along with Simulink program controlling and integrating everything into one system.

Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana.

PubMed

Doornbos, Rogier F; Geraats, Bart P J; Kuramae, Eiko E; Van Loon, L C; Bakker, Peter A H M

2011-04-01

Systemically induced resistance is a promising strategy to control plant diseases, as it affects numerous pathogens. However, since induced resistance reduces one or both growth and activity of plant pathogens, the indigenous microflora may also be affected by an enhanced defensive state of the plant. The aim of this study was to elucidate how much the bacterial rhizosphere microflora of Arabidopsis is affected by induced systemic resistance (ISR) or systemic acquired resistance (SAR). Therefore, the bacterial microflora of wild-type plants and plants affected in their defense signaling was compared. Additionally, ISR was induced by application of methyl jasmonate and SAR by treatment with salicylic acid or benzothiadiazole. As a comparative model, we also used wild type and ethylene-insensitive tobacco. Some of the Arabidopsis genotypes affected in defense signaling showed altered numbers of culturable bacteria in their rhizospheres; however, effects were dependent on soil type. Effects of plant genotype on rhizosphere bacterial community structure could not be related to plant defense because chemical activation of ISR or SAR had no significant effects on density and structure of the rhizosphere bacterial community. These findings support the notion that control of plant diseases by elicitation of systemic resistance will not significantly affect the resident soil bacterial microflora.

Urtica dioica modulates hippocampal insulin signaling and recognition memory deficit in streptozotocin induced diabetic mice.

PubMed

Patel, Sita Sharan; Gupta, Sahil; Udayabanu, Malairaman

2016-06-01

Diabetes mellitus has been associated with functional abnormalities in the hippocampus and performance of cognitive function. Urtica dioica (UD) has been used in the treatment of diabetes. In our previous report we observed that UD extract attenuate diabetes mediated associative and spatial memory dysfunction. The present study aimed to evaluate the effect of UD extract on mouse model of diabetes-induced recognition memory deficit and explore the possible mechanism behind it. Streptozotocin (STZ) (50 mg/kg, i.p. consecutively for 5 days) was used to induce diabetes followed by UD extract (50 mg/kg, oral) or rosiglitazone (ROSI) (5 mg/kg, oral) administration for 8 weeks. STZ induced diabetic mice showed significant decrease in hippocampal insulin signaling and translocation of glucose transporter type 4 (GLUT4) to neuronal membrane resulting in cognitive dysfunction and hypolocomotion. UD treatment effectively improved hippocampal insulin signaling, glucose tolerance and recognition memory performance in diabetic mice, which was comparable to ROSI. Further, diabetes mediated oxidative stress and inflammation was reversed by chronic UD or ROSI administration. UD leaves extract acts via insulin signaling pathway and might prove to be effective for the diabetes mediated central nervous system complications.

Classification of EEG Signals Based on Pattern Recognition Approach.

PubMed

Amin, Hafeez Ullah; Mumtaz, Wajid; Subhani, Ahmad Rauf; Saad, Mohamad Naufal Mohamad; Malik, Aamir Saeed

2017-01-01

Feature extraction is an important step in the process of electroencephalogram (EEG) signal classification. The authors propose a "pattern recognition" approach that discriminates EEG signals recorded during different cognitive conditions. Wavelet based feature extraction such as, multi-resolution decompositions into detailed and approximate coefficients as well as relative wavelet energy were computed. Extracted relative wavelet energy features were normalized to zero mean and unit variance and then optimized using Fisher's discriminant ratio (FDR) and principal component analysis (PCA). A high density EEG dataset validated the proposed method (128-channels) by identifying two classifications: (1) EEG signals recorded during complex cognitive tasks using Raven's Advance Progressive Metric (RAPM) test; (2) EEG signals recorded during a baseline task (eyes open). Classifiers such as, K-nearest neighbors (KNN), Support Vector Machine (SVM), Multi-layer Perceptron (MLP), and Naïve Bayes (NB) were then employed. Outcomes yielded 99.11% accuracy via SVM classifier for coefficient approximations (A5) of low frequencies ranging from 0 to 3.90 Hz. Accuracy rates for detailed coefficients were 98.57 and 98.39% for SVM and KNN, respectively; and for detailed coefficients (D5) deriving from the sub-band range (3.90-7.81 Hz). Accuracy rates for MLP and NB classifiers were comparable at 97.11-89.63% and 91.60-81.07% for A5 and D5 coefficients, respectively. In addition, the proposed approach was also applied on public dataset for classification of two cognitive tasks and achieved comparable classification results, i.e., 93.33% accuracy with KNN. The proposed scheme yielded significantly higher classification performances using machine learning classifiers compared to extant quantitative feature extraction. These results suggest the proposed feature extraction method reliably classifies EEG signals recorded during cognitive tasks with a higher degree of accuracy.

Detection and inhibition of bacterial cell-cell communication.

PubMed

Rice, Scott A; McDougald, Diane; Givskov, Michael; Kjelleberg, Staffan

2008-01-01

Bacteria communicate with other members of their community through the secretion and perception of small chemical cues or signals. The recognition of a signal normally leads to the expression of a large suite of genes, which in some bacteria are involved in the regulation of virulence factors, and as a result, these signaling compounds are key regulatory factors in many disease processes. Thus, it is of interest when studying pathogens to understand the mechanisms used to control the expression of virulence genes so that strategies might be devised for the control of those pathogens. Clearly, the ability to interfere with this process of signaling represents a novel approach for the treatment of bacterial infections. There is a broad range of compounds that bacteria can use for signaling purposes, including fatty acids, peptides, N-acylated homoserine lactones, and the signals collectively called autoinducer 2 (AI-2). This chapter will focus on the latter two signaling systems as they are present in a range of medically relevant bacteria, and here we describe assays for determining whether an organism produces a particular signal and assays that can be used to identify inhibitors of the signaling cascade. Lastly, the signal detection and inhibition assays will be directly linked to the expression of virulence factors of specific pathogens.

Differential Type I Interferon Signaling Is a Master Regulator of Susceptibility to Postinfluenza Bacterial Superinfection

PubMed Central

Larson, Kyle; Morton, Rachelle V.; Prigge, Justin R.; Schmidt, Edward E.; Huber, Victor C.

2016-01-01

ABSTRACT Bacterial superinfections are a primary cause of death during influenza pandemics and epidemics. Type I interferon (IFN) signaling contributes to increased susceptibility of mice to bacterial superinfection around day 7 post-influenza A virus (IAV) infection. Here we demonstrate that the reduced susceptibility to methicillin-resistant Staphylococcus aureus (MRSA) at day 3 post-IAV infection, which we previously reported was due to interleukin-13 (IL-13)/IFN-γ responses, is also dependent on type I IFN signaling and its subsequent requirement for protective IL-13 production. We found, through utilization of blocking antibodies, that reduced susceptibility to MRSA at day 3 post-IAV infection was IFN-β dependent, whereas the increased susceptibility at day 7 was IFN-α dependent. IFN-β signaling early in IAV infection was required for MRSA clearance, whereas IFN-α signaling late in infection was not, though it did mediate increased susceptibility to MRSA at that time. Type I IFN receptor (IFNAR) signaling in CD11c+ and Ly6G+ cells was required for the observed reduced susceptibility at day 3 post-IAV infection. Depletion of Ly6G+ cells in mice in which IFNAR signaling was either blocked or deleted indicated that Ly6G+ cells were responsible for the IFNAR signaling-dependent susceptibility to MRSA superinfection at day 7 post-IAV infection. Thus, during IAV infection, the temporal differences in type I IFN signaling increased bactericidal activity of both CD11c+ and Ly6G+ cells at day 3 and reduced effector function of Ly6G+ cells at day 7. The temporal differential outcomes induced by IFN-β (day 3) and IFN-α (day 7) signaling through the same IFNAR resulted in differential susceptibility to MRSA at 3 and 7 days post-IAV infection. PMID:27143388

On the Measurement of Criterion Noise in Signal Detection Theory: The Case of Recognition Memory

ERIC Educational Resources Information Center

Kellen, David; Klauer, Karl Christoph; Singmann, Henrik

2012-01-01

Traditional approaches within the framework of signal detection theory (SDT; Green & Swets, 1966), especially in the field of recognition memory, assume that the positioning of response criteria is not a noisy process. Recent work (Benjamin, Diaz, & Wee, 2009; Mueller & Weidemann, 2008) has challenged this assumption, arguing not only…

A split recognition mode combined with cascade signal amplification strategy for highly specific, sensitive detection of microRNA.

PubMed

Wang, Rui; Wang, Lei; Zhao, Haiyan; Jiang, Wei

2016-12-15

MicroRNAs (miRNAs) are vital for many biological processes and have been regarded as cancer biomarkers. Specific and sensitive detection of miRNAs is essential for cancer diagnosis and therapy. Herein, a split recognition mode combined with cascade signal amplification strategy is developed for highly specific and sensitive detection of miRNA. The split recognition mode possesses two specific recognition processes, which are based on toehold-mediated strand displacement reaction (TSDR) and direct hybridization reaction. Two recognition probes, hairpin probe (HP) with overhanging toehold domain and assistant probe (AP), are specially designed. Firstly, the toehold domain of HP and AP recognize part of miRNA simultaneously, accompanied with TSDR to unfold the HP and form the stable DNA Y-shaped junction structure (YJS). Then, the AP in YJS can further act as primer to initiate strand displacement amplification, releasing numerous trigger sequences. Finally, the trigger sequences hybridize with padlock DNA to initiate circular rolling circle amplification and generate enhanced fluorescence responses. In this strategy, the dual recognition effect of split recognition mode guarantees the excellent selectivity to discriminate let-7b from high-homology sequences. Furthermore, the high amplification efficiency of cascade signal amplification guarantees a high sensitivity with the detection limit of 3.2 pM and the concentration of let-7b in total RNA sample extracted from Hela cells is determined. These results indicate our strategy will be a promising miRNA detection strategy in clinical diagnosis and disease treatment. Copyright © 2016 Elsevier B.V. All rights reserved.

Pattern-recognition receptors: signaling pathways and dysregulation in canine chronic enteropathies-brief review.

PubMed

Heilmann, Romy M; Allenspach, Karin

2017-11-01

Pattern-recognition receptors (PRRs) are expressed by innate immune cells and recognize pathogen-associated molecular patterns (PAMPs) as well as endogenous damage-associated molecular pattern (DAMP) molecules. With a large potential for synergism or convergence between their signaling pathways, PRRs orchestrate a complex interplay of cellular mediators and transcription factors, and thus play a central role in homeostasis and host defense. Aberrant activation of PRR signaling, mutations of the receptors and/or their downstream signaling molecules, and/or DAMP/PAMP complex-mediated receptor signaling can potentially lead to chronic auto-inflammatory diseases or development of cancer. PRR signaling pathways appear to also present an interesting new avenue for the modulation of inflammatory responses and to serve as potential novel therapeutic targets. Evidence for a dysregulation of the PRR toll-like receptor (TLR)2, TLR4, TLR5, and TLR9, nucleotide-binding oligomerization domain-containing protein (NOD)2, and the receptor of advanced glycation end products (RAGE) exists in dogs with chronic enteropathies. We describe the TLR, NOD2, and RAGE signaling pathways and evaluate the current veterinary literature-in comparison to human medicine-to determine the role of TLRs, NOD2, and RAGE in canine chronic enteropathies.

A type III effector antagonizes death receptor signalling during bacterial gut infection.

PubMed

Pearson, Jaclyn S; Giogha, Cristina; Ong, Sze Ying; Kennedy, Catherine L; Kelly, Michelle; Robinson, Keith S; Lung, Tania Wong Fok; Mansell, Ashley; Riedmaier, Patrice; Oates, Clare V L; Zaid, Ali; Mühlen, Sabrina; Crepin, Valerie F; Marches, Olivier; Ang, Ching-Seng; Williamson, Nicholas A; O'Reilly, Lorraine A; Bankovacki, Aleksandra; Nachbur, Ueli; Infusini, Giuseppe; Webb, Andrew I; Silke, John; Strasser, Andreas; Frankel, Gad; Hartland, Elizabeth L

2013-09-12

Successful infection by enteric bacterial pathogens depends on the ability of the bacteria to colonize the gut, replicate in host tissues and disseminate to other hosts. Pathogens such as Salmonella, Shigella and enteropathogenic and enterohaemorrhagic (EPEC and EHEC, respectively) Escherichia coli use a type III secretion system (T3SS) to deliver virulence effector proteins into host cells during infection that promote colonization and interfere with antimicrobial host responses. Here we report that the T3SS effector NleB1 from EPEC binds to host cell death-domain-containing proteins and thereby inhibits death receptor signalling. Protein interaction studies identified FADD, TRADD and RIPK1 as binding partners of NleB1. NleB1 expressed ectopically or injected by the bacterial T3SS prevented Fas ligand or TNF-induced formation of the canonical death-inducing signalling complex (DISC) and proteolytic activation of caspase-8, an essential step in death-receptor-induced apoptosis. This inhibition depended on the N-acetylglucosamine transferase activity of NleB1, which specifically modified Arg 117 in the death domain of FADD. The importance of the death receptor apoptotic pathway to host defence was demonstrated using mice deficient in the FAS signalling pathway, which showed delayed clearance of the EPEC-like mouse pathogen Citrobacter rodentium and reversion to virulence of an nleB mutant. The activity of NleB suggests that EPEC and other attaching and effacing pathogens antagonize death-receptor-induced apoptosis of infected cells, thereby blocking a major antimicrobial host response.

A type III effector antagonises death receptor signalling during bacterial gut infection

PubMed Central

Pearson, Jaclyn S; Giogha, Cristina; Ong, Sze Ying; Kennedy, Catherine L; Kelly, Michelle; Robinson, Keith S; Wong, Tania; Mansell, Ashley; Riedmaier, Patrice; Oates, Clare VL; Zaid, Ali; Mühlen, Sabrina; Crepin, Valerie F; Marches, Olivier; Ang, Ching-Seng; Williamson, Nicholas A; O’Reilly, Lorraine A; Bankovacki, Aleksandra; Nachbur, Ueli; Infusini, Giuseppe; Webb, Andrew I; Silke, John; Strasser, Andreas; Frankel, Gad; Hartland, Elizabeth L

2013-01-01

Successful infection by enteric bacterial pathogens depends on the ability of the bacteria to colonise the gut, replicate in host tissues and disseminate to other hosts. Pathogens such as Salmonella, Shigella and enteropathogenic and enterohaemorrhagic E. coli (EPEC and EHEC), utilise a type III secretion system (T3SS) to deliver virulence effector proteins into host cells during infection that promote colonisation and interfere with antimicrobial host responses 1-3. Here we report that the T3SS effector NleB1 from EPEC binds to host cell death domain containing proteins and thereby inhibits death receptor signalling. Protein interaction studies identified FADD, TRADD and RIPK1 as binding partners of NleB1. NleB1 expressed ectopically or injected by the bacterial T3SS prevented Fas ligand or TNF-induced formation of the canonical death inducing signalling complex (DISC) and proteolytic activation of caspase-8, an essential step in death receptor induced apoptosis. This inhibition depended on the N-GlcNAc transferase activity of NleB1, which specifically modified Arg117 in the death domain of FADD. The importance of the death receptor apoptotic pathway to host defence was demonstrated using mice deficient in the FAS signalling pathway, which showed delayed clearance of the EPEC-like mouse pathogen Citrobacter rodentium and reversion to virulence of an nleB mutant. The activity of NleB suggests that EPEC and other attaching and effacing (A/E) pathogens antagonise death receptor induced apoptosis of infected cells, thereby blocking a major antimicrobial host response. PMID:24025841

Biomimetic/Optical Sensors for Detecting Bacterial Species

NASA Technical Reports Server (NTRS)

Homer, Margie; Ksendzov, Alexander; Yen, Shiao-Pin; Ryan, Margaret; Lazazzera, Beth

2006-01-01

Biomimetic/optical sensors have been proposed as means of real-time detection of bacteria in liquid samples through real-time detection of compounds secreted by the bacteria. Bacterial species of interest would be identified through detection of signaling compounds unique to those species. The best-characterized examples of quorum-signaling compounds are acyl-homoserine lactones and peptides. Each compound, secreted by each bacterium of an affected species, serves as a signal to other bacteria of the same species to engage in a collective behavior when the population density of that species reaches a threshold level analogous to a quorum. A sensor according to the proposal would include a specially formulated biomimetic film, made of a molecularly imprinted polymer (MIP), that would respond optically to the signaling compound of interest. The MIP film would be integrated directly onto an opticalwaveguide- based ring resonator for optical readout. Optically, the sensor would resemble the one described in Chemical Sensors Based on Optical Ring Resonators (NPO-40601), NASA Tech Briefs, Vol. 29, No. 10 (October 2005), page 32. MIPs have been used before as molecular- recognition compounds, though not in the manner of the present proposal. Molecular imprinting is an approach to making molecularly selective cavities in a polymer matrix. These cavities function much as enzyme receptor sites: the chemical functionality and shape of a cavity in the polymer matrix cause the cavity to bind to specific molecules. An MIP matrix is made by polymerizing monomers in the presence of the compound of interest (template molecule). The polymer forms around the template. After the polymer solidifies, the template molecules are removed from the polymer matrix by decomplexing them from their binding sites and then dissolving them, leaving cavities that are matched to the template molecules in size, shape, and chemical functionality. The cavities thus become molecular-recognition sites

Toll immune signal activates cellular immune response via eicosanoids.

PubMed

Shafeeq, Tahir; Ahmed, Shabbir; Kim, Yonggyun

2018-07-01

Upon immune challenge, insects recognize nonself. The recognition signal will propagate to nearby immune effectors. It is well-known that Toll signal pathway induces antimicrobial peptide (AMP) gene expression. Eicosanoids play crucial roles in mediating the recognition signal to immune effectors by enhancing humoral immune response through activation of AMP synthesis as well as cellular immune responses, suggesting a functional cross-talk between Toll and eicosanoid signals. This study tested a cross-talk between these two signals. Two signal transducing factors (MyD88 and Pelle) of Toll immune pathway were identified in Spodoptera exigua. RNA interference (RNAi) of either SeMyD88 or SePelle expression interfered with the expression of AMP genes under Toll signal pathway. Bacterial challenge induced PLA 2 enzyme activity. However, RNAi of these two immune factors significantly suppressed the induction of PLA 2 enzyme activity. Furthermore, RNAi treatment prevented gene expression of cellular PLA 2 . Inhibition of PLA 2 activity reduced phenoloxidase activity and subsequent suppression in cellular immune response measured by hemocyte nodule formation. However, immunosuppression induced by RNAi of Toll signal molecules was significantly reversed by addition of arachidonic acid (AA), a catalytic product of PLA 2 . The addition also significantly reduced the enhanced fungal susceptibility of S. exigua treated by RNAi against two Toll signal molecules. These results indicate that there is a cross-talk between Toll and eicosanoid signals in insect immunity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Unsupervised pattern recognition methods in ciders profiling based on GCE voltammetric signals.

PubMed

Jakubowska, Małgorzata; Sordoń, Wanda; Ciepiela, Filip

2016-07-15

This work presents a complete methodology of distinguishing between different brands of cider and ageing degrees, based on voltammetric signals, utilizing dedicated data preprocessing procedures and unsupervised multivariate analysis. It was demonstrated that voltammograms recorded on glassy carbon electrode in Britton-Robinson buffer at pH 2 are reproducible for each brand. By application of clustering algorithms and principal component analysis visible homogenous clusters were obtained. Advanced signal processing strategy which included automatic baseline correction, interval scaling and continuous wavelet transform with dedicated mother wavelet, was a key step in the correct recognition of the objects. The results show that voltammetry combined with optimized univariate and multivariate data processing is a sufficient tool to distinguish between ciders from various brands and to evaluate their freshness. Copyright © 2016 Elsevier Ltd. All rights reserved.

Xanthomonas campestris cell–cell signalling molecule DSF (diffusible signal factor) elicits innate immunity in plants and is suppressed by the exopolysaccharide xanthan

PubMed Central

Kakkar, Akanksha; Nizampatnam, Narasimha Rao; Kondreddy, Anil; Pradhan, Binod Bihari; Chatterjee, Subhadeep

2015-01-01

Several secreted and surface-associated conserved microbial molecules are recognized by the host to mount the defence response. One such evolutionarily well-conserved bacterial process is the production of cell–cell signalling molecules which regulate production of multiple virulence functions by a process known as quorum sensing. Here it is shown that a bacterial fatty acid cell–cell signalling molecule, DSF (diffusible signal factor), elicits innate immunity in plants. The DSF family of signalling molecules are highly conserved among many phytopathogenic bacteria belonging to the genus Xanthomonas as well as in opportunistic animal pathogens. Using Arabidopsis, Nicotiana benthamiana, and rice as model systems, it is shown that DSF induces a hypersensitivity reaction (HR)-like response, programmed cell death, the accumulation of autofluorescent compounds, hydrogen peroxide production, and the expression of the PATHOGENESIS-RELATED1 (PR-1) gene. Furthermore, production of the DSF signalling molecule in Pseudomonas syringae, a non-DSF-producing plant pathogen, induces the innate immune response in the N. benthamiana host plant and also affects pathogen growth. By pre- and co-inoculation of DSF, it was demonstrated that the DSF-induced plant defence reduces disease severity and pathogen growth in the host plant. In this study, it was further demonstrated that wild-type Xanthomonas campestris suppresses the DSF-induced innate immunity by secreting xanthan, the main component of extracellular polysaccharide. The results indicate that plants have evolved to recognize a widely conserved bacterial communication system and may have played a role in the co-evolution of host recognition of the pathogen and the communication machinery. PMID:26248667

Bacterial uracil modulates Drosophila DUOX-dependent gut immunity via Hedgehog-induced signaling endosomes.

PubMed

Lee, Kyung-Ah; Kim, Boram; Bhin, Jinhyuk; Kim, Do Hun; You, Hyejin; Kim, Eun-Kyoung; Kim, Sung-Hee; Ryu, Ji-Hwan; Hwang, Daehee; Lee, Won-Jae

2015-02-11

Genetic studies in Drosophila have demonstrated that generation of microbicidal reactive oxygen species (ROS) through the NADPH dual oxidase (DUOX) is a first line of defense in the gut epithelia. Bacterial uracil acts as DUOX-activating ligand through poorly understood mechanisms. Here, we show that the Hedgehog (Hh) signaling pathway modulates uracil-induced DUOX activation. Uracil-induced Hh signaling is required for intestinal expression of the calcium-dependent cell adhesion molecule Cadherin 99C (Cad99C) and subsequent Cad99C-dependent formation of endosomes. These endosomes play essential roles in uracil-induced ROS production by acting as signaling platforms for PLCβ/PKC/Ca2+-dependent DUOX activation. Animals with impaired Hh signaling exhibit abolished Cad99C-dependent endosome formation and reduced DUOX activity, resulting in high mortality during enteric infection. Importantly, endosome formation, DUOX activation, and normal host survival are restored by genetic reintroduction of Cad99C into enterocytes, demonstrating the important role for Hh signaling in host resistance to enteric infection. Copyright © 2015 Elsevier Inc. All rights reserved.

Using Pattern Recognition and Discriminance Analysis to Predict Critical Events in Large Signal Databases

NASA Astrophysics Data System (ADS)

Feller, Jens; Feller, Sebastian; Mauersberg, Bernhard; Mergenthaler, Wolfgang

2009-09-01

Many applications in plant management require close monitoring of equipment performance, in particular with the objective to prevent certain critical events. At each point in time, the information available to classify the criticality of the process, is represented through the historic signal database as well as the actual measurement. This paper presents an approach to detect and predict critical events, based on pattern recognition and discriminance analysis.

The Effect of Elevated Intra-Abdominal Pressure on TLR4 Signaling in Intestinal Mucosa and on Intestinal Bacterial Translocation in a Rat.

PubMed

Strier, Adam; Kravarusic, Dragan; Coran, Arnold G; Srugo, Isaac; Bitterman, Nir; Dorfman, Tatiana; Pollak, Yulia; Matter, Ibrahim; Sukhotnik, Igor

2017-02-01

Recent evidence suggests that elevated intra-abdominal pressure (IAP) may adversely affect the intestinal barrier function. Toll-like receptor 4 (TLR-4) is responsible for the recognition of bacterial endotoxin or lipopolysaccharide and for initiation of the Gram-negative septic shock syndrome. The objective of the current study was to determine the effects of elevated IAP on intestinal bacterial translocation (BT) and TLR-4 signaling in intestinal mucosa in a rat model. Male Sprague-Dawley rats were randomly assigned to one of two experimental groups: sham animals (Sham) and IAP animals who were subjected to a 15 mmHg pressure pneumoperitoneum for 30 minutes. Rats were sacrificed 24 hours later. BT to mesenteric lymph nodes, liver, portal vein blood, and peripheral blood was determined at sacrifice. TLR4-related gene and protein expression (TLR-4; myeloid differentiation factor 88 [Myd88] and TNF-α receptor-associated factor 6 [TRAF6]) expression were determined using real-time PCR, western blotting, and immunohistochemistry. Thirty percent of sham rats developed BT in the mesenteric lymph nodes (level I) and 20% of control rats developed BT in the liver and portal vein (level II). abdominal compartment syndrome (ACS) rats demonstrated an 80% BT in the lymph nodes (Level I) and 40% BT in the liver and portal vein (Level II). Elevated BT was accompanied by a significant increase in TLR-4 immunostaining in jejunum (51%) and ileum (35.9%), and in a number of TRAF6-positive cells in jejunum (2.1%) and ileum (24.01%) compared to control animals. ACS rats demonstrated a significant increase in TLR4 and MYD88 protein levels compared to control animals. Twenty-four hours after the induction of elevated IAP in a rat model, increased BT rates were associated with increased TLR4 signaling in intestinal mucosa.

The Tandem CARDs of NOD2: Intramolecular Interactions and Recognition of RIP2

PubMed Central

Fridh, Veronica; Rittinger, Katrin

2012-01-01

Caspase recruitment domains (CARDs) are homotypic protein interaction modules that link the stimulus-dependent assembly of large signaling platforms such as inflammasomes to the activation of downstream effectors that often include caspases and kinases and thereby play an important role in the regulation of inflammatory and apoptotic signaling pathways. NOD2 belongs to the NOD-like (NLR) family of intracellular pattern recognition receptors (PRR) and induces activation of the NF-κB pathway in response to the recognition of bacterial components. This process requires the specific recognition of the CARD of the protein kinase RIP2 by the tandem CARDs of NOD2. Here we demonstrate that the tandem CARDs of NOD2 are engaged in an intramolecular interaction that is important for the structural stability of this region. Using a combination of ITC and pull-down experiments we identify distinct surface areas that are involved in the intramolecular tandem CARD interaction and the interaction with the downstream effector RIP2. Our findings indicate that while CARDa of NOD2 might be the primary binding partner of RIP2 the two CARDs of NOD2 do not act independently of one another but may cooperate to from a binding surface that is distinct from that of single CARDs. PMID:22470564

Are there differential deficits in facial emotion recognition between paranoid and non-paranoid schizophrenia? A signal detection analysis.

PubMed

Huang, Charles Lung-Cheng; Hsiao, Sigmund; Hwu, Hai-Gwo; Howng, Shen-Long

2013-10-30

This study assessed facial emotion recognition abilities in subjects with paranoid and non-paranoid schizophrenia (NPS) using signal detection theory. We explore the differential deficits in facial emotion recognition in 44 paranoid patients with schizophrenia (PS) and 30 non-paranoid patients with schizophrenia (NPS), compared to 80 healthy controls. We used morphed faces with different intensities of emotion and computed the sensitivity index (d') of each emotion. The results showed that performance differed between the schizophrenia and healthy controls groups in the recognition of both negative and positive affects. The PS group performed worse than the healthy controls group but better than the NPS group in overall performance. Performance differed between the NPS and healthy controls groups in the recognition of all basic emotions and neutral faces; between the PS and healthy controls groups in the recognition of angry faces; and between the PS and NPS groups in the recognition of happiness, anger, sadness, disgust, and neutral affects. The facial emotion recognition impairment in schizophrenia may reflect a generalized deficit rather than a negative-emotion specific deficit. The PS group performed worse than the control group, but better than the NPS group in facial expression recognition, with differential deficits between PS and NPS patients. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Subject-independent emotion recognition based on physiological signals: a three-stage decision method.

PubMed

Chen, Jing; Hu, Bin; Wang, Yue; Moore, Philip; Dai, Yongqiang; Feng, Lei; Ding, Zhijie

2017-12-20

Collaboration between humans and computers has become pervasive and ubiquitous, however current computer systems are limited in that they fail to address the emotional component. An accurate understanding of human emotions is necessary for these computers to trigger proper feedback. Among multiple emotional channels, physiological signals are synchronous with emotional responses; therefore, analyzing physiological changes is a recognized way to estimate human emotions. In this paper, a three-stage decision method is proposed to recognize four emotions based on physiological signals in the multi-subject context. Emotion detection is achieved by using a stage-divided strategy in which each stage deals with a fine-grained goal. The decision method consists of three stages. During the training process, the initial stage transforms mixed training subjects to separate groups, thus eliminating the effect of individual differences. The second stage categorizes four emotions into two emotion pools in order to reduce recognition complexity. The third stage trains a classifier based on emotions in each emotion pool. During the testing process, a test case or test trial will be initially classified to a group followed by classification into an emotion pool in the second stage. An emotion will be assigned to the test trial in the final stage. In this paper we consider two different ways of allocating four emotions into two emotion pools. A comparative analysis is also carried out between the proposal and other methods. An average recognition accuracy of 77.57% was achieved on the recognition of four emotions with the best accuracy of 86.67% to recognize the positive and excited emotion. Using differing ways of allocating four emotions into two emotion pools, we found there is a difference in the effectiveness of a classifier on learning each emotion. When compared to other methods, the proposed method demonstrates a significant improvement in recognizing four emotions in the

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

PubMed Central

Meisel, Joshua D.; Panda, Oishika; Mahanti, Parag; Schroeder, Frank C.; Kim, Dennis H.

2014-01-01

Summary Discrimination among pathogenic and beneficial microbes is essential for host organism immunity and homeostasis. Here, we show that chemosensory detection of two secondary metabolites produced by Pseudomonas aeruginosa modulates a neuroendocrine signaling pathway that promotes avoidance behavior in the simple animal host Caenorhabditis elegans. Secondary metabolites phenazine-1-carboxamide and pyochelin activate a G protein-signaling pathway in the ASJ chemosensory neuron pair that induces expression of the neuromodulator DAF-7/TGF-β. DAF-7, in turn, activates a canonical TGF-β signaling pathway in adjacent interneurons to modulate aerotaxis behavior and promote avoidance of pathogenic P. aeruginosa. Our data provide a chemical, genetic, and neuronal basis for how the behavior and physiology of a simple animal host can be modified by the microbial environment, and suggest that secondary metabolites produced by microbes may provide environmental cues that contribute to pathogen recognition and host survival. PMID:25303524

A novel screen-printed mast cell-based electrochemical sensor for detecting spoilage bacterial quorum signaling molecules (N-acyl-homoserine-lactones) in freshwater fish.

PubMed

Jiang, Donglei; Liu, Yan; Jiang, Hui; Rao, Shengqi; Fang, Wu; Wu, Mangang; Yuan, Limin; Fang, Weiming

2018-04-15

A novel screen-printed cell-based electrochemical sensor was developed to assess bacterial quorum signaling molecules, N-acylhomoserine lactones (AHLs). Screen-printed carbon electrode (SPCE), which possesses excellent properties such as low-cost, disposable and energy-efficient, was modified with multi-walled carbon nanotubes (MWNTs) to improve electrochemical signals and enhance the sensitivity. Rat basophilic leukemia (RBL-2H3) mast cells encapsulated in alginate/graphene oxide (NaAgl/GO) hydrogel were immobilized on the MWNTs/SPCE to serve as recognition element. Electrochemical impedance spectroscopy (EIS) was employed to record the cell impedance signal as-influenced by Pseudomonas aeruginosa quorum-sensing molecule, N-3-oxododecanoyl homoserine lactone (3OC 12 -HSL). Experimental results show that 3OC 12 -HSL caused a significant decrease in cell viability in a dose dependent manner. The EIS value decreased with concentrations of 3OC 12 -HSL in the range of 0.1-1μM, and the detection limit for 3OC 12 -HSL was calculated to be 0.094μM. These results were confirmed via cell viability, SEM, TEM analysis. Next, the sensor was successfully applied to monitoring the production of AHLs by spoilage bacteria in three different freshwater fish juice samples which efficiently proved the practicability of this cell based method. Therefore, the proposed cell sensor may serve as an innovative and effective approach to the measurement of quorum signaling molecule and thus provides a new avenue for real-time monitoring the spoilage bacteria in freshwater fish production. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial Stimulation of Toll-Like Receptor 4 Drives Macrophages To Hemophagocytose

PubMed Central

McDonald, Erin M.; Pilonieta, M. Carolina; Nick, Heidi J.

2015-01-01

During acute infection with bacteria, viruses or parasites, a fraction of macrophages engulf large numbers of red and white blood cells, a process called hemophagocytosis. Hemophagocytes persist into the chronic stage of infection and have an anti-inflammatory phenotype. Salmonella enterica serovar Typhimurium infection of immunocompetent mice results in acute followed by chronic infection, with the accumulation of hemophagocytes. The mechanism(s) that triggers a macrophage to become hemophagocytic is unknown, but it has been reported that the proinflammatory cytokine gamma interferon (IFN-γ) is responsible. We show that primary macrophages become hemophagocytic in the absence or presence of IFN-γ upon infection with Gram-negative bacterial pathogens or prolonged exposure to heat-killed Salmonella enterica, the Gram-positive bacterium Bacillus subtilis, or Mycobacterium marinum. Moreover, conserved microbe-associated molecular patterns are sufficient to stimulate macrophages to hemophagocytose. Purified bacterial lipopolysaccharide (LPS) induced hemophagocytosis in resting and IFN-γ-pretreated macrophages, whereas lipoteichoic acid and synthetic unmethylated deoxycytidine-deoxyguanosine dinucleotides, which mimic bacterial DNA, induced hemophagocytosis only in IFN-γ-pretreated macrophages. Chemical inhibition or genetic deletion of Toll-like receptor 4, a pattern recognition receptor responsive to LPS, prevented both Salmonella- and LPS-stimulated hemophagocytosis. Inhibition of NF-κB also prevented hemophagocytosis. These results indicate that recognition of microbial products by Toll-like receptors stimulates hemophagocytosis, a novel outcome of prolonged Toll-like receptor signaling, suggesting hemophagocytosis is a highly conserved innate immune response. PMID:26459510

Differential Type I Interferon Signaling Is a Master Regulator of Susceptibility to Postinfluenza Bacterial Superinfection.

PubMed

Shepardson, Kelly M; Larson, Kyle; Morton, Rachelle V; Prigge, Justin R; Schmidt, Edward E; Huber, Victor C; Rynda-Apple, Agnieszka

2016-05-03

Bacterial superinfections are a primary cause of death during influenza pandemics and epidemics. Type I interferon (IFN) signaling contributes to increased susceptibility of mice to bacterial superinfection around day 7 post-influenza A virus (IAV) infection. Here we demonstrate that the reduced susceptibility to methicillin-resistant Staphylococcus aureus (MRSA) at day 3 post-IAV infection, which we previously reported was due to interleukin-13 (IL-13)/IFN-γ responses, is also dependent on type I IFN signaling and its subsequent requirement for protective IL-13 production. We found, through utilization of blocking antibodies, that reduced susceptibility to MRSA at day 3 post-IAV infection was IFN-β dependent, whereas the increased susceptibility at day 7 was IFN-α dependent. IFN-β signaling early in IAV infection was required for MRSA clearance, whereas IFN-α signaling late in infection was not, though it did mediate increased susceptibility to MRSA at that time. Type I IFN receptor (IFNAR) signaling in CD11c(+) and Ly6G(+) cells was required for the observed reduced susceptibility at day 3 post-IAV infection. Depletion of Ly6G(+) cells in mice in which IFNAR signaling was either blocked or deleted indicated that Ly6G(+) cells were responsible for the IFNAR signaling-dependent susceptibility to MRSA superinfection at day 7 post-IAV infection. Thus, during IAV infection, the temporal differences in type I IFN signaling increased bactericidal activity of both CD11c(+) and Ly6G(+) cells at day 3 and reduced effector function of Ly6G(+) cells at day 7. The temporal differential outcomes induced by IFN-β (day 3) and IFN-α (day 7) signaling through the same IFNAR resulted in differential susceptibility to MRSA at 3 and 7 days post-IAV infection. Approximately 114,000 hospitalizations and 40,000 annual deaths in the United States are associated with influenza A virus (IAV) infections. Frequently, these deaths are due to community-acquired Gram-positive bacterial

The process of spoken word recognition in the face of signal degradation.

PubMed

Farris-Trimble, Ashley; McMurray, Bob; Cigrand, Nicole; Tomblin, J Bruce

2014-02-01

Though much is known about how words are recognized, little research has focused on how a degraded signal affects the fine-grained temporal aspects of real-time word recognition. The perception of degraded speech was examined in two populations with the goal of describing the time course of word recognition and lexical competition. Thirty-three postlingually deafened cochlear implant (CI) users and 57 normal hearing (NH) adults (16 in a CI-simulation condition) participated in a visual world paradigm eye-tracking task in which their fixations to a set of phonologically related items were monitored as they heard one item being named. Each degraded-speech group was compared with a set of age-matched NH participants listening to unfiltered speech. CI users and the simulation group showed a delay in activation relative to the NH listeners, and there is weak evidence that the CI users showed differences in the degree of peak and late competitor activation. In general, though, the degraded-speech groups behaved statistically similarly with respect to activation levels. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Xanthomonas campestris cell-cell signalling molecule DSF (diffusible signal factor) elicits innate immunity in plants and is suppressed by the exopolysaccharide xanthan.

PubMed

Kakkar, Akanksha; Nizampatnam, Narasimha Rao; Kondreddy, Anil; Pradhan, Binod Bihari; Chatterjee, Subhadeep

2015-11-01

Several secreted and surface-associated conserved microbial molecules are recognized by the host to mount the defence response. One such evolutionarily well-conserved bacterial process is the production of cell-cell signalling molecules which regulate production of multiple virulence functions by a process known as quorum sensing. Here it is shown that a bacterial fatty acid cell-cell signalling molecule, DSF (diffusible signal factor), elicits innate immunity in plants. The DSF family of signalling molecules are highly conserved among many phytopathogenic bacteria belonging to the genus Xanthomonas as well as in opportunistic animal pathogens. Using Arabidopsis, Nicotiana benthamiana, and rice as model systems, it is shown that DSF induces a hypersensitivity reaction (HR)-like response, programmed cell death, the accumulation of autofluorescent compounds, hydrogen peroxide production, and the expression of the PATHOGENESIS-RELATED1 (PR-1) gene. Furthermore, production of the DSF signalling molecule in Pseudomonas syringae, a non-DSF-producing plant pathogen, induces the innate immune response in the N. benthamiana host plant and also affects pathogen growth. By pre- and co-inoculation of DSF, it was demonstrated that the DSF-induced plant defence reduces disease severity and pathogen growth in the host plant. In this study, it was further demonstrated that wild-type Xanthomonas campestris suppresses the DSF-induced innate immunity by secreting xanthan, the main component of extracellular polysaccharide. The results indicate that plants have evolved to recognize a widely conserved bacterial communication system and may have played a role in the co-evolution of host recognition of the pathogen and the communication machinery. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Bartonella henselae engages inside-out and outside-in signaling by integrin β1 and talin1 during invasome-mediated bacterial uptake.

PubMed

Truttmann, Matthias C; Misselwitz, Benjamin; Huser, Sonja; Hardt, Wolf-Dietrich; Critchley, David R; Dehio, Christoph

2011-11-01

The VirB/D4 type IV secretion system (T4SS) of the bacterial pathogen Bartonella henselae (Bhe) translocates seven effector proteins (BepA-BepG) into human cells that subvert host cellular functions. Two redundant pathways dependent on BepG or the combination of BepC and BepF trigger the formation of a bacterial uptake structure termed the invasome. Invasome formation is a multi-step process consisting of bacterial adherence, effector translocation, aggregation of bacteria on the cell surface and engulfment, and eventually, complete internalization of the bacterial aggregate occurs in an F-actin-dependent manner. In the present study, we show that Bhe-triggered invasome formation depends on integrin-β1-mediated signaling cascades that enable assembly of the F-actin invasome structure. We demonstrate that Bhe interacts with integrin β1 in a fibronectin- and VirB/D4 T4SS-independent manner and that activated integrin β1 is essential for both effector translocation and the actin rearrangements leading to invasome formation. Furthermore, we show that talin1, but not talin2, is required for inside-out activation of integrin β1 during invasome formation. Finally, integrin-β1-mediated outside-in signaling by FAK, Src, paxillin and vinculin is necessary for invasome formation. This is the first example of a bacterial entry process that fully exploits the bi-directional signaling capacity of integrin receptors in a talin1-specific manner.

The HD-GYP domain, cyclic di-GMP signaling, and bacterial virulence to plants.

PubMed

Dow, J Maxwell; Fouhy, Yvonne; Lucey, Jean F; Ryan, Robert P

2006-12-01

Cyclic di-GMP is an almost ubiquitous second messenger in bacteria that was first described as an allosteric activator of cellulose synthase but is now known to regulate a range of functions, including virulence in human and animal pathogens. Two protein domains, GGDEF and EAL, are implicated in the synthesis and degradation, respectively, of cyclic di-GMP. These domains are widely distributed in bacteria, including plant pathogens. The majority of proteins with GGDEF and EAL domains contain additional signal input domains, suggesting that their activities are responsive to environmental cues. Recent studies have demonstrated that a third domain, HD-GYP, is also active in cyclic di-GMP degradation. In the plant pathogen Xanthomonas campestris pv. campestris, a two-component signal transduction system comprising the HD-GYP domain regulatory protein RpfG and cognate sensor RpfC positively controls virulence. The signals recognized by RpfC may include the cell-cell signal DSF, which also acts to regulate virulence in X. campestris pv. campestris. Here, we review these recent advances in our understanding of cyclic di-GMP signaling with particular reference to one or more roles in the bacterial pathogenesis of plants.

Bardoxolone methyl prevents high-fat diet-induced alterations in prefrontal cortex signalling molecules involved in recognition memory.

PubMed

Camer, Danielle; Yu, Yinghua; Szabo, Alexander; Fernandez, Francesca; Dinh, Chi H L; Huang, Xu-Feng

2015-06-03

High fat (HF) diets are known to induce changes in synaptic plasticity in the forebrain leading to learning and memory impairments. Previous studies of oleanolic acid derivatives have found that these compounds can cross the blood-brain barrier to prevent neuronal cell death. We examined the hypothesis that the oleanolic acid derivative, bardoxolone methyl (BM) would prevent diet-induced cognitive deficits in mice fed a HF diet. C57BL/6J male mice were fed a lab chow (LC) (5% of energy as fat), a HF (40% of energy as fat), or a HF diet supplemented with 10mg/kg/day BM orally for 21weeks. Recognition memory was assessed by performing a novel object recognition test on the treated mice. Downstream brain-derived neurotrophic factor (BDNF) signalling molecules were examined in the prefrontal cortex (PFC) and hippocampus of mice via Western blotting and N-methyl-d-aspartate (NMDA) receptor binding. BM treatment prevented HF diet-induced impairment in recognition memory (p<0.001). In HF diet fed mice, BM administration attenuated alterations in the NMDA receptor binding density in the PFC (p<0.05), however, no changes were seen in the hippocampus (p>0.05). In the PFC and hippocampus of the HF diet fed mice, BM administration improved downstream BDNF signalling as indicated by increased protein levels of BDNF, phosphorylated tropomyosin related kinase B (pTrkB) and phosphorylated protein kinase B (pAkt), and increased phosphorylated AMP-activated protein kinase (pAMPK) (p<0.05). BM administration also prevented the HF diet-induced increase in the protein levels of inflammatory molecules, phosphorylated c-Jun N-terminal kinase (pJNK) in the PFC, and protein tyrosine phosphatase 1B (PTP1B) in both the PFC and hippocampus. In summary, these findings suggest that BM prevents HF diet-induced impairments in recognition memory by improving downstream BDNF signal transduction, increasing pAMPK, and reducing inflammation in the PFC and hippocampus. Copyright © 2015 Elsevier Inc

Investigating strength and frequency effects in recognition memory using type-2 signal detection theory.

PubMed

Higham, Philip A; Perfect, Timothy J; Bruno, Davide

2009-01-01

Criterion- versus distribution-shift accounts of frequency and strength effects in recognition memory were investigated with Type-2 signal detection receiver operating characteristic (ROC) analysis, which provides a measure of metacognitive monitoring. Experiment 1 demonstrated a frequency-based mirror effect, with a higher hit rate and lower false alarm rate, for low frequency words compared with high frequency words. In Experiment 2, the authors manipulated item strength with repetition, which showed an increased hit rate but no effect on the false alarm rate. Whereas Type-1 indices were ambiguous as to whether these effects were based on a criterion- or distribution-shift model, the two models predict opposite effects on Type-2 distractor monitoring under some assumptions. Hence, Type-2 ROC analysis discriminated between potential models of recognition that could not be discriminated using Type-1 indices alone. In Experiment 3, the authors manipulated Type-1 response bias by varying the number of old versus new response categories to confirm the assumptions made in Experiments 1 and 2. The authors conclude that Type-2 analyses are a useful tool for investigating recognition memory when used in conjunction with more traditional Type-1 analyses.

A novel feature ranking algorithm for biometric recognition with PPG signals.

PubMed

Reşit Kavsaoğlu, A; Polat, Kemal; Recep Bozkurt, M

2014-06-01

This study is intended for describing the application of the Photoplethysmography (PPG) signal and the time domain features acquired from its first and second derivatives for biometric identification. For this purpose, a sum of 40 features has been extracted and a feature-ranking algorithm is proposed. This proposed algorithm calculates the contribution of each feature to biometric recognition and collocates the features, the contribution of which is from great to small. While identifying the contribution of the features, the Euclidean distance and absolute distance formulas are used. The efficiency of the proposed algorithms is demonstrated by the results of the k-NN (k-nearest neighbor) classifier applications of the features. During application, each 15-period-PPG signal belonging to two different durations from each of the thirty healthy subjects were used with a PPG data acquisition card. The first PPG signals recorded from the subjects were evaluated as the 1st configuration; the PPG signals recorded later at a different time as the 2nd configuration and the combination of both were evaluated as the 3rd configuration. When the results were evaluated for the k-NN classifier model created along with the proposed algorithm, an identification of 90.44% for the 1st configuration, 94.44% for the 2nd configuration, and 87.22% for the 3rd configuration has successfully been attained. The obtained results showed that both the proposed algorithm and the biometric identification model based on this developed PPG signal are very promising for contactless recognizing the people with the proposed method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bacterial Signal Transduction by Cyclic Di-GMP and Other Nucleotide Second Messengers

PubMed Central

Gründling, Angelika; Jenal, Urs; Ryan, Robert; Yildiz, Fitnat

2015-01-01

The first International Symposium on c-Di-GMP Signaling in Bacteria (22 to 25 March 2015, Harnack-Haus, Berlin, Germany) brought together 131 molecular microbiologists from 17 countries to discuss recent progress in our knowledge of bacterial nucleotide second messenger signaling. While the focus was on signal input, synthesis, degradation, and the striking diversity of the modes of action of the current second messenger paradigm, i.e., cyclic di-GMP (c-di-GMP), “classics” like cAMP and (p)ppGpp were also presented, in novel facets, and more recent “newcomers,” such as c-di-AMP and c-AMP-GMP, made an impressive appearance. A number of clear trends emerged during the 30 talks, on the 71 posters, and in the lively discussions, including (i) c-di-GMP control of the activities of various ATPases and phosphorylation cascades, (ii) extensive cross talk between c-di-GMP and other nucleotide second messenger signaling pathways, and (iii) a stunning number of novel effectors for nucleotide second messengers that surprisingly include some long-known master regulators of developmental pathways. Overall, the conference made it amply clear that second messenger signaling is currently one of the most dynamic fields within molecular microbiology, with major impacts in research fields ranging from human health to microbial ecology. PMID:26055111

UHF Signal Processing and Pattern Recognition of Partial Discharge in Gas-Insulated Switchgear Using Chromatic Methodology

PubMed Central

Wang, Xiaohua; Li, Xi; Rong, Mingzhe; Xie, Dingli; Ding, Dan; Wang, Zhixiang

2017-01-01

The ultra-high frequency (UHF) method is widely used in insulation condition assessment. However, UHF signal processing algorithms are complicated and the size of the result is large, which hinders extracting features and recognizing partial discharge (PD) patterns. This article investigated the chromatic methodology that is novel in PD detection. The principle of chromatic methodologies in color science are introduced. The chromatic processing represents UHF signals sparsely. The UHF signals obtained from PD experiments were processed using chromatic methodology and characterized by three parameters in chromatic space (H, L, and S representing dominant wavelength, signal strength, and saturation, respectively). The features of the UHF signals were studied hierarchically. The results showed that the chromatic parameters were consistent with conventional frequency domain parameters. The global chromatic parameters can be used to distinguish UHF signals acquired by different sensors, and they reveal the propagation properties of the UHF signal in the L-shaped gas-insulated switchgear (GIS). Finally, typical PD defect patterns had been recognized by using novel chromatic parameters in an actual GIS tank and good performance of recognition was achieved. PMID:28106806

UHF Signal Processing and Pattern Recognition of Partial Discharge in Gas-Insulated Switchgear Using Chromatic Methodology.

PubMed

Wang, Xiaohua; Li, Xi; Rong, Mingzhe; Xie, Dingli; Ding, Dan; Wang, Zhixiang

2017-01-18

The ultra-high frequency (UHF) method is widely used in insulation condition assessment. However, UHF signal processing algorithms are complicated and the size of the result is large, which hinders extracting features and recognizing partial discharge (PD) patterns. This article investigated the chromatic methodology that is novel in PD detection. The principle of chromatic methodologies in color science are introduced. The chromatic processing represents UHF signals sparsely. The UHF signals obtained from PD experiments were processed using chromatic methodology and characterized by three parameters in chromatic space ( H , L , and S representing dominant wavelength, signal strength, and saturation, respectively). The features of the UHF signals were studied hierarchically. The results showed that the chromatic parameters were consistent with conventional frequency domain parameters. The global chromatic parameters can be used to distinguish UHF signals acquired by different sensors, and they reveal the propagation properties of the UHF signal in the L-shaped gas-insulated switchgear (GIS). Finally, typical PD defect patterns had been recognized by using novel chromatic parameters in an actual GIS tank and good performance of recognition was achieved.

Structural basis for signal recognition and transduction by platelet-activating-factor receptor.

PubMed

Cao, Can; Tan, Qiuxiang; Xu, Chanjuan; He, Lingli; Yang, Linlin; Zhou, Ye; Zhou, Yiwei; Qiao, Anna; Lu, Minmin; Yi, Cuiying; Han, Gye Won; Wang, Xianping; Li, Xuemei; Yang, Huaiyu; Rao, Zihe; Jiang, Hualiang; Zhao, Yongfang; Liu, Jianfeng; Stevens, Raymond C; Zhao, Qiang; Zhang, Xuejun C; Wu, Beili

2018-06-01

Platelet-activating-factor receptor (PAFR) responds to platelet-activating factor (PAF), a phospholipid mediator of cell-to-cell communication that exhibits diverse physiological effects. PAFR is considered an important drug target for treating asthma, inflammation and cardiovascular diseases. Here we report crystal structures of human PAFR in complex with the antagonist SR 27417 and the inverse agonist ABT-491 at 2.8-Å and 2.9-Å resolution, respectively. The structures, supported by molecular docking of PAF, provide insights into the signal-recognition mechanisms of PAFR. The PAFR-SR 27417 structure reveals an unusual conformation showing that the intracellular tips of helices II and IV shift outward by 13 Å and 4 Å, respectively, and helix VIII adopts an inward conformation. The PAFR structures, combined with single-molecule FRET and cell-based functional assays, suggest that the conformational change in the helical bundle is ligand dependent and plays a critical role in PAFR activation, thus greatly extending knowledge about signaling by G-protein-coupled receptors.

The effects of digital signal processing features on children's speech recognition and loudness perception.

PubMed

Crukley, Jeffery; Scollie, Susan D

2014-03-01

The purpose of this study was to determine the effects of hearing instruments set to Desired Sensation Level version 5 (DSL v5) hearing instrument prescription algorithm targets and equipped with directional microphones and digital noise reduction (DNR) on children's sentence recognition in noise performance and loudness perception in a classroom environment. Ten children (ages 8-17 years) with stable, congenital sensorineural hearing losses participated in the study. Participants were fitted bilaterally with behind-the-ear hearing instruments set to DSL v5 prescriptive targets. Sentence recognition in noise was evaluated using the Bamford-Kowal-Bench Speech in Noise Test (Niquette et al., 2003). Loudness perception was evaluated using a modified version of the Contour Test of Loudness Perception (Cox, Alexander, Taylor, & Gray, 1997). Children's sentence recognition in noise performance was significantly better when using directional microphones alone or in combination with DNR than when using omnidirectional microphones alone or in combination with DNR. Children's loudness ratings for sounds above 72 dB SPL were lowest when fitted with the DSL v5 Noise prescription combined with directional microphones. DNR use showed no effect on loudness ratings. Use of the DSL v5 Noise prescription with a directional microphone improved sentence recognition in noise performance and reduced loudness perception ratings for loud sounds relative to a typical clinical reference fitting with the DSL v5 Quiet prescription with no digital signal processing features enabled. Potential clinical strategies are discussed.

Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions.

PubMed

Hesketh, Andy; Vergnano, Marta; Wan, Chris; Oliver, Stephen G

2017-07-25

We have engineered Saccharomyces cerevisiae to inducibly synthesize the prokaryotic signaling nucleotides cyclic di-GMP (cdiGMP), cdiAMP, and ppGpp in order to characterize the range of effects these nucleotides exert on eukaryotic cell function during bacterial pathogenesis. Synthetic genetic array (SGA) and transcriptome analyses indicated that, while these compounds elicit some common reactions in yeast, there are also complex and distinctive responses to each of the three nucleotides. All three are capable of inhibiting eukaryotic cell growth, with the guanine nucleotides exhibiting stronger effects than cdiAMP. Mutations compromising mitochondrial function and chromatin remodeling show negative epistatic interactions with all three nucleotides. In contrast, certain mutations that cause defects in chromatin modification and ribosomal protein function show positive epistasis, alleviating growth inhibition by at least two of the three nucleotides. Uniquely, cdiGMP is lethal both to cells growing by respiration on acetate and to obligately fermentative petite mutants. cdiGMP is also synthetically lethal with the ribonucleotide reductase (RNR) inhibitor hydroxyurea. Heterologous expression of the human ppGpp hydrolase Mesh1p prevented the accumulation of ppGpp in the engineered yeast and restored cell growth. Extensive in vivo interactions between bacterial signaling molecules and eukaryotic gene function occur, resulting in outcomes ranging from growth inhibition to death. cdiGMP functions through a mechanism that must be compensated by unhindered RNR activity or by functionally competent mitochondria. Mesh1p may be required for abrogating the damaging effects of ppGpp in human cells subjected to bacterial infection. IMPORTANCE During infections, pathogenic bacteria can release nucleotides into the cells of their eukaryotic hosts. These nucleotides are recognized as signals that contribute to the initiation of defensive immune responses that help the infected

Regulation of the Expression of Bacterial Multidrug Exporters by Two-Component Signal Transduction Systems.

PubMed

Nishino, Kunihiko

2018-01-01

Bacterial multidrug exporters confer resistance to a wide range of antibiotics, dyes, and biocides. Recent studies have shown that there are many multidrug exporters encoded in bacterial genome. For example, it was experimentally identified that E. coli has at least 20 multidrug exporters. Because many of these multidrug exporters have overlapping substrate spectra, it is intriguing that bacteria, with their economically organized genomes, harbor such large sets of multidrug exporter genes. The key to understanding how bacteria utilize these multiple exporters lies in the regulation of exporter expression. Bacteria have developed signaling systems for eliciting a variety of adaptive responses to their environments. These adaptive responses are often mediated by two-component regulatory systems. In this chapter, the method to identify response regulators that affect expression of multidrug exporters is described.

Medical application of artificial immune recognition system (AIRS): diagnosis of atherosclerosis from carotid artery Doppler signals.

PubMed

Latifoğlu, Fatma; Kodaz, Halife; Kara, Sadik; Güneş, Salih

2007-08-01

This study was conducted to distinguish between atherosclerosis and healthy subjects. Hence, we have employed the maximum envelope of the carotid artery Doppler sonograms derived from Fast Fourier Transformation-Welch method and Artificial Immune Recognition System (AIRS). The fuzzy appearance of the carotid artery Doppler signals makes physicians suspicious about the existence of diseases and sometimes causes false diagnosis. Our technique gets around this problem using AIRS to decide and assist the physician to make the final judgment in confidence. AIRS has reached 99.29% classification accuracy using 10-fold cross validation. Results show that the proposed method classified Doppler signals successfully.

Recognition Memory zROC Slopes for Items with Correct versus Incorrect Source Decisions Discriminate the Dual Process and Unequal Variance Signal Detection Models

ERIC Educational Resources Information Center

Starns, Jeffrey J.; Rotello, Caren M.; Hautus, Michael J.

2014-01-01

We tested the dual process and unequal variance signal detection models by jointly modeling recognition and source confidence ratings. The 2 approaches make unique predictions for the slope of the recognition memory zROC function for items with correct versus incorrect source decisions. The standard bivariate Gaussian version of the unequal…

Towards rationally redesigning bacterial signaling systems using information encoded in abundant sequence data

NASA Astrophysics Data System (ADS)

Cheng, Ryan; Morcos, Faruck; Levine, Herbert; Onuchic, Jose

2014-03-01

An important challenge in biology is to distinguish the subset of residues that allow bacterial two-component signaling (TCS) proteins to preferentially interact with their correct TCS partner such that they can bind and transfer signal. Detailed knowledge of this information would allow one to search sequence-space for mutations that can systematically tune the signal transmission between TCS partners as well as re-encode a TCS protein to preferentially transfer signals to a non-partner. Motivated by the notion that this detailed information is found in sequence data, we explore the mutual sequence co-evolution between signaling partners to infer how mutations can positively or negatively alter their interaction. Using Direct Coupling Analysis (DCA) for determining evolutionarily conserved interprotein interactions, we apply a DCA-based metric to quantify mutational changes in the interaction between TCS proteins and demonstrate that it accurately correlates with experimental mutagenesis studies probing the mutational change in the in vitro phosphotransfer. Our methodology serves as a potential framework for the rational design of TCS systems as well as a framework for the system-level study of protein-protein interactions in sequence-rich systems. This research has been supported by the NSF INSPIRE award MCB-1241332 and by the CTBP sponsored by the NSF (Grant PHY-1308264).

Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition.

PubMed

Voogdt, Carlos G P; Bouwman, Lieneke I; Kik, Marja J L; Wagenaar, Jaap A; van Putten, Jos P M

2016-01-07

Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions.

Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition

PubMed Central

Voogdt, Carlos G. P.; Bouwman, Lieneke I.; Kik, Marja J. L.; Wagenaar, Jaap A.; van Putten, Jos P. M.

2016-01-01

Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions. PMID:26738735

Risperidone reverses the spatial object recognition impairment and hippocampal BDNF-TrkB signalling system alterations induced by acute MK-801 treatment

PubMed Central

Chen, Guangdong; Lin, Xiaodong; Li, Gongying; Jiang, Diego; Lib, Zhiruo; Jiang, Ronghuan; Zhuo, Chuanjun

2017-01-01

The aim of the present study was to investigate the effects of a commonly-used atypical antipsychotic, risperidone, on alterations in spatial learning and in the hippocampal brain-derived neurotrophic factor (BDNF)-tyrosine receptor kinase B (TrkB) signalling system caused by acute dizocilpine maleate (MK-801) treatment. In experiment 1, adult male Sprague-Dawley rats subjected to acute treatment of either low-dose MK801 (0.1 mg/kg) or normal saline (vehicle) were tested for spatial object recognition and hippocampal expression levels of BDNF, TrkB and the phophorylation of TrkB (p-TrkB). We found that compared to the vehicle, MK-801 treatment impaired spatial object recognition of animals and downregulated the expression levels of p-TrkB. In experiment 2, MK-801- or vehicle-treated animals were further injected with risperidone (0.1 mg/kg) or vehicle before behavioural testing and sacrifice. Of note, we found that risperidone successfully reversed the deleterious effects of MK-801 on spatial object recognition and upregulated the hippocampal BDNF-TrkB signalling system. Collectively, the findings suggest that cognitive deficits from acute N-methyl-D-aspartate receptor blockade may be associated with the hypofunction of hippocampal BDNF-TrkB signalling system and that risperidone was able to reverse these alterations. PMID:28451387

Behind the lines–actions of bacterial type III effector proteins in plant cells

PubMed Central

Büttner, Daniela

2016-01-01

Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Type III effectors also interfere with additional plant cellular processes including proteasome-dependent protein degradation, phytohormone signaling, the formation of the cytoskeleton, vesicle transport and gene expression. This review summarizes our current knowledge on the molecular functions of type III effector proteins with known plant target molecules. Furthermore, plant defense strategies for the detection of effector protein activities or effector-triggered alterations in plant targets are discussed. PMID:28201715

Bacterial nucleotide-based second messengers.

PubMed

Pesavento, Christina; Hengge, Regine

2009-04-01

In all domains of life nucleotide-based second messengers transduce signals originating from changes in the environment or in intracellular conditions into appropriate cellular responses. In prokaryotes cyclic di-GMP has emerged as an important and ubiquitous second messenger regulating bacterial life-style transitions relevant for biofilm formation, virulence, and many other bacterial functions. This review describes similarities and differences in the architecture of the cAMP, (p)ppGpp, and c-di-GMP signaling systems and their underlying signaling principles. Moreover, recent advances in c-di-GMP-mediated signaling will be presented and the integration of c-di-GMP signaling with other nucleotide-based signaling systems will be discussed.

RIG-I in RNA virus recognition

PubMed Central

Kell, Alison M.; Gale, Michael

2015-01-01

Antiviral immunity is initiated upon host recognition of viral products via non-self molecular patterns known as pathogen-associated molecular patterns (PAMPs). Such recognition initiates signaling cascades that induce intracellular innate immune defenses and an inflammatory response that facilitates development of the acquired immune response. The retinoic acid-inducible gene I (RIG-I) and the RIG-I-like receptor (RLR) protein family are key cytoplasmic pathogen recognition receptors that are implicated in the recognition of viruses across genera and virus families, including functioning as major sensors of RNA viruses, and promoting recognition of some DNA viruses. RIG-I, the charter member of the RLR family, is activated upon binding to PAMP RNA. Activated RIG-I signals by interacting with the adapter protein MAVS leading to a signaling cascade that activates the transcription factors IRF3 and NF-κB. These actions induce the expression of antiviral gene products and the production of type I and III interferons that lead to an antiviral state in the infected cell and surrounding tissue. RIG-I signaling is essential for the control of infection by many RNA viruses. Recently, RIG-I crosstalk with other pathogen recognition receptors and components of the inflammasome has been described. In this review, we discuss the current knowledge regarding the role of RIG-I in recognition of a variety of virus families and its role in programming the adaptive immune response through cross-talk with parallel arms of the innate immune system, including how RIG-I can be leveraged for antiviral therapy. PMID:25749629

Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions

PubMed Central

Vergnano, Marta; Wan, Chris

2017-01-01

ABSTRACT We have engineered Saccharomyces cerevisiae to inducibly synthesize the prokaryotic signaling nucleotides cyclic di-GMP (cdiGMP), cdiAMP, and ppGpp in order to characterize the range of effects these nucleotides exert on eukaryotic cell function during bacterial pathogenesis. Synthetic genetic array (SGA) and transcriptome analyses indicated that, while these compounds elicit some common reactions in yeast, there are also complex and distinctive responses to each of the three nucleotides. All three are capable of inhibiting eukaryotic cell growth, with the guanine nucleotides exhibiting stronger effects than cdiAMP. Mutations compromising mitochondrial function and chromatin remodeling show negative epistatic interactions with all three nucleotides. In contrast, certain mutations that cause defects in chromatin modification and ribosomal protein function show positive epistasis, alleviating growth inhibition by at least two of the three nucleotides. Uniquely, cdiGMP is lethal both to cells growing by respiration on acetate and to obligately fermentative petite mutants. cdiGMP is also synthetically lethal with the ribonucleotide reductase (RNR) inhibitor hydroxyurea. Heterologous expression of the human ppGpp hydrolase Mesh1p prevented the accumulation of ppGpp in the engineered yeast and restored cell growth. Extensive in vivo interactions between bacterial signaling molecules and eukaryotic gene function occur, resulting in outcomes ranging from growth inhibition to death. cdiGMP functions through a mechanism that must be compensated by unhindered RNR activity or by functionally competent mitochondria. Mesh1p may be required for abrogating the damaging effects of ppGpp in human cells subjected to bacterial infection. PMID:28743817

Bacterial recognition of thermal glycation products derived from porcine serum albumin with lactose.

PubMed

Sarabia-Sainz, Andre-I; Ramos-Clamont, Gabriela; Winzerling, Joy; Vázquez-Moreno, Luz

2011-01-01

Recently, glyco-therapy is proposed to prevent the interaction of bacterial lectins with host ligands (glycoconjugates). This interaction represents the first step in infection. Neoglycans referred to as PSA-Lac (PSA-Glu (β1-4) Gal) were obtained by conjugation of porcine serum albumin (PSA) with lactose at 80 °C, 100 °C and 120 ºC. Characterization studies of the products showed that PSA could contain 1, 38 or 41 added lactoses, depending on the reaction temperature. These neoglycans were approximately 10 times more glycated than PSA-Lac obtained in previous work. Lactose conjugation occurred only at lysines and PSA-Lac contained terminal galactoses as confirmed by Ricinus communis lectin recognition. Furthermore, Escherichia coli K88+, K88ab, K88ac and K88ad adhesins showed affinity toward all PSA-Lac neoglycans, and the most effective was the PSA-Lac obtained after 100 ºC treatment. In vitro, this neoglycan partially inhibited the adhesion of E. coli K88+ to piglet mucin (its natural ligand). These results provide support for the hypothesis that glycated proteins can be used as an alternative for bioactive compounds for disease prevention.

Quorum signaling mycotoxins: A new risk strategy for bacterial biocontrol of Fusarium verticillioides and other endophytic fungal species?

USDA-ARS?s Scientific Manuscript database

Bacterial endophytes are used as biocontrol organisms for plant pathogens such as the maize endophyte Fusarium verticillioides and its production of fumonisin mycotoxins. However, such applications are not always predictable and efficient. All bacteria communicate via cell-dependent signals, which...

Signal recognition by green treefrogs (Hyla cinerea) and Cope's gray treefrogs (Hyla chrysoscelis) in naturally fluctuating noise.

PubMed

Vélez, Alejandro; Bee, Mark A

2013-05-01

This study tested three hypotheses about the ability of female frogs to exploit temporal fluctuations in the level of background noise to overcome the problem of recognizing male advertisement calls in noisy breeding choruses. Phonotaxis tests with green treefrogs (Hyla cinerea) and Cope's gray treefrogs (Hyla chrysoscelis) were used to measure thresholds for recognizing calls in the presence of noise maskers with (a) no level fluctuations, (b) random fluctuations, or level fluctuations characteristic of (c) conspecific choruses and (d) heterospecific choruses. The dip-listening hypothesis predicted lower signal recognition thresholds in the presence of fluctuating maskers compared with nonfluctuating maskers. Support for the dip-listening hypothesis was weak; only Cope's gray treefrogs experienced dip listening and only in the presence of randomly fluctuating maskers. The natural soundscapes advantage hypothesis predicted lower recognition thresholds when level fluctuations resembled those of natural soundscapes compared with artificial fluctuations. This hypothesis was rejected. In noise backgrounds with natural fluctuations, the species-specific advantage hypothesis predicted lower recognition thresholds when fluctuations resembled species-specific patterns of conspecific soundscapes. No evidence was found to support this hypothesis. These results corroborate previous findings showing that Cope's gray treefrogs, but not green treefrogs, experience dip listening under some noise conditions. Together, the results suggest level fluctuations in the soundscape of natural breeding choruses may present few dip-listening opportunities. The findings of this study provide little support for the hypothesis that receivers are adapted to exploit level fluctuations of natural soundscapes in recognizing communication signals.

Recognition Imaging with a DNA Aptamer

PubMed Central

Lin, Liyun; Wang, Hongda; Liu, Yan; Yan, Hao; Lindsay, Stuart

2006-01-01

We have used a DNA-aptamer tethered to an atomic force microscope probe to carry out recognition imaging of IgE molecules attached to a mica substrate. The recognition was efficient (∼90%) and specific, being blocked by injection of IgE molecules in solution, and not being interfered with by high concentrations of a second protein. The signal/noise ratio of the recognition signal was better than that obtained with antibodies, despite the fact that the average force required to break the aptamer-protein bonds was somewhat smaller. PMID:16513776

Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi

PubMed Central

Swem, Lee R.; Swem, Danielle L.; Wingreen, Ned S.; Bassler, Bonnie L.

2008-01-01

Summary Quorum sensing, a process of bacterial cell-cell communication, relies on production, detection, and response to autoinducer signaling molecules. Here we focus on LuxN, a nine transmembrane domain protein from Vibrio harveyi, and the founding example of membrane-bound receptors for acyl-homoserine lactone (AHL) autoinducers. Previously, nothing was known about signal recognition by membrane-bound AHL receptors. We used mutagenesis and suppressor analyses to identify the AHL-binding domain of LuxN, and discovered LuxN mutants that confer decreased and increased AHL sensitivity. Our analysis of dose-response curves of multiple LuxN mutants pins these inverse phenotypes on quantifiable opposing shifts in the free-energy bias of LuxN for its kinase and phosphatase states. To extract signaling parameters, we exploited a strong LuxN antagonist, one of fifteen small-molecule antagonists we identified. We find that quorum-sensing-mediated communication can be manipulated positively and negatively to control bacterial behavior, and that signaling parameters can be deduced from in vivo data. PMID:18692469

Recognition- and reactivity-based fluorescent probes for studying transition metal signaling in living systems.

PubMed

Aron, Allegra T; Ramos-Torres, Karla M; Cotruvo, Joseph A; Chang, Christopher J

2015-08-18

Metals are essential for life, playing critical roles in all aspects of the central dogma of biology (e.g., the transcription and translation of nucleic acids and synthesis of proteins). Redox-inactive alkali, alkaline earth, and transition metals such as sodium, potassium, calcium, and zinc are widely recognized as dynamic signals, whereas redox-active transition metals such as copper and iron are traditionally thought of as sequestered by protein ligands, including as static enzyme cofactors, in part because of their potential to trigger oxidative stress and damage via Fenton chemistry. Metals in biology can be broadly categorized into two pools: static and labile. In the former, proteins and other macromolecules tightly bind metals; in the latter, metals are bound relatively weakly to cellular ligands, including proteins and low molecular weight ligands. Fluorescent probes can be useful tools for studying the roles of transition metals in their labile forms. Probes for imaging transition metal dynamics in living systems must meet several stringent criteria. In addition to exhibiting desirable photophysical properties and biocompatibility, they must be selective and show a fluorescence turn-on response to the metal of interest. To meet this challenge, we have pursued two general strategies for metal detection, termed "recognition" and "reactivity". Our design of transition metal probes makes use of a recognition-based approach for copper and nickel and a reactivity-based approach for cobalt and iron. This Account summarizes progress in our laboratory on both the development and application of fluorescent probes to identify and study the signaling roles of transition metals in biology. In conjunction with complementary methods for direct metal detection and genetic and/or pharmacological manipulations, fluorescent probes for transition metals have helped reveal a number of principles underlying transition metal dynamics. In this Account, we give three recent

Bacterial superantigens bypass Lck-dependent T cell receptor signaling by activating a Galpha11-dependent, PLC-beta-mediated pathway.

PubMed

Bueno, Clara; Lemke, Caitlin D; Criado, Gabriel; Baroja, Miren L; Ferguson, Stephen S G; Rahman, A K M Nur-Ur; Tsoukas, Constantine D; McCormick, John K; Madrenas, Joaquin

2006-07-01

The paradigm to explain antigen-dependent T cell receptor (TCR) signaling is based on the activation of the CD4 or CD8 coreceptor-associated kinase Lck. It is widely assumed that this paradigm is also applicable to signaling by bacterial superantigens. However, these bacterial toxins can activate human T cells lacking Lck, suggesting the existence of an additional pathway of TCR signaling. Here we showed that this alternative pathway operates in the absence of Lck-dependent tyrosine-phosphorylation events and was initiated by the TCR-dependent activation of raft-enriched heterotrimeric Galpha11 proteins. This event, in turn, activated a phospholipase C-beta and protein kinase C-mediated cascade that turned on the mitogen-activated protein kinases ERK-1 and ERK-2, triggered Ca(2+) influx, and translocated the transcription factors NF-AT and NF-kappaB to the nucleus, ultimately inducing the production of interleukin-2 in Lck-deficient T cells. The triggering of this alternative pathway by superantigens suggests that these toxins use a G protein-coupled receptor as a coreceptor on T cells.

On the measurement of criterion noise in signal detection theory: the case of recognition memory.

PubMed

Kellen, David; Klauer, Karl Christoph; Singmann, Henrik

2012-07-01

Traditional approaches within the framework of signal detection theory (SDT; Green & Swets, 1966), especially in the field of recognition memory, assume that the positioning of response criteria is not a noisy process. Recent work (Benjamin, Diaz, & Wee, 2009; Mueller & Weidemann, 2008) has challenged this assumption, arguing not only for the existence of criterion noise but also for its large magnitude and substantive contribution to individuals' performance. A review of these recent approaches for the measurement of criterion noise in SDT identifies several shortcomings and confoundings. A reanalysis of Benjamin et al.'s (2009) data sets as well as the results from a new experimental method indicate that the different forms of criterion noise proposed in the recognition memory literature are of very low magnitudes, and they do not provide a significant improvement over the account already given by traditional SDT without criterion noise. Copyright 2012 APA, all rights reserved.

Estradiol-Induced Object Recognition Memory Consolidation Is Dependent on Activation of mTOR Signaling in the Dorsal Hippocampus

ERIC Educational Resources Information Center

Fortress, Ashley M.; Fan, Lu; Orr, Patrick T.; Zhao, Zaorui; Frick, Karyn M.

2013-01-01

The mammalian target of rapamycin (mTOR) signaling pathway is an important regulator of protein synthesis and is essential for various forms of hippocampal memory. Here, we asked whether the enhancement of object recognition memory consolidation produced by dorsal hippocampal infusion of 17[Beta]-estradiol (E[subscript 2]) is dependent on mTOR…

LGP2 Synergy with MDA5 in RLR-Mediated RNA Recognition and Antiviral Signaling

PubMed Central

Bruns, Annie M.; Horvath, Curt M.

2015-01-01

Mammalian cells have the ability to recognize virus infection and mount a powerful antiviral response. Pattern recognition receptor proteins detect molecular signatures of virus infection and activate antiviral signaling. The RIG-I-like receptor (RLR) proteins are expressed in the cytoplasm of nearly all cells and specifically recognize virus-derived RNA species as a molecular feature discriminating the pathogen from the host. The RLR family is composed of three homologous proteins, RIG-I, MDA5, and LGP2. All RLRs have the ability to detect virus-derived dsRNA and hydrolyze ATP, but display individual differences in enzymatic activity, intrinsic ability to recognize RNA, and mechanisms of activation. Emerging evidence suggests that MDA5 and RIG-I utilize distinct mechanisms to form oligomeric complexes along dsRNA. Aligning of their signaling domains creates a platform capable of propagating and amplifying antiviral signaling responses. LGP2 with intact ATP hydrolysis is critical for the MDA5-mediated antiviral response, but LGP2 lacks the domains essential for activation of antiviral signaling, leaving the role of LGP2 in antiviral signaling unclear. Recent studies revealed a mechanistic basis of synergy between LGP2 and MDA5 leading to enhanced antiviral signaling. This review briefly summarizes the RLR system, and focuses on the relationship between LGP2 and MDA5, describing in detail how these two proteins work together to detect foreign RNA and generate a fully functional antiviral response. PMID:25794939

Gut microbial translocation corrupts myeloid cell function to control bacterial infection during liver cirrhosis.

PubMed

Hackstein, Carl-Philipp; Assmus, Lisa Mareike; Welz, Meike; Klein, Sabine; Schwandt, Timo; Schultze, Joachim; Förster, Irmgard; Gondorf, Fabian; Beyer, Marc; Kroy, Daniela; Kurts, Christian; Trebicka, Jonel; Kastenmüller, Wolfgang; Knolle, Percy A; Abdullah, Zeinab

2017-03-01

Patients with liver cirrhosis suffer from increased susceptibility to life-threatening bacterial infections that cause substantial morbidity. Experimental liver fibrosis in mice induced by bile duct ligation or CCl 4 application was used to characterise the mechanisms determining failure of innate immunity to control bacterial infections. In murine liver fibrosis, translocation of gut microbiota induced tonic type I interferon (IFN) expression in the liver. Such tonic IFN expression conditioned liver myeloid cells to produce high concentrations of IFN upon intracellular infection with Listeria that activate cytosolic pattern recognition receptors. Such IFN-receptor signalling caused myeloid cell interleukin (IL)-10 production that corrupted antibacterial immunity, leading to loss of infection-control and to infection-associated mortality. In patients with liver cirrhosis, we also found a prominent liver IFN signature and myeloid cells showed increased IL-10 production after bacterial infection. Thus, myeloid cells are both source and target of IFN-induced and IL-10-mediated immune dysfunction. Antibody-mediated blockade of IFN-receptor or IL-10-receptor signalling reconstituted antibacterial immunity and prevented infection-associated mortality in mice with liver fibrosis. In severe liver fibrosis and cirrhosis, failure to control bacterial infection is caused by augmented IFN and IL-10 expression that incapacitates antibacterial immunity of myeloid cells. Targeted interference with the immune regulatory host factors IL-10 and IFN reconstitutes antibacterial immunity and may be used as therapeutic strategy to control bacterial infections in patients with liver cirrhosis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30T

PubMed Central

Ludewig, Uwe

2013-01-01

The bacterial endophyte Herbaspirillum frisingense GSF30T is a colonizer of several grasses grown in temperate climates, including the highly nitrogen-efficient perennial energy grass Miscanthus. Inoculation of Miscanthus sinensis seedlings with H. frisingense promoted root and shoot growth but had only a minor impact on nutrient concentrations. The bacterium affected the root architecture and increased fine-root structures. Although H. frisingense has the genetic requirements to fix nitrogen, only minor changes in nitrogen concentrations were observed. Herbaspirillum agglomerates were identified primarily in the root apoplast but also in the shoots. The short-term (3h) and long-term (3 weeks) transcriptomic responses of the plant to bacterial inoculation revealed that H. frisingense induced rapid changes in plant hormone signalling, most prominent in jasmonate signalling. Ethylene signalling pathways were also affected and persisted after 3 weeks in the root. Growth stimulation of the root by the ethylene precursor 1-aminocyclopropane 1-carboxylic acid was dose dependent and was affected by H. frisingense inoculation. Minor changes in the proteome were identified after 3 weeks. This study suggests that H. frisingense improves plant growth by modulating plant hormone signalling pathways and provides a framework to understand the beneficial effects of diazotrophic plant-growth-promoting bacteria, such as H. frisingense, on the biomass grass Miscanthus. PMID:24043849

Contemporary cultural evolution of a conspecific recognition signal following serial translocations.

PubMed

Parker, Kevin A; Hauber, Mark E; Brunton, Dianne H

2010-08-01

The divergence of conspecific recognition signals (CRS) among isolated populations facilitates the evolution of behavioral barriers to gene flow. The influence of CRS evolution on signal effectiveness in isolated populations can be assessed by testing the salience of changes in CRS from surviving ancestral populations but founder events are rarely detected. The population history of the North Island (NI) saddleback Philesturnus rufusater is absolutely known following conservation translocations which increased the number of populations from 1 to 15. With one exception there is no gene flow between these populations. The translocations have generated interisland divergence of male rhythmical song (MRS), a culturally transmitted CRS. We conducted an experimental test of behavioral discrimination in NI saddlebacks exposed to familiar and unfamiliar MRS and found that responses were significantly stronger for familiar MRS, consistent with a model of contemporary cultural evolution leading to discrimination between geographic song variants. Significantly, this result demonstrates the rapid tempo with which discrimination of CRS might evolve within isolated populations and supports both bottleneck and cultural mutation hypotheses in CRS evolution. The evolutionary implications of contemporary cultural evolution in the production and perception of CRS merit debate on the time frames over which conservation management is evaluated.

Flexible Piezoelectric Sensor-Based Gait Recognition.

PubMed

Cha, Youngsu; Kim, Hojoon; Kim, Doik

2018-02-05

Most motion recognition research has required tight-fitting suits for precise sensing. However, tight-suit systems have difficulty adapting to real applications, because people normally wear loose clothes. In this paper, we propose a gait recognition system with flexible piezoelectric sensors in loose clothing. The gait recognition system does not directly sense lower-body angles. It does, however, detect the transition between standing and walking. Specifically, we use the signals from the flexible sensors attached to the knee and hip parts on loose pants. We detect the periodic motion component using the discrete time Fourier series from the signal during walking. We adapt the gait detection method to a real-time patient motion and posture monitoring system. In the monitoring system, the gait recognition operates well. Finally, we test the gait recognition system with 10 subjects, for which the proposed system successfully detects walking with a success rate over 93 %.

Individual recognition based on communication behaviour of male fowl.

PubMed

Smith, Carolynn L; Taubert, Jessica; Weldon, Kimberly; Evans, Christopher S

2016-04-01

Correctly directing social behaviour towards a specific individual requires an ability to discriminate between conspecifics. The mechanisms of individual recognition include phenotype matching and familiarity-based recognition. Communication-based recognition is a subset of familiarity-based recognition wherein the classification is based on behavioural or distinctive signalling properties. Male fowl (Gallus gallus) produce a visual display (tidbitting) upon finding food in the presence of a female. Females typically approach displaying males. However, males may tidbit without food. We used the distinctiveness of the visual display and the unreliability of some males to test for communication-based recognition in female fowl. We manipulated the prior experience of the hens with the males to create two classes of males: S(+) wherein the tidbitting signal was paired with a food reward to the female, and S (-) wherein the tidbitting signal occurred without food reward. We then conducted a sequential discrimination test with hens using a live video feed of a familiar male. The results of the discrimination tests revealed that hens discriminated between categories of males based on their signalling behaviour. These results suggest that fowl possess a communication-based recognition system. This is the first demonstration of live-to-video transfer of recognition in any species of bird. Copyright © 2016 Elsevier B.V. All rights reserved.

Call recognition and individual identification of fish vocalizations based on automatic speech recognition: An example with the Lusitanian toadfish.

PubMed

Vieira, Manuel; Fonseca, Paulo J; Amorim, M Clara P; Teixeira, Carlos J C

2015-12-01

The study of acoustic communication in animals often requires not only the recognition of species specific acoustic signals but also the identification of individual subjects, all in a complex acoustic background. Moreover, when very long recordings are to be analyzed, automatic recognition and identification processes are invaluable tools to extract the relevant biological information. A pattern recognition methodology based on hidden Markov models is presented inspired by successful results obtained in the most widely known and complex acoustical communication signal: human speech. This methodology was applied here for the first time to the detection and recognition of fish acoustic signals, specifically in a stream of round-the-clock recordings of Lusitanian toadfish (Halobatrachus didactylus) in their natural estuarine habitat. The results show that this methodology is able not only to detect the mating sounds (boatwhistles) but also to identify individual male toadfish, reaching an identification rate of ca. 95%. Moreover this method also proved to be a powerful tool to assess signal durations in large data sets. However, the system failed in recognizing other sound types.

Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling

PubMed Central

Park, Chang-Jin; Caddell, Daniel F.; Ronald, Pamela C.

2012-01-01

Plants are continuously challenged by pathogens including viruses, bacteria, and fungi. The plant immune system recognizes invading pathogens and responds by activating an immune response. These responses occur rapidly and often involve post-translational modifications (PTMs) within the proteome. Protein phosphorylation is a common and intensively studied form of these PTMs and regulates many plant processes including plant growth, development, and immunity. Most well-characterized pattern recognition receptors (PRRs), including Xanthomonas resistance 21, flagellin sensitive 2, and elongation factor-Tu receptor, possess intrinsic protein kinase activity and regulate downstream signaling through phosphorylation events. Here, we focus on the phosphorylation events of plant PRRs that play important roles in the immune response. We also discuss the role of phosphorylation in regulating mitogen-associated protein kinase cascades and transcription factors in plant immune signaling. PMID:22876255

Arabidopsis EDS1 connects pathogen effector recognition to cell compartment-specific immune responses.

PubMed

Heidrich, Katharina; Wirthmueller, Lennart; Tasset, Céline; Pouzet, Cécile; Deslandes, Laurent; Parker, Jane E

2011-12-09

Pathogen effectors are intercepted by plant intracellular nucleotide binding-leucine-rich repeat (NB-LRR) receptors. However, processes linking receptor activation to downstream defenses remain obscure. Nucleo-cytoplasmic basal resistance regulator EDS1 (ENHANCED DISEASE SUSCEPTIBILITY1) is indispensible for immunity mediated by TIR (Toll-interleukin-1 receptor)-NB-LRR receptors. We show that Arabidopsis EDS1 molecularly connects TIR-NB-LRR disease resistance protein RPS4 recognition of bacterial effector AvrRps4 to defense pathways. RPS4-EDS1 and AvrRps4-EDS1 complexes are detected inside nuclei of living tobacco cells after transient coexpression and in Arabidopsis soluble leaf extracts after resistance activation. Forced AvrRps4 localization to the host cytoplasm or nucleus reveals cell compartment-specific RPS4-EDS1 defense branches. Although nuclear processes restrict bacterial growth, programmed cell death and transcriptional resistance reinforcement require nucleo-cytoplasmic coordination. Thus, EDS1 behaves as an effector target and activated TIR-NB-LRR signal transducer for defenses across cell compartments.

Activation of the immune system by bacterial CpG-DNA

PubMed Central

Häcker, Georg; Redecke, Vanessa; Häcker, Hans

2002-01-01

The past decade has seen a remarkable process of refocusing in immunology. Cells of the innate immune system, especially macrophages and dendritic cells, have been at the centre of this process. These cells had been regarded by some scientists as non-specific, sometimes perhaps even confined to the menial job of serving T cells by scavenging antigen and presenting it to the sophisticated adaptive immune system. Only over the last few years has it become unequivocally clear that cells of the innate immunity hold, by variation of context and mode of antigen presentation, the power of shaping an adaptive immune response. The innate immune response, in turn, is to a significant degree the result of stimulation by so-called pathogen-associated molecular patterns (PAMPs). One compound with high stimulatory potential for the innate immune system is bacterial DNA. Here we will review recent evidence that bacterial DNA should be ranked with other PAMPs such as lipopolysaccharide (LPS) and lipoteichoic acid. We will further review our present knowledge of DNA recognition and DNA-dependent signal transduction in cells of the immune system. PMID:11918685

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria

NASA Astrophysics Data System (ADS)

Amin, S. A.; Hmelo, L. R.; van Tol, H. M.; Durham, B. P.; Carlson, L. T.; Heal, K. R.; Morales, R. L.; Berthiaume, C. T.; Parker, M. S.; Djunaedi, B.; Ingalls, A. E.; Parsek, M. R.; Moran, M. A.; Armbrust, E. V.

2015-06-01

Interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape ecosystem diversity. In marine ecosystems, these interactions are difficult to study partly because the major photosynthetic organisms are microscopic, unicellular phytoplankton. Coastal phytoplankton communities are dominated by diatoms, which generate approximately 40% of marine primary production and form the base of many marine food webs. Diatoms co-occur with specific bacterial taxa, but the mechanisms of potential interactions are mostly unknown. Here we tease apart a bacterial consortium associated with a globally distributed diatom and find that a Sulfitobacter species promotes diatom cell division via secretion of the hormone indole-3-acetic acid, synthesized by the bacterium using both diatom-secreted and endogenous tryptophan. Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia. The potential prevalence of this mode of signalling in the oceans is corroborated by metabolite and metatranscriptome analyses that show widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments. Our study expands on the emerging recognition that marine microbial communities are part of tightly connected networks by providing evidence that these interactions are mediated through production and exchange of infochemicals.

Essential role of mitochondrial antiviral signaling, IFN regulatory factor (IRF)3, and IRF7 in Chlamydophila pneumoniae-mediated IFN-beta response and control of bacterial replication in human endothelial cells.

PubMed

Buss, Claudia; Opitz, Bastian; Hocke, Andreas C; Lippmann, Juliane; van Laak, Vincent; Hippenstiel, Stefan; Krüll, Matthias; Suttorp, Norbert; Eitel, Julia

2010-03-15

Chlamydophila pneumoniae infection of the vascular wall as well as activation of the transcription factor IFN regulatory factor (IRF)3 have been linked to development of chronic vascular lesions and atherosclerosis. The innate immune system detects invading pathogens by use of pattern recognition receptors, some of which are able to stimulate IRF3/7 activation and subsequent type I IFN production (e. g., IFN-beta). In this study, we show that infection of human endothelial cells with C. pneumoniae-induced production of IFN-beta, a cytokine that so far has been mainly associated with antiviral immunity. Moreover, C. pneumoniae infection led to IRF3 and IRF7 nuclear translocation in HUVECs and RNA interference experiments showed that IRF3 and IRF7 as well as the mitochondrial antiviral signaling (MAVS) were essential for IFN-beta induction. Finally, C. pneumoniae replication was enhanced in endothelial cells in which IRF3, IRF7, or MAVS expression was inhibited by small interfering RNA and attenuated by IFN-beta treatment. In conclusion, C. pneumoniae infection of endothelial cells activates an MAVS-, IRF3-, and IRF7-dependent signaling, which controls bacterial growth and might modulate development of vascular lesions.

Human β‐defensin 3 increases the TLR9‐dependent response to bacterial DNA

PubMed Central

McGlasson, Sarah L.; Semple, Fiona; MacPherson, Heather; Gray, Mohini; Davidson, Donald J.

2017-01-01

Human β‐defensin 3 (hBD3) is a cationic antimicrobial peptide with potent bactericidal activity in vitro. HBD3 is produced in response to pathogen challenge and can modulate immune responses. The amplified recognition of self‐DNA by human plasmacytoid dendritic cells has been previously reported, but we show here that hBD3 preferentially enhances the response to bacterial DNA in mouse Flt‐3 induced dendritic cells (FLDCs) and in human peripheral blood mononuclear cells. We show the effect is mediated through TLR9 and although hBD3 significantly increases the cellular uptake of both E. coli and self‐DNA in mouse FLDCs, only the response to bacterial DNA is enhanced. Liposome transfection also increases uptake of bacterial DNA and amplifies the TLR9‐dependent response. In contrast to hBD3, lipofection of self‐DNA enhances inflammatory signaling, but the response is predominantly TLR9‐independent. Together, these data show that hBD3 has a role in the innate immune‐mediated response to pathogen DNA, increasing inflammatory signaling and promoting activation of the adaptive immune system via antigen presenting cells including dendritic cells. Therefore, our data identify an additional immunomodulatory role for this copy‐number variable defensin, of relevance to host defence against infection and indicate a potential for the inclusion of HBD3 in pathogen DNA‐based vaccines. PMID:28102569

Human β-defensin 3 increases the TLR9-dependent response to bacterial DNA.

PubMed

McGlasson, Sarah L; Semple, Fiona; MacPherson, Heather; Gray, Mohini; Davidson, Donald J; Dorin, Julia R

2017-04-01

Human β-defensin 3 (hBD3) is a cationic antimicrobial peptide with potent bactericidal activity in vitro. HBD3 is produced in response to pathogen challenge and can modulate immune responses. The amplified recognition of self-DNA by human plasmacytoid dendritic cells has been previously reported, but we show here that hBD3 preferentially enhances the response to bacterial DNA in mouse Flt-3 induced dendritic cells (FLDCs) and in human peripheral blood mononuclear cells. We show the effect is mediated through TLR9 and although hBD3 significantly increases the cellular uptake of both E. coli and self-DNA in mouse FLDCs, only the response to bacterial DNA is enhanced. Liposome transfection also increases uptake of bacterial DNA and amplifies the TLR9-dependent response. In contrast to hBD3, lipofection of self-DNA enhances inflammatory signaling, but the response is predominantly TLR9-independent. Together, these data show that hBD3 has a role in the innate immune-mediated response to pathogen DNA, increasing inflammatory signaling and promoting activation of the adaptive immune system via antigen presenting cells including dendritic cells. Therefore, our data identify an additional immunomodulatory role for this copy-number variable defensin, of relevance to host defence against infection and indicate a potential for the inclusion of HBD3 in pathogen DNA-based vaccines. © 2017 The Authors. European Journal of Immunology published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multifunctionality of a Picornavirus Polymerase Domain: Nuclear Localization Signal and Nucleotide Recognition

PubMed Central

Ferrer-Orta, Cristina; de la Higuera, Ignacio; Caridi, Flavia; Sánchez-Aparicio, María Teresa; Moreno, Elena; Perales, Celia; Singh, Kamalendra; Sarafianos, Stefan G.; Sobrino, Francisco; Domingo, Esteban

2015-01-01

ABSTRACT The N-terminal region of the foot-and-mouth disease virus (FMDV) 3D polymerase contains the sequence MRKTKLAPT (residues 16 to 24) that acts as a nuclear localization signal. A previous study showed that substitutions K18E and K20E diminished the transport to the nucleus of 3D and 3CD and severely impaired virus infectivity. These residues have also been implicated in template binding, as seen in the crystal structures of different 3D-RNA elongation complexes. Here, we report the biochemical and structural characterization of different mutant polymerases harboring substitutions at residues 18 and 20, in particular, K18E, K18A, K20E, K20A, and the double mutant K18A K20A (KAKA). All mutant enzymes exhibit low RNA binding activity, low processivity, and alterations in nucleotide recognition, including increased incorporation of ribavirin monophosphate (RMP) relative to the incorporation of cognate nucleotides compared with the wild-type enzyme. The structural analysis shows an unprecedented flexibility of the 3D mutant polymerases, including both global rearrangements of the closed-hand architecture and local conformational changes at loop β9-α11 (within the polymerase motif B) and at the template-binding channel. Specifically, in 3D bound to RNA, both K18E and K20E induced the opening of new pockets in the template channel where the downstream templating nucleotide at position +2 binds. The comparisons of free and RNA-bound enzymes suggest that the structural rearrangements may occur in a concerted mode to regulate RNA replication, processivity, and fidelity. Thus, the N-terminal region of FMDV 3D that acts as a nuclear localization signal (NLS) and in template binding is also involved in nucleotide recognition and can affect the incorporation of nucleotide analogues. IMPORTANCE The study documents multifunctionality of a nuclear localization signal (NLS) located at the N-terminal region of the foot-and-mouth disease viral polymerase (3D). Amino acid

RIG-I detects infection with live Listeria by sensing secreted bacterial nucleic acids

PubMed Central

Abdullah, Zeinab; Schlee, Martin; Roth, Susanne; Mraheil, Mobarak Abu; Barchet, Winfried; Böttcher, Jan; Hain, Torsten; Geiger, Sergej; Hayakawa, Yoshihiro; Fritz, Jörg H; Civril, Filiz; Hopfner, Karl-Peter; Kurts, Christian; Ruland, Jürgen; Hartmann, Gunther; Chakraborty, Trinad; Knolle, Percy A

2012-01-01

Immunity against infection with Listeria monocytogenes is not achieved from innate immune stimulation by contact with killed but requires viable Listeria gaining access to the cytosol of infected cells. It has remained ill-defined how such immune sensing of live Listeria occurs. Here, we report that efficient cytosolic immune sensing requires access of nucleic acids derived from live Listeria to the cytoplasm of infected cells. We found that Listeria released nucleic acids and that such secreted bacterial RNA/DNA was recognized by the cytosolic sensors RIG-I, MDA5 and STING thereby triggering interferon β production. Secreted Listeria nucleic acids also caused RIG-I-dependent IL-1β-production and inflammasome activation. The signalling molecule CARD9 contributed to IL-1β production in response to secreted nucleic acids. In conclusion, cytosolic recognition of secreted bacterial nucleic acids by RIG-I provides a mechanistic explanation for efficient induction of immunity by live bacteria. PMID:23064150

Messing with Bacterial Quorum Sensing

PubMed Central

González, Juan E.; Keshavan, Neela D.

2006-01-01

Quorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. Several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. Interestingly, eukaryotes produce quorum-sensing-interfering (QSI) compounds that have a positive or negative influence on the bacterial signaling network. This eukaryotic interference could result in further fine-tuning of bacterial quorum sensing. Furthermore, recent work involving the synthesis of structural homologs to the various quorum-sensing signal molecules has resulted in the development of additional QSI compounds that could be used to control pathogenic bacteria. The creation of transgenic plants that express bacterial quorum-sensing genes is yet another strategy to interfere with bacterial behavior. Further investigation on the manipulation of quorum-sensing systems could provide us with powerful tools against harmful bacteria. PMID:17158701

Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

PubMed Central

Paget, Mark S.

2015-01-01

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2–4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor. PMID:26131973

Implementation theory of distortion-invariant pattern recognition for optical and digital signal processing systems

NASA Astrophysics Data System (ADS)

Lhamon, Michael Earl

A pattern recognition system which uses complex correlation filter banks requires proportionally more computational effort than single-real valued filters. This introduces increased computation burden but also introduces a higher level of parallelism, that common computing platforms fail to identify. As a result, we consider algorithm mapping to both optical and digital processors. For digital implementation, we develop computationally efficient pattern recognition algorithms, referred to as, vector inner product operators that require less computational effort than traditional fast Fourier methods. These algorithms do not need correlation and they map readily onto parallel digital architectures, which imply new architectures for optical processors. These filters exploit circulant-symmetric matrix structures of the training set data representing a variety of distortions. By using the same mathematical basis as with the vector inner product operations, we are able to extend the capabilities of more traditional correlation filtering to what we refer to as "Super Images". These "Super Images" are used to morphologically transform a complicated input scene into a predetermined dot pattern. The orientation of the dot pattern is related to the rotational distortion of the object of interest. The optical implementation of "Super Images" yields feature reduction necessary for using other techniques, such as artificial neural networks. We propose a parallel digital signal processor architecture based on specific pattern recognition algorithms but general enough to be applicable to other similar problems. Such an architecture is classified as a data flow architecture. Instead of mapping an algorithm to an architecture, we propose mapping the DSP architecture to a class of pattern recognition algorithms. Today's optical processing systems have difficulties implementing full complex filter structures. Typically, optical systems (like the 4f correlators) are limited to phase

Signal Recognition by Green Treefrogs (Hyla cinerea) and Cope’s Gray Treefrogs (Hyla chrysoscelis) in Naturally Fluctuating Noise

PubMed Central

Vélez, Alejandro; Bee, Mark A.

2013-01-01

This study tested three hypotheses about the ability of female frogs to exploit temporal fluctuations in the level of background noise to overcome the problem of recognizing male advertisement calls in noisy breeding choruses. Phonotaxis tests with green treefrogs (Hyla cinerea) and Cope’s gray treefrogs (Hyla chrysoscelis) were used to measure thresholds for recognizing calls in the presence of noise maskers with (i) no level fluctuations, (ii) random fluctuations, or level fluctuations characteristic of (iii) conspecific choruses and (iv) heterospecific choruses. The dip-listening hypothesis predicted lower signal recognition thresholds in the presence of fluctuating maskers compared with non-fluctuating maskers. Support for the dip listening hypothesis was weak; only Cope’s gray treefrogs experienced dip listening and only in the presence of randomly fluctuating maskers. The natural soundscapes advantage hypothesis predicted lower recognition thresholds when level fluctuations resembled those of natural soundscapes compared with artificial fluctuations. This hypothesis was rejected. In noise backgrounds with natural fluctuations, the species-specific advantage hypothesis predicted lower recognition thresholds when fluctuations resembled species-specific patterns of conspecific soundscapes. No evidence was found to support this hypothesis. These results corroborate previous findings showing that Cope’s gray treefrogs, but not green treefrogs, experience dip listening under some noise conditions. Together, the results suggest level fluctuations in the soundscape of natural breeding choruses may present few dip-listening opportunities. The findings of this study provide little support for the hypothesis that receivers are adapted to exploit level fluctuations of natural soundscapes in recognizing communication signals. PMID:23106802

Transcriptional response of Musca domestica larvae to bacterial infection.

PubMed

Tang, Ting; Li, Xiang; Yang, Xue; Yu, Xue; Wang, Jianhui; Liu, Fengsong; Huang, Dawei

2014-01-01

The house fly Musca domestica, a cosmopolitan dipteran insect, is a significant vector for human and animal bacterial pathogens, but little is known about its immune response to these pathogens. To address this issue, we inoculated the larvae with a mixture of Escherichia coli and Staphylococcus aureus and profiled the transcriptome 6, 24, and 48 h thereafter. Many genes known to controlling innate immunity in insects were induced following infection, including genes encoding pattern recognition proteins (PGRPs), various components of the Toll and IMD signaling pathways and of the proPO-activating and redox systems, and multiple antimicrobial peptides. Interestingly, we also uncovered a large set of novel immune response genes including two broad-spectrum antimicrobial peptides (muscin and domesticin), which might have evolved to adapt to house-fly's unique ecological environments. Finally, genes mediating oxidative phosphorylation were repressed at 48 h post-infection, suggesting disruption of energy homeostasis and mitochondrial function at the late stages of infection. Collectively, our data reveal dynamic changes in gene expression following bacterial infection in the house fly, paving the way for future in-depth analysis of M. domestica's immune system.

Leucine-rich Repeats of Bacterial Surface Proteins Serve as Common Pattern Recognition Motifs of Human Scavenger Receptor gp340*

PubMed Central

Loimaranta, Vuokko; Hytönen, Jukka; Pulliainen, Arto T.; Sharma, Ashu; Tenovuo, Jorma; Strömberg, Nicklas; Finne, Jukka

2009-01-01

Scavenger receptors are innate immune molecules recognizing and inducing the clearance of non-host as well as modified host molecules. To recognize a wide pattern of invading microbes, many scavenger receptors bind to common pathogen-associated molecular patterns, such as lipopolysaccharides and lipoteichoic acids. Similarly, the gp340/DMBT1 protein, a member of the human scavenger receptor cysteine-rich protein family, displays a wide ligand repertoire. The peptide motif VEVLXXXXW derived from its scavenger receptor cysteine-rich domains is involved in some of these interactions, but most of the recognition mechanisms are unknown. In this study, we used mass spectrometry sequencing, gene inactivation, and recombinant proteins to identify Streptococcus pyogenes protein Spy0843 as a recognition receptor of gp340. Antibodies against Spy0843 are shown to protect against S. pyogenes infection, but no function or host receptor have been identified for the protein. Spy0843 belongs to the leucine-rich repeat (Lrr) family of eukaryotic and prokaryotic proteins. Experiments with truncated forms of the recombinant proteins confirmed that the Lrr region is needed in the binding of Spy0843 to gp340. The same motif of two other Lrr proteins, LrrG from the Gram-positive S. agalactiae and BspA from the Gram-negative Tannerella forsythia, also mediated binding to gp340. Moreover, inhibition of Spy0843 binding occurred with peptides containing the VEVLXXXXW motif, but also peptides devoid of the XXXXW motif inhibited binding of Lrr proteins. These results thus suggest that the conserved Lrr motif in bacterial proteins serves as a novel pattern recognition motif for unique core peptides of human scavenger receptor gp340. PMID:19465482

Acoustic interference and recognition space within a complex assemblage of dendrobatid frogs

PubMed Central

Amézquita, Adolfo; Flechas, Sandra Victoria; Lima, Albertina Pimentel; Gasser, Herbert; Hödl, Walter

2011-01-01

In species-rich assemblages of acoustically communicating animals, heterospecific sounds may constrain not only the evolution of signal traits but also the much less-studied signal-processing mechanisms that define the recognition space of a signal. To test the hypothesis that the recognition space is optimally designed, i.e., that it is narrower toward the species that represent the higher potential for acoustic interference, we studied an acoustic assemblage of 10 diurnally active frog species. We characterized their calls, estimated pairwise correlations in calling activity, and, to model the recognition spaces of five species, conducted playback experiments with 577 synthetic signals on 531 males. Acoustic co-occurrence was not related to multivariate distance in call parameters, suggesting a minor role for spectral or temporal segregation among species uttering similar calls. In most cases, the recognition space overlapped but was greater than the signal space, indicating that signal-processing traits do not act as strictly matched filters against sounds other than homospecific calls. Indeed, the range of the recognition space was strongly predicted by the acoustic distance to neighboring species in the signal space. Thus, our data provide compelling evidence of a role of heterospecific calls in evolutionarily shaping the frogs' recognition space within a complex acoustic assemblage without obvious concomitant effects on the signal. PMID:21969562

Effects of cue modality and emotional category on recognition of nonverbal emotional signals in schizophrenia.

PubMed

Vogel, Bastian D; Brück, Carolin; Jacob, Heike; Eberle, Mark; Wildgruber, Dirk

2016-07-07

Impaired interpretation of nonverbal emotional cues in patients with schizophrenia has been reported in several studies and a clinical relevance of these deficits for social functioning has been assumed. However, it is unclear to what extent the impairments depend on specific emotions or specific channels of nonverbal communication. Here, the effect of cue modality and emotional categories on accuracy of emotion recognition was evaluated in 21 patients with schizophrenia and compared to a healthy control group (n = 21). To this end, dynamic stimuli comprising speakers of both genders in three different sensory modalities (auditory, visual and audiovisual) and five emotional categories (happy, alluring, neutral, angry and disgusted) were used. Patients with schizophrenia were found to be impaired in emotion recognition in comparison to the control group across all stimuli. Considering specific emotions more severe deficits were revealed in the recognition of alluring stimuli and less severe deficits in the recognition of disgusted stimuli as compared to all other emotions. Regarding cue modality the extent of the impairment in emotional recognition did not significantly differ between auditory and visual cues across all emotional categories. However, patients with schizophrenia showed significantly more severe disturbances for vocal as compared to facial cues when sexual interest is expressed (alluring stimuli), whereas more severe disturbances for facial as compared to vocal cues were observed when happiness or anger is expressed. Our results confirmed that perceptual impairments can be observed for vocal as well as facial cues conveying various social and emotional connotations. The observed differences in severity of impairments with most severe deficits for alluring expressions might be related to specific difficulties in recognizing the complex social emotional information of interpersonal intentions as compared to "basic" emotional states. Therefore

Orexin signaling during social defeat stress influences subsequent social interaction behaviour and recognition memory.

PubMed

Eacret, Darrell; Grafe, Laura A; Dobkin, Jane; Gotter, Anthony L; Rengerb, John J; Winrow, Christopher J; Bhatnagar, Seema

2018-06-11

Orexins are neuropeptides synthesized in the lateral hypothalamus that influence arousal, feeding, reward pathways, and the response to stress. However, the role of orexins in repeated stress is not fully characterized. Here, we examined how orexins and their receptors contribute to the coping response during repeated social defeat and subsequent anxiety-like and memory-related behaviors. Specifically, we used Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) to stimulate orexins prior to each of five consecutive days of social defeat stress in adult male rats. Additionally, we determined the role of the orexin 2 receptor in these behaviors by using a selective orexin 2 receptor antagonist (MK-1064) administered prior to each social defeat. Following the 5 day social defeat conditioning period, rats were evaluated in social interaction and novel object recognition paradigms to assess anxiety-like behavior and recognition memory, respectively. Activation of orexin neurons by DREADDs prior to each social defeat decreased the average latency to become defeated across 5 days, indicative of a passive coping strategy that we have previously linked to a stress vulnerable phenotype. Moreover, stimulation of orexin signaling during defeat conditioning decreased subsequent social interaction and performance in the novel object recognition test indicating increased subsequent anxiety-like behavior and reduced working memory. Blocking the orexin 2 receptor during repeated defeat did not alter these effects. Together, our results suggest that orexin neuron activation produces a passive coping phenotype during social defeat leading to subsequent anxiety-like behaviors and memory deficits. Copyright © 2018. Published by Elsevier B.V.

Intercellular and intracellular signalling systems that globally control the expression of virulence genes in plant pathogenic bacteria.

PubMed

Ham, Jong Hyun

2013-04-01

Plant pathogenic bacteria utilize complex signalling systems to control the expression of virulence genes at the cellular level and within populations. Quorum sensing (QS), an important intercellular communication mechanism, is mediated by different types of small molecules, including N-acyl homoserine lactones (AHLs), fatty acids and small proteins. AHL-mediated signalling systems dependent on the LuxI and LuxR family proteins play critical roles in the virulence of a wide range of Gram-negative plant pathogenic bacteria belonging to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Xanthomonas spp. and Xylella fastidiosa, members of the Gammaproteobacteria, however, possess QS systems that are mediated by fatty acid-type diffusible signal factors (DSFs). Recent studies have demonstrated that Ax21, a 194-amino-acid protein in Xanthomonas oryzae pv. oryzae, plays dual functions in activating a rice innate immune pathway through binding to the rice XA21 pattern recognition receptor and in regulating bacterial virulence and biofilm formation as a QS signal molecule. In xanthomonads, DSF-mediated QS systems are connected with the signalling pathways mediated by cyclic diguanosine monophosphate (c-di-GMP), which functions as a second messenger for the control of virulence gene expression in these bacterial pathogens. © 2012 BSPP AND BLACKWELL PUBLISHING LTD.

DNA recognition by an RNA-guided bacterial Argonaute

PubMed Central

Doudna, Jennifer A.

2017-01-01

Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5′-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 Å resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate. Comparison of this ternary complex to other target-bound Argonaute structures reveals a unique orientation of the N-terminal domain, resulting in a straight helical axis of the entire RNA-DNA heteroduplex through the central cleft of the protein. Additionally, mismatches introduced into the heteroduplex reduce MpAgo cleavage efficiency with a symmetric profile centered around the middle of the helix. This pattern differs from the canonical mismatch tolerance of other Argonautes, which display decreased cleavage efficiency for substrates bearing sequence mismatches to the 5′ region of the guide strand. This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins. PMID:28520746

Shigella flexneri type III secreted effector OspF reveals new crosstalks of proinflammatory signaling pathways during bacterial infection.

PubMed

Reiterer, Veronika; Grossniklaus, Lars; Tschon, Therese; Kasper, Christoph Alexander; Sorg, Isabel; Arrieumerlou, Cécile

2011-07-01

Shigella flexneri type III secreted effector OspF harbors a phosphothreonine lyase activity that irreversibly dephosphorylates MAP kinases (MAPKs) p38 and ERK in infected epithelial cells and thereby, dampens innate immunity. Whereas this activity has been well characterized, the impact of OspF on other host signaling pathways that control inflammation was unknown. Here we report that OspF potentiates the activation of the MAPK JNK and the transcription factor NF-κB during S. flexneri infection. This unexpected effect of OspF was dependent on the phosphothreonine lyase activity of OspF on p38, and resulted from the disruption of a negative feedback loop regulation between p38 and TGF-beta activated kinase 1 (TAK1), mediated via the phosphorylation of TAK1-binding protein 1. Interestingly, potentiated JNK activation was not associated with enhanced c-Jun signaling as OspF also inhibits c-Jun expression at the transcriptional level. Altogether, our data reveal the impact of OspF on the activation of NF-κB, JNK and c-Jun, and demonstrate the existence of a negative feedback loop regulation between p38 and TAK1 during S. flexneri infection. Furthermore, this study validates the use of bacterial effectors as molecular tools to identify the crosstalks that connect important host signaling pathways induced upon bacterial infection. Copyright © 2011 Elsevier Inc. All rights reserved.

Recognition of LPS by TLR4: Potential for Anti-Inflammatory Therapies

PubMed Central

Nijland, Reindert; Hofland, Tom; van Strijp, Jos A. G.

2014-01-01

LPS molecules of marine bacteria show structures distinct from terrestrial bacteria, due to the different environment that marine bacteria live in. Because of these different structures, lipid A molecules from marine bacteria are most often poor stimulators of the Toll-like receptor 4 (TLR4) pathway. Due to their low stimulatory potential, these lipid A molecules are suggested to be applicable as antagonists of TLR4 signaling in sepsis patients, where this immune response is amplified and unregulated. Antagonizing lipid A molecules might be used for future therapies against sepsis, therapies that currently do not exist. In this review, we will discuss these differences in lipid A structures and their recognition by the immune system. The modifications present in marine lipid A structures are described, and their potential as LPS antagonists will be discussed. Finally, since clinical trials built on antagonizing lipid A molecules have proven unsuccessful, we propose to also focus on different aspects of the TLR4 signaling pathway when searching for new potential drugs. Furthermore, we put forward the notion that bacteria probably already produce inhibitors of TLR4 signaling, making these bacterial products interesting molecules to investigate for future sepsis therapies. PMID:25056632

Group A Streptococcus tissue invasion by CD44-mediated cell signalling

NASA Astrophysics Data System (ADS)

Cywes, Colette; Wessels, Michael R.

2001-12-01

Streptococcus pyogenes (also known as group A Streptococcus, GAS), the agent of streptococcal sore throat and invasive soft-tissue infections, attaches to human pharyngeal or skin epithelial cells through specific recognition of its hyaluronic acid capsular polysaccharide by the hyaluronic-acid-binding protein CD44 (refs 1, 2). Because ligation of CD44 by hyaluronic acid can induce epithelial cell movement on extracellular matrix, we investigated whether molecular mimicry by the GAS hyaluronic acid capsule might induce similar cellular responses. Here we show that CD44-dependent GAS binding to polarized monolayers of human keratinocytes induced marked cytoskeletal rearrangements manifested by membrane ruffling and disruption of intercellular junctions. Transduction of the signal induced by GAS binding to CD44 on the keratinocyte surface involved Rac1 and the cytoskeleton linker protein ezrin, as well as tyrosine phosphorylation of cellular proteins. Studies of bacterial translocation in two models of human skin indicated that cell signalling triggered by interaction of the GAS capsule with CD44 opened intercellular junctions and promoted tissue penetration by GAS through a paracellular route. These results support a model of host cytoskeleton manipulation and tissue invasion by an extracellular bacterial pathogen.

Perceptual Plasticity for Auditory Object Recognition

PubMed Central

Heald, Shannon L. M.; Van Hedger, Stephen C.; Nusbaum, Howard C.

2017-01-01

In our auditory environment, we rarely experience the exact acoustic waveform twice. This is especially true for communicative signals that have meaning for listeners. In speech and music, the acoustic signal changes as a function of the talker (or instrument), speaking (or playing) rate, and room acoustics, to name a few factors. Yet, despite this acoustic variability, we are able to recognize a sentence or melody as the same across various kinds of acoustic inputs and determine meaning based on listening goals, expectations, context, and experience. The recognition process relates acoustic signals to prior experience despite variability in signal-relevant and signal-irrelevant acoustic properties, some of which could be considered as “noise” in service of a recognition goal. However, some acoustic variability, if systematic, is lawful and can be exploited by listeners to aid in recognition. Perceivable changes in systematic variability can herald a need for listeners to reorganize perception and reorient their attention to more immediately signal-relevant cues. This view is not incorporated currently in many extant theories of auditory perception, which traditionally reduce psychological or neural representations of perceptual objects and the processes that act on them to static entities. While this reduction is likely done for the sake of empirical tractability, such a reduction may seriously distort the perceptual process to be modeled. We argue that perceptual representations, as well as the processes underlying perception, are dynamically determined by an interaction between the uncertainty of the auditory signal and constraints of context. This suggests that the process of auditory recognition is highly context-dependent in that the identity of a given auditory object may be intrinsically tied to its preceding context. To argue for the flexible neural and psychological updating of sound-to-meaning mappings across speech and music, we draw upon examples

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

PubMed Central

Fouts, Derrick E.; Matthias, Michael A.; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E.; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L.; Haake, David A.; Haft, Daniel H.; Hartskeerl, Rudy; Ko, Albert I.; Levett, Paul N.; Matsunaga, James; Mechaly, Ariel E.; Monk, Jonathan M.; Nascimento, Ana L. T.; Nelson, Karen E.; Palsson, Bernhard; Peacock, Sharon J.; Picardeau, Mathieu; Ricaldi, Jessica N.; Thaipandungpanit, Janjira; Wunder, Elsio A.; Yang, X. Frank; Zhang, Jun-Jie; Vinetz, Joseph M.

2016-01-01

Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade’s refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

PubMed

Fouts, Derrick E; Matthias, Michael A; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L; Haake, David A; Haft, Daniel H; Hartskeerl, Rudy; Ko, Albert I; Levett, Paul N; Matsunaga, James; Mechaly, Ariel E; Monk, Jonathan M; Nascimento, Ana L T; Nelson, Karen E; Palsson, Bernhard; Peacock, Sharon J; Picardeau, Mathieu; Ricaldi, Jessica N; Thaipandungpanit, Janjira; Wunder, Elsio A; Yang, X Frank; Zhang, Jun-Jie; Vinetz, Joseph M

2016-02-01

Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic

Dynamic chemical communication between plants and bacteria through airborne signals: induced resistance by bacterial volatiles.

PubMed

Farag, Mohamed A; Zhang, Huiming; Ryu, Choong-Min

2013-07-01

Certain plant growth-promoting rhizobacteria (PGPR) elicit induced systemic resistance (ISR) and plant growth promotion in the absence of physical contact with plants via volatile organic compound (VOC) emissions. In this article, we review the recent progess made by research into the interactions between PGPR VOCs and plants, focusing on VOC emission by PGPR strains in plants. Particular attention is given to the mechanisms by which these bacterial VOCs elicit ISR. We provide an overview of recent progress in the elucidation of PGPR VOC interactions from studies utilizing transcriptome, metabolome, and proteome analyses. By monitoring defense gene expression patterns, performing 2-dimensional electrophoresis, and studying defense signaling null mutants, salicylic acid and ethylene have been found to be key players in plant signaling pathways involved in the ISR response. Bacterial VOCs also confer induced systemic tolerance to abiotic stresses, such as drought and heavy metals. A review of current analytical approaches for PGPR volatile profiling is also provided with needed future developments emphasized. To assess potential utilization of PGPR VOCs for crop plants, volatile suspensions have been applied to pepper and cucumber roots and found to be effective at protecting plants against plant pathogens and insect pests in the field. Taken together, these studies provide further insight into the biological and ecological potential of PGPR VOCs for enhancing plant self-immunity and/or adaptation to biotic and abiotic stresses in modern agriculture.

Indole-based novel small molecules for the modulation of bacterial signalling pathways.

PubMed

Biswas, Nripendra Nath; Kutty, Samuel K; Barraud, Nicolas; Iskander, George M; Griffith, Renate; Rice, Scott A; Willcox, Mark; Black, David StC; Kumar, Naresh

2015-01-21

Gram-negative bacteria such as Pseudomonas aeruginosa use N-acylated L-homoserine lactones (AHLs) as autoinducers (AIs) for quorum sensing (QS), a major regulatory and cell-to-cell communication system for social adaptation, virulence factor production, biofilm formation and antibiotic resistance. Some bacteria use indole moieties for intercellular signaling and as regulators of various bacterial phenotypes important for evading the innate host immune response and antimicrobial resistance. A range of natural and synthetic indole derivatives have been found to act as inhibitors of QS-dependent bacterial phenotypes, complementing the bactericidal ability of traditional antibiotics. In this work, various indole-based AHL mimics were designed and synthesized via the 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC·HCl) and N,N'-dicyclohexylcarbodiimide (DCC) mediated coupling reactions of a variety of substituted or unsubstituted aminoindoles with different alkanoic acids. All synthesized compounds were tested for QS inhibition using a P. aeruginosa QS reporter strain by measuring the amount of green fluorescent protein (GFP) production. Docking studies were performed to examine their potential to bind and therefore inhibit the target QS receptor protein. The most potent compounds 11a, 11d and 16a showed 44 to 65% inhibition of QS activity at 250 μM concentration, and represent promising drug leads for the further development of anti-QS antimicrobial compounds.

Autophagic clearance of bacterial pathogens: molecular recognition of intracellular microorganisms.

PubMed

Pareja, Maria Eugenia Mansilla; Colombo, Maria I

2013-01-01

Autophagy is involved in several physiological and pathological processes. One of the key roles of the autophagic pathway is to participate in the first line of defense against the invasion of pathogens, as part of the innate immune response. Targeting of intracellular bacteria by the autophagic machinery, either in the cytoplasm or within vacuolar compartments, helps to control bacterial proliferation in the host cell, controlling also the spreading of the infection. In this review we will describe the means used by diverse bacterial pathogens to survive intracellularly and how they are recognized by the autophagic molecular machinery, as well as the mechanisms used to avoid autophagic clearance.

Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition.

PubMed

Ferrer-Orta, Cristina; de la Higuera, Ignacio; Caridi, Flavia; Sánchez-Aparicio, María Teresa; Moreno, Elena; Perales, Celia; Singh, Kamalendra; Sarafianos, Stefan G; Sobrino, Francisco; Domingo, Esteban; Verdaguer, Nuria

2015-07-01

The N-terminal region of the foot-and-mouth disease virus (FMDV) 3D polymerase contains the sequence MRKTKLAPT (residues 16 to 24) that acts as a nuclear localization signal. A previous study showed that substitutions K18E and K20E diminished the transport to the nucleus of 3D and 3CD and severely impaired virus infectivity. These residues have also been implicated in template binding, as seen in the crystal structures of different 3D-RNA elongation complexes. Here, we report the biochemical and structural characterization of different mutant polymerases harboring substitutions at residues 18 and 20, in particular, K18E, K18A, K20E, K20A, and the double mutant K18A K20A (KAKA). All mutant enzymes exhibit low RNA binding activity, low processivity, and alterations in nucleotide recognition, including increased incorporation of ribavirin monophosphate (RMP) relative to the incorporation of cognate nucleotides compared with the wild-type enzyme. The structural analysis shows an unprecedented flexibility of the 3D mutant polymerases, including both global rearrangements of the closed-hand architecture and local conformational changes at loop β9-α11 (within the polymerase motif B) and at the template-binding channel. Specifically, in 3D bound to RNA, both K18E and K20E induced the opening of new pockets in the template channel where the downstream templating nucleotide at position +2 binds. The comparisons of free and RNA-bound enzymes suggest that the structural rearrangements may occur in a concerted mode to regulate RNA replication, processivity, and fidelity. Thus, the N-terminal region of FMDV 3D that acts as a nuclear localization signal (NLS) and in template binding is also involved in nucleotide recognition and can affect the incorporation of nucleotide analogues. The study documents multifunctionality of a nuclear localization signal (NLS) located at the N-terminal region of the foot-and-mouth disease viral polymerase (3D). Amino acid substitutions at this

Fractal and twin SVM-based handgrip recognition for healthy subjects and trans-radial amputees using myoelectric signal.

PubMed

Arjunan, Sridhar Poosapadi; Kumar, Dinesh Kant; Jayadeva J

2016-02-01

Identifying functional handgrip patterns using surface electromygram (sEMG) signal recorded from amputee residual muscle is required for controlling the myoelectric prosthetic hand. In this study, we have computed the signal fractal dimension (FD) and maximum fractal length (MFL) during different grip patterns performed by healthy and transradial amputee subjects. The FD and MFL of the sEMG, referred to as the fractal features, were classified using twin support vector machines (TSVM) to recognize the handgrips. TSVM requires fewer support vectors, is suitable for data sets with unbalanced distributions, and can simultaneously be trained for improving both sensitivity and specificity. When compared with other methods, this technique resulted in improved grip recognition accuracy, sensitivity, and specificity, and this improvement was significant (κ=0.91).

Intelligent signal analysis and recognition

NASA Technical Reports Server (NTRS)

Levinson, Robert; Helman, Daniel; Oswalt, Edward

1987-01-01

Progress in the research and development of self-organizing database system that can support the identification and characterization of signals in an RF environment is described. As the radio frequency spectrum becomes more crowded, there are a number of situations that require a characterization of the RF environment. This database system is designed to be practical in applications where communications and other instruments encounter a time varying and complex RF environment. The primary application of this system is the guidance and control of NASA's SETI Microwave Observing Project. Other possible applications include selection of telemety bands for communication with spacecraft, and the scheduling of antenna for radio astronomy are two examples where characterization of the RF environment is required. In these applications, the RF environment is constantly changing, and even experienced operators cannot quickly identify the multitude of signals that can be encountered. Some of these signals are repetitive, others appear to occur sporadically.

Deep learning approach to bacterial colony classification.

PubMed

Zieliński, Bartosz; Plichta, Anna; Misztal, Krzysztof; Spurek, Przemysław; Brzychczy-Włoch, Monika; Ochońska, Dorota

2017-01-01

In microbiology it is diagnostically useful to recognize various genera and species of bacteria. It can be achieved using computer-aided methods, which make the recognition processes more automatic and thus significantly reduce the time necessary for the classification. Moreover, in case of diagnostic uncertainty (the misleading similarity in shape or structure of bacterial cells), such methods can minimize the risk of incorrect recognition. In this article, we apply the state of the art method for texture analysis to classify genera and species of bacteria. This method uses deep Convolutional Neural Networks to obtain image descriptors, which are then encoded and classified with Support Vector Machine or Random Forest. To evaluate this approach and to make it comparable with other approaches, we provide a new dataset of images. DIBaS dataset (Digital Image of Bacterial Species) contains 660 images with 33 different genera and species of bacteria.

Bacterial surface adaptation

NASA Astrophysics Data System (ADS)

Utada, Andrew

2014-03-01

Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

Systemic cytokine signaling via IL-17 in smokers with obstructive pulmonary disease: a link to bacterial colonization?

PubMed Central

Andelid, Kristina; Tengvall, Sara; Andersson, Anders; Levänen, Bettina; Christenson, Karin; Jirholt, Pernilla; Åhrén, Christina; Qvarfordt, Ingemar; Ekberg-Jansson, Ann; Lindén, Anders

2015-01-01

We examined whether systemic cytokine signaling via interleukin (IL)-17 and growth-related oncogene-α (GRO-α) is impaired in smokers with obstructive pulmonary disease including chronic bronchitis (OPD-CB). We also examined how this systemic cytokine signaling relates to bacterial colonization in the airways of the smokers with OPD-CB. Currently smoking OPD-CB patients (n=60, corresponding to Global initiative for chronic Obstructive Lung Disease [GOLD] stage I–IV) underwent recurrent blood and sputum sampling over 60 weeks, during stable conditions and at exacerbations. We characterized cytokine protein concentrations in blood and bacterial growth in sputum. Asymptomatic smokers (n=10) and never-smokers (n=10) were included as control groups. During stable clinical conditions, the protein concentrations of IL-17 and GRO-α were markedly lower among OPD-CB patients compared with never-smoker controls, whereas the asymptomatic smoker controls displayed intermediate concentrations. Notably, among OPD-CB patients, colonization by opportunistic pathogens was associated with markedly lower IL-17 and GRO-α, compared with colonization by common respiratory pathogens or oropharyngeal flora. During exacerbations in the OPD-CB patients, GRO-α and neutrophil concentrations were increased, whereas protein concentrations and messenger RNA for IL-17 were not detectable in a reproducible manner. In smokers with OPD-CB, systemic cytokine signaling via IL-17 and GRO-α is impaired and this alteration may be linked to colonization by opportunistic pathogens in the airways. Given the potential pathogenic and therapeutic implications, these findings deserve to be validated in new and larger patient cohorts. PMID:25848245

Individual recognition between mother and infant bats (Myotis)

NASA Technical Reports Server (NTRS)

Turner, D.; Shaughnessy, A.; Gould, E.

1972-01-01

The recognition process and the basis for that recognition, in brown bats, between mother and infant are analyzed. Two parameters, ultrasonic communication and olfactory stimuli, are investigated. The test animals were not allowed any visual contact. It was concluded that individual recognition between mother and infant occurred. However, it could not be determined if the recognition was based on ultrasonic signals or olfactory stimuli.

OsLYP4 and OsLYP6 play critical roles in rice defense signal transduction.

PubMed

Liu, Bing; Li, Jian-Feng; Ao, Ying; Li, Zhangqun; Liu, Jun; Feng, Dongru; Qi, Kangbiao; He, Yanming; Zeng, Liexian; Wang, Jinfa; Wang, Hong-Bin

2013-02-01

Plant innate immunity relies on successful detection of trespassing pathogens through recognizing their microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) at the cell surface. We recently reported two rice lysin motif (LysM)-containing proteins, OsLYP4 and OsLYP6, as dual functional PRRs sensing bacterial peptidoglycan (PGN) and fungal chitin. Here we further demonstrated the important roles of OsLYP4 and OsLYP6 in rice defense signaling, as silencing of either LYP impaired the defense marker gene activation induced by either bacterial pathogen Xanthomonas oryzaecola or fungal pathogen Magnaporthe oryzae. Moreover, we found that OsLYP4 and OsLYP6 could form homo- and hetero-dimers, and could interact with CEBiP, suggesting an unexpected complexity of chitin perception in rice.

STATUS OF THE SYSTEM OF SIGNALING PATTERN RECOGNITION RECEPTORS OF MONOCYTES AND GRANULOCYTES IN COSMONAUTS' PERIPHERAL BLOOD BEFORE AND AFTER LONG-DURATION MISSIONS TO THE INTERNATIONAL SPACE STATION.

PubMed

Ponomarev, S A; Berendeeva, T A; Kalinin, S A; Muranova, A V

The system of signaling pattern recognition receptors was studied in 8 cosmonauts aged 35 to 56 years before and after (R+) long-duration missions to the International space station. Peripheral blood samples were analyzed for the content of monocytes and granulocytes that express the signaling pattern recognition Toll- like (TLR) receptors localized as on cell surface (TLR1, TLR2, TLR4, TLR5, TLR6), so inside cells (TLR3, TLR8, TLR9). In parallel, serum concentrations of TLR2 (HSP60) and TLR4 ligands (HSP70, HMGB1) were measured. The results of investigations showed growth of HSP60, HSP70 and HMGB1 concentrations on R+1. In the;majority of cosmonauts increases in endogenous ligands were followed by growth in the number of both monocytes and granulocytes that express TLR2 1 TLR4. This consistency gives ground to assume that changes in the system of signaling pattern recognition receptors can stem .from the predominantly endogenous ligands' response to the effects of long-duration space flight on human organism.

Engineered fluorescent proteins illuminate the bacterial periplasm

PubMed Central

Dammeyer, Thorben; Tinnefeld, Philip

2012-01-01

The bacterial periplasm is of special interest whenever cell factories are designed and engineered. Recombinantely produced proteins are targeted to the periplasmic space of Gram negative bacteria to take advantage of the authentic N-termini, disulfide bridge formation and easy accessibility for purification with less contaminating cellular proteins. The oxidizing environment of the periplasm promotes disulfide bridge formation - a prerequisite for proper folding of many proteins into their active conformation. In contrast, the most popular reporter protein in all of cell biology, Green Fluorescent Protein (GFP), remains inactive if translocated to the periplasmic space prior to folding. Here, the self-catalyzed chromophore maturation is blocked by formation of covalent oligomers via interchain disulfide bonds in the oxidizing environment. However, different protein engineering approaches addressing folding and stability of GFP resulted in improved proteins with enhanced folding properties. Recent studies describe GFP variants that are not only active if translocated in their folded form via the twin-arginine translocation (Tat) pathway, but actively fold in the periplasm following general secretory pathway (Sec) and signal recognition particle (SRP) mediated secretion. This mini-review highlights the progress that enables new insights into bacterial export and periplasmic protein organization, as well as new biotechnological applications combining the advantages of the periplasmic production and the Aequorea-based fluorescent reporter proteins. PMID:24688673

micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules.

PubMed

Holt, Dennis B; Gupta, Vikas; Meyer, Dörte; Abel, Nikolaj B; Andersen, Stig U; Stougaard, Jens; Markmann, Katharina

2015-10-01

Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. japonicus sRNA-ome and isolate infection-responsive sRNAs, followed by candidate-based functional characterization. Sequences from four libraries revealed 219 novel L. japonicus micro RNAs (miRNAs) from 114 newly assigned families, and 76 infection-responsive sRNAs. Unlike infection-associated coding genes such as NODULE INCEPTION (NIN), a micro RNA 172 (miR172) isoform showed strong accumulation in dependency of both Nodulation (Nod) factor and compatible rhizobia. The genetics of miR172 induction support the existence of distinct epidermal and cortical signalling events. MIR172a promoter activity followed a previously unseen pattern preceding infection thread progression in epidermal and cortical cells. Nodule-associated miR172a expression was infection-independent, representing the second of two genetically separable activity waves. The combined data provide a valuable resource for further study, and identify miR172 as an sRNA marking successful epidermal infection. We show that miR172 acts upstream of several APETALA2-type (AP2) transcription factors, and suggest that it has a role in fine-tuning AP2 levels during bacterial symbiosis. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Structural Insights Into the Recognition of Peroxisomal Targeting Signal 1 By Trypanosoma Brucei Peroxin 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sampathkumar, P.; Roach, C.; Michels, P.A.M.

2009-05-27

Glycosomes are peroxisome-like organelles essential for trypanosomatid parasites. Glycosome biogenesis is mediated by proteins called 'peroxins,' which are considered to be promising drug targets in pathogenic Trypanosomatidae. The first step during protein translocation across the glycosomal membrane of peroxisomal targeting signal 1 (PTS1)-harboring proteins is signal recognition by the cytosolic receptor peroxin 5 (PEX5). The C-terminal PTS1 motifs interact with the PTS1 binding domain (P1BD) of PEX5, which is made up of seven tetratricopeptide repeats. Obtaining diffraction-quality crystals of the P1BD of Trypanosoma brucei PEX5 (TbPEX5) required surface entropy reduction mutagenesis. Each of the seven tetratricopeptide repeats appears to havemore » a residue in the alpha(L) conformation in the loop connecting helices A and B. Five crystal structures of the P1BD of TbPEX5 were determined, each in complex with a hepta- or decapeptide corresponding to a natural or nonnatural PTS1 sequence. The PTS1 peptides are bound between the two subdomains of the P1BD. These structures indicate precise recognition of the C-terminal Leu of the PTS1 motif and important interactions between the PTS1 peptide main chain and up to five invariant Asn side chains of PEX5. The TbPEX5 structures reported here reveal a unique hydrophobic pocket in the subdomain interface that might be explored to obtain compounds that prevent relative motions of the subdomains and interfere selectively with PTS1 motif binding or release in trypanosomatids, and would therefore disrupt glycosome biogenesis and prevent parasite growth.« less

Structural Basis for Ligand Recognition and Discrimination of a Quorum-quenching Antibody*

PubMed Central

Kirchdoerfer, Robert N.; Garner, Amanda L.; Flack, Caralyn E.; Mee, Jenny M.; Horswill, Alexander R.; Janda, Kim D.; Kaufmann, Gunnar F.; Wilson, Ian A.

2011-01-01

In the postantibiotic era, available treatment options for severe bacterial infections caused by methicillin-resistant Staphylococcus aureus have become limited. Therefore, new and innovative approaches are needed to combat such life-threatening infections. Virulence factor expression in S. aureus is regulated in a cell density-dependent manner using “quorum sensing,” which involves generation and secretion of autoinducing peptides (AIPs) into the surrounding environment to activate a bacterial sensor kinase at a particular threshold concentration. Mouse monoclonal antibody AP4-24H11 was shown previously to blunt quorum sensing-mediated changes in gene expression in vitro and protect mice from a lethal dose of S. aureus by sequestering the AIP signal. We have elucidated the crystal structure of the AP4-24H11 Fab in complex with AIP-4 at 2.5 Å resolution to determine its mechanism of ligand recognition. A key GluH95 provides much of the binding specificity through formation of hydrogen bonds with each of the four amide nitrogens in the AIP-4 macrocyclic ring. Importantly, these structural data give clues as to the interactions between the cognate staphylococcal AIP receptors AgrC and the AIPs, as AP4-24H11·AIP-4 binding recapitulates features that have been proposed for AgrC-AIP recognition. Additionally, these structural insights may enable the engineering of AIP cross-reactive antibodies or quorum quenching vaccines for use in active or passive immunotherapy for prevention or treatment of S. aureus infections. PMID:21454495

Structural Basis for Ligand Recognition and Discrimination of a Quorum-quenching Antibody

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirchdoerfer, Robert N.; Garner, Amanda L.; Flack, Caralyn E.

2011-09-16

In the postantibiotic era, available treatment options for severe bacterial infections caused by methicillin-resistant Staphylococcus aureus have become limited. Therefore, new and innovative approaches are needed to combat such life-threatening infections. Virulence factor expression in S. aureus is regulated in a cell density-dependent manner using 'quorum sensing,' which involves generation and secretion of autoinducing peptides (AIPs) into the surrounding environment to activate a bacterial sensor kinase at a particular threshold concentration. Mouse monoclonal antibody AP4-24H11 was shown previously to blunt quorum sensing-mediated changes in gene expression in vitro and protect mice from a lethal dose of S. aureus by sequesteringmore » the AIP signal. We have elucidated the crystal structure of the AP4-24H11 Fab in complex with AIP-4 at 2.5 {angstrom} resolution to determine its mechanism of ligand recognition. A key GluH95 provides much of the binding specificity through formation of hydrogen bonds with each of the four amide nitrogens in the AIP-4 macrocyclic ring. Importantly, these structural data give clues as to the interactions between the cognate staphylococcal AIP receptors AgrC and the AIPs, as AP4-24H11 {center_dot} AIP-4 binding recapitulates features that have been proposed for AgrC-AIP recognition. Additionally, these structural insights may enable the engineering of AIP cross-reactive antibodies or quorum quenching vaccines for use in active or passive immunotherapy for prevention or treatment of S. aureus infections.« less

Detection and recognition of mechanical, digging and vehicle signals in the optical fiber pre-warning system

NASA Astrophysics Data System (ADS)

Tian, Qing; Yang, Dan; Zhang, Yuan; Qu, Hongquan

2018-04-01

This paper presents detection and recognition method to locate and identify harmful intrusions in the optical fiber pre-warning system (OFPS). Inspired by visual attention architecture (VAA), the process flow is divided into two parts, i.e., data-driven process and task-driven process. At first, data-driven process takes all the measurements collected by the system as input signals, which is handled by detection method to locate the harmful intrusion in both spatial domain and time domain. Then, these detected intrusion signals are taken over by task-driven process. Specifically, we get pitch period (PP) and duty cycle (DC) of the intrusion signals to identify the mechanical and manual digging (MD) intrusions respectively. For the passing vehicle (PV) intrusions, their strong low frequency component can be used as good feature. In generally, since the harmful intrusion signals only account for a small part of whole measurements, the data-driven process reduces the amount of input data for subsequent task-driven process considerably. Furthermore, the task-driven process determines the harmful intrusions orderly according to their severity, which makes a priority mechanism for the system as well as targeted processing for different harmful intrusion. At last, real experiments are performed to validate the effectiveness of this method.

Self-recognition, color signals, and cycles of greenbeard mutualism and altruism

PubMed Central

Sinervo, Barry; Chaine, Alexis; Clobert, Jean; Calsbeek, Ryan; Hazard, Lisa; Lancaster, Lesley; McAdam, Andrew G.; Alonzo, Suzanne; Corrigan, Gwynne; Hochberg, Michael E.

2006-01-01

Altruism presents a challenge to evolutionary theory because selection should favor selfish over caring strategies. Greenbeard altruism resolves this paradox by allowing cooperators to identify individuals carrying similar alleles producing a form of genic selection. In side-blotched lizards, genetically similar but unrelated blue male morphs settle on adjacent territories and cooperate. Here we show that payoffs of cooperation depend on asymmetric costs of orange neighbors. One blue male experiences low fitness and buffers his unrelated partner from aggressive orange males despite the potential benefits of defection. We show that recognition behavior is highly heritable in nature, and we map genetic factors underlying color and self-recognition behavior of genetic similarity in both sexes. Recognition and cooperation arise from genome-wide factors based on our mapping study of the location of genes responsible for self-recognition behavior, recognition of blue color, and the color locus. Our results provide an example of greenbeard interactions in a vertebrate that are typified by cycles of greenbeard mutualism interspersed with phases of transient true altruism. Such cycles provide a mechanism encouraging the origin and stability of true altruism. PMID:16651531

"Multiple partial recognitions in dynamic equilibrium" in the binding sites of proteins form the molecular basis of promiscuous recognition of structurally diverse ligands.

PubMed

Kohda, Daisuke

2018-04-01

Promiscuous recognition of ligands by proteins is as important as strict recognition in numerous biological processes. In living cells, many short, linear amino acid motifs function as targeting signals in proteins to specify the final destination of the protein transport. In general, the target signal is defined by a consensus sequence containing wild-characters, and hence represented by diverse amino acid sequences. The classical lock-and-key or induced-fit/conformational selection mechanism may not cover all aspects of the promiscuous recognition. On the basis of our crystallographic and NMR studies on the mitochondrial Tom20 protein-presequence interaction, we proposed a new hypothetical mechanism based on "a rapid equilibrium of multiple states with partial recognitions". This dynamic, multiple recognition mode enables the Tom20 receptor to recognize diverse mitochondrial presequences with nearly equal affinities. The plant Tom20 is evolutionally unrelated to the animal Tom20 in our study, but is a functional homolog of the animal/fungal Tom20. NMR studies by another research group revealed that the presequence binding by the plant Tom20 was not fully explained by simple interaction modes, suggesting the presence of a similar dynamic, multiple recognition mode. Circumstantial evidence also suggested that similar dynamic mechanisms may be applicable to other promiscuous recognitions of signal peptides by the SRP54/Ffh and SecA proteins.

An Ancient Bacterial Signaling Pathway Regulates Chloroplast Function to Influence Growth and Development in Arabidopsis.

PubMed

Sugliani, Matteo; Abdelkefi, Hela; Ke, Hang; Bouveret, Emmanuelle; Robaglia, Christophe; Caffarri, Stefano; Field, Ben

2016-03-01

The chloroplast originated from the endosymbiosis of an ancient photosynthetic bacterium by a eukaryotic cell. Remarkably, the chloroplast has retained elements of a bacterial stress response pathway that is mediated by the signaling nucleotides guanosine penta- and tetraphosphate (ppGpp). However, an understanding of the mechanism and outcomes of ppGpp signaling in the photosynthetic eukaryotes has remained elusive. Using the model plant Arabidopsis thaliana, we show that ppGpp is a potent regulator of chloroplast gene expression in vivo that directly reduces the quantity of chloroplast transcripts and chloroplast-encoded proteins. We then go on to demonstrate that the antagonistic functions of different plant RelA SpoT homologs together modulate ppGpp levels to regulate chloroplast function and show that they are required for optimal plant growth, chloroplast volume, and chloroplast breakdown during dark-induced and developmental senescence. Therefore, our results show that ppGpp signaling is not only linked to stress responses in plants but is also an important mediator of cooperation between the chloroplast and the nucleocytoplasmic compartment during plant growth and development. © 2016 American Society of Plant Biologists. All rights reserved.

Intra-pulse modulation recognition using short-time ramanujan Fourier transform spectrogram

NASA Astrophysics Data System (ADS)

Ma, Xiurong; Liu, Dan; Shan, Yunlong

2017-12-01

Intra-pulse modulation recognition under negative signal-to-noise ratio (SNR) environment is a research challenge. This article presents a robust algorithm for the recognition of 5 types of radar signals with large variation range in the signal parameters in low SNR using the combination of the Short-time Ramanujan Fourier transform (ST-RFT) and pseudo-Zernike moments invariant features. The ST-RFT provides the time-frequency distribution features for 5 modulations. The pseudo-Zernike moments provide invariance properties that are able to recognize different modulation schemes on different parameter variation conditions from the ST-RFT spectrograms. Simulation results demonstrate that the proposed algorithm achieves the probability of successful recognition (PSR) of over 90% when SNR is above -5 dB with large variation range in the signal parameters: carrier frequency (CF) for all considered signals, hop size (HS) for frequency shift keying (FSK) signals, and the time-bandwidth product for Linear Frequency Modulation (LFM) signals.

Spatial organization shapes the turnover of a bacterial transcriptome

PubMed Central

Moffitt, Jeffrey R; Pandey, Shristi; Boettiger, Alistair N; Wang, Siyuan; Zhuang, Xiaowei

2016-01-01

Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Time-resolved RNA-sequencing revealed that degradation rates of inner-membrane-protein mRNAs are on average greater that those of the other mRNAs and that this selective destabilization of inner-membrane-protein mRNAs is abolished by dissociating the RNA degradosome from the membrane. Together, these results demonstrate that the bacterial transcriptome is spatially organized and suggest that this organization shapes the post-transcriptional dynamics of mRNAs. DOI: http://dx.doi.org/10.7554/eLife.13065.001 PMID:27198188

An Ancient Bacterial Signaling Pathway Regulates Chloroplast Function to Influence Growth and Development in Arabidopsis[OPEN

PubMed Central

Sugliani, Matteo; Ke, Hang; Bouveret, Emmanuelle; Robaglia, Christophe; Caffarri, Stefano

2016-01-01

The chloroplast originated from the endosymbiosis of an ancient photosynthetic bacterium by a eukaryotic cell. Remarkably, the chloroplast has retained elements of a bacterial stress response pathway that is mediated by the signaling nucleotides guanosine penta- and tetraphosphate (ppGpp). However, an understanding of the mechanism and outcomes of ppGpp signaling in the photosynthetic eukaryotes has remained elusive. Using the model plant Arabidopsis thaliana, we show that ppGpp is a potent regulator of chloroplast gene expression in vivo that directly reduces the quantity of chloroplast transcripts and chloroplast-encoded proteins. We then go on to demonstrate that the antagonistic functions of different plant RelA SpoT homologs together modulate ppGpp levels to regulate chloroplast function and show that they are required for optimal plant growth, chloroplast volume, and chloroplast breakdown during dark-induced and developmental senescence. Therefore, our results show that ppGpp signaling is not only linked to stress responses in plants but is also an important mediator of cooperation between the chloroplast and the nucleocytoplasmic compartment during plant growth and development. PMID:26908759

[Recognition of walking stance phase and swing phase based on moving window].

PubMed

Geng, Xiaobo; Yang, Peng; Wang, Xinran; Geng, Yanli; Han, Yu

2014-04-01

Wearing transfemoral prosthesis is the only way to complete daily physical activity for amputees. Motion pattern recognition is important for the control of prosthesis, especially in the recognizing swing phase and stance phase. In this paper, it is reported that surface electromyography (sEMG) signal is used in swing and stance phase recognition. sEMG signal of related muscles was sampled by Infiniti of a Canadian company. The sEMG signal was then filtered by weighted filtering window and analyzed by height permitted window. The starting time of stance phase and swing phase is determined through analyzing special muscles. The sEMG signal of rectus femoris was used in stance phase recognition and sEMG signal of tibialis anterior is used in swing phase recognition. In a certain tolerating range, the double windows theory, including weighted filtering window and height permitted window, can reach a high accuracy rate. Through experiments, the real walking consciousness of the people was reflected by sEMG signal of related muscles. Using related muscles to recognize swing and stance phase is reachable. The theory used in this paper is useful for analyzing sEMG signal and actual prosthesis control.

Robot Command Interface Using an Audio-Visual Speech Recognition System

NASA Astrophysics Data System (ADS)

Ceballos, Alexánder; Gómez, Juan; Prieto, Flavio; Redarce, Tanneguy

In recent years audio-visual speech recognition has emerged as an active field of research thanks to advances in pattern recognition, signal processing and machine vision. Its ultimate goal is to allow human-computer communication using voice, taking into account the visual information contained in the audio-visual speech signal. This document presents a command's automatic recognition system using audio-visual information. The system is expected to control the laparoscopic robot da Vinci. The audio signal is treated using the Mel Frequency Cepstral Coefficients parametrization method. Besides, features based on the points that define the mouth's outer contour according to the MPEG-4 standard are used in order to extract the visual speech information.

Preliminary Study on Continuous Recognition of Elbow Flexion/Extension Using sEMG Signals for Bilateral Rehabilitation

PubMed Central

Song, Zhibin; Zhang, Songyuan

2016-01-01

Surface electromyography (sEMG) signals are closely related to the activation of human muscles and the motion of the human body, which can be used to estimate the dynamics of human limbs in the rehabilitation field. They also have the potential to be used in the application of bilateral rehabilitation, where hemiplegic patients can train their affected limbs following the motion of unaffected limbs via some rehabilitation devices. Traditional methods to process the sEMG focused on motion pattern recognition, namely, discrete patterns, which are not satisfactory for use in bilateral rehabilitation. In order to overcome this problem, in this paper, we built a relationship between sEMG signals and human motion in elbow flexion and extension on the sagittal plane. During the conducted experiments, four participants were required to perform elbow flexion and extension on the sagittal plane smoothly with only an inertia sensor in their hands, where forearm dynamics were not considered. In these circumstances, sEMG signals were weak compared to those with heavy loads or high acceleration. The contrastive experimental results show that continuous motion can also be obtained within an acceptable precision range. PMID:27775573

Preliminary Study on Continuous Recognition of Elbow Flexion/Extension Using sEMG Signals for Bilateral Rehabilitation.

PubMed

Song, Zhibin; Zhang, Songyuan

2016-10-19

Surface electromyography (sEMG) signals are closely related to the activation of human muscles and the motion of the human body, which can be used to estimate the dynamics of human limbs in the rehabilitation field. They also have the potential to be used in the application of bilateral rehabilitation, where hemiplegic patients can train their affected limbs following the motion of unaffected limbs via some rehabilitation devices. Traditional methods to process the sEMG focused on motion pattern recognition, namely, discrete patterns, which are not satisfactory for use in bilateral rehabilitation. In order to overcome this problem, in this paper, we built a relationship between sEMG signals and human motion in elbow flexion and extension on the sagittal plane. During the conducted experiments, four participants were required to perform elbow flexion and extension on the sagittal plane smoothly with only an inertia sensor in their hands, where forearm dynamics were not considered. In these circumstances, sEMG signals were weak compared to those with heavy loads or high acceleration. The contrastive experimental results show that continuous motion can also be obtained within an acceptable precision range.

Hybrid Radar Emitter Recognition Based on Rough k-Means Classifier and Relevance Vector Machine

PubMed Central

Yang, Zhutian; Wu, Zhilu; Yin, Zhendong; Quan, Taifan; Sun, Hongjian

2013-01-01

Due to the increasing complexity of electromagnetic signals, there exists a significant challenge for recognizing radar emitter signals. In this paper, a hybrid recognition approach is presented that classifies radar emitter signals by exploiting the different separability of samples. The proposed approach comprises two steps, namely the primary signal recognition and the advanced signal recognition. In the former step, a novel rough k-means classifier, which comprises three regions, i.e., certain area, rough area and uncertain area, is proposed to cluster the samples of radar emitter signals. In the latter step, the samples within the rough boundary are used to train the relevance vector machine (RVM). Then RVM is used to recognize the samples in the uncertain area; therefore, the classification accuracy is improved. Simulation results show that, for recognizing radar emitter signals, the proposed hybrid recognition approach is more accurate, and presents lower computational complexity than traditional approaches. PMID:23344380

Interference in Bacterial Quorum Sensing: A Biopharmaceutical Perspective

PubMed Central

Rémy, Benjamin; Mion, Sonia; Plener, Laure; Elias, Mikael; Chabrière, Eric; Daudé, David

2018-01-01

Numerous bacteria utilize molecular communication systems referred to as quorum sensing (QS) to synchronize the expression of certain genes regulating, among other aspects, the expression of virulence factors and the synthesis of biofilm. To achieve this process, bacteria use signaling molecules, known as autoinducers (AIs), as chemical messengers to share information. Naturally occurring strategies that interfere with bacterial signaling have been extensively studied in recent years, examining their potential to control bacteria. To interfere with QS, bacteria use quorum sensing inhibitors (QSIs) to block the action of AIs and quorum quenching (QQ) enzymes to degrade signaling molecules. Recent studies have shown that these strategies are promising routes to decrease bacterial pathogenicity and decrease biofilms, potentially enhancing bacterial susceptibility to antimicrobial agents including antibiotics and bacteriophages. The efficacy of QSIs and QQ enzymes has been demonstrated in various animal models and are now considered in the development of new medical devices against bacterial infections, including dressings, and catheters for enlarging the therapeutic arsenal against bacteria. PMID:29563876

Optical Pattern Recognition With Self-Amplification

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang

1994-01-01

In optical pattern recognition system with self-amplification, no reference beam used in addressing mode. Polarization of laser beam and orientation of photorefractive crystal chosen to maximize photorefractive effect. Intensity of recognition signal is orders of magnitude greater than other optical correlators. Apparatus regarded as real-time or quasi-real-time optical pattern recognizer with memory and reprogrammability.

Lipopolysaccharide Clearance, Bacterial Clearance, and Systemic Inflammatory Responses Are Regulated by Cell Type–Specific Functions of TLR4 during Sepsis

PubMed Central

Deng, Meihong; Loughran, Patricia; Gibson, Gregory; Sodhi, Chhinder; Watkins, Simon; Hackam, David

2013-01-01

The morbidity associated with bacterial sepsis is the result of host immune responses to pathogens, which are dependent on pathogen recognition by pattern recognition receptors, such as TLR4. TLR4 is expressed on a range of cell types, yet the mechanisms by which cell-specific functions of TLR4 lead to an integrated sepsis response are poorly understood. To address this, we generated mice in which TLR4 was specifically deleted from myeloid cells (LysMTLR4KO) or hepatocytes (HCTLR4KO) and then determined survival, bacterial counts, host inflammatory responses, and organ injury in a model of cecal ligation and puncture (CLP), with or without antibiotics. LysM-TLR4 was required for phagocytosis and efficient bacterial clearance in the absence of antibiotics. Survival, the magnitude of the systemic and local inflammatory responses, and liver damage were associated with bacterial levels. HCTLR4 was required for efficient LPS clearance from the circulation, and deletion of HCTLR4 was associated with enhanced macrophage phagocytosis, lower bacterial levels, and improved survival in CLP without antibiotics. Antibiotic administration during CLP revealed an important role for hepatocyte LPS clearance in limiting sepsis-induced inflammation and organ injury. Our work defines cell type–selective roles for TLR4 in coordinating complex immune responses to bacterial sepsis and suggests that future strategies for modulating microbial molecule recognition should account for varying roles of pattern recognition receptors in multiple cell populations. PMID:23562812

Neutrophil cell surface receptors and their intracellular signal transduction pathways☆

PubMed Central

Futosi, Krisztina; Fodor, Szabina; Mócsai, Attila

2013-01-01

Neutrophils play a critical role in the host defense against bacterial and fungal infections, but their inappropriate activation also contributes to tissue damage during autoimmune and inflammatory diseases. Neutrophils express a large number of cell surface receptors for the recognition of pathogen invasion and the inflammatory environment. Those include G-protein-coupled chemokine and chemoattractant receptors, Fc-receptors, adhesion receptors such as selectins/selectin ligands and integrins, various cytokine receptors, as well as innate immune receptors such as Toll-like receptors and C-type lectins. The various cell surface receptors trigger very diverse signal transduction pathways including activation of heterotrimeric and monomeric G-proteins, receptor-induced and store-operated Ca2 + signals, protein and lipid kinases, adapter proteins and cytoskeletal rearrangement. Here we provide an overview of the receptors involved in neutrophil activation and the intracellular signal transduction processes they trigger. This knowledge is crucial for understanding how neutrophils participate in antimicrobial host defense and inflammatory tissue damage and may also point to possible future targets of the pharmacological therapy of neutrophil-mediated autoimmune or inflammatory diseases. PMID:23994464

Type I interferon and pattern recognition receptor signaling following particulate matter inhalation

PubMed Central

2012-01-01

Background Welding, a process that generates an aerosol containing gases and metal-rich particulates, induces adverse physiological effects including inflammation, immunosuppression and cardiovascular dysfunction. This study utilized microarray technology and subsequent pathway analysis as an exploratory search for markers/mechanisms of in vivo systemic effects following inhalation. Mice were exposed by inhalation to gas metal arc – stainless steel (GMA-SS) welding fume at 40 mg/m3 for 3 hr/d for 10 d and sacrificed 4 hr, 14 d and 28 d post-exposure. Whole blood cells, aorta and lung were harvested for global gene expression analysis with subsequent Ingenuity Pathway Analysis and confirmatory qRT-PCR. Serum was collected for protein profiling. Results The novel finding was a dominant type I interferon signaling network with the transcription factor Irf7 as a central component maintained through 28 d. Remarkably, these effects showed consistency across all tissues indicating a systemic type I interferon response that was complemented by changes in serum proteins (decreased MMP-9, CRP and increased VCAM1, oncostatin M, IP-10). In addition, pulmonary expression of interferon α and β and Irf7 specific pattern recognition receptors (PRR) and signaling molecules (Ddx58, Ifih1, Dhx58, ISGF3) were induced, an effect that showed specificity when compared to other inflammatory exposures. Also, a canonical pathway indicated a coordinated response of multiple PRR and associated signaling molecules (Tlr7, Tlr2, Clec7a, Nlrp3, Myd88) to inhalation of GMA-SS. Conclusion This methodological approach has the potential to identify consistent, prominent and/or novel pathways and provides insight into mechanisms that contribute to pulmonary and systemic effects following toxicant exposure. PMID:22776377

Type I interferon and pattern recognition receptor signaling following particulate matter inhalation.

PubMed

Erdely, Aaron; Antonini, James M; Salmen-Muniz, Rebecca; Liston, Angie; Hulderman, Tracy; Simeonova, Petia P; Kashon, Michael L; Li, Shengqiao; Gu, Ja K; Stone, Samuel; Chen, Bean T; Frazer, David G; Zeidler-Erdely, Patti C

2012-07-09

Welding, a process that generates an aerosol containing gases and metal-rich particulates, induces adverse physiological effects including inflammation, immunosuppression and cardiovascular dysfunction. This study utilized microarray technology and subsequent pathway analysis as an exploratory search for markers/mechanisms of in vivo systemic effects following inhalation. Mice were exposed by inhalation to gas metal arc - stainless steel (GMA-SS) welding fume at 40 mg/m3 for 3 hr/d for 10 d and sacrificed 4 hr, 14 d and 28 d post-exposure. Whole blood cells, aorta and lung were harvested for global gene expression analysis with subsequent Ingenuity Pathway Analysis and confirmatory qRT-PCR. Serum was collected for protein profiling. The novel finding was a dominant type I interferon signaling network with the transcription factor Irf7 as a central component maintained through 28 d. Remarkably, these effects showed consistency across all tissues indicating a systemic type I interferon response that was complemented by changes in serum proteins (decreased MMP-9, CRP and increased VCAM1, oncostatin M, IP-10). In addition, pulmonary expression of interferon α and β and Irf7 specific pattern recognition receptors (PRR) and signaling molecules (Ddx58, Ifih1, Dhx58, ISGF3) were induced, an effect that showed specificity when compared to other inflammatory exposures. Also, a canonical pathway indicated a coordinated response of multiple PRR and associated signaling molecules (Tlr7, Tlr2, Clec7a, Nlrp3, Myd88) to inhalation of GMA-SS. This methodological approach has the potential to identify consistent, prominent and/or novel pathways and provides insight into mechanisms that contribute to pulmonary and systemic effects following toxicant exposure.

Improved Open-Microphone Speech Recognition

NASA Astrophysics Data System (ADS)

Abrash, Victor

2002-12-01

Many current and future NASA missions make extreme demands on mission personnel both in terms of work load and in performing under difficult environmental conditions. In situations where hands are impeded or needed for other tasks, eyes are busy attending to the environment, or tasks are sufficiently complex that ease of use of the interface becomes critical, spoken natural language dialog systems offer unique input and output modalities that can improve efficiency and safety. They also offer new capabilities that would not otherwise be available. For example, many NASA applications require astronauts to use computers in micro-gravity or while wearing space suits. Under these circumstances, command and control systems that allow users to issue commands or enter data in hands-and eyes-busy situations become critical. Speech recognition technology designed for current commercial applications limits the performance of the open-ended state-of-the-art dialog systems being developed at NASA. For example, today's recognition systems typically listen to user input only during short segments of the dialog, and user input outside of these short time windows is lost. Mistakes detecting the start and end times of user utterances can lead to mistakes in the recognition output, and the dialog system as a whole has no way to recover from this, or any other, recognition error. Systems also often require the user to signal when that user is going to speak, which is impractical in a hands-free environment, or only allow a system-initiated dialog requiring the user to speak immediately following a system prompt. In this project, SRI has developed software to enable speech recognition in a hands-free, open-microphone environment, eliminating the need for a push-to-talk button or other signaling mechanism. The software continuously captures a user's speech and makes it available to one or more recognizers. By constantly monitoring and storing the audio stream, it provides the spoken

Improved Open-Microphone Speech Recognition

NASA Technical Reports Server (NTRS)

Abrash, Victor

2002-01-01

Many current and future NASA missions make extreme demands on mission personnel both in terms of work load and in performing under difficult environmental conditions. In situations where hands are impeded or needed for other tasks, eyes are busy attending to the environment, or tasks are sufficiently complex that ease of use of the interface becomes critical, spoken natural language dialog systems offer unique input and output modalities that can improve efficiency and safety. They also offer new capabilities that would not otherwise be available. For example, many NASA applications require astronauts to use computers in micro-gravity or while wearing space suits. Under these circumstances, command and control systems that allow users to issue commands or enter data in hands-and eyes-busy situations become critical. Speech recognition technology designed for current commercial applications limits the performance of the open-ended state-of-the-art dialog systems being developed at NASA. For example, today's recognition systems typically listen to user input only during short segments of the dialog, and user input outside of these short time windows is lost. Mistakes detecting the start and end times of user utterances can lead to mistakes in the recognition output, and the dialog system as a whole has no way to recover from this, or any other, recognition error. Systems also often require the user to signal when that user is going to speak, which is impractical in a hands-free environment, or only allow a system-initiated dialog requiring the user to speak immediately following a system prompt. In this project, SRI has developed software to enable speech recognition in a hands-free, open-microphone environment, eliminating the need for a push-to-talk button or other signaling mechanism. The software continuously captures a user's speech and makes it available to one or more recognizers. By constantly monitoring and storing the audio stream, it provides the spoken

SIGIRR, a negative regulator of TLR/IL-1R signalling promotes Microbiota dependent resistance to colonization by enteric bacterial pathogens.

PubMed

Sham, Ho Pan; Yu, Emily Yi Shan; Gulen, Muhammet F; Bhinder, Ganive; Stahl, Martin; Chan, Justin M; Brewster, Lara; Morampudi, Vijay; Gibson, Deanna L; Hughes, Michael R; McNagny, Kelly M; Li, Xiaoxia; Vallance, Bruce A

2013-01-01

Enteric bacterial pathogens such as enterohemorrhagic E. coli (EHEC) and Salmonella Typhimurium target the intestinal epithelial cells (IEC) lining the mammalian gastrointestinal tract. Despite expressing innate Toll-like receptors (TLRs), IEC are innately hypo-responsive to most bacterial products. This is thought to prevent maladaptive inflammatory responses against commensal bacteria, but it also limits antimicrobial responses by IEC to invading bacterial pathogens, potentially increasing host susceptibility to infection. One reason for the innate hypo-responsiveness of IEC is their expression of Single Ig IL-1 Related Receptor (SIGIRR), a negative regulator of interleukin (IL)-1 and TLR signaling. To address whether SIGIRR expression and the innate hypo-responsiveness of IEC impacts on enteric host defense, Sigirr deficient (-/-) mice were infected with the EHEC related pathogen Citrobacter rodentium. Sigirr -/- mice responded with accelerated IEC proliferation and strong pro-inflammatory and antimicrobial responses but surprisingly, Sigirr -/- mice proved dramatically more susceptible to infection than wildtype mice. Through haematopoietic transplantation studies, it was determined that SIGIRR expression by non-haematopoietic cells (putative IEC) regulated these responses. Moreover, the exaggerated responses were found to be primarily dependent on IL-1R signaling. Whilst exploring the basis for their susceptibility, Sigirr -/- mice were found to be unusually susceptible to intestinal Salmonella Typhimurium colonization, developing enterocolitis without the typical requirement for antibiotic based removal of competing commensal microbes. Strikingly, the exaggerated antimicrobial responses seen in Sigirr -/- mice were found to cause a rapid and dramatic loss of commensal microbes from the infected intestine. This depletion appears to reduce the ability of the microbiota to compete for space and nutrients (colonization resistance) with the invading pathogens

Protobiological informatoin, bidirectional recognition and reverse translation

NASA Technical Reports Server (NTRS)

Fox, S. W.; Nakashima, T.; Przybylski, A.; Vaughan, G.

1986-01-01

Emergence of protobiological information has been suggested by experiments in which heated mixtures of alpha-amino acids order themselves into a self limited array of thermal proteins. The polymers display selective catalytic, hormonal, and other activities. Interactions of varied cationic thermal proteins with polynucleotides indicate selective recognition in both directions. Reverse translation is partly a missing link in the molecular evolution flowsheet. The self ordering of amino acids serves conceptually as a deterministic evolutionary precursor of the modern coding mechanism. The possibility for the evolution of information at an early nontemplated protein stage is supported by findings of electrical signals from proteinoid microspheres prepared with no DNA/RNA in their history. The deposition of thermal copolyamino acids on lipid membranes in the Mueller-Rudin apparatus has here been found to produce electrical behavior like that evoked by bacterial EIM polypeptide. A new procedure is to make a film of membrane on the electrode; the results provide maximal repeatability. The principle of nonrandom biomacromolecular specificity identified by these studies in molecular evolution have been extrapolated to principles of evolution of advanced organisms.

Identification of novel binding partners (annexins) for the cell death signal phosphatidylserine and definition of their recognition motif.

PubMed

Rosenbaum, Sabrina; Kreft, Sandra; Etich, Julia; Frie, Christian; Stermann, Jacek; Grskovic, Ivan; Frey, Benjamin; Mielenz, Dirk; Pöschl, Ernst; Gaipl, Udo; Paulsson, Mats; Brachvogel, Bent

2011-02-18

Identification and clearance of apoptotic cells prevents the release of harmful cell contents thereby suppressing inflammation and autoimmune reactions. Highly conserved annexins may modulate the phagocytic cell removal by acting as bridging molecules to phosphatidylserine, a characteristic phagocytosis signal of dying cells. In this study five members of the structurally and functionally related annexin family were characterized for their capacity to interact with phosphatidylserine and dying cells. The results showed that AnxA3, AnxA4, AnxA13, and the already described interaction partner AnxA5 can bind to phosphatidylserine and apoptotic cells, whereas AnxA8 lacks this ability. Sequence alignment experiments located the essential amino residues for the recognition of surface exposed phosphatidylserine within the calcium binding motifs common to all annexins. These amino acid residues were missing in the evolutionary young AnxA8 and when they were reintroduced by site directed mutagenesis AnxA8 gains the capability to interact with phosphatidylserine containing liposomes and apoptotic cells. By defining the evolutionary conserved amino acid residues mediating phosphatidylserine binding of annexins we show that the recognition of dying cells represent a common feature of most annexins. Hence, the individual annexin repertoire bound to the cell surface of dying cells may fulfil opsonin-like function in cell death recognition.

Two-step membrane binding by the bacterial SRP receptor enable efficient and accurate Co-translational protein targeting.

PubMed

Hwang Fu, Yu-Hsien; Huang, William Y C; Shen, Kuang; Groves, Jay T; Miller, Thomas; Shan, Shu-Ou

2017-07-28

The signal recognition particle (SRP) delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum, or the bacterial plasma membrane. The precise mechanism by which the bacterial SRP receptor, FtsY, interacts with and is regulated at the target membrane remain unclear. Here, quantitative analysis of FtsY-lipid interactions at single-molecule resolution revealed a two-step mechanism in which FtsY initially contacts membrane via a Dynamic mode, followed by an SRP-induced conformational transition to a Stable mode that activates FtsY for downstream steps. Importantly, mutational analyses revealed extensive auto-inhibitory mechanisms that prevent free FtsY from engaging membrane in the Stable mode; an engineered FtsY pre-organized into the Stable mode led to indiscriminate targeting in vitro and disrupted FtsY function in vivo. Our results show that the two-step lipid-binding mechanism uncouples the membrane association of FtsY from its conformational activation, thus optimizing the balance between the efficiency and fidelity of co-translational protein targeting.

Recognition- and Reactivity-Based Fluorescent Probes for Studying Transition Metal Signaling in Living Systems

PubMed Central

2015-01-01

Conspectus Metals are essential for life, playing critical roles in all aspects of the central dogma of biology (e.g., the transcription and translation of nucleic acids and synthesis of proteins). Redox-inactive alkali, alkaline earth, and transition metals such as sodium, potassium, calcium, and zinc are widely recognized as dynamic signals, whereas redox-active transition metals such as copper and iron are traditionally thought of as sequestered by protein ligands, including as static enzyme cofactors, in part because of their potential to trigger oxidative stress and damage via Fenton chemistry. Metals in biology can be broadly categorized into two pools: static and labile. In the former, proteins and other macromolecules tightly bind metals; in the latter, metals are bound relatively weakly to cellular ligands, including proteins and low molecular weight ligands. Fluorescent probes can be useful tools for studying the roles of transition metals in their labile forms. Probes for imaging transition metal dynamics in living systems must meet several stringent criteria. In addition to exhibiting desirable photophysical properties and biocompatibility, they must be selective and show a fluorescence turn-on response to the metal of interest. To meet this challenge, we have pursued two general strategies for metal detection, termed “recognition” and “reactivity”. Our design of transition metal probes makes use of a recognition-based approach for copper and nickel and a reactivity-based approach for cobalt and iron. This Account summarizes progress in our laboratory on both the development and application of fluorescent probes to identify and study the signaling roles of transition metals in biology. In conjunction with complementary methods for direct metal detection and genetic and/or pharmacological manipulations, fluorescent probes for transition metals have helped reveal a number of principles underlying transition metal dynamics. In this Account, we give

Bacterial and parasitic diseases of parrots.

PubMed

Doneley, Robert J T

2009-09-01

As wild-caught birds become increasingly rare in aviculture, there is a corresponding decline in the incidence of bacterial and parasitic problems and an increase in the recognition of the importance of maintaining health through better nutrition and husbandry. Nevertheless, the relatively close confines of captivity mean an increased pathogen load in the environment in which companion and aviary parrots live. This increased pathogen load leads to greater exposure of these birds to bacteria and parasites, and consequently a greater risk of infection and disease. This article discusses bacterial and parasitic infections in companion and aviary parrots. It includes the origins, pathogens, diagnosis, treatment, and some of the associated risk factors.

Lateralization of kin recognition signals in the human face

PubMed Central

Dal Martello, Maria F.; Maloney, Laurence T.

2010-01-01

When human subjects view photographs of faces, their judgments of identity, gender, emotion, age, and attractiveness depend more on one side of the face than the other. We report an experiment testing whether allocentric kin recognition (the ability to judge the degree of kinship between individuals other than the observer) is also lateralized. One hundred and twenty-four observers judged whether or not pairs of children were biological siblings by looking at photographs of their faces. In three separate conditions, (1) the right hemi-face was masked, (2) the left hemi-face was masked, or (3) the face was fully visible. The d′ measures for the masked left hemi-face and masked right hemi-face were 1.024 and 1.004, respectively (no significant difference), and the d′ measure for the unmasked face was 1.079, not significantly greater than that for either of the masked conditions. We conclude, first, that there is no superiority of one or the other side of the observed face in kin recognition, second, that the information present in the left and right hemi-faces relevant to recognizing kin is completely redundant, and last that symmetry cues are not used for kin recognition. PMID:20884584

The Emotion Recognition System Based on Autoregressive Model and Sequential Forward Feature Selection of Electroencephalogram Signals

PubMed Central

Hatamikia, Sepideh; Maghooli, Keivan; Nasrabadi, Ali Motie

2014-01-01

Electroencephalogram (EEG) is one of the useful biological signals to distinguish different brain diseases and mental states. In recent years, detecting different emotional states from biological signals has been merged more attention by researchers and several feature extraction methods and classifiers are suggested to recognize emotions from EEG signals. In this research, we introduce an emotion recognition system using autoregressive (AR) model, sequential forward feature selection (SFS) and K-nearest neighbor (KNN) classifier using EEG signals during emotional audio-visual inductions. The main purpose of this paper is to investigate the performance of AR features in the classification of emotional states. To achieve this goal, a distinguished AR method (Burg's method) based on Levinson-Durbin's recursive algorithm is used and AR coefficients are extracted as feature vectors. In the next step, two different feature selection methods based on SFS algorithm and Davies–Bouldin index are used in order to decrease the complexity of computing and redundancy of features; then, three different classifiers include KNN, quadratic discriminant analysis and linear discriminant analysis are used to discriminate two and three different classes of valence and arousal levels. The proposed method is evaluated with EEG signals of available database for emotion analysis using physiological signals, which are recorded from 32 participants during 40 1 min audio visual inductions. According to the results, AR features are efficient to recognize emotional states from EEG signals, and KNN performs better than two other classifiers in discriminating of both two and three valence/arousal classes. The results also show that SFS method improves accuracies by almost 10-15% as compared to Davies–Bouldin based feature selection. The best accuracies are %72.33 and %74.20 for two classes of valence and arousal and %61.10 and %65.16 for three classes, respectively. PMID:25298928

Peptidoglycan microarray as a novel tool to explore protein-ligand recognition.

PubMed

Wang, Ning; Hirata, Akiyoshi; Nokihara, Kiyoshi; Fukase, Koichi; Fujimoto, Yukari

2016-11-04

Peptidoglycan is a giant bag-shaped molecule essential for bacterial cell shape and resistance to osmotic stresses. The activity of a large number of bacterial surface proteins involved in cell growth and division requires binding to this macromolecule. Recognition of peptidoglycan by immune effectors is also crucial for the establishment of the immune response against pathogens. The availability of pure and chemically defined peptidoglycan fragments is a major technical bottleneck that has precluded systematic studies of the mechanisms underpinning protein-mediated peptidoglycan recognition. Here, we report a microarray strategy suitable to carry out comprehensive studies to characterize proteins-peptidoglycan interactions. We describe a method to introduce a functional group on peptidoglycan fragments allowing their stable immobilization on amorphous carbon chip plates to minimize nonspecific binding. Such peptidoglycan microarrays were used with a model peptidoglycan binding protein-the human peptidoglycan recognition protein-S (hPGRP-S). We propose that this strategy could be implemented to carry out high-throughput analyses to study peptidoglycan binding proteins. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 422-429, 2016. © 2016 Wiley Periodicals, Inc.

Myopericarditis in a case of anti-signal recognition particle (anti-SRP) antibody-positive myopathy.

PubMed

Tanaka, Mariko; Gamou, Naoki; Shizukawa, Hirohiko; Tsuda, Emiko; Shimohama, Shun

2016-12-28

A 79 year-old female was admitted to our hospital because of high serum creatine kinase level together with proximal muscle weakness and pain on grasping. MRI revealed inflammatory changes in femoral muscles on both sides. Muscle biopsy showed size irregularity of muscle cells, and necrosis and regeneration of fibers. Study of antibodies was also consistent with the diagnostic criteria of anti-signal recognition particle (anti-SRP) antibody-positive myopathy. On admission, the patient required pericardiocentesis for the management of exudative pericarditis. Accompanying the aggravation of myositis, negative T wave in precordial leads on ECG, ventricular extrasystoles and non-sustained ventricular tachycardia were observed. These abnormalities were resolved with the improvement of myositis by immunosuppressive treatment. These observations suggest that the myopericarditis was associated with anti-SRP antibody-positive myopathy.

Terahertz spectroscopy for the isothermal detection of bacterial DNA by magnetic bead-based rolling circle amplification.

PubMed

Yang, Xiang; Yang, Ke; Zhao, Xiang; Lin, Zhongquan; Liu, Zhiyong; Luo, Sha; Zhang, Yang; Wang, Yunxia; Fu, Weiling

2017-12-04

The demand for rapid and sensitive bacterial detection is continuously increasing due to the significant requirements of various applications. In this study, a terahertz (THz) biosensor based on rolling circle amplification (RCA) was developed for the isothermal detection of bacterial DNA. The synthetic bacterium-specific sequence of 16S rDNA hybridized with a padlock probe (PLP) that contains a sequence fully complementary to the target sequence at the 5' and 3' ends. The linear PLP was circularized by ligation to form a circular PLP upon recognition of the target sequence; then the capture probe (CP) immobilized on magnetic beads (MBs) acted as a primer to initialize RCA. As DNA molecules are much less absorptive than water molecules in the THz range, the RCA products on the surface of the MBs cause a significant decrease in THz absorption, which can be sensitively probed by THz spectroscopy. Our results showed that 0.12 fmol of synthetic bacterial DNA and 0.05 ng μL -1 of genomic DNA could be effectively detected using this assay. In addition, the specificity of this strategy was demonstrated by its low signal response to interfering bacteria. The proposed strategy not only represents a new method for the isothermal detection of the target bacterial DNA but also provides a general methodology for sensitive and specific DNA biosensing using THz spectroscopy.

Processing Electromyographic Signals to Recognize Words

NASA Technical Reports Server (NTRS)

Jorgensen, C. C.; Lee, D. D.

2009-01-01

A recently invented speech-recognition method applies to words that are articulated by means of the tongue and throat muscles but are otherwise not voiced or, at most, are spoken sotto voce. This method could satisfy a need for speech recognition under circumstances in which normal audible speech is difficult, poses a hazard, is disturbing to listeners, or compromises privacy. The method could also be used to augment traditional speech recognition by providing an additional source of information about articulator activity. The method can be characterized as intermediate between (1) conventional speech recognition through processing of voice sounds and (2) a method, not yet developed, of processing electroencephalographic signals to extract unspoken words directly from thoughts. This method involves computational processing of digitized electromyographic (EMG) signals from muscle innervation acquired by surface electrodes under a subject's chin near the tongue and on the side of the subject s throat near the larynx. After preprocessing, digitization, and feature extraction, EMG signals are processed by a neural-network pattern classifier, implemented in software, that performs the bulk of the recognition task as described.

Dissecting Bacterial Cell Wall Entry and Signaling in Eukaryotic Cells: an Actin-Dependent Pathway Parallels Platelet-Activating Factor Receptor-Mediated Endocytosis.

PubMed

Loh, Lip Nam; Gao, Geli; Tuomanen, Elaine I

2017-01-03

The Gram-positive bacterial cell wall (CW) peptidoglycan-teichoic acid complex is released into the host environment during bacterial metabolism or death. It is a highly inflammatory Toll-like receptor 2 (TLR2) ligand, and previous in vivo studies have demonstrated its ability to recapitulate pathological features of pneumonia and meningitis. We report that an actin-dependent pathway is involved in the internalization of the CW by epithelial and endothelial cells, in addition to the previously described platelet-activating factor receptor (PAFr)-dependent uptake pathway. Unlike the PAFr-dependent pathway, which is mediated by clathrin and dynamin and does not lead to signaling, the alternative pathway is sensitive to 5-(N-ethyl-N-isopropyl) amiloride (EIPA) and engenders Rac1, Cdc42, and phosphatidylinositol 3-kinase (PI3K) signaling. Upon internalization by this macropinocytosis-like pathway, CW is trafficked to lysosomes. Intracellular CW trafficking is more complex than previously recognized and suggests multiple points of interaction with and without innate immune signaling. Streptococcus pneumoniae is a major human pathogen infecting the respiratory tract and brain. It is an established model organism for understanding how infection injures the host. During infection or bacterial growth, bacteria shed their cell wall (CW) into the host environment and trigger inflammation. A previous study has shown that CW enters and crosses cell barriers by interacting with a receptor on the surfaces of host cells, termed platelet-activating factor receptor (PAFr). In the present study, by using cells that are depleted of PAFr, we identified a second pathway with features of macropinocytosis, which is a receptor-independent fluid uptake mechanism by cells. Each pathway contributes approximately the same amount of cell wall trafficking, but the PAFr pathway is silent, while the new pathway appears to contribute to the host inflammatory response to CW insult. Copyright © 2017

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PubMed Central

Damienikan, Aliaksandr U.

2016-01-01

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

Models of Recognition, Repetition Priming, and Fluency : Exploring a New Framework

ERIC Educational Resources Information Center

Berry, Christopher J.; Shanks, David R.; Speekenbrink, Maarten; Henson, Richard N. A.

2012-01-01

We present a new modeling framework for recognition memory and repetition priming based on signal detection theory. We use this framework to specify and test the predictions of 4 models: (a) a single-system (SS) model, in which one continuous memory signal drives recognition and priming; (b) a multiple-systems-1 (MS1) model, in which completely…

The ARTT motif and a unified structural understanding of substraterecognition in ADP ribosylating bacterial toxins and eukaryotic ADPribosyltransferases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, S.; Tainer, J.A.

2001-08-01

ADP-ribosylation is a widely occurring and biologically critical covalent chemical modification process in pathogenic mechanisms, intracellular signaling systems, DNA repair, and cell division. The reaction is catalyzed by ADP-ribosyltransferases, which transfer the ADP-ribose moiety of NAD to a target protein with nicotinamide release. A family of bacterial toxins and eukaryotic enzymes has been termed the mono-ADP-ribosyltransferases, in distinction to the poly-ADP-ribosyltransferases, which catalyze the addition of multiple ADP-ribose groups to the carboxyl terminus of eukaryotic nucleoproteins. Despite the limited primary sequence homology among the different ADP-ribosyltransferases, a central cleft bearing NAD-binding pocket formed by the two perpendicular b-sheet core hasmore » been remarkably conserved between bacterial toxins and eukaryotic mono- and poly-ADP-ribosyltransferases. The majority of bacterial toxins and eukaryotic mono-ADP-ribosyltransferases are characterized by conserved His and catalytic Glu residues. In contrast, Diphtheria toxin, Pseudomonas exotoxin A, and eukaryotic poly-ADP-ribosyltransferases are characterized by conserved Arg and catalytic Glu residues. The NAD-binding core of a binary toxin and a C3-like toxin family identified an ARTT motif (ADP-ribosylating turn-turn motif) that is implicated in substrate specificity and recognition by structural and mutagenic studies. Here we apply structure-based sequence alignment and comparative structural analyses of all known structures of ADP-ribosyltransfeases to suggest that this ARTT motif is functionally important in many ADP-ribosylating enzymes that bear a NAD binding cleft as characterized by conserved Arg and catalytic Glu residues. Overall, structure-based sequence analysis reveals common core structures and conserved active sites of ADP-ribosyltransferases to support similar NAD binding mechanisms but differing mechanisms of target protein binding via sequence variations within

Exploratory data analysis of acceleration signals to select light-weight and accurate features for real-time activity recognition on smartphones.

PubMed

Khan, Adil Mehmood; Siddiqi, Muhammad Hameed; Lee, Seok-Won

2013-09-27

Smartphone-based activity recognition (SP-AR) recognizes users' activities using the embedded accelerometer sensor. Only a small number of previous works can be classified as online systems, i.e., the whole process (pre-processing, feature extraction, and classification) is performed on the device. Most of these online systems use either a high sampling rate (SR) or long data-window (DW) to achieve high accuracy, resulting in short battery life or delayed system response, respectively. This paper introduces a real-time/online SP-AR system that solves this problem. Exploratory data analysis was performed on acceleration signals of 6 activities, collected from 30 subjects, to show that these signals are generated by an autoregressive (AR) process, and an accurate AR-model in this case can be built using a low SR (20 Hz) and a small DW (3 s). The high within class variance resulting from placing the phone at different positions was reduced using kernel discriminant analysis to achieve position-independent recognition. Neural networks were used as classifiers. Unlike previous works, true subject-independent evaluation was performed, where 10 new subjects evaluated the system at their homes for 1 week. The results show that our features outperformed three commonly used features by 40% in terms of accuracy for the given SR and DW.

Signal processing method and system for noise removal and signal extraction

DOEpatents

Fu, Chi Yung; Petrich, Loren

2009-04-14

A signal processing method and system combining smooth level wavelet pre-processing together with artificial neural networks all in the wavelet domain for signal denoising and extraction. Upon receiving a signal corrupted with noise, an n-level decomposition of the signal is performed using a discrete wavelet transform to produce a smooth component and a rough component for each decomposition level. The n.sup.th level smooth component is then inputted into a corresponding neural network pre-trained to filter out noise in that component by pattern recognition in the wavelet domain. Additional rough components, beginning at the highest level, may also be retained and inputted into corresponding neural networks pre-trained to filter out noise in those components also by pattern recognition in the wavelet domain. In any case, an inverse discrete wavelet transform is performed on the combined output from all the neural networks to recover a clean signal back in the time domain.

Effects of Pre-Experimental Knowledge on Recognition Memory

ERIC Educational Resources Information Center

Bird, Chris M.; Davies, Rachel A.; Ward, Jamie; Burgess, Neil

2011-01-01

The influence of pre-experimental autobiographical knowledge on recognition memory was investigated using as memoranda faces that were either personally known or unknown to the participant. Under a dual process theory, such knowledge boosted both recollection- and familiarity-based recognition judgements. Under an unequal variance signal detection…

Pathogen espionage: multiple bacterial adrenergic sensors eavesdrop on host communication systems.

PubMed

Karavolos, Michail H; Winzer, Klaus; Williams, Paul; Khan, C M Anjam

2013-02-01

The interactions between bacterial pathogens and their eukaryotic hosts are vital in determining the outcome of infections. Bacterial pathogens employ molecular sensors to detect and facilitate adaptation to changes in their niche. The sensing of these extracellular signals enables the pathogen to navigate within mammalian hosts. Intercellular bacterial communication is facilitated by the production and sensing of autoinducer (AI) molecules via quorum sensing. More recently, AI-3 and the host neuroendocrine (NE) hormones adrenaline and noradrenaline were reported to display cross-talk for the activation of the same signalling pathways. Remarkably, there is increasing evidence to suggest that enteric bacteria sense and respond to the host NE stress hormones adrenaline and noradrenaline to modulate virulence. These responses can be inhibited by α and β-adrenergic receptor antagonists implying a bacterial receptor-based sensing and signalling cascade. In Escherichia coli O157:H7 and Salmonella, QseC has been proposed as the adrenergic receptor. Strikingly, there is an increasing body of evidence that not all the bacterial adrenergic responses require signalling through QseC. Here we provide additional hypotheses to reconcile these observations implicating the existence of alternative adrenergic receptors including BasS, QseE and CpxA and their associated signalling cascades with major roles in interkingdom communication. © 2012 Blackwell Publishing Ltd.

One process is not enough! A speed-accuracy tradeoff study of recognition memory.

PubMed

Boldini, Angela; Russo, Riccardo; Avons, S E

2004-04-01

Speed-accuracy tradeoff (SAT) methods have been used to contrast single- and dual-process accounts of recognition memory. In these procedures, subjects are presented with individual test items and are required to make recognition decisions under various time constraints. In this experiment, we presented word lists under incidental learning conditions, varying the modality of presentation and level of processing. At test, we manipulated the interval between each visually presented test item and a response signal, thus controlling the amount of time available to retrieve target information. Study-test modality match had a beneficial effect on recognition accuracy at short response-signal delays (< or =300 msec). Conversely, recognition accuracy benefited more from deep than from shallow processing at study only at relatively long response-signal delays (> or =300 msec). The results are congruent with views suggesting that both fast familiarity and slower recollection processes contribute to recognition memory.

Get rich quick: the signal to respond procedure reveals the time course of semantic richness effects during visual word recognition.

PubMed

Hargreaves, Ian S; Pexman, Penny M

2014-05-01

According to several current frameworks, semantic processing involves an early influence of language-based information followed by later influences of object-based information (e.g., situated simulations; Santos, Chaigneau, Simmons, & Barsalou, 2011). In the present study we examined whether these predictions extend to the influence of semantic variables in visual word recognition. We investigated the time course of semantic richness effects in visual word recognition using a signal-to-respond (STR) paradigm fitted to a lexical decision (LDT) and a semantic categorization (SCT) task. We used linear mixed effects to examine the relative contributions of language-based (number of senses, ARC) and object-based (imageability, number of features, body-object interaction ratings) descriptions of semantic richness at four STR durations (75, 100, 200, and 400ms). Results showed an early influence of number of senses and ARC in the SCT. In both LDT and SCT, object-based effects were the last to influence participants' decision latencies. We interpret our results within a framework in which semantic processes are available to influence word recognition as a function of their availability over time, and of their relevance to task-specific demands. Copyright © 2014 Elsevier B.V. All rights reserved.

Dynamic Gesture Recognition with a Terahertz Radar Based on Range Profile Sequences and Doppler Signatures

PubMed Central

Pi, Yiming

2017-01-01

The frequency of terahertz radar ranges from 0.1 THz to 10 THz, which is higher than that of microwaves. Multi-modal signals, including high-resolution range profile (HRRP) and Doppler signatures, can be acquired by the terahertz radar system. These two kinds of information are commonly used in automatic target recognition; however, dynamic gesture recognition is rarely discussed in the terahertz regime. In this paper, a dynamic gesture recognition system using a terahertz radar is proposed, based on multi-modal signals. The HRRP sequences and Doppler signatures were first achieved from the radar echoes. Considering the electromagnetic scattering characteristics, a feature extraction model is designed using location parameter estimation of scattering centers. Dynamic Time Warping (DTW) extended to multi-modal signals is used to accomplish the classifications. Ten types of gesture signals, collected from a terahertz radar, are applied to validate the analysis and the recognition system. The results of the experiment indicate that the recognition rate reaches more than 91%. This research verifies the potential applications of dynamic gesture recognition using a terahertz radar. PMID:29267249

Dynamic Gesture Recognition with a Terahertz Radar Based on Range Profile Sequences and Doppler Signatures.

PubMed

Zhou, Zhi; Cao, Zongjie; Pi, Yiming

2017-12-21

The frequency of terahertz radar ranges from 0.1 THz to 10 THz, which is higher than that of microwaves. Multi-modal signals, including high-resolution range profile (HRRP) and Doppler signatures, can be acquired by the terahertz radar system. These two kinds of information are commonly used in automatic target recognition; however, dynamic gesture recognition is rarely discussed in the terahertz regime. In this paper, a dynamic gesture recognition system using a terahertz radar is proposed, based on multi-modal signals. The HRRP sequences and Doppler signatures were first achieved from the radar echoes. Considering the electromagnetic scattering characteristics, a feature extraction model is designed using location parameter estimation of scattering centers. Dynamic Time Warping (DTW) extended to multi-modal signals is used to accomplish the classifications. Ten types of gesture signals, collected from a terahertz radar, are applied to validate the analysis and the recognition system. The results of the experiment indicate that the recognition rate reaches more than 91%. This research verifies the potential applications of dynamic gesture recognition using a terahertz radar.

Fuzzy Logic-Based Audio Pattern Recognition

NASA Astrophysics Data System (ADS)

Malcangi, M.

2008-11-01

Audio and audio-pattern recognition is becoming one of the most important technologies to automatically control embedded systems. Fuzzy logic may be the most important enabling methodology due to its ability to rapidly and economically model such application. An audio and audio-pattern recognition engine based on fuzzy logic has been developed for use in very low-cost and deeply embedded systems to automate human-to-machine and machine-to-machine interaction. This engine consists of simple digital signal-processing algorithms for feature extraction and normalization, and a set of pattern-recognition rules manually tuned or automatically tuned by a self-learning process.

Interspecific aggression and character displacement of competitor recognition in Hetaerina damselflies.

PubMed

Anderson, Christopher N; Grether, Gregory F

2010-02-22

In zones of sympatry between closely related species, species recognition errors in a competitive context can cause character displacement in agonistic signals and competitor recognition functions, just as species recognition errors in a mating context can cause character displacement in mating signals and mate recognition. These two processes are difficult to distinguish because the same traits can serve as both agonistic and mating signals. One solution is to test for sympatric shifts in recognition functions. We studied competitor recognition in Hetaerina damselflies by challenging territory holders with live tethered conspecific and heterospecific intruders. Heterospecific intruders elicited less aggression than conspecific intruders in species pairs with dissimilar wing coloration (H. occisa/H. titia, H. americana/H. titia) but not in species pairs with similar wing coloration (H. occisa/H. cruentata, H. americana/H. cruentata). Natural variation in the area of black wing pigmentation on H. titia intruders correlated negatively with heterospecific aggression. To directly examine the role of wing coloration, we blackened the wings of H. occisa or H. americana intruders and measured responses of conspecific territory holders. This treatment reduced territorial aggression at multiple sites where H. titia is present, but not at allopatric sites. These results provide strong evidence for agonistic character displacement.

Molecular structure of EmbR, a response element of Ser/Thr kinase signaling in Mycobacterium tuberculosis

PubMed Central

Alderwick, Luke J.; Molle, Virginie; Kremer, Laurent; Cozzone, Alain J.; Dafforn, Timothy R.; Besra, Gurdyal S.; Fütterer, Klaus

2006-01-01

Ser/Thr phosphorylation has emerged as a critical regulatory mechanism in a number of bacteria, including Mycobacterium tuberculosis. This problematic pathogen encodes 11 eukaryotic-like Ser/Thr kinases, yet few substrates or signaling targets have been characterized. Here, we report the structure of EmbR (2.0 Å), a putative transcriptional regulator of key arabinosyltransferases (EmbC, -A, and -B), and an endogenous substrate of the Ser/Thr-kinase PknH. EmbR presents a unique domain architecture: the N-terminal winged-helix DNA-binding domain forms an extensive interface with the all-helical central bacterial transcriptional activation domain and is positioned adjacent to the regulatory C-terminal forkhead-associated (FHA) domain, which mediates binding to a Thr-phosphorylated site in PknH. The structure in complex with a phospho-peptide (1.9 Å) reveals a conserved mode of phospho-threonine recognition by the FHA domain and evidence for specific recognition of the cognate kinase. The present structures suggest hypotheses as to how EmbR might propagate the phospho-relay signal from its cognate kinase, while serving as a template for the structurally uncharacterized Streptomyces antibiotic regulatory protein family of transcription factors. PMID:16477027

Method of synthesized phase objects for pattern recognition with rotation invariance

NASA Astrophysics Data System (ADS)

Ostroukh, Alexander P.; Butok, Alexander M.; Shvets, Rostislav A.; Yezhov, Pavel V.; Kim, Jin-Tae; Kuzmenko, Alexander V.

2015-11-01

We present a development of the method of synthesized phase objects (SPO-method) [1] for the rotation-invariant pattern recognition. For the standard method of recognition and the SPO-method, the comparison of the parameters of correlation signals for a number of amplitude objects is executed at the realization of a rotation in an optical-digital correlator with the joint Fourier transformation. It is shown that not only the invariance relative to a rotation at a realization of the joint correlation for synthesized phase objects (SP-objects) but also the main advantage of the method of SP-objects over the reference one such as the unified δ-like recognition signal with the largest possible signal-to-noise ratio independent of the type of an object are attained.

Structural correlates of carrier protein recognition in tetanus toxoid-conjugated bacterial polysaccharide vaccines.

PubMed

Lockyer, Kay; Gao, Fang; Derrick, Jeremy P; Bolgiano, Barbara

2015-03-10

An analysis of structure-antibody recognition relationships in nine licenced polysaccharide-tetanus toxoid (TT) conjugate vaccines was performed. The panel of conjugates used included vaccine components to protect against disease caused by Haemophilus influenzae type b, Neisseria meningitidis groups A, C, W and Y and Streptococcus pneumoniae serotype 18C. Conformation and structural analysis included size exclusion chromatography with multi-angle light scattering to determine size, and intrinsic fluorescence spectroscopy and fluorescence quenching to evaluate the protein folding and exposure of Trp residues. A capture ELISA measured the recognition of TT epitopes in the conjugates, using four rat monoclonal antibodies: 2 localised to the HC domain, and 2 of which were holotoxoid conformation-dependent. The conjugates had a wide range of average molecular masses ranging from 1.8×10(6) g/mol to larger than 20×10(6) g/mol. The panel of conjugates were found to be well folded, and did not have spectral features typical of aggregated TT. A partial correlation was found between molecular mass and epitope recognition. Recognition of the epitopes either on the HC domain or the whole toxoid was not necessarily hampered by the size of the molecule. Correlation was also found between the accessibility of Trp side chains and polysaccharide loading, suggesting also that a higher level of conjugated PS does not necessarily interfere with toxoid accessibility. There were different levels of carrier protein Trp side-chain and epitope accessibility that were localised to the HC domain; these were related to the saccharide type, despite the conjugates being independently manufactured. These findings extend our understanding of the molecular basis for carrier protein recognition in TT conjugate vaccines. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Structural correlates of carrier protein recognition in tetanus toxoid-conjugated bacterial polysaccharide vaccines

PubMed Central

Lockyer, Kay; Gao, Fang; Derrick, Jeremy P.; Bolgiano, Barbara

2015-01-01

An analysis of structure-antibody recognition relationships in nine licenced polysaccharide-tetanus toxoid (TT) conjugate vaccines was performed. The panel of conjugates used included vaccine components to protect against disease caused by Haemophilus influenzae type b, Neisseria meningitidis groups A, C, W and Y and Streptococcus pneumoniae serotype 18C. Conformation and structural analysis included size exclusion chromatography with multi-angle light scattering to determine size, and intrinsic fluorescence spectroscopy and fluorescence quenching to evaluate the protein folding and exposure of Trp residues. A capture ELISA measured the recognition of TT epitopes in the conjugates, using four rat monoclonal antibodies: 2 localised to the HC domain, and 2 of which were holotoxoid conformation-dependent. The conjugates had a wide range of average molecular masses ranging from 1.8 × 106 g/mol to larger than 20 × 106 g/mol. The panel of conjugates were found to be well folded, and did not have spectral features typical of aggregated TT. A partial correlation was found between molecular mass and epitope recognition. Recognition of the epitopes either on the HC domain or the whole toxoid was not necessarily hampered by the size of the molecule. Correlation was also found between the accessibility of Trp side chains and polysaccharide loading, suggesting also that a higher level of conjugated PS does not necessarily interfere with toxoid accessibility. There were different levels of carrier protein Trp side-chain and epitope accessibility that were localised to the HC domain; these were related to the saccharide type, despite the conjugates being independently manufactured. These findings extend our understanding of the molecular basis for carrier protein recognition in TT conjugate vaccines. PMID:25640334

Orientation Encoding and Viewpoint Invariance in Face Recognition: Inferring Neural Properties from Large-Scale Signals.

PubMed

Ramírez, Fernando M

2018-05-01

Viewpoint-invariant face recognition is thought to be subserved by a distributed network of occipitotemporal face-selective areas that, except for the human anterior temporal lobe, have been shown to also contain face-orientation information. This review begins by highlighting the importance of bilateral symmetry for viewpoint-invariant recognition and face-orientation perception. Then, monkey electrophysiological evidence is surveyed describing key tuning properties of face-selective neurons-including neurons bimodally tuned to mirror-symmetric face-views-followed by studies combining functional magnetic resonance imaging (fMRI) and multivariate pattern analyses to probe the representation of face-orientation and identity information in humans. Altogether, neuroimaging studies suggest that face-identity is gradually disentangled from face-orientation information along the ventral visual processing stream. The evidence seems to diverge, however, regarding the prevalent form of tuning of neural populations in human face-selective areas. In this context, caveats possibly leading to erroneous inferences regarding mirror-symmetric coding are exposed, including the need to distinguish angular from Euclidean distances when interpreting multivariate pattern analyses. On this basis, this review argues that evidence from the fusiform face area is best explained by a view-sensitive code reflecting head angular disparity, consistent with a role of this area in face-orientation perception. Finally, the importance is stressed of explicit models relating neural properties to large-scale signals.

Deep Learning Methods for Underwater Target Feature Extraction and Recognition

PubMed Central

Peng, Yuan; Qiu, Mengran; Shi, Jianfei; Liu, Liangliang

2018-01-01

The classification and recognition technology of underwater acoustic signal were always an important research content in the field of underwater acoustic signal processing. Currently, wavelet transform, Hilbert-Huang transform, and Mel frequency cepstral coefficients are used as a method of underwater acoustic signal feature extraction. In this paper, a method for feature extraction and identification of underwater noise data based on CNN and ELM is proposed. An automatic feature extraction method of underwater acoustic signals is proposed using depth convolution network. An underwater target recognition classifier is based on extreme learning machine. Although convolution neural networks can execute both feature extraction and classification, their function mainly relies on a full connection layer, which is trained by gradient descent-based; the generalization ability is limited and suboptimal, so an extreme learning machine (ELM) was used in classification stage. Firstly, CNN learns deep and robust features, followed by the removing of the fully connected layers. Then ELM fed with the CNN features is used as the classifier to conduct an excellent classification. Experiments on the actual data set of civil ships obtained 93.04% recognition rate; compared to the traditional Mel frequency cepstral coefficients and Hilbert-Huang feature, recognition rate greatly improved. PMID:29780407

A Signal Peptide Derived from hsp60 Binds HLA-E and Interferes with CD94/NKG2A Recognition

PubMed Central

Michaëlsson, Jakob; Teixeira de Matos, Cristina; Achour, Adnane; Lanier, Lewis L.; Kärre, Klas; Söderström, Kalle

2002-01-01

Human histocompatibility leukocyte antigen (HLA)-E is a nonclassical major histocompatibility complex (MHC) class I molecule which presents a restricted set of nonameric peptides, derived mainly from the signal sequence of other MHC class I molecules. It interacts with CD94/NKG2 receptors expressed on the surface of natural killer (NK) cells and T cell subsets. Here we demonstrate that HLA-E also presents a peptide derived from the leader sequence of human heat shock protein 60 (hsp60). This peptide gains access to HLA-E intracellularly, resulting in up-regulated HLA-E/hsp60 signal peptide cell-surface levels on stressed cells. Notably, HLA-E molecules in complex with the hsp60 signal peptide are no longer recognized by CD94/NKG2A inhibitory receptors. Thus, during cellular stress an increased proportion of HLA-E molecules may bind the nonprotective hsp60 signal peptide, leading to a reduced capacity to inhibit a major NK cell population. Such stress induced peptide interference would gradually uncouple CD94/NKG2A inhibitory recognition and provide a mechanism for NK cells to detect stressed cells in a peptide-dependent manner. PMID:12461076

Chemical sensing in mammalian host-bacterial commensal associations

USDA-ARS?s Scientific Manuscript database

The mammalian gastrointestinal (GI) tract is colonized by a complex consortium of bacterial species. Bacteria engage in chemical signaling to coordinate population-wide behavior. However, it is unclear if chemical sensing plays a role in establishing mammalian host–bacterial commensal relationships....

Pattern-Recognition Algorithm for Locking Laser Frequency

NASA Technical Reports Server (NTRS)

Karayan, Vahag; Klipstein, William; Enzer, Daphna; Yates, Philip; Thompson, Robert; Wells, George

2006-01-01

A computer program serves as part of a feedback control system that locks the frequency of a laser to one of the spectral peaks of cesium atoms in an optical absorption cell. The system analyzes a saturation absorption spectrum to find a target peak and commands a laser-frequency-control circuit to minimize an error signal representing the difference between the laser frequency and the target peak. The program implements an algorithm consisting of the following steps: Acquire a saturation absorption signal while scanning the laser through the frequency range of interest. Condition the signal by use of convolution filtering. Detect peaks. Match the peaks in the signal to a pattern of known spectral peaks by use of a pattern-recognition algorithm. Add missing peaks. Tune the laser to the desired peak and thereafter lock onto this peak. Finding and locking onto the desired peak is a challenging problem, given that the saturation absorption signal includes noise and other spurious signal components; the problem is further complicated by nonlinearity and shifting of the voltage-to-frequency correspondence. The pattern-recognition algorithm, which is based on Hausdorff distance, is what enables the program to meet these challenges.

Particle Swarm Optimization Based Feature Enhancement and Feature Selection for Improved Emotion Recognition in Speech and Glottal Signals

PubMed Central

Muthusamy, Hariharan; Polat, Kemal; Yaacob, Sazali

2015-01-01

In the recent years, many research works have been published using speech related features for speech emotion recognition, however, recent studies show that there is a strong correlation between emotional states and glottal features. In this work, Mel-frequency cepstralcoefficients (MFCCs), linear predictive cepstral coefficients (LPCCs), perceptual linear predictive (PLP) features, gammatone filter outputs, timbral texture features, stationary wavelet transform based timbral texture features and relative wavelet packet energy and entropy features were extracted from the emotional speech (ES) signals and its glottal waveforms(GW). Particle swarm optimization based clustering (PSOC) and wrapper based particle swarm optimization (WPSO) were proposed to enhance the discerning ability of the features and to select the discriminating features respectively. Three different emotional speech databases were utilized to gauge the proposed method. Extreme learning machine (ELM) was employed to classify the different types of emotions. Different experiments were conducted and the results show that the proposed method significantly improves the speech emotion recognition performance compared to previous works published in the literature. PMID:25799141

Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling

PubMed Central

Podgornaia, Anna I.; Casino, Patricia; Marina, Alberto; Laub, Michael T.

2013-01-01

Summary Two-component signal transduction systems typically involve a sensor histidine kinase that specifically phosphorylates a single, cognate response regulator. This protein-protein interaction relies on molecular recognition via a small set of residues in each protein. To better understand how these residues determine the specificity of kinase-substrate interactions, we rationally rewired the interaction interface of a Thermotoga maritima two-component system, HK853-RR468, to match that found in a different two-component system, E. coli PhoR-PhoB. The rewired proteins interacted robustly with each other, but no longer interacted with the parent proteins. Analysis of the crystal structures of the wild-type and mutant protein complexes, along with a systematic mutagenesis study, reveals how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions, protein evolution, and the design of novel protein interfaces. PMID:23954504

Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds

NASA Astrophysics Data System (ADS)

Oh, Yoo Jin; Hubauer-Brenner, Michael; Gruber, Hermann J.; Cui, Yidan; Traxler, Lukas; Siligan, Christine; Park, Sungsu; Hinterdorfer, Peter

2016-09-01

Many enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.

Genetic Evidence for a Tight Cooperation of TatB and TatC during Productive Recognition of Twin-Arginine (Tat) Signal Peptides in Escherichia coli

PubMed Central

Lausberg, Frank; Fleckenstein, Stefan; Kreutzenbeck, Peter; Fröbel, Julia; Rose, Patrick; Müller, Matthias; Freudl, Roland

2012-01-01

The twin arginine translocation (Tat) pathway transports folded proteins across the cytoplasmic membrane of bacteria. Tat signal peptides contain a consensus motif (S/T-R-R-X-F-L-K) that is thought to play a crucial role in substrate recognition by the Tat translocase. Replacement of the phenylalanine at the +2 consensus position in the signal peptide of a Tat-specific reporter protein (TorA-MalE) by aspartate blocked export of the corresponding TorA(D+2)-MalE precursor, indicating that this mutation prevents a productive binding of the TorA(D+2) signal peptide to the Tat translocase. Mutations were identified in the extreme amino-terminal regions of TatB and TatC that synergistically suppressed the export defect of TorA(D+2)-MalE when present in pairwise or triple combinations. The observed synergistic suppression activities were even more pronounced in the restoration of membrane translocation of another export-defective precursor, TorA(KQ)-MalE, in which the conserved twin arginine residues had been replaced by lysine-glutamine. Collectively, these findings indicate that the extreme amino-terminal regions of TatB and TatC cooperate tightly during recognition and productive binding of Tat-dependent precursor proteins and, furthermore, that TatB and TatC are both involved in the formation of a specific signal peptide binding site that reaches out as far as the end of the TatB transmembrane segment. PMID:22761916

Genetic evidence for a tight cooperation of TatB and TatC during productive recognition of twin-arginine (Tat) signal peptides in Escherichia coli.

PubMed

Lausberg, Frank; Fleckenstein, Stefan; Kreutzenbeck, Peter; Fröbel, Julia; Rose, Patrick; Müller, Matthias; Freudl, Roland

2012-01-01

The twin arginine translocation (Tat) pathway transports folded proteins across the cytoplasmic membrane of bacteria. Tat signal peptides contain a consensus motif (S/T-R-R-X-F-L-K) that is thought to play a crucial role in substrate recognition by the Tat translocase. Replacement of the phenylalanine at the +2 consensus position in the signal peptide of a Tat-specific reporter protein (TorA-MalE) by aspartate blocked export of the corresponding TorA(D(+2))-MalE precursor, indicating that this mutation prevents a productive binding of the TorA(D(+2)) signal peptide to the Tat translocase. Mutations were identified in the extreme amino-terminal regions of TatB and TatC that synergistically suppressed the export defect of TorA(D(+2))-MalE when present in pairwise or triple combinations. The observed synergistic suppression activities were even more pronounced in the restoration of membrane translocation of another export-defective precursor, TorA(KQ)-MalE, in which the conserved twin arginine residues had been replaced by lysine-glutamine. Collectively, these findings indicate that the extreme amino-terminal regions of TatB and TatC cooperate tightly during recognition and productive binding of Tat-dependent precursor proteins and, furthermore, that TatB and TatC are both involved in the formation of a specific signal peptide binding site that reaches out as far as the end of the TatB transmembrane segment.

Experimental study on GMM-based speaker recognition

NASA Astrophysics Data System (ADS)

Ye, Wenxing; Wu, Dapeng; Nucci, Antonio

2010-04-01

Speaker recognition plays a very important role in the field of biometric security. In order to improve the recognition performance, many pattern recognition techniques have be explored in the literature. Among these techniques, the Gaussian Mixture Model (GMM) is proved to be an effective statistic model for speaker recognition and is used in most state-of-the-art speaker recognition systems. The GMM is used to represent the 'voice print' of a speaker through modeling the spectral characteristic of speech signals of the speaker. In this paper, we implement a speaker recognition system, which consists of preprocessing, Mel-Frequency Cepstrum Coefficients (MFCCs) based feature extraction, and GMM based classification. We test our system with TIDIGITS data set (325 speakers) and our own recordings of more than 200 speakers; our system achieves 100% correct recognition rate. Moreover, we also test our system under the scenario that training samples are from one language but test samples are from a different language; our system also achieves 100% correct recognition rate, which indicates that our system is language independent.

Activation of mitogen-activated protein kinase/extracellular signal-regulated kinase in hippocampal circuitry is required for consolidation and reconsolidation of recognition memory.

PubMed

Kelly, Aine; Laroche, Serge; Davis, Sabrina

2003-06-15

Consolidation and reconsolidation of long-term memory have been shown to be dependent on the synthesis of new proteins, but the specific molecular mechanisms underlying these events remain to be elucidated. The mitogen-activated protein kinase (MAPK) pathway can trigger genomic responses in neurons, leading to changes in protein synthesis, and several studies have identified its pivotal role in synaptic plasticity and long-term memory formation. In this study, we analyze the involvement of this pathway in the consolidation and reconsolidation of long-term recognition memory, using an object recognition task. We show that inhibition of the MAPK pathway by intracerebroventricular injection of the MEK [MAPK/extracellular signal-regulated kinase (ERK)] inhibitor UO126 blocks consolidation of object recognition memory but does not affect short-term memory. Brain regions of the entorhinal cortex-hippocampal circuitry were analyzed for ERK activation, and it was shown that consolidation of recognition memory was associated with increased phosphorylation of ERK in the dentate gyrus and entorhinal cortex, although total expression of ERK was unchanged. We also report that inhibition of the MAPK pathway blocks reconsolidation of recognition memory, and this was shown to be dependent on reactivation of the memory trace by brief reexposure to the objects. In addition, reconsolidation of memory was associated with an increase in the phosphorylation of ERK in entorhinal cortex and CA1. In summary, our data show that the MAPK kinase pathway is required for both consolidation and reconsolidation of long-term recognition memory, and that this is associated with hyperphosphorylation of ERK in different subregions of the entorhinal cortex-hippocampal circuitry.

Aminoglycosides: Molecular Insights on the Recognition of RNA and Aminoglycoside Mimics

PubMed Central

Chittapragada, Maruthi; Roberts, Sarah; Ham, Young Wan

2009-01-01

RNA is increasingly recognized for its significant functions in biological systems and has recently become an important molecular target for therapeutics development. Aminoglycosides, a large class of clinically significant antibiotics, exert their biological functions by binding to prokaryotic ribosomal RNA (rRNA) and interfering with protein translation, resulting in bacterial cell death. They are also known to bind to viral mRNAs such as HIV-1 RRE and TAR. Consequently, aminoglycosides are accepted as the single most important model in understanding the principles that govern small molecule-RNA recognition, which is essential for the development of novel antibacterial, antiviral or even anti-oncogenic agents. This review outlines the chemical structures and mechanisms of molecular recognition and antibacterial activity of aminoglycosides and various aminoglycoside mimics that have recently been devised to improve biological efficacy, binding affinity and selectivity, or to circumvent bacterial resistance. PMID:19812740

Gesture recognition by instantaneous surface EMG images

PubMed Central

Geng, Weidong; Du, Yu; Jin, Wenguang; Wei, Wentao; Hu, Yu; Li, Jiajun

2016-01-01

Gesture recognition in non-intrusive muscle-computer interfaces is usually based on windowed descriptive and discriminatory surface electromyography (sEMG) features because the recorded amplitude of a myoelectric signal may rapidly fluctuate between voltages above and below zero. Here, we present that the patterns inside the instantaneous values of high-density sEMG enables gesture recognition to be performed merely with sEMG signals at a specific instant. We introduce the concept of an sEMG image spatially composed from high-density sEMG and verify our findings from a computational perspective with experiments on gesture recognition based on sEMG images with a classification scheme of a deep convolutional network. Without any windowed features, the resultant recognition accuracy of an 8-gesture within-subject test reached 89.3% on a single frame of sEMG image and reached 99.0% using simple majority voting over 40 frames with a 1,000 Hz sampling rate. Experiments on the recognition of 52 gestures of NinaPro database and 27 gestures of CSL-HDEMG database also validated that our approach outperforms state-of-the-arts methods. Our findings are a starting point for the development of more fluid and natural muscle-computer interfaces with very little observational latency. For example, active prostheses and exoskeletons based on high-density electrodes could be controlled with instantaneous responses. PMID:27845347

Gesture recognition by instantaneous surface EMG images.

PubMed

Geng, Weidong; Du, Yu; Jin, Wenguang; Wei, Wentao; Hu, Yu; Li, Jiajun

2016-11-15

Gesture recognition in non-intrusive muscle-computer interfaces is usually based on windowed descriptive and discriminatory surface electromyography (sEMG) features because the recorded amplitude of a myoelectric signal may rapidly fluctuate between voltages above and below zero. Here, we present that the patterns inside the instantaneous values of high-density sEMG enables gesture recognition to be performed merely with sEMG signals at a specific instant. We introduce the concept of an sEMG image spatially composed from high-density sEMG and verify our findings from a computational perspective with experiments on gesture recognition based on sEMG images with a classification scheme of a deep convolutional network. Without any windowed features, the resultant recognition accuracy of an 8-gesture within-subject test reached 89.3% on a single frame of sEMG image and reached 99.0% using simple majority voting over 40 frames with a 1,000 Hz sampling rate. Experiments on the recognition of 52 gestures of NinaPro database and 27 gestures of CSL-HDEMG database also validated that our approach outperforms state-of-the-arts methods. Our findings are a starting point for the development of more fluid and natural muscle-computer interfaces with very little observational latency. For example, active prostheses and exoskeletons based on high-density electrodes could be controlled with instantaneous responses.

Lysozyme as a recognition element for monitoring of bacterial population.

PubMed

Zheng, Laibao; Wan, Yi; Yu, Liangmin; Zhang, Dun

2016-01-01

Bacterial infections remain a significant challenge in biomedicine and environment safety. Increasing worldwide demand for point-of-care techniques and increasing concern on their safe development and use, require a simple and sensitive bioanalysis for pathogen detection. However, this goal is not yet achieved. A design for fluorescein isothiocyanate-labeled lysozyme (FITC-LYZ), which provides quantitative binding information for gram-positive bacteria, Micrococcus luteus, and detects pathogen concentration, is presented. The functional lysozyme is used not only as the pathogenic detection platform, but also as a tracking reagent for microbial population in antibacterial tests. A nonlinear relationship between the system response and the logarithm of the bacterial concentration was observed in the range of 1.2×10(2)-1.2×10(5) cfu mL(-1). The system has a potential for further applications and provides a facile and simple method for detection of pathogenic bacteria. Meanwhile, the fluorescein isothiocyanate -labeled lysozyme is also employed as the tracking agent for antibacterial dynamic assay, which show a similar dynamic curve compared with UV-vis test. Copyright © 2015 Elsevier B.V. All rights reserved.

Binding of Signal Recognition Particle Gives Ribosome/Nascent Chain Complexes a Competitive Advantage in Endoplasmic Reticulum Membrane Interaction

PubMed Central

Neuhof, Andrea; Rolls, Melissa M.; Jungnickel, Berit; Kalies, Kai-Uwe; Rapoport, Tom A.

1998-01-01

Most secretory and membrane proteins are sorted by signal sequences to the endoplasmic reticulum (ER) membrane early during their synthesis. Targeting of the ribosome-nascent chain complex (RNC) involves the binding of the signal sequence to the signal recognition particle (SRP), followed by an interaction of ribosome-bound SRP with the SRP receptor. However, ribosomes can also independently bind to the ER translocation channel formed by the Sec61p complex. To explain the specificity of membrane targeting, it has therefore been proposed that nascent polypeptide-associated complex functions as a cytosolic inhibitor of signal sequence- and SRP-independent ribosome binding to the ER membrane. We report here that SRP-independent binding of RNCs to the ER membrane can occur in the presence of all cytosolic factors, including nascent polypeptide-associated complex. Nontranslating ribosomes competitively inhibit SRP-independent membrane binding of RNCs but have no effect when SRP is bound to the RNCs. The protective effect of SRP against ribosome competition depends on a functional signal sequence in the nascent chain and is also observed with reconstituted proteoliposomes containing only the Sec61p complex and the SRP receptor. We conclude that cytosolic factors do not prevent the membrane binding of ribosomes. Instead, specific ribosome targeting to the Sec61p complex is provided by the binding of SRP to RNCs, followed by an interaction with the SRP receptor, which gives RNC–SRP complexes a selective advantage in membrane targeting over nontranslating ribosomes. PMID:9436994

Pattern recognition applied to seismic signals of Llaima volcano (Chile): An evaluation of station-dependent classifiers

NASA Astrophysics Data System (ADS)

Curilem, Millaray; Huenupan, Fernando; Beltrán, Daniel; San Martin, Cesar; Fuentealba, Gustavo; Franco, Luis; Cardona, Carlos; Acuña, Gonzalo; Chacón, Max; Khan, M. Salman; Becerra Yoma, Nestor

2016-04-01

Automatic pattern recognition applied to seismic signals from volcanoes may assist seismic monitoring by reducing the workload of analysts, allowing them to focus on more challenging activities, such as producing reports, implementing models, and understanding volcanic behaviour. In a previous work, we proposed a structure for automatic classification of seismic events in Llaima volcano, one of the most active volcanoes in the Southern Andes, located in the Araucanía Region of Chile. A database of events taken from three monitoring stations on the volcano was used to create a classification structure, independent of which station provided the signal. The database included three types of volcanic events: tremor, long period, and volcano-tectonic and a contrast group which contains other types of seismic signals. In the present work, we maintain the same classification scheme, but we consider separately the stations information in order to assess whether the complementary information provided by different stations improves the performance of the classifier in recognising seismic patterns. This paper proposes two strategies for combining the information from the stations: i) combining the features extracted from the signals from each station and ii) combining the classifiers of each station. In the first case, the features extracted from the signals from each station are combined forming the input for a single classification structure. In the second, a decision stage combines the results of the classifiers for each station to give a unique output. The results confirm that the station-dependent strategies that combine the features and the classifiers from several stations improves the classification performance, and that the combination of the features provides the best performance. The results show an average improvement of 9% in the classification accuracy when compared with the station-independent method.

Applications of Wavelet Transform and Fuzzy Neural Network on Power Quality Recognition

NASA Astrophysics Data System (ADS)

Liao, Chiung-Chou; Yang, Hong-Tzer; Lin, Ying-Chun

2008-10-01

The wavelet transform coefficients (WTCs) contain plenty of information needed for transient event identification of power quality (PQ) events. However, adopting WTCs directly has the drawbacks of taking a longer time and too much memory for the recognition system. To solve the abovementioned recognition problems and to effectively reduce the number of features representing power transients, spectrum energies of WTCs in different scales are calculated by Parseval's Theorem. Through the proposed approach, features of the original power signals can be reserved and not influenced by occurring points of PQ events. The fuzzy neural classification systems are then used for signal recognition and fuzzy rule construction. Success rates of recognizing PQ events from noise-riding signals are proven to be feasible in power system applications in this paper.

Induction of Mincle by Helicobacter pylori and consequent anti-inflammatory signaling denote a bacterial survival strategy

PubMed Central

Devi, Savita; Rajakumara, Eerappa; Ahmed, Niyaz

2015-01-01

Evasion of innate immune recognition is one of the key strategies for persistence of Helicobacter pylori, by virtue of its ability to modulate or escape the host innate immune receptors and signaling pathways. C-type lectin receptors (CLRs) predominantly expressed by macrophages are pivotal in tailoring immune response against pathogens. The recognition of glyco or carbohydrate moieties by Mincle (Macrophage inducible C-type lectin) is emerging as a crucial element in anti-fungal and anti-mycobacterial immunity. Herein, we demonstrate the role of Mincle in modulation of innate immune response against H. pylori infection. Our results revealed an upregulated expression of Mincle which was independent of direct host cell contact. Upon computational modelling, Mincle was observed to interact with the Lewis antigens of H. pylori LPS and possibly activating an anti-inflammatory cytokine production, thereby maintaining a balance between pro- and anti-inflammatory cytokine production. Furthermore, siRNA mediated knockdown of Mincle in human macrophages resulted in up regulation of pro-inflammatory cytokines and consequent down regulation of anti-inflammatory cytokines. Collectively, our study demonstrates a novel mechanism employed by H. pylori to escape clearance by exploiting functional plasticity of Mincle to strike a balance between pro-and anti-inflammatory responses ensuring its persistence in the host. PMID:26456705

Door latching recognition apparatus and process

DOEpatents

Eakle, Jr., Robert F.

2012-05-15

An acoustic door latch detector is provided in which a sound recognition sensor is integrated into a door or door lock mechanism. The programmable sound recognition sensor can be trained to recognize the acoustic signature of the door and door lock mechanism being properly engaged and secured. The acoustic sensor will signal a first indicator indicating that proper closure was detected or sound an alarm condition if the proper acoustic signature is not detected within a predetermined time interval.

Mapping the signal peptide binding and oligomer contact sites of the core subunit of the pea twin arginine protein translocase.

PubMed

Ma, Xianyue; Cline, Kenneth

2013-03-01

Twin arginine translocation (Tat) systems of thylakoid and bacterial membranes transport folded proteins using the proton gradient as the sole energy source. Tat substrates have hydrophobic signal peptides with an essential twin arginine (RR) recognition motif. The multispanning cpTatC plays a central role in Tat operation: It binds the signal peptide, directs translocase assembly, and may facilitate translocation. An in vitro assay with pea (Pisum sativum) chloroplasts was developed to conduct mutagenesis and analysis of cpTatC functions. Ala scanning mutagenesis identified mutants defective in substrate binding and receptor complex assembly. Mutations in the N terminus (S1) and first stromal loop (S2) caused specific defects in signal peptide recognition. Cys matching between substrate and imported cpTatC confirmed that S1 and S2 directly and specifically bind the RR proximal region of the signal peptide. Mutations in four lumen-proximal regions of cpTatC were defective in receptor complex assembly. Copurification and Cys matching analyses suggest that several of the lumen proximal regions may be important for cpTatC-cpTatC interactions. Surprisingly, RR binding domains of adjacent cpTatCs directed strong cpTatC-cpTatC cross-linking. This suggests clustering of binding sites on the multivalent receptor complex and explains the ability of Tat to transport cross-linked multimers. Transport of substrate proteins cross-linked to the signal peptide binding site tentatively identified mutants impaired in the translocation step.

Host-induced bacterial cell wall decomposition mediates pattern-triggered immunity in Arabidopsis

PubMed Central

Liu, Xiaokun; Grabherr, Heini M; Willmann, Roland; Kolb, Dagmar; Brunner, Frédéric; Bertsche, Ute; Kühner, Daniel; Franz-Wachtel, Mirita; Amin, Bushra; Felix, Georg; Ongena, Marc; Nürnberger, Thorsten; Gust, Andrea A

2014-01-01

Peptidoglycans (PGNs) are immunogenic bacterial surface patterns that trigger immune activation in metazoans and plants. It is generally unknown how complex bacterial structures such as PGNs are perceived by plant pattern recognition receptors (PRRs) and whether host hydrolytic activities facilitate decomposition of bacterial matrices and generation of soluble PRR ligands. Here we show that Arabidopsis thaliana, upon bacterial infection or exposure to microbial patterns, produces a metazoan lysozyme-like hydrolase (lysozyme 1, LYS1). LYS1 activity releases soluble PGN fragments from insoluble bacterial cell walls and cleavage products are able to trigger responses typically associated with plant immunity. Importantly, LYS1 mutant genotypes exhibit super-susceptibility to bacterial infections similar to that observed on PGN receptor mutants. We propose that plants employ hydrolytic activities for the decomposition of complex bacterial structures, and that soluble pattern generation might aid PRR-mediated immune activation in cell layers adjacent to infection sites. DOI: http://dx.doi.org/10.7554/eLife.01990.001 PMID:24957336

Emotional expression recognition and attribution bias among sexual and violent offenders: a signal detection analysis

PubMed Central

Gillespie, Steven M.; Rotshtein, Pia; Satherley, Rose-Marie; Beech, Anthony R.; Mitchell, Ian J.

2015-01-01

Research with violent offenders has consistently shown impaired recognition of other’s facial expressions of emotion. However, the extent to which similar problems can be observed among sexual offenders remains unknown. Using a computerized task, we presented sexual and violent offenders, and non-offenders, with male and female expressions of anger, disgust, fear, happiness, sadness, and surprise, morphed with neutral expressions at varying levels of intensity (10, 55, and 90% expressive). Based on signal detection theory, we used hit rates and false alarms to calculate the sensitivity index d-prime (d′) and criterion (c) for each emotional expression. Overall, sexual offenders showed reduced sensitivity to emotional expressions across intensity, sex, and type of expression, compared with non-offenders, while both sexual and violent offenders showed particular reduced sensitivity to fearful expressions. We also observed specific effects for high (90%) intensity female faces, with sexual offenders showing reduced sensitivity to anger compared with non-offenders and violent offenders, and reduced sensitivity to disgust compared with non-offenders. Furthermore, both sexual and violent offenders showed impaired sensitivity to high intensity female fearful expressions compared with non-offenders. Violent offenders also showed a higher criterion for classifying moderate and high intensity male expressions as fearful, indicative of a more conservative response style, compared with angry, happy, or sad. These results suggest that both types of offender show problems in emotion recognition, and may have implications for understanding the inhibition of violent and sexually violent behaviors. PMID:26029137

Emotional expression recognition and attribution bias among sexual and violent offenders: a signal detection analysis.

PubMed

Gillespie, Steven M; Rotshtein, Pia; Satherley, Rose-Marie; Beech, Anthony R; Mitchell, Ian J

2015-01-01

Research with violent offenders has consistently shown impaired recognition of other's facial expressions of emotion. However, the extent to which similar problems can be observed among sexual offenders remains unknown. Using a computerized task, we presented sexual and violent offenders, and non-offenders, with male and female expressions of anger, disgust, fear, happiness, sadness, and surprise, morphed with neutral expressions at varying levels of intensity (10, 55, and 90% expressive). Based on signal detection theory, we used hit rates and false alarms to calculate the sensitivity index d-prime (d') and criterion (c) for each emotional expression. Overall, sexual offenders showed reduced sensitivity to emotional expressions across intensity, sex, and type of expression, compared with non-offenders, while both sexual and violent offenders showed particular reduced sensitivity to fearful expressions. We also observed specific effects for high (90%) intensity female faces, with sexual offenders showing reduced sensitivity to anger compared with non-offenders and violent offenders, and reduced sensitivity to disgust compared with non-offenders. Furthermore, both sexual and violent offenders showed impaired sensitivity to high intensity female fearful expressions compared with non-offenders. Violent offenders also showed a higher criterion for classifying moderate and high intensity male expressions as fearful, indicative of a more conservative response style, compared with angry, happy, or sad. These results suggest that both types of offender show problems in emotion recognition, and may have implications for understanding the inhibition of violent and sexually violent behaviors.

Phylogenetic analysis and expression profiling of the pattern recognition receptors: insights into molecular recognition of invading pathogens in Manduca sexta

PubMed Central

Zhang, Xiufeng; He, Yan; Cao, Xiaolong; Gunaratna, Ramesh T.; Chen, Yun-ru; Blissard, Gary; Kanost, Michael R.; Jiang, Haobo

2015-01-01

Pattern recognition receptors (PRRs) detect microbial pathogens and trigger innate immune responses. Previous biochemical studies have elucidated the physiological functions of eleven PRRs in Manduca sexta but our understanding of the recognition process is still limited, lacking genomic perspectives. While 34 C-type lectin-domain proteins and 16 Toll-like receptors are reported in the companion papers, we present here 120 other putative PRRs identified through the genome annotation. These include 76 leucine-rich repeat (LRR) proteins, 14 peptidoglycan recognition proteins, 6 EGF/Nim-domain proteins, 5 β-1,3-glucanase-related proteins, 4 galectins, 4 fibrinogen-related proteins, 3 thioester proteins, 5 immunoglobulin-domain proteins, 2 hemocytins, and 1 Reeler. Sequence alignment and phylogenetic analysis reveal the evolution history of a diverse repertoire of proteins for pathogen recognition. While functions of insect LRR proteins are mostly unknown, their structure diversification is phenomenal: In addition to the Toll homologs, 22 LRR proteins with a signal peptide are expected to be secreted; 18 LRR proteins lacking signal peptides may be cytoplasmic; 36 LRRs with a signal peptide and a transmembrane segment may be non-Toll receptors on the surface of cells. Expression profiles of the 120 genes in 52 tissue samples reflect complex regulation in various developmental stages and physiological states, including some likely by Rel family transcription factors via κB motifs in the promoter regions. This collection of information is expected to facilitate future biochemical studies detailing their respective roles in this model insect. PMID:25701384

Inhibition of Nod2 Signaling and Target Gene Expression by Curcumin

PubMed Central

Huang, Shurong; Zhao, Ling; Kim, Kihoon; Lee, Dong Seok; Hwang, Daniel H.

2008-01-01

Nod2 is an intracellular pattern recognition receptor that detects a conserved moiety of bacterial peptidoglycan and subsequently activates proinflammatory signaling pathways. Mutations in Nod2 have been implicated to be linked to inflammatory granulomatous disorders, such as Crohn's disease and Blau syndrome. Many phytochemicals possess anti-inflammatory properties. However, it is not known whether any of these phytochemicals might modulate Nod2-mediated immune responses and thus might be of therapeutic value for the intervention of these inflammatory diseases. In this report, we demonstrate that curcumin, a polyphenol found in the plant Curcuma longa, and parthenolide, a sesquiterpene lactone, suppress both ligand-induced and lauric acid-induced Nod2 signaling, leading to the suppression of nuclear factor-κB activation and target gene interleukin-8 expression. We provide molecular and biochemical evidence that the suppression is mediated through the inhibition of Nod2 oligomerization and subsequent inhibition of downstream signaling. These results demonstrate for the first time that curcumin and parthenolide can directly inhibit Nod2-mediated signaling pathways at the receptor level and suggest that Nod2-mediated inflammatory responses can be modulated by these phytochemicals. It remains to be determined whether these phytochemicals possess protective or therapeutic efficacy against Nod2-mediated inflammatory disorders. PMID:18413660

MDMA (Ecstasy) use is associated with reduced BOLD signal change during semantic recognition in abstinent human polydrug users: a preliminary fMRI study

PubMed Central

Raj, Vidya; Liang, Han-Chun; Woodward, Neil D.; Bauernfeind, Amy L.; Lee, Junghee; Dietrich, Mary; Park, Sohee; Cowan, Ronald L.

2011-01-01

Objectives MDMA users have impaired verbal memory, and voxel-based morphometry has demonstrated decreased gray matter in Brodmann area (BA) 18, 21 and 45. Because these regions play a role in verbal memory, we hypothesized that MDMA users would show altered brain activation in these areas during performance of an fMRI task that probed semantic verbal memory. Methods Polysubstance users enriched for MDMA exposure participated in a semantic memory encoding and recognition fMRI task that activated left BA 9, 18, 21/22 and 45. Primary outcomes were percent BOLD signal change in left BA 9, 18, 21/22 and 45, accuracy and response time. Results During semantic recognition, lifetime MDMA use was associated with decreased activation in left BA 9, 18 and 21/22 but not 45. This was partly influenced by contributions from cannabis and cocaine use. MDMA exposure was not associated with accuracy or response time during the semantic recognition task. Conclusions During semantic recognition, MDMA exposure is associated with reduced regional brain activation in regions mediating verbal memory. These findings partially overlap with prior structural evidence for reduced gray matter in MDMA users and may, in part, explain the consistent verbal memory impairments observed in other studies of MDMA users. PMID:19304866

Defense Against Cannibalism: The SdpI Family of Bacterial Immunity/Signal Transduction Proteins

PubMed Central

Povolotsky, Tatyana Leonidovna; Orlova, Ekaterina; Tamang, Dorjee G.

2010-01-01

The SdpI family consists of putative bacterial toxin immunity and signal transduction proteins. One member of the family in Bacillus subtilis, SdpI, provides immunity to cells from cannibalism in times of nutrient limitation. SdpI family members are transmembrane proteins with 3, 4, 5, 6, 7, 8, or 12 putative transmembrane α-helical segments (TMSs). These varied topologies appear to be genuine rather than artifacts due to sequencing or annotation errors. The basic and most frequently occurring element of the SdpI family has 6 TMSs. Homologues of all topological types were aligned to determine the homologous TMSs and loop regions, and the positive-inside rule was used to determine sidedness. The two most conserved motifs were identified between TMSs 1 and 2 and TMSs 4 and 5 of the 6 TMS proteins. These showed significant sequence similarity, leading us to suggest that the primordial precursor of these proteins was a 3 TMS–encoding genetic element that underwent intragenic duplication. Various deletional and fusional events, as well as intragenic duplications and inversions, may have yielded SdpI homologues with topologies of varying numbers and positions of TMSs. We propose a specific evolutionary pathway that could have given rise to these distantly related bacterial immunity proteins. We further show that genes encoding SdpI homologues often appear in operons with genes for homologues of SdpR, SdpI’s autorepressor. Our analyses allow us to propose structure–function relationships that may be applicable to most family members. Electronic supplementary material The online version of this article (doi:10.1007/s00232-010-9260-7) contains supplementary material, which is available to authorized users. PMID:20563570

Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle.

PubMed

Wang, Connie Y; Miller, Thomas F

2014-10-31

We characterize the conformational dynamics and substrate selectivity of the signal recognition particle (SRP) using a thermodynamic free energy cycle approach and microsecond timescale molecular dynamics simulations. The SRP is a central component of the co-translational protein targeting machinery that binds to the N-terminal signal peptide (SP) of nascent proteins. We determined the shift in relative conformational stability of the SRP upon substrate binding to quantify allosteric coupling between SRP domains. In particular, for dipeptidyl aminopeptidase, an SP that is recognized by the SRP for co-translational targeting, it is found that substrate binding induces substantial changes in the SRP toward configurations associated with targeting of the nascent protein, and it is found that the changes are modestly enhanced by a mutation that increases the hydrophobicity of the SP. However, for alkaline phosphatase, an SP that is recognized for post-translational targeting, substrate binding induces the reverse change in the SRP conformational distribution away from targeting configurations. Microsecond timescale trajectories reveal the intrinsic flexibility of the SRP conformational landscape and provide insight into recent single molecule studies by illustrating that 10-nm lengthscale changes between FRET pairs occur via the rigid-body movement of SRP domains connected by the flexible linker region. In combination, these results provide direct evidence for the hypothesis that substrate-controlled conformational switching in the SRP provides a mechanism for discriminating between different SPs and for connecting substrate binding to downstream steps in the protein targeting pathway. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Waveguide-type optical circuits for recognition of optical 8QAM-coded label

NASA Astrophysics Data System (ADS)

Surenkhorol, Tumendemberel; Kishikawa, Hiroki; Goto, Nobuo; Gonchigsumlaa, Khishigjargal

2017-10-01

Optical signal processing is expected to be applied in network nodes. In photonic routers, label recognition is one of the important functions. We have studied different kinds of label recognition methods so far for on-off keying, binary phase-shift keying, quadrature phase-shift keying, and 16 quadrature amplitude modulation-coded labels. We propose a method based on waveguide circuits to recognize an optical eight quadrature amplitude modulation (8QAM)-coded label by simple passive optical signal processing. The recognition of the proposed method is theoretically analyzed and numerically simulated by the finite difference beam propagation method. The noise tolerance is discussed, and bit-error rate against optical signal-to-noise ratio is evaluated. The scalability of the proposed method is also discussed theoretically for two-symbol length 8QAM-coded labels.

A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing.

PubMed

Ismail, Anisa S; Valastyan, Julie S; Bassler, Bonnie L

2016-04-13

Host-microbial symbioses are vital to health; nonetheless, little is known about the role crosskingdom signaling plays in these relationships. In a process called quorum sensing, bacteria communicate with one another using extracellular signal molecules called autoinducers. One autoinducer, AI-2, is proposed to promote interspecies bacterial communication, including in the mammalian gut. We show that mammalian epithelia produce an AI-2 mimic activity in response to bacteria or tight-junction disruption. This AI-2 mimic is detected by the bacterial AI-2 receptor, LuxP/LsrB, and can activate quorum-sensing-controlled gene expression, including in the enteric pathogen Salmonella typhimurium. AI-2 mimic activity is induced when epithelia are directly or indirectly exposed to bacteria, suggesting that a secreted bacterial component(s) stimulates its production. Mutagenesis revealed genes required for bacteria to both detect and stimulate production of the AI-2 mimic. These findings uncover a potential role for the mammalian AI-2 mimic in fostering crosskingdom signaling and host-bacterial symbioses. Copyright © 2016 Elsevier Inc. All rights reserved.

Signal recognition particle RNA in dinoflagellates and the Perkinsid Perkinsus marinus.

PubMed

Zhang, Huan; Campbell, David A; Sturm, Nancy R; Rosenblad, Magnus A; Dungan, Christopher F; Lin, Senjie

2013-09-01

In dinoflagellates and perkinsids, the molecular structure of the protein translocating machinery is unclear. Here, we identified several types of full-length signal recognition particle (SRP) RNA genes from Karenia brevis (dinoflagellate) and Perkinsus marinus (perkinsid). We also identified the four SRP S-domain proteins, but not the two Alu domain proteins, from P. marinus and several dinoflagellates. We mapped both ends of SRP RNA transcripts from K. brevis and P. marinus, and obtained the 3' end from four other dinoflagellates. The lengths of SRP RNA are predicted to be ∼260-300 nt in dinoflagellates and 280-285 nt in P. marinus. Although these SRP RNA sequences are substantially variable, the predicted structures are similar. The genomic organization of the SRP RNA gene differs among species. In K. brevis, this gene is located downstream of the spliced leader (SL) RNA, either as SL RNA-SRP RNA-tRNA gene tandem repeats, or within a SL RNA-SRP RNA-tRNA-U6-5S rRNA gene cluster. In other dinoflagellates, SRP RNA does not cluster with SL RNA or 5S rRNA genes. The majority of P. marinus SRP RNA genes array as tandem repeats without the above-mentioned small RNA genes. Our results capture a snapshot of a potentially complex evolutionary history of SRP RNA in alveolates. Copyright © 2013 Elsevier GmbH. All rights reserved.

Emotional recognition from the speech signal for a virtual education agent

NASA Astrophysics Data System (ADS)

Tickle, A.; Raghu, S.; Elshaw, M.

2013-06-01

This paper explores the extraction of features from the speech wave to perform intelligent emotion recognition. A feature extract tool (openSmile) was used to obtain a baseline set of 998 acoustic features from a set of emotional speech recordings from a microphone. The initial features were reduced to the most important ones so recognition of emotions using a supervised neural network could be performed. Given that the future use of virtual education agents lies with making the agents more interactive, developing agents with the capability to recognise and adapt to the emotional state of humans is an important step.

Robust Radar Emitter Recognition Based on the Three-Dimensional Distribution Feature and Transfer Learning

PubMed Central

Yang, Zhutian; Qiu, Wei; Sun, Hongjian; Nallanathan, Arumugam

2016-01-01

Due to the increasing complexity of electromagnetic signals, there exists a significant challenge for radar emitter signal recognition. To address this challenge, multi-component radar emitter recognition under a complicated noise environment is studied in this paper. A novel radar emitter recognition approach based on the three-dimensional distribution feature and transfer learning is proposed. The cubic feature for the time-frequency-energy distribution is proposed to describe the intra-pulse modulation information of radar emitters. Furthermore, the feature is reconstructed by using transfer learning in order to obtain the robust feature against signal noise rate (SNR) variation. Last, but not the least, the relevance vector machine is used to classify radar emitter signals. Simulations demonstrate that the approach proposed in this paper has better performances in accuracy and robustness than existing approaches. PMID:26927111

Robust Radar Emitter Recognition Based on the Three-Dimensional Distribution Feature and Transfer Learning.

PubMed

Yang, Zhutian; Qiu, Wei; Sun, Hongjian; Nallanathan, Arumugam

2016-02-25

Due to the increasing complexity of electromagnetic signals, there exists a significant challenge for radar emitter signal recognition. To address this challenge, multi-component radar emitter recognition under a complicated noise environment is studied in this paper. A novel radar emitter recognition approach based on the three-dimensional distribution feature and transfer learning is proposed. The cubic feature for the time-frequency-energy distribution is proposed to describe the intra-pulse modulation information of radar emitters. Furthermore, the feature is reconstructed by using transfer learning in order to obtain the robust feature against signal noise rate (SNR) variation. Last, but not the least, the relevance vector machine is used to classify radar emitter signals. Simulations demonstrate that the approach proposed in this paper has better performances in accuracy and robustness than existing approaches.

Four-Channel Biosignal Analysis and Feature Extraction for Automatic Emotion Recognition

NASA Astrophysics Data System (ADS)

Kim, Jonghwa; André, Elisabeth

This paper investigates the potential of physiological signals as a reliable channel for automatic recognition of user's emotial state. For the emotion recognition, little attention has been paid so far to physiological signals compared to audio-visual emotion channels such as facial expression or speech. All essential stages of automatic recognition system using biosignals are discussed, from recording physiological dataset up to feature-based multiclass classification. Four-channel biosensors are used to measure electromyogram, electrocardiogram, skin conductivity and respiration changes. A wide range of physiological features from various analysis domains, including time/frequency, entropy, geometric analysis, subband spectra, multiscale entropy, etc., is proposed in order to search the best emotion-relevant features and to correlate them with emotional states. The best features extracted are specified in detail and their effectiveness is proven by emotion recognition results.

Recognition and processing of randomly fluctuating electric signals by Na,K-ATPase.

PubMed Central

Xie, T. D.; Marszalek, P.; Chen, Y. D.; Tsong, T. Y.

1994-01-01

Previous work has shown that Na,K-ATPase of human erythrocytes can extract free energy from sinusoidal electric fields to pump cations up their respective concentration gradients. Because regularly oscillating waveform is not a feature of the transmembrane electric potential of cells, questions have been raised whether these observed effects are biologically relevant. Here we show that a random-telegraph fluctuating electric field (RTF) consisting of alternating square electric pulses with random lifetimes can also stimulate the Rb(+)-pumping mode of the Na,K-ATPase. The net RTF-stimulated, ouabain-sensitive Rb+ pumping was monitored with 86Rb+. The tracer-measured, Rb+ influx exhibited frequency and amplitude dependencies that peaked at the mean frequency of 1.0 kHz and amplitude of 20 V/cm. At 4 degrees C, the maximal pumping activity under these optimal conditions was 28 Rb+/RBC-hr, which is approximately 50% higher than that obtained with the sinusoidal electric field. These findings indicate that Na,K-ATPase can recognize an electric signal, either regularly oscillatory or randomly fluctuating, for energy coupling, with high fidelity. The use of RTF for activation also allowed a quantitative theoretical analysis of kinetics of a membrane transport model of any complexity according to the theory of electroconformational coupling (ECC) by the diagram methods. A four-state ECC model was shown to produce the amplitude and the frequency windows of the Rb(+)-pumping if the free energy of interaction of the transporter with the membrane potential was to include a nonlinear quadratic term. Kinetic constants for the ECC model have been derived. These results indicate that the ECC is a plausible mechanism for the recognition and processing of electric signals by proteins of the cell membrane. PMID:7811939

Exploiting Quorum Sensing To Confuse Bacterial Pathogens

PubMed Central

LaSarre, Breah

2013-01-01

SUMMARY Cell-cell communication, or quorum sensing, is a widespread phenomenon in bacteria that is used to coordinate gene expression among local populations. Its use by bacterial pathogens to regulate genes that promote invasion, defense, and spread has been particularly well documented. With the ongoing emergence of antibiotic-resistant pathogens, there is a current need for development of alternative therapeutic strategies. An antivirulence approach by which quorum sensing is impeded has caught on as a viable means to manipulate bacterial processes, especially pathogenic traits that are harmful to human and animal health and agricultural productivity. The identification and development of chemical compounds and enzymes that facilitate quorum-sensing inhibition (QSI) by targeting signaling molecules, signal biogenesis, or signal detection are reviewed here. Overall, the evidence suggests that QSI therapy may be efficacious against some, but not necessarily all, bacterial pathogens, and several failures and ongoing concerns that may steer future studies in productive directions are discussed. Nevertheless, various QSI successes have rightfully perpetuated excitement surrounding new potential therapies, and this review highlights promising QSI leads in disrupting pathogenesis in both plants and animals. PMID:23471618

Bacterial autolysins trim cell surface peptidoglycan to prevent detection by the Drosophila innate immune system

PubMed Central

Atilano, Magda Luciana; Pereira, Pedro Matos; Vaz, Filipa; Catalão, Maria João; Reed, Patricia; Grilo, Inês Ramos; Sobral, Rita Gonçalves; Ligoxygakis, Petros; Pinho, Mariana Gomes; Filipe, Sérgio Raposo

2014-01-01

Bacteria have to avoid recognition by the host immune system in order to establish a successful infection. Peptidoglycan, the principal constituent of virtually all bacterial surfaces, is a specific molecular signature recognized by dedicated host receptors, present in animals and plants, which trigger an immune response. Here we report that autolysins from Gram-positive pathogenic bacteria, enzymes capable of hydrolyzing peptidoglycan, have a major role in concealing this inflammatory molecule from Drosophila peptidoglycan recognition proteins (PGRPs). We show that autolysins trim the outermost peptidoglycan fragments and that in their absence bacterial virulence is impaired, as PGRPs can directly recognize leftover peptidoglycan extending beyond the external layers of bacterial proteins and polysaccharides. The activity of autolysins is not restricted to the producer cells but can also alter the surface of neighboring bacteria, facilitating the survival of the entire population in the infected host. DOI: http://dx.doi.org/10.7554/eLife.02277.001 PMID:24692449

Virus recognition by Toll-7 activates antiviral autophagy in Drosophila.

PubMed

Nakamoto, Margaret; Moy, Ryan H; Xu, Jie; Bambina, Shelly; Yasunaga, Ari; Shelly, Spencer S; Gold, Beth; Cherry, Sara

2012-04-20

Innate immunity is highly conserved and relies on pattern recognition receptors (PRRs) such as Toll-like receptors (identified through their homology to Drosophila Toll) for pathogen recognition. Although Drosophila Toll is vital for immune recognition and defense, roles for the other eight Drosophila Tolls in immunity have remained elusive. Here we have shown that Toll-7 is a PRR both in vitro and in adult flies; loss of Toll-7 led to increased vesicular stomatitis virus (VSV) replication and mortality. Toll-7, along with additional uncharacterized Drosophila Tolls, was transcriptionally induced by VSV infection. Furthermore, Toll-7 interacted with VSV at the plasma membrane and induced antiviral autophagy independently of the canonical Toll signaling pathway. These data uncover an evolutionarily conserved role for a second Drosophila Toll receptor that links viral recognition to autophagy and defense and suggest that other Drosophila Tolls may restrict specific as yet untested pathogens, perhaps via noncanonical signaling pathways. Copyright © 2012 Elsevier Inc. All rights reserved.

Noise tolerance in optical waveguide circuits for recognition of optical 16 quadrature amplitude modulation codes

NASA Astrophysics Data System (ADS)

Inoshita, Kensuke; Hama, Yoshimitsu; Kishikawa, Hiroki; Goto, Nobuo

2016-12-01

In photonic label routers, various optical signal processing functions are required; these include optical label extraction, recognition of the label, optical switching and buffering controlled by signals based on the label information and network routing tables, and label rewriting. Among these functions, we focus on photonic label recognition. We have proposed two kinds of optical waveguide circuits to recognize 16 quadrature amplitude modulation codes, i.e., recognition from the minimum output port and from the maximum output port. The recognition function was theoretically analyzed and numerically simulated by finite-difference beam-propagation method. We discuss noise tolerance in the circuit and show numerically simulated results to evaluate bit-error-rate (BER) characteristics against optical signal-to-noise ratio (OSNR). The OSNR required to obtain a BER less than 1.0×10-3 for the symbol rate of 2.5 GBaud was 14.5 and 27.0 dB for recognition from the minimum and maximum output, respectively.

The macrophage pattern recognition scavenger receptors SR-A and CD36 protect against microbial induced pregnancy loss

PubMed Central

Ebersole, Jeffery L.; de Villiers, Willem J. S.

2014-01-01

Objectives and design Microbial products can act via stress-induced signaling cascades to link dysregulated endogenous microbiota to immune activation (e.g., macrophages) and pregnancy loss. Our previous studies demonstrated that mice deficient in the macrophage pattern recognition scavenger receptors, SR-A and CD36, are more susceptible to inflammatory complications including gut leakiness and experimental colitis. We hypothesized that bacterial penetration of the maternal mucosal surfaces and replication in embryonic fluids compromise the fetal status and can result in miscarriage. Materials and methods Eighty pregnant ICR and SR-A/CD36-deficient mice were injected via tail vein or intraperitoneally with commensal bacteria (Streptococcus cricetus and/or Actinobacillus sp.) or sham controls. Dams were monitored daily for physical distress, pain and abortion. Results Dams injected with single dose bacterial inoculum did not develop clinical symptoms. Day old pups injected with bacteria developed internal focal abscesses, lost weight but recovered after 1 week. Dams receiving a second bacterial inoculum delivered dead fetuses. However, SR-A/CD36-deficnet dams demonstrated 100% fetal death via aborted fetuses, and significant up-regulation of the proinflammatory markers (IL-6, serum Amyloid A) 24–74 h after single inoculum. Conclusions These data indicate that macrophage scavenger receptors are required for the fetal protection against microbial attack and support that maternal transfer of innate immunity contributes to this protection. PMID:20711846

Enhancing speech recognition using improved particle swarm optimization based hidden Markov model.

PubMed

Selvaraj, Lokesh; Ganesan, Balakrishnan

2014-01-01

Enhancing speech recognition is the primary intention of this work. In this paper a novel speech recognition method based on vector quantization and improved particle swarm optimization (IPSO) is suggested. The suggested methodology contains four stages, namely, (i) denoising, (ii) feature mining (iii), vector quantization, and (iv) IPSO based hidden Markov model (HMM) technique (IP-HMM). At first, the speech signals are denoised using median filter. Next, characteristics such as peak, pitch spectrum, Mel frequency Cepstral coefficients (MFCC), mean, standard deviation, and minimum and maximum of the signal are extorted from the denoised signal. Following that, to accomplish the training process, the extracted characteristics are given to genetic algorithm based codebook generation in vector quantization. The initial populations are created by selecting random code vectors from the training set for the codebooks for the genetic algorithm process and IP-HMM helps in doing the recognition. At this point the creativeness will be done in terms of one of the genetic operation crossovers. The proposed speech recognition technique offers 97.14% accuracy.

Self-organizing neural network models for visual pattern recognition.

PubMed

Fukushima, K

1987-01-01

Two neural network models for visual pattern recognition are discussed. The first model, called a "neocognitron", is a hierarchical multilayered network which has only afferent synaptic connections. It can acquire the ability to recognize patterns by "learning-without-a-teacher": the repeated presentation of a set of training patterns is sufficient, and no information about the categories of the patterns is necessary. The cells of the highest stage eventually become "gnostic cells", whose response shows the final result of the pattern-recognition of the network. Pattern recognition is performed on the basis of similarity in shape between patterns, and is not affected by deformation, nor by changes in size, nor by shifts in the position of the stimulus pattern. The second model has not only afferent but also efferent synaptic connections, and is endowed with the function of selective attention. The afferent and the efferent signals interact with each other in the hierarchical network: the efferent signals, that is, the signals for selective attention, have a facilitating effect on the afferent signals, and at the same time, the afferent signals gate efferent signal flow. When a complex figure, consisting of two patterns or more, is presented to the model, it is segmented into individual patterns, and each pattern is recognized separately. Even if one of the patterns to which the models is paying selective attention is affected by noise or defects, the model can "recall" the complete pattern from which the noise has been eliminated and the defects corrected.

Hybrid Speaker Recognition Using Universal Acoustic Model

NASA Astrophysics Data System (ADS)

Nishimura, Jun; Kuroda, Tadahiro

We propose a novel speaker recognition approach using a speaker-independent universal acoustic model (UAM) for sensornet applications. In sensornet applications such as “Business Microscope”, interactions among knowledge workers in an organization can be visualized by sensing face-to-face communication using wearable sensor nodes. In conventional studies, speakers are detected by comparing energy of input speech signals among the nodes. However, there are often synchronization errors among the nodes which degrade the speaker recognition performance. By focusing on property of the speaker's acoustic channel, UAM can provide robustness against the synchronization error. The overall speaker recognition accuracy is improved by combining UAM with the energy-based approach. For 0.1s speech inputs and 4 subjects, speaker recognition accuracy of 94% is achieved at the synchronization error less than 100ms.

LL37 and Cationic Peptides Enhance TLR3 Signaling by Viral Double-stranded RNAs

PubMed Central

Lai, Yvonne; Adhikarakunnathu, Sreedevi; Bhardwaj, Kanchan; Ranjith-Kumar, C. T.; Wen, Yahong; Jordan, Jarrat L.; Wu, Linda H.; Dragnea, Bogdan; Mateo, Lani San; Kao, C. Cheng

2011-01-01

Background Toll-like Receptor 3 (TLR3) detects viral dsRNA during viral infection. However, most natural viral dsRNAs are poor activators of TLR3 in cell-based systems, leading us to hypothesize that TLR3 needs additional factors to be activated by viral dsRNAs. The anti-microbial peptide LL37 is the only known human member of the cathelicidin family of anti-microbial peptides. LL37 complexes with bacterial lipopolysaccharide (LPS) to prevent activation of TLR4, binds to ssDNA to modulate TLR9 and ssRNA to modulate TLR7 and 8. It synergizes with TLR2/1, TLR3 and TLR5 agonists to increase IL8 and IL6 production. This work seeks to determine whether LL37 enhances viral dsRNA recognition by TLR3. Methodology/Principal Findings Using a human bronchial epithelial cell line (BEAS2B) and human embryonic kidney cells (HEK 293T) transiently transfected with TLR3, we found that LL37 enhanced poly(I:C)-induced TLR3 signaling and enabled the recognition of viral dsRNAs by TLR3. The presence of LL37 also increased the cytokine response to rhinovirus infection in BEAS2B cells and in activated human peripheral blood mononuclear cells. Confocal microscopy determined that LL37 could co-localize with TLR3. Electron microscopy showed that LL37 and poly(I:C) individually formed globular structures, but a complex of the two formed filamentous structures. To separate the effects of LL37 on TLR3 and TLR4, other peptides that bind RNA and transport the complex into cells were tested and found to activate TLR3 signaling in response to dsRNAs, but had no effect on TLR4 signaling. This is the first demonstration that LL37 and other RNA-binding peptides with cell penetrating motifs can activate TLR3 signaling and facilitate the recognition of viral ligands. Conclusions/Significance LL37 and several cell-penetrating peptides can enhance signaling by TLR3 and enable TLR3 to respond to viral dsRNA. PMID:22039520

Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta.

PubMed

Zhang, Xiufeng; He, Yan; Cao, Xiaolong; Gunaratna, Ramesh T; Chen, Yun-ru; Blissard, Gary; Kanost, Michael R; Jiang, Haobo

2015-07-01

Pattern recognition receptors (PRRs) detect microbial pathogens and trigger innate immune responses. Previous biochemical studies have elucidated the physiological functions of eleven PRRs in Manduca sexta but our understanding of the recognition process is still limited, lacking genomic perspectives. While 34 C-type lectin-domain proteins and 16 Toll-like receptors are reported in the companion papers, we present here 120 other putative PRRs identified through the genome annotation. These include 76 leucine-rich repeat (LRR) proteins, 14 peptidoglycan recognition proteins, 6 EGF/Nim-domain proteins, 5 β-1,3-glucanase-related proteins, 4 galectins, 4 fibrinogen-related proteins, 3 thioester proteins, 5 immunoglobulin-domain proteins, 2 hemocytins, and 1 Reeler. Sequence alignment and phylogenetic analysis reveal the evolution history of a diverse repertoire of proteins for pathogen recognition. While functions of insect LRR proteins are mostly unknown, their structure diversification is phenomenal: In addition to the Toll homologs, 22 LRR proteins with a signal peptide are expected to be secreted; 18 LRR proteins lacking signal peptides may be cytoplasmic; 36 LRRs with a signal peptide and a transmembrane segment may be non-Toll receptors on the surface of cells. Expression profiles of the 120 genes in 52 tissue samples reflect complex regulation in various developmental stages and physiological states, including some likely by Rel family transcription factors via κB motifs in the promoter regions. This collection of information is expected to facilitate future biochemical studies detailing their respective roles in this model insect. Copyright © 2015 Elsevier Ltd. All rights reserved.

A functional glycoprotein competitive recognition and signal amplification strategy for carbohydrate-protein interaction profiling and cell surface carbohydrate expression evaluation

NASA Astrophysics Data System (ADS)

Wang, Yangzhong; Chen, Zhuhai; Liu, Yang; Li, Jinghong

2013-07-01

A simple and sensitive carbohydrate biosensor has been suggested as a potential tool for accurate analysis of cell surface carbohydrate expression as well as carbohydrate-based therapeutics for a variety of diseases and infections. In this work, a sensitive biosensor for carbohydrate-lectin profiling and in situ cell surface carbohydrate expression was designed by taking advantage of a functional glycoprotein of glucose oxidase acting as both a multivalent recognition unit and a signal amplification probe. Combining the gold nanoparticle catalyzed luminol electrogenerated chemiluminescence and nanocarrier for active biomolecules, the number of cell surface carbohydrate groups could be conveniently read out. The apparent dissociation constant between GOx@Au probes and Con A was detected to be 1.64 nM and was approximately 5 orders of magnitude smaller than that of mannose and Con A, which would arise from the multivalent effect between the probe and Con A. Both glycoproteins and gold nanoparticles contribute to the high affinity between carbohydrates and lectin. The as-proposed biosensor exhibits excellent analytical performance towards the cytosensing of K562 cells with a detection limit of 18 cells, and the mannose moieties on a single K562 cell were determined to be 1.8 × 1010. The biosensor can also act as a useful tool for antibacterial drug screening and mechanism investigation. This strategy integrates the excellent biocompatibility and multivalent recognition of glycoproteins as well as the significant enzymatic catalysis and gold nanoparticle signal amplification, and avoids the cell pretreatment and labelling process. This would contribute to the glycomic analysis and the understanding of complex native glycan-related biological processes.A simple and sensitive carbohydrate biosensor has been suggested as a potential tool for accurate analysis of cell surface carbohydrate expression as well as carbohydrate-based therapeutics for a variety of diseases and

Testing Theories of Recognition Memory by Predicting Performance Across Paradigms

ERIC Educational Resources Information Center

Smith, David G.; Duncan, Matthew J. J.

2004-01-01

Signal-detection theory (SDT) accounts of recognition judgments depend on the assumption that recognition decisions result from a single familiarity-based process. However, fits of a hybrid SDT model, called dual-process theory (DPT), have provided evidence for the existence of a second, recollection-based process. In 2 experiments, the authors…

Short temporal asynchrony disrupts visual object recognition

PubMed Central

Singer, Jedediah M.; Kreiman, Gabriel

2014-01-01

Humans can recognize objects and scenes in a small fraction of a second. The cascade of signals underlying rapid recognition might be disrupted by temporally jittering different parts of complex objects. Here we investigated the time course over which shape information can be integrated to allow for recognition of complex objects. We presented fragments of object images in an asynchronous fashion and behaviorally evaluated categorization performance. We observed that visual recognition was significantly disrupted by asynchronies of approximately 30 ms, suggesting that spatiotemporal integration begins to break down with even small deviations from simultaneity. However, moderate temporal asynchrony did not completely obliterate recognition; in fact, integration of visual shape information persisted even with an asynchrony of 100 ms. We describe the data with a concise model based on the dynamic reduction of uncertainty about what image was presented. These results emphasize the importance of timing in visual processing and provide strong constraints for the development of dynamical models of visual shape recognition. PMID:24819738

Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins.

PubMed

Pombo, Marina A; Zheng, Yi; Fernandez-Pozo, Noe; Dunham, Diane M; Fei, Zhangjun; Martin, Gregory B

2014-01-01

Plants have two related immune systems to defend themselves against pathogen attack. Initially,pattern-triggered immunity is activated upon recognition of microbe-associated molecular patterns by pattern recognition receptors. Pathogenic bacteria deliver effector proteins into the plant cell that interfere with this immune response and promote disease. However, some plants express resistance proteins that detect the presence of specific effectors leading to a robust defense response referred to as effector-triggered immunity. The interaction of tomato with Pseudomonas syringae pv. tomato is an established model system for understanding the molecular basis of these plant immune responses. We apply high-throughput RNA sequencing to this pathosystem to identify genes whose expression changes specifically during pattern-triggered or effector-triggered immunity. We then develop reporter genes for each of these responses that will enable characterization of the host response to the large collection of P. s. pv. tomato strains that express different combinations of effectors. Virus-induced gene silencing of 30 of the effector-triggered immunity-specific genes identifies Epk1 which encodes a predicted protein kinase from a family previously unknown to be involved in immunity. Knocked-down expression of Epk1 compromises effector-triggered immunity triggered by three bacterial effectors but not by effectors from non-bacterial pathogens. Epistasis experiments indicate that Epk1 acts upstream of effector-triggered immunity-associated MAP kinase signaling. Using RNA-seq technology we identify genes involved in specific immune responses. A functional genomics screen led to the discovery of Epk1, a novel predicted protein kinase required for plant defense activation upon recognition of three different bacterial effectors.

A conserved juxtacrine signal regulates synaptic partner recognition in Caenorhabditis elegans

PubMed Central

2011-01-01

. Furthermore, an artificially membrane-tethered UNC-6 expressed in the postsynaptic neurons promotes SPR, consistent with a short-range signal between adjacent synaptic partners. Conclusions These results indicate that the conserved UNC-6/Netrin-UNC-40/DCC ligand-receptor pair has a previously unknown function, acting in a juxtacrine manner to specify recognition of individual postsynaptic neurons. Furthermore, they illustrate the potential of this new approach, combining NLG-1 GRASP and behavioral analysis, in gene discovery and characterization. PMID:21663630

Effects of pre-experimental knowledge on recognition memory.

PubMed

Bird, Chris M; Davies, Rachel A; Ward, Jamie; Burgess, Neil

2011-01-01

The influence of pre-experimental autobiographical knowledge on recognition memory was investigated using as memoranda faces that were either personally known or unknown to the participant. Under a dual process theory, such knowledge boosted both recollection- and familiarity-based recognition judgements. Under an unequal variance signal detection model, pre-experimental knowledge increased both the variance and the separation of the target and foil memory strength distributions, boosting hits and correct rejections. Thus, pre-experimental knowledge has profound effects on the multiple, interacting processes that subserve recognition memory, and likely in the neural systems that underpin them.

Are Bacterial Volatile Compounds Poisonous Odors to a Fungal Pathogen Botrytis cinerea, Alarm Signals to Arabidopsis Seedlings for Eliciting Induced Resistance, or Both?

PubMed Central

Sharifi, Rouhallah; Ryu, Choong-Min

2016-01-01

Biological control (biocontrol) agents act on plants via numerous mechanisms, and can be used to protect plants from pathogens. Biocontrol agents can act directly as pathogen antagonists or competitors or indirectly to promote plant induced systemic resistance (ISR). Whether a biocontrol agent acts directly or indirectly depends on the specific strain and the pathosystem type. We reported previously that bacterial volatile organic compounds (VOCs) are determinants for eliciting plant ISR. Emerging data suggest that bacterial VOCs also can directly inhibit fungal and plant growth. The aim of the current study was to differentiate direct and indirect mechanisms of bacterial VOC effects against Botrytis cinerea infection of Arabidopsis. Volatile emissions from Bacillus subtilis GB03 successfully protected Arabidopsis seedlings against B. cinerea. First, we investigated the direct effects of bacterial VOCs on symptom development and different phenological stages of B. cinerea including spore germination, mycelial attachment to the leaf surface, mycelial growth, and sporulation in vitro and in planta. Volatile emissions inhibited hyphal growth in a dose-dependent manner in vitro, and interfered with fungal attachment on the hydrophobic leaf surface. Second, the optimized bacterial concentration that did not directly inhibit fungal growth successfully protected Arabidopsis from fungal infection, which indicates that bacterial VOC-elicited plant ISR has a more important role in biocontrol than direct inhibition of fungal growth on Arabidopsis. We performed qRT-PCR to investigate the priming of the defense-related genes PR1, PDF1.2, and ChiB at 0, 12, 24, and 36 h post-infection and 14 days after the start of plant exposure to bacterial VOCs. The results indicate that bacterial VOCs potentiate expression of PR1 and PDF1.2 but not ChiB, which stimulates SA- and JA-dependent signaling pathways in plant ISR and protects plants against pathogen colonization. This study

Single-trial EEG-informed fMRI reveals spatial dependency of BOLD signal on early and late IC-ERP amplitudes during face recognition.

PubMed

Wirsich, Jonathan; Bénar, Christian; Ranjeva, Jean-Philippe; Descoins, Médéric; Soulier, Elisabeth; Le Troter, Arnaud; Confort-Gouny, Sylviane; Liégeois-Chauvel, Catherine; Guye, Maxime

2014-10-15

Simultaneous EEG-fMRI has opened up new avenues for improving the spatio-temporal resolution of functional brain studies. However, this method usually suffers from poor EEG quality, especially for evoked potentials (ERPs), due to specific artifacts. As such, the use of EEG-informed fMRI analysis in the context of cognitive studies has particularly focused on optimizing narrow ERP time windows of interest, which ignores the rich diverse temporal information of the EEG signal. Here, we propose to use simultaneous EEG-fMRI to investigate the neural cascade occurring during face recognition in 14 healthy volunteers by using the successive ERP peaks recorded during the cognitive part of this process. N170, N400 and P600 peaks, commonly associated with face recognition, were successfully and reproducibly identified for each trial and each subject by using a group independent component analysis (ICA). For the first time we use this group ICA to extract several independent components (IC) corresponding to the sequence of activation and used single-trial peaks as modulation parameters in a general linear model (GLM) of fMRI data. We obtained an occipital-temporal-frontal stream of BOLD signal modulation, in accordance with the three successive IC-ERPs providing an unprecedented spatio-temporal characterization of the whole cognitive process as defined by BOLD signal modulation. By using this approach, the pattern of EEG-informed BOLD modulation provided improved characterization of the network involved than the fMRI-only analysis or the source reconstruction of the three ERPs; the latter techniques showing only two regions in common localized in the occipital lobe. Copyright © 2014 Elsevier Inc. All rights reserved.

Looking for myself: current multisensory input alters self-face recognition.

PubMed

Tsakiris, Manos

2008-01-01

How do I know the person I see in the mirror is really me? Is it because I know the person simply looks like me, or is it because the mirror reflection moves when I move, and I see it being touched when I feel touch myself? Studies of face-recognition suggest that visual recognition of stored visual features inform self-face recognition. In contrast, body-recognition studies conclude that multisensory integration is the main cue to selfhood. The present study investigates for the first time the specific contribution of current multisensory input for self-face recognition. Participants were stroked on their face while they were looking at a morphed face being touched in synchrony or asynchrony. Before and after the visuo-tactile stimulation participants performed a self-recognition task. The results show that multisensory signals have a significant effect on self-face recognition. Synchronous tactile stimulation while watching another person's face being similarly touched produced a bias in recognizing one's own face, in the direction of the other person included in the representation of one's own face. Multisensory integration can update cognitive representations of one's body, such as the sense of ownership. The present study extends this converging evidence by showing that the correlation of synchronous multisensory signals also updates the representation of one's face. The face is a key feature of our identity, but at the same time is a source of rich multisensory experiences used to maintain or update self-representations.

Towards Contactless Silent Speech Recognition Based on Detection of Active and Visible Articulators Using IR-UWB Radar

PubMed Central

Shin, Young Hoon; Seo, Jiwon

2016-01-01

People with hearing or speaking disabilities are deprived of the benefits of conventional speech recognition technology because it is based on acoustic signals. Recent research has focused on silent speech recognition systems that are based on the motions of a speaker’s vocal tract and articulators. Because most silent speech recognition systems use contact sensors that are very inconvenient to users or optical systems that are susceptible to environmental interference, a contactless and robust solution is hence required. Toward this objective, this paper presents a series of signal processing algorithms for a contactless silent speech recognition system using an impulse radio ultra-wide band (IR-UWB) radar. The IR-UWB radar is used to remotely and wirelessly detect motions of the lips and jaw. In order to extract the necessary features of lip and jaw motions from the received radar signals, we propose a feature extraction algorithm. The proposed algorithm noticeably improved speech recognition performance compared to the existing algorithm during our word recognition test with five speakers. We also propose a speech activity detection algorithm to automatically select speech segments from continuous input signals. Thus, speech recognition processing is performed only when speech segments are detected. Our testbed consists of commercial off-the-shelf radar products, and the proposed algorithms are readily applicable without designing specialized radar hardware for silent speech processing. PMID:27801867

Towards Contactless Silent Speech Recognition Based on Detection of Active and Visible Articulators Using IR-UWB Radar.

PubMed

Shin, Young Hoon; Seo, Jiwon

2016-10-29

People with hearing or speaking disabilities are deprived of the benefits of conventional speech recognition technology because it is based on acoustic signals. Recent research has focused on silent speech recognition systems that are based on the motions of a speaker's vocal tract and articulators. Because most silent speech recognition systems use contact sensors that are very inconvenient to users or optical systems that are susceptible to environmental interference, a contactless and robust solution is hence required. Toward this objective, this paper presents a series of signal processing algorithms for a contactless silent speech recognition system using an impulse radio ultra-wide band (IR-UWB) radar. The IR-UWB radar is used to remotely and wirelessly detect motions of the lips and jaw. In order to extract the necessary features of lip and jaw motions from the received radar signals, we propose a feature extraction algorithm. The proposed algorithm noticeably improved speech recognition performance compared to the existing algorithm during our word recognition test with five speakers. We also propose a speech activity detection algorithm to automatically select speech segments from continuous input signals. Thus, speech recognition processing is performed only when speech segments are detected. Our testbed consists of commercial off-the-shelf radar products, and the proposed algorithms are readily applicable without designing specialized radar hardware for silent speech processing.

Character displacement of Cercopithecini primate visual signals

PubMed Central

Allen, William L.; Stevens, Martin; Higham, James P.

2014-01-01

Animal visual signals have the potential to act as an isolating barrier to prevent interbreeding of populations through a role in species recognition. Within communities of competing species, species recognition signals are predicted to undergo character displacement, becoming more visually distinctive from each other, however this pattern has rarely been identified. Using computational face recognition algorithms to model primate face processing, we demonstrate that the face patterns of guenons (tribe: Cercopithecini) have evolved under selection to become more visually distinctive from those of other guenon species with whom they are sympatric. The relationship between the appearances of sympatric species suggests that distinguishing conspecifics from other guenon species has been a major driver of diversification in guenon face appearance. Visual signals that have undergone character displacement may have had an important role in the tribe’s radiation, keeping populations that became geographically separated reproductively isolated on secondary contact. PMID:24967517

Novel Blind Recognition Algorithm of Frame Synchronization Words Based on Soft-Decision in Digital Communication Systems.

PubMed

Qin, Jiangyi; Huang, Zhiping; Liu, Chunwu; Su, Shaojing; Zhou, Jing

2015-01-01

A novel blind recognition algorithm of frame synchronization words is proposed to recognize the frame synchronization words parameters in digital communication systems. In this paper, a blind recognition method of frame synchronization words based on the hard-decision is deduced in detail. And the standards of parameter recognition are given. Comparing with the blind recognition based on the hard-decision, utilizing the soft-decision can improve the accuracy of blind recognition. Therefore, combining with the characteristics of Quadrature Phase Shift Keying (QPSK) signal, an improved blind recognition algorithm based on the soft-decision is proposed. Meanwhile, the improved algorithm can be extended to other signal modulation forms. Then, the complete blind recognition steps of the hard-decision algorithm and the soft-decision algorithm are given in detail. Finally, the simulation results show that both the hard-decision algorithm and the soft-decision algorithm can recognize the parameters of frame synchronization words blindly. What's more, the improved algorithm can enhance the accuracy of blind recognition obviously.

Speech emotion recognition methods: A literature review

NASA Astrophysics Data System (ADS)

Basharirad, Babak; Moradhaseli, Mohammadreza

2017-10-01

Recently, attention of the emotional speech signals research has been boosted in human machine interfaces due to availability of high computation capability. There are many systems proposed in the literature to identify the emotional state through speech. Selection of suitable feature sets, design of a proper classifications methods and prepare an appropriate dataset are the main key issues of speech emotion recognition systems. This paper critically analyzed the current available approaches of speech emotion recognition methods based on the three evaluating parameters (feature set, classification of features, accurately usage). In addition, this paper also evaluates the performance and limitations of available methods. Furthermore, it highlights the current promising direction for improvement of speech emotion recognition systems.

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

PubMed

Fuchs, Julian E; Huber, Roland G; Waldner, Birgit J; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

PubMed Central

Fuchs, Julian E.; Huber, Roland G.; Waldner, Birgit J.; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R.

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm “dynamics govern specificity” might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design. PMID:26496636

Complex Event Recognition Architecture

NASA Technical Reports Server (NTRS)

Fitzgerald, William A.; Firby, R. James

2009-01-01

Complex Event Recognition Architecture (CERA) is the name of a computational architecture, and software that implements the architecture, for recognizing complex event patterns that may be spread across multiple streams of input data. One of the main components of CERA is an intuitive event pattern language that simplifies what would otherwise be the complex, difficult tasks of creating logical descriptions of combinations of temporal events and defining rules for combining information from different sources over time. In this language, recognition patterns are defined in simple, declarative statements that combine point events from given input streams with those from other streams, using conjunction, disjunction, and negation. Patterns can be built on one another recursively to describe very rich, temporally extended combinations of events. Thereafter, a run-time matching algorithm in CERA efficiently matches these patterns against input data and signals when patterns are recognized. CERA can be used to monitor complex systems and to signal operators or initiate corrective actions when anomalous conditions are recognized. CERA can be run as a stand-alone monitoring system, or it can be integrated into a larger system to automatically trigger responses to changing environments or problematic situations.

SSVEP recognition using common feature analysis in brain-computer interface.

PubMed

Zhang, Yu; Zhou, Guoxu; Jin, Jing; Wang, Xingyu; Cichocki, Andrzej

2015-04-15

Canonical correlation analysis (CCA) has been successfully applied to steady-state visual evoked potential (SSVEP) recognition for brain-computer interface (BCI) application. Although the CCA method outperforms the traditional power spectral density analysis through multi-channel detection, it requires additionally pre-constructed reference signals of sine-cosine waves. It is likely to encounter overfitting in using a short time window since the reference signals include no features from training data. We consider that a group of electroencephalogram (EEG) data trials recorded at a certain stimulus frequency on a same subject should share some common features that may bear the real SSVEP characteristics. This study therefore proposes a common feature analysis (CFA)-based method to exploit the latent common features as natural reference signals in using correlation analysis for SSVEP recognition. Good performance of the CFA method for SSVEP recognition is validated with EEG data recorded from ten healthy subjects, in contrast to CCA and a multiway extension of CCA (MCCA). Experimental results indicate that the CFA method significantly outperformed the CCA and the MCCA methods for SSVEP recognition in using a short time window (i.e., less than 1s). The superiority of the proposed CFA method suggests it is promising for the development of a real-time SSVEP-based BCI. Copyright © 2014 Elsevier B.V. All rights reserved.

Optical signal processing

NASA Technical Reports Server (NTRS)

Casasent, D.

1978-01-01

The article discusses several optical configurations used for signal processing. Electronic-to-optical transducers are outlined, noting fixed window transducers and moving window acousto-optic transducers. Folded spectrum techniques are considered, with reference to wideband RF signal analysis, fetal electroencephalogram analysis, engine vibration analysis, signal buried in noise, and spatial filtering. Various methods for radar signal processing are described, such as phased-array antennas, the optical processing of phased-array data, pulsed Doppler and FM radar systems, a multichannel one-dimensional optical correlator, correlations with long coded waveforms, and Doppler signal processing. Means for noncoherent optical signal processing are noted, including an optical correlator for speech recognition and a noncoherent optical correlator.

Response-related fMRI of veridical and false recognition of words.

PubMed

Heun, Reinhard; Jessen, Frank; Klose, Uwe; Erb, Michael; Granath, Dirk-Oliver; Grodd, Wolfgang

2004-02-01

Studies on the relation between local cerebral activation and retrieval success usually compared high and low performance conditions, and thus showed performance-related activation of different brain areas. Only a few studies directly compared signal intensities of different response categories during retrieval. During verbal recognition, we recently observed increased parieto-occipital activation related to false alarms. The present study intends to replicate and extend this observation by investigating common and differential activation by veridical and false recognition. Fifteen healthy volunteers performed a verbal recognition paradigm using 160 learned target and 160 new distractor words. The subjects had to indicate whether they had learned the word before or not. Echo-planar MRI of blood-oxygen-level-dependent signal changes was performed during this recognition task. Words were classified post hoc according to the subjects' responses, i.e. hits, false alarms, correct rejections and misses. Response-related fMRI-analysis was used to compare activation associated with the subjects' recognition success, i.e. signal intensities related to the presentation of words were compared by the above-mentioned four response types. During recognition, all word categories showed increased bilateral activation of the inferior frontal gyrus, the inferior temporal gyrus, the occipital lobe and the brainstem in comparison with the control condition. Hits and false alarms activated several areas including the left medial and lateral parieto-occipital cortex in comparison with subjectively unknown items, i.e. correct rejections and misses. Hits showed more pronounced activation in the medial, false alarms in the lateral parts of the left parieto-occipital cortex. Veridical and false recognition show common as well as different areas of cerebral activation in the left parieto-occipital lobe: increased activation of the medial parietal cortex by hits may correspond to true

Fifty years of progress in speech and speaker recognition

NASA Astrophysics Data System (ADS)

Furui, Sadaoki

2004-10-01

Speech and speaker recognition technology has made very significant progress in the past 50 years. The progress can be summarized by the following changes: (1) from template matching to corpus-base statistical modeling, e.g., HMM and n-grams, (2) from filter bank/spectral resonance to Cepstral features (Cepstrum + DCepstrum + DDCepstrum), (3) from heuristic time-normalization to DTW/DP matching, (4) from gdistanceh-based to likelihood-based methods, (5) from maximum likelihood to discriminative approach, e.g., MCE/GPD and MMI, (6) from isolated word to continuous speech recognition, (7) from small vocabulary to large vocabulary recognition, (8) from context-independent units to context-dependent units for recognition, (9) from clean speech to noisy/telephone speech recognition, (10) from single speaker to speaker-independent/adaptive recognition, (11) from monologue to dialogue/conversation recognition, (12) from read speech to spontaneous speech recognition, (13) from recognition to understanding, (14) from single-modality (audio signal only) to multi-modal (audio/visual) speech recognition, (15) from hardware recognizer to software recognizer, and (16) from no commercial application to many practical commercial applications. Most of these advances have taken place in both the fields of speech recognition and speaker recognition. The majority of technological changes have been directed toward the purpose of increasing robustness of recognition, including many other additional important techniques not noted above.

Motion-based signaling in sympatric species of Australian agamid lizards.

PubMed

Ramos, Jose A; Peters, Richard A

2017-08-01

Signaling species occurring in sympatry are often exposed to similar environmental constraints, so similar adaptations to enhance signal efficacy are expected. However, potentially opposing selective pressures might be present to ensure species recognition. Here, we analyzed the movement-based signals of two pairs of sympatric lizard species to consider how reliable communication is maintained while avoiding misidentification. Our novel approach allows us to quantify signal contrast with plant motion noise at any site we measure, including those utilized by other species. Ctenophorus caudicinctus and Gowidon longirostris differed in display complexity and motor pattern use. They also differed in overall morphology, but their signal contrast scores are strikingly similar. These results demonstrate similar adaptations to their shared environment while maintaining species recognition cues. In contrast, Ctenophorus fordi and Ctenophorus pictus are much closer in appearance, but C. pictus produces considerably higher signal contrast scores, which we suggest is attributable to the absence of territoriality in C. fordi. Taken together, our data provide evidence for adaptation to the local environment in movement-based signals, while also meeting species recognition requirements, but the selective pressure to deal with local conditions is mediated by signal function.

Transient Receptor Potential Channel 1 Deficiency Impairs Host Defense and Proinflammatory Responses to Bacterial Infection by Regulating Protein Kinase Cα Signaling.

PubMed

Zhou, Xikun; Ye, Yan; Sun, Yuyang; Li, Xuefeng; Wang, Wenxue; Privratsky, Breanna; Tan, Shirui; Zhou, Zongguang; Huang, Canhua; Wei, Yu-Quan; Birnbaumer, Lutz; Singh, Brij B; Wu, Min

2015-08-01

Transient receptor potential channel 1 (TRPC1) is a nonselective cation channel that is required for Ca(2+) homeostasis necessary for cellular functions. However, whether TRPC1 is involved in infectious disease remains unknown. Here, we report a novel function for TRPC1 in host defense against Gram-negative bacteria. TRPC1(-/-) mice exhibited decreased survival, severe lung injury, and systemic bacterial dissemination upon infection. Furthermore, silencing of TRPC1 showed decreased Ca(2+) entry, reduced proinflammatory cytokines, and lowered bacterial clearance. Importantly, TRPC1 functioned as an endogenous Ca(2+) entry channel critical for proinflammatory cytokine production in both alveolar macrophages and epithelial cells. We further identified that bacterium-mediated activation of TRPC1 was dependent on Toll-like receptor 4 (TLR4), which induced endoplasmic reticulum (ER) store depletion. After activation of phospholipase Cγ (PLC-γ), TRPC1 mediated Ca(2+) entry and triggered protein kinase Cα (PKCα) activity to facilitate nuclear translocation of NF-κB/Jun N-terminal protein kinase (JNK) and augment the proinflammatory response, leading to tissue damage and eventually mortality. These findings reveal that TRPC1 is required for host defense against bacterial infections through the TLR4-TRPC1-PKCα signaling circuit. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Single-Walled Carbon Nanotubes as Fluorescence Biosensors for Pathogen Recognition in Water Systems

DOE PAGES

Upadhyayula, Venkata K. K.; Ghoshroy, Soumitra; Nair, Vinod S.; ...

2008-01-01

Tmore » he possibility of using single-walled carbon nanotubes (SWCNs) aggregates as fluorescence sensors for pathogen recognition in drinking water treatment applications has been studied. Batch adsorption study is conducted to adsorb large concentrations of Staphylococcus aureus aureus SH 1000 and Escherichia coli pKV-11 on single-walled carbon nanotubes. Subsequently the immobilized bacteria are detected with confocal microscopy by coating the nanotubes with fluorescence emitting antibodies. he Freundlich adsorption equilibrium constant ( k ) for S.aureus and E.coli determined from batch adsorption study was found to be 9 × 10 8 and 2 × 10 8  ml/g, respectively. he visualization of bacterial cells adsorbed on fluorescently modified carbon nanotubes is also clearly seen. he results indicate that hydrophobic single-walled carbon nanotubes have excellent bacterial adsorption capacity and fluorescent detection capability. his is an important advancement in designing fluorescence biosensors for pathogen recognition in water systems.« less

Bacterial Serine/Threonine Protein Kinases in Host-Pathogen Interactions*

PubMed Central

Canova, Marc J.; Molle, Virginie

2014-01-01

In bacterial pathogenesis, monitoring and adapting to the dynamically changing environment in the host and an ability to disrupt host immune responses are critical. The virulence determinants of pathogenic bacteria include the sensor/signaling proteins of the serine/threonine protein kinase (STPK) family that have a dual role of sensing the environment and subverting specific host defense processes. STPKs can sense a wide range of signals and coordinate multiple cellular processes to mount an appropriate response. Here, we review some of the well studied bacterial STPKs that are essential virulence factors and that modify global host responses during infection. PMID:24554701

Bacterial serine/threonine protein kinases in host-pathogen interactions.

PubMed

Canova, Marc J; Molle, Virginie

2014-04-04

In bacterial pathogenesis, monitoring and adapting to the dynamically changing environment in the host and an ability to disrupt host immune responses are critical. The virulence determinants of pathogenic bacteria include the sensor/signaling proteins of the serine/threonine protein kinase (STPK) family that have a dual role of sensing the environment and subverting specific host defense processes. STPKs can sense a wide range of signals and coordinate multiple cellular processes to mount an appropriate response. Here, we review some of the well studied bacterial STPKs that are essential virulence factors and that modify global host responses during infection.

Paracrine signaling in a bacterium.

PubMed

López, Daniel; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

2009-07-15

Cellular differentiation is triggered by extracellular signals that cause target cells to adopt a particular fate. Differentiation in bacteria typically involves autocrine signaling in which all cells in the population produce and respond to the same signal. Here we present evidence for paracrine signaling in bacterial populations-some cells produce a signal to which only certain target cells respond. Biofilm formation in Bacillus involves two centrally important signaling molecules, ComX and surfactin. ComX triggers the production of surfactin. In turn, surfactin causes a subpopulation of cells to produce an extracellular matrix. Cells that produced surfactin were themselves unable to respond to it. Likewise, once surfactin-responsive cells commenced matrix production, they no longer responded to ComX and could not become surfactin producers. Insensitivity to ComX was the consequence of the extracellular matrix as mutant cells unable to make matrix responded to both ComX and surfactin. Our results demonstrate that extracellular signaling was unidirectional, with one subpopulation producing a signal and a different subpopulation responding to it. Paracrine signaling in a bacterial population ensures the maintenance, over generations, of particular cell types even in the presence of molecules that would otherwise cause those cells to differentiate into other cell types.

Toll like receptor 4: an important molecule in recognition and induction of appropriate immune responses against Chlamydia infection.

PubMed

Nosratababadi, Reza; Bagheri, Vahid; Zare-Bidaki, Mohammad; Hakimi, Hamid; Zainodini, Nahid; Kazemi Arababadi, Mohammad

2017-04-01

Chlamydia species are obligate intracellular pathogens causing different infectious diseases particularly asymptomatic genital infections and are also responsible for a wide range of complications. Previous studies showed that there are different immune responses to Chlamydia species and their infections are limited to some cases. Moreover, Chlamydia species are able to alter immune responses through modulating the expression of some immune system related molecules including cytokines. Toll like receptors (TLRs) belonge to pathogen recognition receptors (PRRs) and play vital roles in recognition of microbes and stimulation of appropriate immune responses. Therefore, it appears that TLRs may be considered as important sensors for recognition of Chlamydia and promotion of immune responses against these bacterial infections. Accordingly, TLR4 detects several microbial PAMPs such as bacterial lipopolysacharide (LPS) and subsequently activates transcription from pro-inflammatory cytokines in both MYD88 and TRIF pathways dependent manner. The purpose of this review is to provide the recent data about the status and major roles played by TLR4 in Chlamydia species recognition and promotion of immune responses against these infections and also the relationship between TLR4 activities and pathogenesis of Chlamydia infections. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evidence for a bacterial lipopolysaccharide-recognizing G-protein-coupled receptor in the bacterial engulfment by Entamoeba histolytica.

PubMed

Brewer, Matthew T; Agbedanu, Prince N; Zamanian, Mostafa; Day, Tim A; Carlson, Steve A

2013-11-01

Entamoeba histolytica is the causative agent of amoebic dysentery, a worldwide protozoal disease that results in approximately 100,000 deaths annually. The virulence of E. histolytica may be due to interactions with the host bacterial flora, whereby trophozoites engulf colonic bacteria as a nutrient source. The engulfment process depends on trophozoite recognition of bacterial epitopes that activate phagocytosis pathways. E. histolytica GPCR-1 (EhGPCR-1) was previously recognized as a putative G-protein-coupled receptor (GPCR) used by Entamoeba histolytica during phagocytosis. In the present study, we attempted to characterize EhGPCR-1 by using heterologous GPCR expression in Saccharomyces cerevisiae. We discovered that bacterial lipopolysaccharide (LPS) is an activator of EhGPCR-1 and that LPS stimulates EhGPCR-1 in a concentration-dependent manner. Additionally, we demonstrated that Entamoeba histolytica prefers to engulf bacteria with intact LPS and that this engulfment process is sensitive to suramin, which prevents the interactions of GPCRs and G-proteins. Thus, EhGPCR-1 is an LPS-recognizing GPCR that is a potential drug target for treatment of amoebiasis, especially considering the well-established drug targeting to GPCRs.

Modafinil improves methamphetamine-induced object recognition deficits and restores prefrontal cortex ERK signaling in mice.

PubMed

González, Betina; Raineri, Mariana; Cadet, Jean Lud; García-Rill, Edgar; Urbano, Francisco J; Bisagno, Veronica

2014-12-01

Chronic use of methamphetamine (METH) leads to long-lasting cognitive dysfunction in humans and in animal models. Modafinil is a wake-promoting compound approved for the treatment of sleeping disorders. It is also prescribed off label to treat METH dependence. In the present study, we investigated whether modafinil could improve cognitive deficits induced by sub-chronic METH treatment in mice by measuring visual retention in a Novel Object Recognition (NOR) task. After sub-chronic METH treatment (1 mg/kg, once a day for 7 days), mice performed the NOR task, which consisted of habituation to the object recognition arena (5 min a day, 3 consecutive days), training session (2 equal objects, 10 min, day 4), and a retention session (1 novel object, 5 min, day 5). One hour before the training session, mice were given a single dose of modafinil (30 or 90 mg/kg). METH-treated mice showed impairments in visual memory retention, evidenced by equal preference of familiar and novel objects during the retention session. The lower dose of modafinil (30 mg/kg) had no effect on visual retention scores in METH-treated mice, while the higher dose (90 mg/kg) rescued visual memory retention to control values. We also measured extracellular signal-regulated kinase (ERK) phosphorylation in medial prefrontal cortex (mPFC), hippocampus, and nucleus accumbens (NAc) of METH- and vehicle-treated mice that received modafinil 1 h before exposure to novel objects in the training session, compared to mice placed in the arena without objects. Elevated ERK phosphorylation was found in the mPFC of vehicle-treated mice, but not in METH-treated mice, exposed to objects. The lower dose of modafinil had no effect on ERK phosphorylation in METH-treated mice, while 90 mg/kg modafinil treatment restored the ERK phosphorylation induced by novelty in METH-treated mice to values comparable to controls. We found neither a novelty nor treatment effect on ERK phosphorylation in hippocampus or NAc of vehicle

Phosphotyrosine recognition domains: the typical, the atypical and the versatile

PubMed Central

2012-01-01

SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCδ and PKCθ C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases. PMID:23134684

Recall and recognition hypermnesia for Socratic stimuli.

PubMed

Kazén, Miguel; Solís-Macías, Víctor M

2016-01-01

In two experiments, we investigate hypermnesia, net memory improvements with repeated testing of the same material after a single study trial. In the first experiment, we found hypermnesia across three trials for the recall of word solutions to Socratic stimuli (dictionary-like definitions of concepts) replicating Erdelyi, Buschke, and Finkelstein and, for the first time using these materials, for their recognition. In the second experiment, we had two "yes/no" recognition groups, a Socratic stimuli group presented with concrete and abstract verbal materials and a word-only control group. Using signal detection measures, we found hypermnesia for concrete Socratic stimuli-and stable performance for abstract stimuli across three recognition tests. The control group showed memory decrements across tests. We interpret these findings with the alternative retrieval pathways (ARP) hypothesis, contrasting it with alternative theories of hypermnesia, such as depth of processing, generation and retrieve-recognise. We conclude that recognition hypermnesia for concrete Socratic stimuli is a reliable phenomenon, which we found in two experiments involving both forced-choice and yes/no recognition procedures.

Gut-derived commensal bacterial products inhibit liver dendritic cell maturation by stimulating hepatic interleukin-6/signal transducer and activator of transcription 3 activity.

PubMed

Lunz, John G; Specht, Susan M; Murase, Noriko; Isse, Kumiko; Demetris, Anthony J

2007-12-01

Intraorgan dendritic cells (DCs) monitor the environment and help translate triggers of innate immunity into adaptive immune responses. Liver-based DCs are continually exposed, via gut-derived portal venous blood, to potential antigens and bacterial products that can trigger innate immunity. However, somehow the liver avoids a state of perpetual inflammation and protects central immune organs from overstimulation. In this study, we tested the hypothesis that hepatic interleukin-6 (IL-6)/signal transducer and activator of transcription 3 (STAT3) activity increases the activation/maturation threshold of hepatic DCs toward innate immune signals. The results show that the liver nuclear STAT3 activity is significantly higher than that of other organs and is IL-6-dependent. Hepatic DCs in normal IL-6 wild-type (IL-6(+/+)) mice are phenotypically and functionally less mature than DCs from IL-6-deficient (IL-6(-/-)) or STAT3-inhibited IL-6(+/+) mice, as determined by surface marker expression, proinflammatory cytokine secretion, and allogeneic T-cell stimulation. IL-6(+/+) liver DCs produce IL-6 in response to exposure to lipopolysaccharide (LPS) and cytidine phosphate guanosine oligonucleotides (CpG) but are resistant to maturation compared with IL-6(-/-) liver DCs. Conversely, exogenous IL-6 inhibits LPS-induced IL-6(-/-) liver DC maturation. IL-6/STAT3 signaling influences the liver DC expression of toll-like receptor 9 and IL-1 receptor associated kinase-M. The depletion of gut commensal bacteria in IL-6(+/+) mice with oral antibiotics decreased portal blood endotoxin levels, lowered the expression of IL-6 and phospho-STAT3, and significantly increased liver DC maturation. Gut-derived bacterial products, by stimulating hepatic IL-6/STAT3 signaling, inhibit hepatic DC activation/maturation and thereby elevate the threshold needed for translating triggers of innate immunity into adaptive immune responses. Manipulating gut bacteria may therefore be an effective strategy

Access to Ribosomal Protein Rpl25p by the Signal Recognition Particle Is Required for Efficient Cotranslational Translocation

PubMed Central

Dalley, Jane A.; Selkirk, Alexander

2008-01-01

Targeting of proteins to the endoplasmic reticulum (ER) occurs cotranslationally necessitating the interaction of the signal recognition particle (SRP) and the translocon with the ribosome. Biochemical and structural studies implicate ribosomal protein Rpl25p as a major ribosome interaction site for both these factors. Here we characterize an RPL25GFP fusion, which behaves as a dominant mutant leading to defects in co- but not posttranslational translocation in vivo. In these cells, ribosomes still interact with ER membrane and the translocon, but are defective in binding SRP. Overexpression of SRP can restore ribosome binding of SRP, but only partially rescues growth and translocation defects. Our results indicate that Rpl25p plays a critical role in the recruitment of SRP to the ribosome. PMID:18448667

Carbon nanotubes as in vivo bacterial probes.

PubMed

Bardhan, Neelkanth M; Ghosh, Debadyuti; Belcher, Angela M

2014-09-17

With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F'-positive and F'-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F'-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

Carbon nanotubes as in vivo bacterial probes

NASA Astrophysics Data System (ADS)

Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

2014-09-01

With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F‧-positive and F‧-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F‧-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

Carbon Nanotubes as in vivo Bacterial Probes

PubMed Central

Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

2014-01-01

With the rise in antibiotic-resistant infections, noninvasive sensing of infectious diseases is increasingly important. Optical imaging, while safer and simpler, is less developed than other modalities like radioimaging; due to low availability of target-specific molecular probes. Here, we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F'-positive and F'-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F’-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4× enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08×, and higher signal amplification ~1.4×, compared to conventional dyes. We show the probe offers greater ~5.7× enhancement in imaging of S. aureus infective endocarditis. These biologically-functionalized, aqueous-dispersed, actively-targeted, modularly-tunable SWNT probes offer new avenues for exploration of deeply-buried infections. PMID:25230005

Feature Selection in Classification of Eye Movements Using Electrooculography for Activity Recognition

PubMed Central

Mala, S.; Latha, K.

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition. PMID:25574185

Feature selection in classification of eye movements using electrooculography for activity recognition.

PubMed

Mala, S; Latha, K

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition.

Visual environment recognition for robot path planning using template matched filters

NASA Astrophysics Data System (ADS)

Orozco-Rosas, Ulises; Picos, Kenia; Díaz-Ramírez, Víctor H.; Montiel, Oscar; Sepúlveda, Roberto

2017-08-01

A visual approach in environment recognition for robot navigation is proposed. This work includes a template matching filtering technique to detect obstacles and feasible paths using a single camera to sense a cluttered environment. In this problem statement, a robot can move from the start to the goal by choosing a single path between multiple possible ways. In order to generate an efficient and safe path for mobile robot navigation, the proposal employs a pseudo-bacterial potential field algorithm to derive optimal potential field functions using evolutionary computation. Simulation results are evaluated in synthetic and real scenes in terms of accuracy of environment recognition and efficiency of path planning computation.

Suppression of bacterial cell-cell signalling, biofilm formation and type III secretion system by citrus flavonoids.

PubMed

Vikram, A; Jayaprakasha, G K; Jesudhasan, P R; Pillai, S D; Patil, B S

2010-08-01

This study investigated the quorum sensing, biofilm and type three secretion system (TTSS) inhibitory properties of citrus flavonoids. Flavonoids were tested for their ability to inhibit quorum sensing using Vibrio harveyi reporter assay. Biofilm assays were carried out in 96-well plates. Inhibition of biofilm formation in Escherichia coli O157:H7 and V. harveyi by citrus flavonoids was measured. Furthermore, effect of naringenin on expression of V. harveyi TTSS was investigated by semi-quantitative PCR. Differential responses for different flavonoids were observed for different cell-cell signalling systems. Among the tested flavonoids, naringenin, kaempferol, quercetin and apigenin were effective antagonists of cell-cell signalling. Furthermore, these flavonoids suppressed the biofilm formation in V. harveyi and E. coli O157:H7. In addition, naringenin altered the expression of genes encoding TTSS in V. harveyi. The results of the study indicate a potential modulation of bacterial cell-cell communication, E. coli O157:H7 biofilm and V. harveyi virulence, by flavonoids especially naringenin, quercetin, sinensetin and apigenin. Among the tested flavonoids, naringenin emerged as potent and possibly a nonspecific inhibitor of autoinducer-mediated cell-cell signalling. Naringenin and other flavonoids are prominent secondary metabolites present in citrus species. Therefore, citrus, being a major source of some of these flavonoids and by virtue of widely consumed fruit, may modulate the intestinal microflora. Currently, a limited number of naturally occurring compounds have demonstrated their potential in inhibition of cell-cell communications; therefore, citrus flavonoids may be useful as lead compounds for the development of antipathogenic agents.

Anti-signal recognition particle autoantibody ELISA validation and clinical associations.

PubMed

Aggarwal, Rohit; Oddis, Chester V; Goudeau, Danielle; Fertig, Noreen; Metes, Ilinca; Stephens, Chad; Qi, Zengbiao; Koontz, Diane; Levesque, Marc C

2015-07-01

The aim of this study was to develop and validate a quantitative anti-signal recognition particle (SRP) autoantibody serum ELISA in patients with myositis and longitudinal association with myositis disease activity. We developed a serum ELISA using recombinant purified full-length human SRP coated on ELISA plates and a secondary antibody that bound human IgG to detect anti-SRP binding. Protein immunoprecipitation was used as the gold standard for the presence of anti-SRP. Serum samples from three groups were analysed: SRP(+) myositis subjects by immunoprecipitation, SRP(-) myositis subjects by immunoprecipitation and non-myositis controls. The ELISA's sensitivity, specificity, positive predictive value and negative predictive value were evaluated. Percentage agreement and test-retest reliability were assessed. Serial samples from seven SRP immunoprecipitation-positive subjects were also tested, along with serum muscle enzymes and manual muscle testing. Using immunoprecipitation, we identified 26 SRP(+) myositis patients and 77 SRP(-) controls (including 38 patients with necrotizing myopathy). Non-myositis control patients included SLE (n = 4) and SSc (n = 7) patients. Anti-SRP positivity by ELISA showed strong agreement (97.1%) with immunoprecipitation (κ = 0.94). The sensitivity, specificity, positive predictive value, and negative predictive value of the anti-SRP ELISA were 88, 100, 100 and 96, respectively. The area under the curve was 0.94, and test-retest reliability was strong (r = 0.91, P < 0.001). Serial samples showed that anti-SRP levels paralleled changes in muscle enzymes and manual muscle testing. We developed a quantitative ELISA for detecting serum anti-SRP autoantibodies and validated the assay in myositis. Longitudinal assessment of SRP levels by ELISA may be a useful biomarker for disease activity. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions

Prevention of bacterial foodborne disease using nanobiotechnology.

PubMed

Billington, Craig; Hudson, J Andrew; D'Sa, Elaine

2014-01-01

Foodborne disease is an important source of expense, morbidity, and mortality for society. Detection and control constitute significant components of the overall management of foodborne bacterial pathogens, and this review focuses on the use of nanosized biological entities and molecules to achieve these goals. There is an emphasis on the use of organisms called bacteriophages (phages: viruses that infect bacteria), which are increasingly being used in pathogen detection and biocontrol applications. Detection of pathogens in foods by conventional techniques is time-consuming and expensive, although it can also be sensitive and accurate. Nanobiotechnology is being used to decrease detection times and cost through the development of biosensors, exploiting specific cell-recognition properties of antibodies and phage proteins. Although sensitivity per test can be excellent (eg, the detection of one cell), the very small volumes tested mean that sensitivity per sample is less compelling. An ideal detection method needs to be inexpensive, sensitive, and accurate, but no approach yet achieves all three. For nanobiotechnology to displace existing methods (culture-based, antibody-based rapid methods, or those that detect amplified nucleic acid) it will need to focus on improving sensitivity. Although manufactured nonbiological nanoparticles have been used to kill bacterial cells, nanosized organisms called phages are increasingly finding favor in food safety applications. Phages are amenable to protein and nucleic acid labeling, and can be very specific, and the typical large "burst size" resulting from phage amplification can be harnessed to produce a rapid increase in signal to facilitate detection. There are now several commercially available phages for pathogen control, and many reports in the literature demonstrate efficacy against a number of foodborne pathogens on diverse foods. As a method for control of pathogens, nanobiotechnology is therefore flourishing.

2016: Signaling Breakthroughs of the Year.

PubMed

Adler, Elizabeth M

2017-01-03

Signaling breakthroughs of 2016 clustered mainly in the areas of neuroscience, immunology, and metabolism, with excursions into plant hormone signaling and bacterial manipulation of host signaling pathways. Perhaps reflecting the growing maturity of the discipline of cell signaling, many of this year's breakthroughs have implications for the pathogenesis or treatment of human disease. Copyright © 2017, American Association for the Advancement of Science.

Gram Positive Bacterial Superantigen Outside-In Signaling Causes Toxic Shock Syndrome

PubMed Central

Brosnahan, Amanda J.; Schlievert, Patrick M.

2011-01-01

Staphylococcus aureus and Streptococcus pyogenes (group A streptococci) are gram-positive pathogens capable of producing a variety of bacterial exotoxins known as superantigens. Superantigens interact with antigen-presenting cells (APCs) and T cells to induce T cell proliferation and massive cytokine production, which leads to fever, rash, capillary leak, and subsequent hypotension, the major symptoms of toxic shock syndrome. Both S. aureus and group A streptococci colonize mucosal surfaces, including the anterior nares and vagina for S. aureus, and the oropharynx and less commonly the vagina for group A streptococci. However, due to their abilities to secrete a variety of virulence factors, the organisms can also cause illnesses from the mucosa. This review provides an updated discussion of the biochemical and structural features of one group of secreted virulence factors, the staphylococcal and group A streptococcal superantigens, and their abilities to cause toxic shock syndrome from a mucosal surface. The main focus of this review, however, is the abilities of superantigens to induce cytokines and chemokines from epithelial cells, which has been linked to a dodecapeptide region that is relatively conserved among all superantigens and is distinct from the binding sites required for interactions with APCs and T cells. This phenomenon, termed outside-in signaling, acts to recruit adaptive immune cells to the submucosa, where the superantigens can then interact with those cells to initiate the final cytokine cascades that lead to toxic shock syndrome. PMID:21535475

Gram-positive bacterial superantigen outside-in signaling causes toxic shock syndrome.

PubMed

Brosnahan, Amanda J; Schlievert, Patrick M

2011-12-01

Staphylococcus aureus and Streptococcus pyogenes (group A streptococci) are Gram-positive pathogens capable of producing a variety of bacterial exotoxins known as superantigens. Superantigens interact with antigen-presenting cells (APCs) and T cells to induce T cell proliferation and massive cytokine production, which leads to fever, rash, capillary leak and subsequent hypotension, the major symptoms of toxic shock syndrome. Both S. aureus and group A streptococci colonize mucosal surfaces, including the anterior nares and vagina for S. aureus, and the oropharynx and less commonly the vagina for group A streptococci. However, due to their abilities to secrete a variety of virulence factors, the organisms can also cause illnesses from the mucosa. This review provides an updated discussion of the biochemical and structural features of one group of secreted virulence factors, the staphylococcal and group A streptococcal superantigens, and their abilities to cause toxic shock syndrome from a mucosal surface. The main focus of this review, however, is the abilities of superantigens to induce cytokines and chemokines from epithelial cells, which has been linked to a dodecapeptide region that is relatively conserved among all superantigens and is distinct from the binding sites required for interactions with APCs and T cells. This phenomenon, termed outside-in signaling, acts to recruit adaptive immune cells to the submucosa, where the superantigens can then interact with those cells to initiate the final cytokine cascades that lead to toxic shock syndrome. © 2011 The Authors Journal compilation © 2011 FEBS.

Selection of peptidoglycan-specific aptamers for bacterial cells identification.

PubMed

Ferreira, Iêda Mendes; de Souza Lacerda, Camila Maria; de Faria, Lígia Santana; Corrêa, Cristiane Rodrigues; de Andrade, Antero Silva Ribeiro

2014-12-01

Peptidoglycan is a highly complex and essential macromolecule of bacterial outer cell wall; it is a heteropolymer made up of linear glycan strands cross-linked by peptides. Peptidoglycan has a particular composition which makes it a possible target for specific bacterial recognition. Aptamers are single-stranded DNA or RNA oligonucleotides that bind to target molecules with high affinity and specificity. Aptamers can be labeled with different radioisotopes and possess several properties that make them suitable for molecular imaging. The purpose of this study was to obtain aptamers for use as radiopharmaceutical in bacterial infection diagnosis. Two aptamers (Antibac1 and Antibac2) against peptidoglycan were selected through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology. The dissociation constant (Kd) for Antibac1 was 0.415 + 0.047 μM and for Antibac2 was 1.261 + 0.280 μM. These aptamers labeled with (32)P showed high affinity for Staphylococcus aureus cells. The binding to S. aureus and Escherichia coli in vitro were significantly higher than for Candida albicans and human fibroblasts, demonstrating their specificity for bacterial cells. These results point Antibac1 and Antibac2 as promising tools for bacterial infections identification.

The chemical structure of DNA sequence signals for RNA transcription

NASA Technical Reports Server (NTRS)

George, D. G.; Dayhoff, M. O.

1982-01-01

The proposed recognition sites for RNA transcription for E. coli NRA polymerase, bacteriophage T7 RNA polymerase, and eukaryotic RNA polymerase Pol II are evaluated in the light of the requirements for efficient recognition. It is shown that although there is good experimental evidence that specific nucleic acid sequence patterns are involved in transcriptional regulation in bacteria and bacterial viruses, among the sequences now available, only in the case of the promoters recognized by bacteriophage T7 polymerase does it seem likely that the pattern is sufficient. It is concluded that the eukaryotic pattern that is investigated is not restrictive enough to serve as a recognition site.

Structural basis of host recognition and biofilm formation by Salmonella Saf pili

PubMed Central

2017-01-01

Pili are critical in host recognition, colonization and biofilm formation during bacterial infection. Here, we report the crystal structures of SafD-dsc and SafD-SafA-SafA (SafDAA-dsc) in Saf pili. Cell adherence assays show that SafD and SafA are both required for host recognition, suggesting a poly-adhesive mechanism for Saf pili. Moreover, the SafDAA-dsc structure, as well as SAXS characterization, reveals an unexpected inter-molecular oligomerization, prompting the investigation of Saf-driven self-association in biofilm formation. The bead/cell aggregation and biofilm formation assays are used to demonstrate the novel function of Saf pili. Structure-based mutants targeting the inter-molecular hydrogen bonds and complementary architecture/surfaces in SafDAA-dsc dimers significantly impaired the Saf self-association activity and biofilm formation. In summary, our results identify two novel functions of Saf pili: the poly-adhesive and self-associating activities. More importantly, Saf-Saf structures and functional characterizations help to define a pili-mediated inter-cellular oligomerizaiton mechanism for bacterial aggregation, colonization and ultimate biofilm formation. PMID:29125121

Quorum sensing is a language of chemical signals and plays an ecological role in algal-bacterial interactions

PubMed Central

Zhou, Jin; Lyu, Yihua; Richlen, Mindy; Anderson, Donald M.; Cai, Zhonghua

2017-01-01

Algae are ubiquitous in the marine environment, and the ways in which they interact with bacteria are of particular interest in marine ecology field. The interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape microbial diversity. Although algal-bacterial interactions are well known and studied, information regarding the chemical-ecological role of this relationship remains limited, particularly with respect to quorum sensing (QS), which is a system of stimuli and response correlated to population density. In the microbial biosphere, QS is pivotal in driving community structure and regulating behavioral ecology, including biofilm formation, virulence, antibiotic resistance, swarming motility, and secondary metabolite production. Many marine habitats, such as the phycosphere, harbour diverse populations of microorganisms and various signal languages (such as QS-based autoinducers). QS-mediated interactions widely influence algal-bacterial symbiotic relationships, which in turn determine community organization, population structure, and ecosystem functioning. Understanding infochemicals-mediated ecological processes may shed light on the symbiotic interactions between algae host and associated microbes. In this review, we summarize current achievements about how QS modulates microbial behavior, affects symbiotic relationships, and regulates phytoplankton chemical ecological processes. Additionally, we present an overview of QS-modulated co-evolutionary relationships between algae and bacterioplankton, and consider the potential applications and future perspectives of QS. PMID:28966438

Toll-like receptor 4 mediates inflammatory signaling by bacterial lipopolysaccharide in human hepatic stellate cells.

PubMed

Paik, Yong-Han; Schwabe, Robert F; Bataller, Ramón; Russo, Maria P; Jobin, Christian; Brenner, David A

2003-05-01

Bacterial lipopolysaccharide (LPS) stimulates Kupffer cells and participates in the pathogenesis of alcohol-induced liver injury. However, it is unknown whether LPS directly affects hepatic stellate cells (HSCs), the main fibrogenic cell type in the injured liver. This study characterizes LPS-induced signal transduction and proinflammatory gene expression in activated human HSCs. Culture-activated HSCs and HSCs isolated from patients with hepatitis C virus-induced cirrhosis express LPS-associated signaling molecules, including CD14, toll-like receptor (TLR) 4, and MD2. Stimulation of culture-activated HSCs with LPS results in a rapid and marked activation of NF-kappaB, as assessed by in vitro kinase assays for IkappaB kinase (IKK), IkappaBalpha steady-state levels, p65 nuclear translocation, NF-kappaB-dependent luciferase reporter gene assays, and electrophoretic mobility shift assays. Lipid A induces NF-kappaB activation in a similar manner. Both LPS- and lipid A-induced NF-kappaB activation is blocked by preincubation with either anti-TLR4 blocking antibody (HTA125) or Polymyxin B. Lipid A induces NF-kappaB activation in HSCs from TLR4-sufficient (C3H/OuJ) mice but not from TLR4-deficient (C3H/HeJ) mice. LPS also activates c-Jun N-terminal kinase (JNK), as assessed by in vitro kinase assays. LPS up-regulates IL-8 and MCP-1 gene expression and secretion. LPS-induced IL-8 secretion is completely inhibited by the IkappaB super repressor (Ad5IkappaB) and partially inhibited by a specific JNK inhibitor, SP600125. LPS also up-regulates cell surface expression of ICAM-1 and VCAM-1. In conclusion, human activated HSCs utilize components of TLR4 signal transduction cascade to stimulate NF-kappaB and JNK and up-regulate chemokines and adhesion molecules. Thus, HSCs are a potential mediator of LPS-induced liver injury.

The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among-population signal diversity?

PubMed Central

Van Damme, Raoul

2018-01-01

Animal signalling structures are amongst the most variable characteristics, as they are subjected to a diversity of selection pressures. A well-known example of a diverse signalling system in the animal kingdom is the dewlap of Anolis lizards. Dewlap characteristics can vary remarkably among and within species, and also between sexes. Although a considerable amount of studies have attempted to disentangle the functional significance of the staggering dewlap diversity in Anolis, the underlying evolutionary processes remain elusive. In this study, we focus on the contribution of biotic selective pressures in shaping geographic variation in dewlap design (size, colour, and pattern) and dewlap display behaviour at the intraspecific level. Notably, we have tried to replicate and extend previously reported results hereof in both sexes of the brown anole lizard (Anolis sagrei). To do this, we assembled a dataset consisting of 17 A. sagrei heterogeneous island populations from the Caribbean and specifically tested whether predation pressure, sexual selection, or species recognition could explain interpopulational variation in an array of dewlap characteristics. Our findings show that in neither males nor females estimates of predation pressure (island size, tail break frequency, model attack rate, presence of predatory Leiocephalus lizards) or sexual selection (sexual size dimorphism) could explain variation in dewlap design. We did find that A. sagrei males from larger islands showed higher dewlap display intensities than males from smaller islands, but the direct connection with predation pressure remains ambiguous and demands further investigation. Last, we could show indirect support for species recognition only in males, as they are more likely to have a ‘spotted’ dewlap pattern when co-occurring with a higher number of syntopic Anolis species. In conclusion, we found overall limited support for the idea that the extensive interpopulational variability in dewlap

Mechanism of pathogen recognition by human dectin-2.

PubMed

Feinberg, Hadar; Jégouzo, Sabine A F; Rex, Maximus J; Drickamer, Kurt; Weis, William I; Taylor, Maureen E

2017-08-11

Dectin-2, a C-type lectin on macrophages and other cells of the innate immune system, functions in response to pathogens, particularly fungi. The carbohydrate-recognition domain (CRD) in dectin-2 is linked to a transmembrane sequence that interacts with the common Fc receptor γ subunit to initiate immune signaling. The molecular mechanism by which dectin-2 selectively binds to pathogens has been investigated by characterizing the CRD expressed in a bacterial system. Competition binding studies indicated that the CRD binds to monosaccharides with modest affinity and that affinity was greatly enhanced for mannose-linked α1-2 or α1-4 to a second mannose residue. Glycan array analysis confirmed selective binding of the CRD to glycans that contain Manα1-2Man epitopes. Crystals of the CRD in complex with a mammalian-type high-mannose Man 9 GlcNAc 2 oligosaccharide exhibited interaction with Manα1-2Man on two different termini of the glycan, with the reducing-end mannose residue ligated to Ca 2+ in a primary binding site and the nonreducing terminal mannose residue occupying an adjacent secondary site. Comparison of the binding sites in DC-SIGN and langerin, two other pathogen-binding receptors of the innate immune system, revealed why these two binding sites accommodate only terminal Manα1-2Man structures, whereas dectin-2 can bind Manα1-2Man in internal positions in mannans and other polysaccharides. The specificity and geometry of the dectin-2-binding site provide the molecular mechanism for binding of dectin-2 to fungal mannans and also to bacterial lipopolysaccharides, capsular polysaccharides, and lipoarabinomannans that contain the Manα1-2Man disaccharide unit. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

A PP2A-B55 recognition signal controls substrate dephosphorylation kinetics during mitotic exit

PubMed Central

Cundell, Michael J.; Holder, James

2016-01-01

PP2A-B55 is one of the major phosphatases regulating cell division. Despite its importance for temporal control during mitotic exit, how B55 substrates are recognized and differentially dephosphorylated is unclear. Using phosphoproteomics combined with kinetic modeling to extract B55-dependent rate constants, we have systematically identified B55 substrates and assigned their temporal order in mitotic exit. These substrates share a bipartite polybasic recognition determinant (BPR) flanking a Cdk1 phosphorylation site. Experiments and modeling show that dephosphorylation rate is encoded into B55 substrates, including its inhibitor ENSA, by cooperative action of basic residues within the BPR. A complementary acidic surface on B55 decodes this signal, supporting a cooperative electrostatic mechanism for substrate selection. A further level of specificity is encoded into B55 substrates because B55 displays selectivity for phosphothreonine. These simple biochemical properties, combined with feedback control of B55 activity by the phosphoserine-containing substrate/inhibitor ENSA, can help explain the temporal sequence of events during exit from mitosis. PMID:27551054

Isolation of bacterial metabolites as natural inducers for larval settlement in the marine polychaete Hydroides elegans (Haswell).

PubMed

Harder, Tilmann; Lau, Stanley Chun Kwan; Dahms, Hans-Uwe; Qian, Pei-Yuan

2002-10-01

The bacterial component of marine biofilms plays an important role in the induction of larval settlement in the polychaete Hydroides elegans. In this study, we provide experimental evidence that bacterial metabolites comprise the chemical signal for larval settlement. Bacteria were isolated from biofilms, purified and cultured according to standard procedures. Bacterial metabolites were isolated from spent culture broth by chloroform extraction as well as by closed-loop stripping and adsorption of volatile components on surface-modified silica gel. A pronounced biological activity was exclusively observed when concentrated metabolites were adsorbed on activated charcoal. Larvae did not respond to waterbome metabolites when prevented from contacting the bacterial film surface. These results indicate that an association of the chemical signal with a sorbent-like substratum may be an essential cofactor for the expression of biological activity. The functional role of bacterial exopolymers as an adsorptive matrix for larval settlement signals is discussed.

De Novo Transcriptome Analysis Shows That SAV-3 Infection Upregulates Pattern Recognition Receptors of the Endosomal Toll-Like and RIG-I-Like Receptor Signaling Pathways in Macrophage/Dendritic Like TO-Cells.

PubMed

Xu, Cheng; Evensen, Øystein; Munang'andu, Hetron

2016-04-21

A fundamental step in cellular defense mechanisms is the recognition of "danger signals" made of conserved pathogen associated molecular patterns (PAMPs) expressed by invading pathogens, by host cell germ line coded pattern recognition receptors (PRRs). In this study, we used RNA-seq and the Kyoto encyclopedia of genes and genomes (KEGG) to identify PRRs together with the network pathway of differentially expressed genes (DEGs) that recognize salmonid alphavirus subtype 3 (SAV-3) infection in macrophage/dendritic like TO-cells derived from Atlantic salmon (Salmo salar L) headkidney leukocytes. Our findings show that recognition of SAV-3 in TO-cells was restricted to endosomal Toll-like receptors (TLRs) 3 and 8 together with RIG-I-like receptors (RLRs) and not the nucleotide-binding oligomerization domain-like receptors NOD-like receptor (NLRs) genes. Among the RLRs, upregulated genes included the retinoic acid inducible gene I (RIG-I), melanoma differentiation association 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2). The study points to possible involvement of the tripartite motif containing 25 (TRIM25) and mitochondrial antiviral signaling protein (MAVS) in modulating RIG-I signaling being the first report that links these genes to the RLR pathway in SAV-3 infection in TO-cells. Downstream signaling suggests that both the TLR and RLR pathways use interferon (IFN) regulatory factors (IRFs) 3 and 7 to produce IFN-a2. The validity of RNA-seq data generated in this study was confirmed by quantitative real time qRT-PCR showing that genes up- or downregulated by RNA-seq were also up- or downregulated by RT-PCR. Overall, this study shows that de novo transcriptome assembly identify key receptors of the TLR and RLR sensors engaged in host pathogen interaction at cellular level. We envisage that data presented here can open a road map for future intervention strategies in SAV infection of salmon.

Recognition intent and visual word recognition.

PubMed

Wang, Man-Ying; Ching, Chi-Le

2009-03-01

This study adopted a change detection task to investigate whether and how recognition intent affects the construction of orthographic representation in visual word recognition. Chinese readers (Experiment 1-1) and nonreaders (Experiment 1-2) detected color changes in radical components of Chinese characters. Explicit recognition demand was imposed in Experiment 2 by an additional recognition task. When the recognition was implicit, a bias favoring the radical location informative of character identity was found in Chinese readers (Experiment 1-1), but not nonreaders (Experiment 1-2). With explicit recognition demands, the effect of radical location interacted with radical function and word frequency (Experiment 2). An estimate of identification performance under implicit recognition was derived in Experiment 3. These findings reflect the joint influence of recognition intent and orthographic regularity in shaping readers' orthographic representation. The implication for the role of visual attention in word recognition was also discussed.

ReliefF-Based EEG Sensor Selection Methods for Emotion Recognition.

PubMed

Zhang, Jianhai; Chen, Ming; Zhao, Shaokai; Hu, Sanqing; Shi, Zhiguo; Cao, Yu

2016-09-22

Electroencephalogram (EEG) signals recorded from sensor electrodes on the scalp can directly detect the brain dynamics in response to different emotional states. Emotion recognition from EEG signals has attracted broad attention, partly due to the rapid development of wearable computing and the needs of a more immersive human-computer interface (HCI) environment. To improve the recognition performance, multi-channel EEG signals are usually used. A large set of EEG sensor channels will add to the computational complexity and cause users inconvenience. ReliefF-based channel selection methods were systematically investigated for EEG-based emotion recognition on a database for emotion analysis using physiological signals (DEAP). Three strategies were employed to select the best channels in classifying four emotional states (joy, fear, sadness and relaxation). Furthermore, support vector machine (SVM) was used as a classifier to validate the performance of the channel selection results. The experimental results showed the effectiveness of our methods and the comparison with the similar strategies, based on the F-score, was given. Strategies to evaluate a channel as a unity gave better performance in channel reduction with an acceptable loss of accuracy. In the third strategy, after adjusting channels' weights according to their contribution to the classification accuracy, the number of channels was reduced to eight with a slight loss of accuracy (58.51% ± 10.05% versus the best classification accuracy 59.13% ± 11.00% using 19 channels). In addition, the study of selecting subject-independent channels, related to emotion processing, was also implemented. The sensors, selected subject-independently from frontal, parietal lobes, have been identified to provide more discriminative information associated with emotion processing, and are distributed symmetrically over the scalp, which is consistent with the existing literature. The results will make a contribution to the

Manipulation of host membranes by bacterial effectors.

PubMed

Ham, Hyeilin; Sreelatha, Anju; Orth, Kim

2011-07-18

Bacterial pathogens interact with host membranes to trigger a wide range of cellular processes during the course of infection. These processes include alterations to the dynamics between the plasma membrane and the actin cytoskeleton, and subversion of the membrane-associated pathways involved in vesicle trafficking. Such changes facilitate the entry and replication of the pathogen, and prevent its phagocytosis and degradation. In this Review, we describe the manipulation of host membranes by numerous bacterial effectors that target phosphoinositide metabolism, GTPase signalling and autophagy.

Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.

PubMed

Han, S; Arvai, A S; Clancy, S B; Tainer, J A

2001-01-05

Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors

EMG-based speech recognition using hidden markov models with global control variables.

PubMed

Lee, Ki-Seung

2008-03-01

It is well known that a strong relationship exists between human voices and the movement of articulatory facial muscles. In this paper, we utilize this knowledge to implement an automatic speech recognition scheme which uses solely surface electromyogram (EMG) signals. The sequence of EMG signals for each word is modelled by a hidden Markov model (HMM) framework. The main objective of the work involves building a model for state observation density when multichannel observation sequences are given. The proposed model reflects the dependencies between each of the EMG signals, which are described by introducing a global control variable. We also develop an efficient model training method, based on a maximum likelihood criterion. In a preliminary study, 60 isolated words were used as recognition variables. EMG signals were acquired from three articulatory facial muscles. The findings indicate that such a system may have the capacity to recognize speech signals with an accuracy of up to 87.07%, which is superior to the independent probabilistic model.

Time and timing in the acoustic recognition system of crickets

PubMed Central

Hennig, R. Matthias; Heller, Klaus-Gerhard; Clemens, Jan

2014-01-01

The songs of many insects exhibit precise timing as the result of repetitive and stereotyped subunits on several time scales. As these signals encode the identity of a species, time and timing are important for the recognition system that analyzes these signals. Crickets are a prominent example as their songs are built from sound pulses that are broadcast in a long trill or as a chirped song. This pattern appears to be analyzed on two timescales, short and long. Recent evidence suggests that song recognition in crickets relies on two computations with respect to time; a short linear-nonlinear (LN) model that operates as a filter for pulse rate and a longer integration time window for monitoring song energy over time. Therefore, there is a twofold role for timing. A filter for pulse rate shows differentiating properties for which the specific timing of excitation and inhibition is important. For an integrator, however, the duration of the time window is more important than the precise timing of events. Here, we first review evidence for the role of LN-models and integration time windows for song recognition in crickets. We then parameterize the filter part by Gabor functions and explore the effects of duration, frequency, phase, and offset as these will correspond to differently timed patterns of excitation and inhibition. These filter properties were compared with known preference functions of crickets and katydids. In a comparative approach, the power for song discrimination by LN-models was tested with the songs of over 100 cricket species. It is demonstrated how the acoustic signals of crickets occupy a simple 2-dimensional space for song recognition that arises from timing, described by a Gabor function, and time, the integration window. Finally, we discuss the evolution of recognition systems in insects based on simple sensory computations. PMID:25161622

Ionotropic receptors signal host recognition in the salmon louse (Lepeophtheirus salmonis, Copepoda).

PubMed

Komisarczuk, Anna Z; Grotmol, Sindre; Nilsen, Frank

2017-01-01

A remarkable feature of many parasites is a high degree of host specificity but the mechanisms behind are poorly understood. A major challenge for parasites is to identify and infect a suitable host. Many species show a high degree of host specificity, being able to survive only on one or a few related host species. To facilitate transmission, parasite's behavior and reproduction has been fine tuned to maximize the likelihood of infection of a suitable host. For some species chemical cues that trigger or attract the parasite in question have been identified but how metazoan parasites themselves receive these signals remains unknown. In the present study we show that ionotropic receptors (IRs) in the salmon louse are likely responsible for identification of a specific host. By using RNAi to knock down the expression level of different co-receptors, a significant change of infectivity and settlement of lice larvae was achieved on Atlantic salmon. More remarkably, knock down of the IRs changed the host specificity of the salmon louse and lice larvae settled at a significant rate on host that the wild type lice rejected within minutes. To our knowledge, this has never before been demonstrated for any metazoan parasite. Our results show that the parasites are able to identify the host quickly upon settlement, settle and initiate the parasitic life style if they are on the right host. This novel discovery opens up for utilizing the host recognition system for future parasite control.

Ionotropic receptors signal host recognition in the salmon louse (Lepeophtheirus salmonis, Copepoda)

PubMed Central

Grotmol, Sindre; Nilsen, Frank

2017-01-01

A remarkable feature of many parasites is a high degree of host specificity but the mechanisms behind are poorly understood. A major challenge for parasites is to identify and infect a suitable host. Many species show a high degree of host specificity, being able to survive only on one or a few related host species. To facilitate transmission, parasite’s behavior and reproduction has been fine tuned to maximize the likelihood of infection of a suitable host. For some species chemical cues that trigger or attract the parasite in question have been identified but how metazoan parasites themselves receive these signals remains unknown. In the present study we show that ionotropic receptors (IRs) in the salmon louse are likely responsible for identification of a specific host. By using RNAi to knock down the expression level of different co-receptors, a significant change of infectivity and settlement of lice larvae was achieved on Atlantic salmon. More remarkably, knock down of the IRs changed the host specificity of the salmon louse and lice larvae settled at a significant rate on host that the wild type lice rejected within minutes. To our knowledge, this has never before been demonstrated for any metazoan parasite. Our results show that the parasites are able to identify the host quickly upon settlement, settle and initiate the parasitic life style if they are on the right host. This novel discovery opens up for utilizing the host recognition system for future parasite control. PMID:28582411

Bacterial RNA induces myocyte cellular dysfunction through the activation of PKR

PubMed Central

Bleiblo, Farag; Michael, Paul; Brabant, Danielle; Ramana, Chilakamarti V.; Tai, TC; Saleh, Mazen; Parrillo, Joseph E.; Kumar, Anand

2012-01-01

Severe sepsis and the ensuing septic shock are serious life threatening conditions. These diseases are triggered by the host's over exuberant systemic response to the infecting pathogen. Several surveillance mechanisms have evolved to discriminate self from foreign RNA and accordingly trigger effective cellular responses to target the pathogenic threats. The RNA-dependent protein kinase (PKR) is a key component of the cytoplasmic RNA sensors involved in the recognition of viral double-stranded RNA (dsRNA). Here, we identify bacterial RNA as a distinct pathogenic pattern recognized by PKR. Our results indicate that natural RNA derived from bacteria directly binds to and activates PKR. We further show that bacterial RNA induces human cardiac myocyte apoptosis and identify the requirement for PKR in mediating this response. In addition to bacterial immunity, the results presented here may also have implications in cardiac pathophysiology. PMID:22833816

Prokaryotic RNA Associated to Bacterial Viability Induces Polymorphonuclear Neutrophil Activation.

PubMed

Rodriguez-Rodrigues, Nahuel; Castillo, Luis A; Landoni, Verónica I; Martire-Greco, Daiana; Milillo, M Ayelén; Barrionuevo, Paula; Fernández, Gabriela C

2017-01-01

Polymorphonuclear neutrophils (PMN) are the first cellular line of antibacterial host defense. They sense pathogens through recognition of pathogen-associated molecular patterns (PAMPs) by innate pattern recognition receptors, such as Toll-like receptors (TLR). The aim of this study was to investigate whether PMN sense bacterial viability and explore which viability factor could be involved in this phenomenon. For this purpose, different functions were evaluated in isolated human PMN using live Escherichia coli (Ec) and heat-killed Ec (HK-Ec). We found that bacterial viability was indispensable to induce PMN activation, as measured by forward-scatter (FSC) increase, CD11b surface expression, chemotaxis, reactive oxygen species (ROS) generation and neutrophil extracellular trap (NET) formation. As uncapped non-polyadenylated prokaryotic mRNA has been recognized as a PAMP associated to bacterial viability by macrophages and dendritic cells, total prokaryotic RNA (pRNA) from live Ec was purified and used as a stimulus for PMN. pRNA triggered similar responses to those observed with live bacteria. No RNA could be isolated from HK-Ec, explaining the lack of effect of dead bacteria. Moreover, the supernatant of dead bacteria was able to induce PMN activation, and this was associated with the presence of pRNA in this supernatant, which is released in the killing process. The induction of bactericidal functions (ROS and NETosis) by pRNA were abolished when the supernatant of dead bacteria or isolated pRNA were treated with RNAse. Moreover, endocytosis was necessary for pRNA-induced ROS generation and NETosis, and priming was required for the induction of pRNA-induced ROS in whole blood. However, responses related to movement and degranulation (FSC increase, CD11b up-regulation, and chemotaxis) were still triggered when pRNA was digested with RNase, and were not dependent on pRNA endocytosis or PMN priming. In conclusion, our results indicate that PMN sense live bacteria

Prokaryotic RNA Associated to Bacterial Viability Induces Polymorphonuclear Neutrophil Activation

PubMed Central

Rodriguez-Rodrigues, Nahuel; Castillo, Luis A.; Landoni, Verónica I.; Martire-Greco, Daiana; Milillo, M. Ayelén; Barrionuevo, Paula; Fernández, Gabriela C.

2017-01-01

Polymorphonuclear neutrophils (PMN) are the first cellular line of antibacterial host defense. They sense pathogens through recognition of pathogen-associated molecular patterns (PAMPs) by innate pattern recognition receptors, such as Toll-like receptors (TLR). The aim of this study was to investigate whether PMN sense bacterial viability and explore which viability factor could be involved in this phenomenon. For this purpose, different functions were evaluated in isolated human PMN using live Escherichia coli (Ec) and heat-killed Ec (HK-Ec). We found that bacterial viability was indispensable to induce PMN activation, as measured by forward-scatter (FSC) increase, CD11b surface expression, chemotaxis, reactive oxygen species (ROS) generation and neutrophil extracellular trap (NET) formation. As uncapped non-polyadenylated prokaryotic mRNA has been recognized as a PAMP associated to bacterial viability by macrophages and dendritic cells, total prokaryotic RNA (pRNA) from live Ec was purified and used as a stimulus for PMN. pRNA triggered similar responses to those observed with live bacteria. No RNA could be isolated from HK-Ec, explaining the lack of effect of dead bacteria. Moreover, the supernatant of dead bacteria was able to induce PMN activation, and this was associated with the presence of pRNA in this supernatant, which is released in the killing process. The induction of bactericidal functions (ROS and NETosis) by pRNA were abolished when the supernatant of dead bacteria or isolated pRNA were treated with RNAse. Moreover, endocytosis was necessary for pRNA-induced ROS generation and NETosis, and priming was required for the induction of pRNA-induced ROS in whole blood. However, responses related to movement and degranulation (FSC increase, CD11b up-regulation, and chemotaxis) were still triggered when pRNA was digested with RNase, and were not dependent on pRNA endocytosis or PMN priming. In conclusion, our results indicate that PMN sense live bacteria

Random Deep Belief Networks for Recognizing Emotions from Speech Signals.

PubMed

Wen, Guihua; Li, Huihui; Huang, Jubing; Li, Danyang; Xun, Eryang

2017-01-01

Now the human emotions can be recognized from speech signals using machine learning methods; however, they are challenged by the lower recognition accuracies in real applications due to lack of the rich representation ability. Deep belief networks (DBN) can automatically discover the multiple levels of representations in speech signals. To make full of its advantages, this paper presents an ensemble of random deep belief networks (RDBN) method for speech emotion recognition. It firstly extracts the low level features of the input speech signal and then applies them to construct lots of random subspaces. Each random subspace is then provided for DBN to yield the higher level features as the input of the classifier to output an emotion label. All outputted emotion labels are then fused through the majority voting to decide the final emotion label for the input speech signal. The conducted experimental results on benchmark speech emotion databases show that RDBN has better accuracy than the compared methods for speech emotion recognition.

Random Deep Belief Networks for Recognizing Emotions from Speech Signals

PubMed Central

Li, Huihui; Huang, Jubing; Li, Danyang; Xun, Eryang

2017-01-01

Now the human emotions can be recognized from speech signals using machine learning methods; however, they are challenged by the lower recognition accuracies in real applications due to lack of the rich representation ability. Deep belief networks (DBN) can automatically discover the multiple levels of representations in speech signals. To make full of its advantages, this paper presents an ensemble of random deep belief networks (RDBN) method for speech emotion recognition. It firstly extracts the low level features of the input speech signal and then applies them to construct lots of random subspaces. Each random subspace is then provided for DBN to yield the higher level features as the input of the classifier to output an emotion label. All outputted emotion labels are then fused through the majority voting to decide the final emotion label for the input speech signal. The conducted experimental results on benchmark speech emotion databases show that RDBN has better accuracy than the compared methods for speech emotion recognition. PMID:28356908

Speech Recognition in Noise by Children with and without Dyslexia: How is it Related to Reading?

PubMed

Nittrouer, Susan; Krieg, Letitia M; Lowenstein, Joanna H

2018-06-01

Developmental dyslexia is commonly viewed as a phonological deficit that makes it difficult to decode written language. But children with dyslexia typically exhibit other problems, as well, including poor speech recognition in noise. The purpose of this study was to examine whether the speech-in-noise problems of children with dyslexia are related to their reading problems, and if so, if a common underlying factor might explain both. The specific hypothesis examined was that a spectral processing disorder results in these children receiving smeared signals, which could explain both the diminished sensitivity to phonological structure - leading to reading problems - and the speech recognition in noise difficulties. The alternative hypothesis tested in this study was that children with dyslexia simply have broadly based language deficits. Ninety-seven children between the ages of 7 years; 10 months and 12 years; 9 months participated: 46 with dyslexia and 51 without dyslexia. Children were tested on two dependent measures: word reading and recognition in noise with two types of sentence materials: as unprocessed (UP) signals, and as spectrally smeared (SM) signals. Data were collected for four predictor variables: phonological awareness, vocabulary, grammatical knowledge, and digit span. Children with dyslexia showed deficits on both dependent and all predictor variables. Their scores for speech recognition in noise were poorer than those of children without dyslexia for both the UP and SM signals, but by equivalent amounts across signal conditions indicating that they were not disproportionately hindered by spectral distortion. Correlation analyses on scores from children with dyslexia showed that reading ability and speech-in-noise recognition were only mildly correlated, and each skill was related to different underlying abilities. No substantial evidence was found to support the suggestion that the reading and speech recognition in noise problems of children with

Bacterial Chemotaxis: The Early Years of Molecular Studies

PubMed Central

Hazelbauer, Gerald L.

2014-01-01

This review focuses on the early years of molecular studies of bacterial chemotaxis and motility, beginning in the 1960s with Julius Adler's pioneering work. It describes key observations that established the field and made bacterial chemotaxis a paradigm for the molecular understanding of biological signaling. Consideration of those early years includes aspects of science seldom described in journals: the accidental findings, personal interactions, and scientific culture that often drive scientific progress. PMID:22994495

A real time mobile-based face recognition with fisherface methods

NASA Astrophysics Data System (ADS)

Arisandi, D.; Syahputra, M. F.; Putri, I. L.; Purnamawati, S.; Rahmat, R. F.; Sari, P. P.

2018-03-01

Face Recognition is a field research in Computer Vision that study about learning face and determine the identity of the face from a picture sent to the system. By utilizing this face recognition technology, learning process about people’s identity between students in a university will become simpler. With this technology, student won’t need to browse student directory in university’s server site and look for the person with certain face trait. To obtain this goal, face recognition application use image processing methods consist of two phase, pre-processing phase and recognition phase. In pre-processing phase, system will process input image into the best image for recognition phase. Purpose of this pre-processing phase is to reduce noise and increase signal in image. Next, to recognize face phase, we use Fisherface Methods. This methods is chosen because of its advantage that would help system of its limited data. Therefore from experiment the accuracy of face recognition using fisherface is 90%.

Nitric oxide functions as a signal in plant disease resistance.

PubMed

Delledonne, M; Xia, Y; Dixon, R A; Lamb, C

1998-08-06

Recognition of an avirulent pathogen triggers the rapid production of the reactive oxygen intermediates superoxide (O2-) and hydrogen peroxide (H2O2). This oxidative burst drives crosslinking of the cell wall, induces several plant genes involved in cellular protection and defence, and is necessary for the initiation of host cell death in the hypersensitive disease-resistance response. However, this burst is not enough to support a strong disease-resistance response. Here we show that nitric oxide, which acts as a signal in the immune, nervous and vascular systems, potentiates the induction of hypersensitive cell death in soybean cells by reactive oxygen intermediates and functions independently of such intermediates to induce genes for the synthesis of protective natural products. Moreover, inhibitors of nitric oxide synthesis compromise the hypersensitive disease-resistance response of Arabidopsis leaves to Pseudomonas syringae, promoting disease and bacterial growth. We conclude that nitric oxide plays a key role in disease resistance in plants.

Galectin-9 Signaling through TIM-3 Is Involved in Neutrophil-Mediated Gram-Negative Bacterial Killing: An Effect Abrogated within the Cystic Fibrosis Lung

PubMed Central

Vega-Carrascal, Isabel; Bergin, David A.; McElvaney, Oliver J.; McCarthy, Cormac; Banville, Nessa; Pohl, Kerstin; Hirashima, Mitsuomi; Kuchroo, Vijay K.; Reeves, Emer P.; McElvaney, Noel G.

2016-01-01

The T cell Ig and mucin domain–containing molecule (TIM) family of receptors have emerged as potential therapeutic targets to correct abnormal immune function in chronic inflammatory conditions. TIM-3 serves as a functional receptor in structural cells of the airways and via the ligand galectin-9 (Gal-9) can modulate the inflammatory response. The aim of this study was to investigate TIM-3 expression and function in neutrophils, focusing on its potential role in cystic fibrosis (CF) lung disease. Results revealed that TIM-3 mRNA and protein expression values of circulating neutrophils were equal between healthy controls (n = 20) and people with CF (n = 26). TIM-3 was detected on resting neutrophil membranes by FACS analysis, and expression levels significantly increased post IL-8 or TNF-α exposure (p < 0.05). Our data suggest a novel role for TIM-3/Gal-9 signaling involving modulation of cytosolic calcium levels. Via TIM-3 interaction, Gal-9 induced neutrophil degranulation and primed the cell for enhanced NADPH oxidase activity. Killing of Pseudomonas aeruginosa was significantly increased upon bacterial opsonization with Gal-9 (p < 0.05), an effect abrogated by blockade of TIM-3 receptors. This mechanism appeared to be Gram-negative bacteria specific and mediated via Gal-9/ LPS binding. Additionally, we have demonstrated that neutrophil TIM-3/Gal-9 signaling is perturbed in the CF airways due to proteolytic degradation of the receptor. In conclusion, results suggest a novel neutrophil defect potentially contributing to the defective bacterial clearance observed in the CF airways and suggest that manipulation of the TIM-3 signaling pathway may be of therapeutic value in CF, preferably in conjunction with antiprotease treatment. PMID:24477913

Tunneling readout of hydrogen-bonding based recognition

PubMed Central

Chang, Shuai; He, Jin; Kibel, Ashley; Lee, Myeong; Sankey, Otto; Zhang, Peiming; Lindsay, Stuart

2009-01-01

Hydrogen bonding has a ubiquitous role in electron transport1,2 and in molecular recognition, with DNA base-pairing being the best known example.3 Scanning tunneling microscope (STM) images4 and measurements of the decay of tunnel-current as a molecular junction is pulled apart by the STM tip, 5 are sensitive to hydrogen-bonded interactions. Here we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA basepairs. Junctions that are held together by three hydrogen bonds per basepair (e.g., guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per basepair (e.g., adenine-thymine interactions). Similar, but less-pronounced, effects are observed on the approach of the tunneling probe, implying that hydrogen-bond dependent attractive forces also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal. PMID:19421214

Modeling Fan Effects on the Time Course of Associative Recognition

ERIC Educational Resources Information Center

Schneider, Darryl W.; Anderson, John R.

2012-01-01

We investigated the time course of associative recognition using the response signal procedure, whereby a stimulus is presented and followed after a variable lag by a signal indicating that an immediate response is required. More specifically, we examined the effects of associative fan (the number of associations that an item has with other items…

LYK4, a Lysin Motif Receptor-Like Kinase, Is Important for Chitin Signaling and Plant Innate Immunity in Arabidopsis1[C][W][OA

PubMed Central

Wan, Jinrong; Tanaka, Kiwamu; Zhang, Xue-Cheng; Son, Geon Hui; Brechenmacher, Laurent; Nguyen, Tran Hong Nha; Stacey, Gary

2012-01-01

Chitin is commonly found in fungal cell walls and is one of the well-studied microbe/pathogen-associated molecular patterns. Previous studies showed that lysin motif (LysM)-containing proteins are essential for plant recognition of chitin, leading to the activation of plant innate immunity. In Arabidopsis (Arabidopsis thaliana), the LYK1/CERK1 (for LysM-containing receptor-like kinase1/chitin elicitor receptor kinase1) was shown to be essential for chitin recognition, whereas in rice (Oryza sativa), the LysM-containing protein, CEBiP (for chitin elicitor-binding protein), was shown to be involved in chitin recognition. Unlike LYK1/CERK1, CEBiP lacks an intracellular kinase domain. Arabidopsis possesses three CEBiP-like genes. Our data show that mutations in these genes, either singly or in combination, did not compromise the response to chitin treatment. Arabidopsis also contains five LYK genes. Analysis of mutations in LYK2, -3, -4, or -5 showed that LYK4 is also involved in chitin signaling. The lyk4 mutants showed reduced induction of chitin-responsive genes and diminished chitin-induced cytosolic calcium elevation as well as enhanced susceptibility to both the bacterial pathogen Pseudomonas syringae pv tomato DC3000 and the fungal pathogen Alternaria brassicicola, although these phenotypes were not as dramatic as that seen in the lyk1/cerk1 mutants. Similar to LYK1/CERK1, the LYK4 protein was also localized to the plasma membrane. Therefore, LYK4 may play a role in the chitin recognition receptor complex to assist chitin signal transduction and plant innate immunity. PMID:22744984

Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins.

PubMed

Thirumalai, D; Hyeon, Changbong

2018-06-19

Signal transmission at the molecular level in many biological complexes occurs through allosteric transitions. Allostery describes the responses of a complex to binding of ligands at sites that are spatially well separated from the binding region. We describe the structural perturbation method, based on phonon propagation in solids, which can be used to determine the signal-transmitting allostery wiring diagram (AWD) in large but finite-sized biological complexes. Application to the bacterial chaperonin GroEL-GroES complex shows that the AWD determined from structures also drives the allosteric transitions dynamically. From both a structural and dynamical perspective these transitions are largely determined by formation and rupture of salt-bridges. The molecular description of allostery in GroEL provides insights into its function, which is quantitatively described by the iterative annealing mechanism. Remarkably, in this complex molecular machine, a deep connection is established between the structures, reaction cycle during which GroEL undergoes a sequence of allosteric transitions, and function, in a self-consistent manner.This article is part of a discussion meeting issue 'Allostery and molecular machines'. © 2018 The Author(s).

Process dissociation between contextual retrieval and item recognition.

PubMed

Weis, Susanne; Specht, Karsten; Klaver, Peter; Tendolkar, Indira; Willmes, Klaus; Ruhlmann, Jürgen; Elger, Christian E; Fernández, Guillén

2004-12-22

We employed a source memory task in an event related fMRI study to dissociate MTL processes associated with either contextual retrieval or item recognition. To introduce context during study, stimuli (photographs of buildings and natural landscapes) were transformed into one of four single-color-scales: red, blue, yellow, or green. In the subsequent old/new recognition memory test, all stimuli were presented as gray scale photographs, and old-responses were followed by a four-alternative source judgment referring to the color in which the stimulus was presented during study. Our results suggest a clear-cut process dissociation within the human MTL. While an activity increase accompanies successful retrieval of contextual information, an activity decrease provides a familiarity signal that is sufficient for successful item recognition.

Signal Detection with Criterion Noise: Applications to Recognition Memory

ERIC Educational Resources Information Center

Benjamin, Aaron S.; Diaz, Michael; Wee, Serena

2009-01-01

A tacit but fundamental assumption of the theory of signal detection is that criterion placement is a noise-free process. This article challenges that assumption on theoretical and empirical grounds and presents the noisy decision theory of signal detection (ND-TSD). Generalized equations for the isosensitivity function and for measures of…

Anti-synthetase syndrome associated with anti PL-12 and anti-Signal recognition particle antibodies and a necrotizing auto-immune myositis.

PubMed

Malkan, Ashish; Cappelen-Smith, Cecilia; Beran, Roy; Griffith, Neil; Toong, Catherine; Wang, Min-Xia; Cordato, Dennis

2015-02-01

We report a 37-year-old woman with a 2 month history of proximal muscle weakness and extremely high creatine kinase (21,808 U/L) due to necrotizing auto-immune myositis (NAM) in association with anti-synthetase syndrome. Myositis-specific auto-immune antibody panel was positive for anti-Signal recognition particle and anti-PL-12. CT scan of the chest confirmed interstitial lung disease. Prednisolone, intravenous immunoglobulin and cyclophosphamide therapy was given with gradual improvement. This patient is notable for the unusual combination of NAM and anti-synthetase syndrome with the rare finding of two myositis-specific autoantibodies, which directed testing for associated extramuscular features and management with more aggressive immunotherapy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Binding of a C-type lectin’s coiled-coil domain to the Domeless receptor directly activates the JAK/STAT pathway in the shrimp immune response to bacterial infection

PubMed Central

Zhao, Xiao-Fan; Vasta, Gerardo R.

2017-01-01

C-type lectins (CTLs) are characterized by the presence of a C-type carbohydrate recognition domain (CTLD) that by recognizing microbial glycans, is responsible for their roles as pattern recognition receptors in the immune response to bacterial infection. In addition to the CTLD, however, some CTLs display additional domains that can carry out effector functions, such as the collagenous domain of the mannose-binding lectin. While in vertebrates, the mechanisms involved in these effector functions have been characterized in considerable detail, in invertebrates they remain poorly understood. In this study, we identified in the kuruma shrimp (Marsupenaeus japonicus) a structurally novel CTL (MjCC-CL) that in addition to the canonical CTLD, contains a coiled-coil domain (CCD) responsible for the effector functions that are key to the shrimp’s antibacterial response mediated by antimicrobial peptides (AMPs). By the use of in vitro and in vivo experimental approaches we elucidated the mechanism by which the recognition of bacterial glycans by the CTLD of MjCC-CL leads to activation of the JAK/STAT pathway via interaction of the CCD with the surface receptor Domeless, and upregulation of AMP expression. Thus, our study of the shrimp MjCC-CL revealed a striking functional difference with vertebrates, in which the JAK/STAT pathway is indirectly activated by cell death and stress signals through cytokines or growth factors. Instead, by cross-linking microbial pathogens with the cell surface receptor Domeless, a lectin directly activates the JAK/STAT pathway, which plays a central role in the shrimp antibacterial immune responses by upregulating expression of selected AMPs. PMID:28931061

Solid-state NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization.

PubMed

Takahashi, Hiroki; Ayala, Isabel; Bardet, Michel; De Paëpe, Gaël; Simorre, Jean-Pierre; Hediger, Sabine

2013-04-03

Dynamic nuclear polarization (DNP) enhanced solid-state nuclear magnetic resonance (NMR) has recently emerged as a powerful technique for the study of material surfaces. In this study, we demonstrate its potential to investigate cell surface in intact cells. Using Bacillus subtilis bacterial cells as an example, it is shown that the polarizing agent 1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol (TOTAPOL) has a strong binding affinity to cell wall polymers (peptidoglycan). This particular interaction is thoroughly investigated with a systematic study on extracted cell wall materials, disrupted cells, and entire cells, which proved that TOTAPOL is mainly accumulating in the cell wall. This property is used on one hand to selectively enhance or suppress cell wall signals by controlling radical concentrations and on the other hand to improve spectral resolution by means of a difference spectrum. Comparing DNP-enhanced and conventional solid-state NMR, an absolute sensitivity ratio of 24 was obtained on the entire cell sample. This important increase in sensitivity together with the possibility of enhancing specifically cell wall signals and improving resolution really opens new avenues for the use of DNP-enhanced solid-state NMR as an on-cell investigation tool.

Development of bacterial display peptides for use in biosensing applications

NASA Astrophysics Data System (ADS)

Stratis-Cullum, Dimitra N.; Kogot, Joshua M.; Sellers, Michael S.; Hurley, Margaret M.; Sarkes, Deborah A.; Pennington, Joseph M.; Val-Addo, Irene; Adams, Bryn L.; Warner, Candice R.; Carney, James P.; Brown, Rebecca L.; Pellegrino, Paul M.

2012-06-01

Recent advances in synthetic library engineering continue to show promise for the rapid production of reagent technology in response to biological threats. A synthetic library of peptide mutants built off a bacterial host offers a convenient means to link the peptide sequence, (i.e., identity of individual library members) with the desired molecular recognition traits, but also allows for a relatively simple protocol, amenable to automation. An improved understanding of the mechanisms of recognition and control of synthetic reagent isolation and evolution remain critical to success. In this paper, we describe our approach to development of peptide affinity reagents based on peptide bacterial display technology with improved control of binding interactions for stringent evolution of reagent candidates, and tailored performance capabilities. There are four key elements to the peptide affinity reagent program including: (1) the diverse bacterial library technology, (2) advanced reagent screening amenable to laboratory automation and control, (3) iterative characterization and feedback on both affinity and specificity of the molecular interactions, and (3) integrated multiscale computational prescreening of candidate peptide ligands including in silico prediction of improved binding performance. Specific results on peptides binders to Protective Antigen (PA) protein of Bacillus anthracis and Staphylococcal Enterotoxin B (SEB) will be presented. Recent highlights of on cell vs. off-cell affinity behavior and correlation of the results with advanced docking simulations on the protein-peptide system(s) are included. The potential of this technology and approach to enable rapid development of a new affinity reagent with unprecedented speed (less than one week) would allow for rapid response to new and constantly emerging threats.

Localization of adhesins on the surface of a pathogenic bacterial envelope through atomic force microscopy

NASA Astrophysics Data System (ADS)

Arnal, L.; Longo, G.; Stupar, P.; Castez, M. F.; Cattelan, N.; Salvarezza, R. C.; Yantorno, O. M.; Kasas, S.; Vela, M. E.

2015-10-01

Bacterial adhesion is the first and a significant step in establishing infection. This adhesion normally occurs in the presence of flow of fluids. Therefore, bacterial adhesins must be able to provide high strength interactions with their target surface in order to maintain the adhered bacteria under hydromechanical stressing conditions. In the case of B. pertussis, a Gram-negative bacterium responsible for pertussis, a highly contagious human respiratory tract infection, an important protein participating in the adhesion process is a 220 kDa adhesin named filamentous haemagglutinin (FHA), an outer membrane and also secreted protein that contains recognition domains to adhere to ciliated respiratory epithelial cells and macrophages. In this work, we obtained information on the cell-surface localization and distribution of the B. pertussis adhesin FHA using an antibody-functionalized AFM tip. Through the analysis of specific molecular recognition events we built a map of the spatial distribution of the adhesin which revealed a non-homogeneous pattern. Moreover, our experiments showed a force induced reorganization of the adhesin on the surface of the cells, which could explain a reinforced adhesive response under external forces. This single-molecule information contributes to the understanding of basic molecular mechanisms used by bacterial pathogens to cause infectious disease and to gain insights into the structural features by which adhesins can act as force sensors under mechanical shear conditions.Bacterial adhesion is the first and a significant step in establishing infection. This adhesion normally occurs in the presence of flow of fluids. Therefore, bacterial adhesins must be able to provide high strength interactions with their target surface in order to maintain the adhered bacteria under hydromechanical stressing conditions. In the case of B. pertussis, a Gram-negative bacterium responsible for pertussis, a highly contagious human respiratory tract

Hyperspectral face recognition with spatiospectral information fusion and PLS regression.

PubMed

Uzair, Muhammad; Mahmood, Arif; Mian, Ajmal

2015-03-01

Hyperspectral imaging offers new opportunities for face recognition via improved discrimination along the spectral dimension. However, it poses new challenges, including low signal-to-noise ratio, interband misalignment, and high data dimensionality. Due to these challenges, the literature on hyperspectral face recognition is not only sparse but is limited to ad hoc dimensionality reduction techniques and lacks comprehensive evaluation. We propose a hyperspectral face recognition algorithm using a spatiospectral covariance for band fusion and partial least square regression for classification. Moreover, we extend 13 existing face recognition techniques, for the first time, to perform hyperspectral face recognition.We formulate hyperspectral face recognition as an image-set classification problem and evaluate the performance of seven state-of-the-art image-set classification techniques. We also test six state-of-the-art grayscale and RGB (color) face recognition algorithms after applying fusion techniques on hyperspectral images. Comparison with the 13 extended and five existing hyperspectral face recognition techniques on three standard data sets show that the proposed algorithm outperforms all by a significant margin. Finally, we perform band selection experiments to find the most discriminative bands in the visible and near infrared response spectrum.

Chemical signaling between plants and plant-pathogenic bacteria.

PubMed

Venturi, Vittorio; Fuqua, Clay

2013-01-01

Studies of chemical signaling between plants and bacteria in the past have been largely confined to two models: the rhizobial-legume symbiotic association and pathogenesis between agrobacteria and their host plants. Recent studies are beginning to provide evidence that many plant-associated bacteria undergo chemical signaling with the plant host via low-molecular-weight compounds. Plant-produced compounds interact with bacterial regulatory proteins that then affect gene expression. Similarly, bacterial quorum-sensing signals result in a range of functional responses in plants. This review attempts to highlight current knowledge in chemical signaling that takes place between pathogenic bacteria and plants. This chemical communication between plant and bacteria, also referred to as interkingdom signaling, will likely become a major research field in the future, as it allows the design of specific strategies to create plants that are resistant to plant pathogens.

Anthrapyrazolone analogues intercept inflammatory JNK signals to moderate endotoxin induced septic shock

NASA Astrophysics Data System (ADS)

Prasad, Karothu Durga; Trinath, Jamma; Biswas, Ansuman; Sekar, Kanagaraj; Balaji, Kithiganahalli N.; Guru Row, Tayur N.

2014-11-01

Severe sepsis or septic shock is one of the rising causes for mortality worldwide representing nearly 10% of intensive care unit admissions. Susceptibility to sepsis is identified to be mediated by innate pattern recognition receptors and responsive signaling pathways of the host. The c-Jun N-terminal Kinase (JNK)-mediated signaling events play critical role in bacterial infection triggered multi-organ failure, cardiac dysfunction and mortality. In the context of kinase specificities, an extensive library of anthrapyrazolone analogues has been investigated for the selective inhibition of c-JNK and thereby to gain control over the inflammation associated risks. In our comprehensive biochemical characterization, it is observed that alkyl and halogen substitution on the periphery of anthrapyrazolone increases the binding potency of the inhibitors specifically towards JNK. Further, it is demonstrated that hydrophobic and hydrophilic interactions generated by these small molecules effectively block endotoxin-induced inflammatory genes expression in in vitro and septic shock in vivo, in a mouse model, with remarkable efficacies. Altogether, the obtained results rationalize the significance of the diversity oriented synthesis of small molecules for selective inhibition of JNK and their potential in the treatment of severe sepsis.

The Effect of Lexical Content on Dichotic Speech Recognition in Older Adults.

PubMed

Findlen, Ursula M; Roup, Christina M

2016-01-01

Age-related auditory processing deficits have been shown to negatively affect speech recognition for older adult listeners. In contrast, older adults gain benefit from their ability to make use of semantic and lexical content of the speech signal (i.e., top-down processing), particularly in complex listening situations. Assessment of auditory processing abilities among aging adults should take into consideration semantic and lexical content of the speech signal. The purpose of this study was to examine the effects of lexical and attentional factors on dichotic speech recognition performance characteristics for older adult listeners. A repeated measures design was used to examine differences in dichotic word recognition as a function of lexical and attentional factors. Thirty-five older adults (61-85 yr) with sensorineural hearing loss participated in this study. Dichotic speech recognition was evaluated using consonant-vowel-consonant (CVC) word and nonsense CVC syllable stimuli administered in the free recall, directed recall right, and directed recall left response conditions. Dichotic speech recognition performance for nonsense CVC syllables was significantly poorer than performance for CVC words. Dichotic recognition performance varied across response condition for both stimulus types, which is consistent with previous studies on dichotic speech recognition. Inspection of individual results revealed that five listeners demonstrated an auditory-based left ear deficit for one or both stimulus types. Lexical content of stimulus materials affects performance characteristics for dichotic speech recognition tasks in the older adult population. The use of nonsense CVC syllable material may provide a way to assess dichotic speech recognition performance while potentially lessening the effects of lexical content on performance (i.e., measuring bottom-up auditory function both with and without top-down processing). American Academy of Audiology.

Crystal Structure of a Bacterial Signal Peptide Peptidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim,A.; Oliver, D.; Paetzel, M.

2008-01-01

Signal peptide peptidase (Spp) is the enzyme responsible for cleaving the remnant signal peptides left behind in the membrane following Sec-dependent protein secretion. Spp activity appears to be present in all cell types, eukaryotic, prokaryotic and archaeal. Here we report the first structure of a signal peptide peptidase, that of the Escherichia coli SppA (SppAEC). SppAEC forms a tetrameric assembly with a novel bowl-shaped architecture. The bowl has a dramatically hydrophobic interior and contains four separate active sites that utilize a Ser/Lys catalytic dyad mechanism. Our structural analysis of SppA reveals that while in many Gram-negative bacteria as well asmore » characterized plant variants, a tandem duplication in the protein fold creates an intact active site at the interface between the repeated domains, other species, particularly Gram-positive and archaeal organisms, encode half-size, unduplicated SppA variants that could form similar oligomers to their duplicated counterparts, but using an octamer arrangement and with the catalytic residues provided by neighboring monomers. The structure reveals a similarity in the protein fold between the domains in the periplasmic Ser/Lys protease SppA and the monomers seen in the cytoplasmic Ser/His/Asp protease ClpP. We propose that SppA may, in addition to its role in signal peptide hydrolysis, have a role in the quality assurance of periplasmic and membrane-bound proteins, similar to the role that ClpP plays for cytoplasmic proteins.« less

Real-Time Reconfigurable Adaptive Speech Recognition Command and Control Apparatus and Method

NASA Technical Reports Server (NTRS)

Salazar, George A. (Inventor); Haynes, Dena S. (Inventor); Sommers, Marc J. (Inventor)

1998-01-01

An adaptive speech recognition and control system and method for controlling various mechanisms and systems in response to spoken instructions and in which spoken commands are effective to direct the system into appropriate memory nodes, and to respective appropriate memory templates corresponding to the voiced command is discussed. Spoken commands from any of a group of operators for which the system is trained may be identified, and voice templates are updated as required in response to changes in pronunciation and voice characteristics over time of any of the operators for which the system is trained. Provisions are made for both near-real-time retraining of the system with respect to individual terms which are determined not be positively identified, and for an overall system training and updating process in which recognition of each command and vocabulary term is checked, and in which the memory templates are retrained if necessary for respective commands or vocabulary terms with respect to an operator currently using the system. In one embodiment, the system includes input circuitry connected to a microphone and including signal processing and control sections for sensing the level of vocabulary recognition over a given period and, if recognition performance falls below a given level, processing audio-derived signals for enhancing recognition performance of the system.

Context retrieval and description benefits for recognition of unfamiliar faces.

PubMed

Jones, Todd C; Robinson, Kealagh; Steel, Brenna C

2018-04-19

Describing unfamiliar faces during or immediately after their presentation in a study phase can produce better recognition memory performance compared with a view-only control condition. We treated descriptions as elaborative information that is part of the study context and investigated how context retrieval influences recognition memory. Following general dual-process theories, we hypothesized that recollection would be used to recall descriptions and that description recall would influence recognition decisions, including the level of recognition confidence. In four experiments description conditions produced higher hit rates and higher levels of recognition confidence than control conditions. Participants recalled descriptive content on some trials, and this context retrieval was linked to an increase in the recognition confidence level. Repeating study faces in description conditions increased recognition scores, recognition confidence level, and context retrieval. Estimates of recollection from Yonelinas' (1994) dual-process signal detection ROCs were, on average, very close to the measures of context recall. Description conditions also produced higher estimates of familiarity. Finally, we found evidence that participants engaged in description activity in some ostensibly view-only trials. An emphasis on the information participants use in making their recognition decisions can advance understanding on description effects when descriptions are part of the study trial context. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis

PubMed Central

An, Shi-Qi; Febrer, Melanie; McCarthy, Yvonne; Tang, Dong-Jie; Clissold, Leah; Kaithakottil, Gemy; Swarbreck, David; Tang, Ji-Liang; Rogers, Jane; Dow, J Maxwell; Ryan, Robert P

2013-01-01

The bacterium Xanthomonas campestris is an economically important pathogen of many crop species and a model for the study of bacterial phytopathogenesis. In X. campestris, a regulatory system mediated by the signal molecule DSF controls virulence to plants. The synthesis and recognition of the DSF signal depends upon different Rpf proteins. DSF signal generation requires RpfF whereas signal perception and transduction depends upon a system comprising the sensor RpfC and regulator RpfG. Here we have addressed the action and role of Rpf/DSF signalling in phytopathogenesis by high-resolution transcriptional analysis coupled to functional genomics. We detected transcripts for many genes that were unidentified by previous computational analysis of the genome sequence. Novel transcribed regions included intergenic transcripts predicted as coding or non-coding as well as those that were antisense to coding sequences. In total, mutation of rpfF, rpfG and rpfC led to alteration in transcript levels (more than fourfold) of approximately 480 genes. The regulatory influence of RpfF and RpfC demonstrated considerable overlap. Contrary to expectation, the regulatory influence of RpfC and RpfG had limited overlap, indicating complexities of the Rpf signalling system. Importantly, functional analysis revealed over 160 new virulence factors within the group of Rpf-regulated genes. PMID:23617851

An analysis of the influence of deep neural network (DNN) topology in bottleneck feature based language recognition.

PubMed

Lozano-Diez, Alicia; Zazo, Ruben; Toledano, Doroteo T; Gonzalez-Rodriguez, Joaquin

2017-01-01

Language recognition systems based on bottleneck features have recently become the state-of-the-art in this research field, showing its success in the last Language Recognition Evaluation (LRE 2015) organized by NIST (U.S. National Institute of Standards and Technology). This type of system is based on a deep neural network (DNN) trained to discriminate between phonetic units, i.e. trained for the task of automatic speech recognition (ASR). This DNN aims to compress information in one of its layers, known as bottleneck (BN) layer, which is used to obtain a new frame representation of the audio signal. This representation has been proven to be useful for the task of language identification (LID). Thus, bottleneck features are used as input to the language recognition system, instead of a classical parameterization of the signal based on cepstral feature vectors such as MFCCs (Mel Frequency Cepstral Coefficients). Despite the success of this approach in language recognition, there is a lack of studies analyzing in a systematic way how the topology of the DNN influences the performance of bottleneck feature-based language recognition systems. In this work, we try to fill-in this gap, analyzing language recognition results with different topologies for the DNN used to extract the bottleneck features, comparing them and against a reference system based on a more classical cepstral representation of the input signal with a total variability model. This way, we obtain useful knowledge about how the DNN configuration influences bottleneck feature-based language recognition systems performance.

Autophagic control of RLR signaling

PubMed Central

Tal, Michal Caspi; Iwasaki, Akiko

2013-01-01

Innate immunity to viral infection is initiated within the infected cells through the recognition of unique viral signatures by pattern recognition receptors (PRRs) that mediate the induction of potent antiviral factor, type I interferons (IFNs). Infection with RNA viruses is recognized by the members of the retinoic acid inducible gene I (RIG-I)-like receptor (RLR) family in the cytosol. Our recent study demonstrates that IFN production in response to RNA viral ligands is increased in the absence of autophagy. The process of autophagy functions as an internal clean-up crew within the cell, shuttling damaged cellular organelles and long-lived proteins to the lysosomes for degradation. Our data show that the absence of autophagy leads to the amplification of RLR signaling in two ways. First, in the absence of autophagy, mitochondria accumulate within the cell leading to the build up of mitochondrial associated protein, IPS-1, a key signaling protein for RLRs. Second, damaged mitochondria that are not degraded in the absence of autophagy provide a source of reactive oxygen species (ROS), which amplify RLR signaling in Atg5 knockout cells. Our study provides the first link between ROS and cytosolic signaling mediated by the RLRs, and suggests the importance of autophagy in the regulation of signaling emanating from mitochondria. PMID:19571662

Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection

PubMed Central

Valkov, Eugene; Stamp, Anna; DiMaio, Frank; Baker, David; Verstak, Brett; Roversi, Pietro; Kellie, Stuart; Sweet, Matthew J.; Mansell, Ashley; Gay, Nicholas J.; Martin, Jennifer L.; Kobe, Bostjan

2011-01-01

Initiation of the innate immune response requires agonist recognition by pathogen-recognition receptors such as the Toll-like receptors (TLRs). Toll/interleukin-1 receptor (TIR) domain-containing adaptors are critical in orchestrating the signal transduction pathways after TLR and interleukin-1 receptor activation. Myeloid differentiation primary response gene 88 (MyD88) adaptor-like (MAL)/TIR domain-containing adaptor protein (TIRAP) is involved in bridging MyD88 to TLR2 and TLR4 in response to bacterial infection. Genetic studies have associated a number of unique single-nucleotide polymorphisms in MAL with protection against invasive microbial infection, but a molecular understanding has been hampered by a lack of structural information. The present study describes the crystal structure of MAL TIR domain. Significant structural differences exist in the overall fold of MAL compared with other TIR domain structures: A sequence motif comprising a β-strand in other TIR domains instead corresponds to a long loop, placing the functionally important “BB loop” proline motif in a unique surface position in MAL. The structure suggests possible dimerization and MyD88-interacting interfaces, and we confirm the key interface residues by coimmunoprecipitation using site-directed mutants. Jointly, our results provide a molecular and structural basis for the role of MAL in TLR signaling and disease protection. PMID:21873236

Evidence for calcium-mediated perception of plant symbiotic signals in aequorin-expressing Mesorhizobium loti

PubMed Central

2009-01-01

Background During the interaction between rhizobia and leguminous plants the two partners engage in a molecular conversation that leads to reciprocal recognition and ensures the beginning of a successful symbiotic integration. In host plants, intracellular Ca2+ changes are an integral part of the signalling mechanism. In rhizobia it is not yet known whether Ca2+ can act as a transducer of symbiotic signals. Results A plasmid encoding the bioluminescent Ca2+ probe aequorin was introduced into Mesorhizobium loti USDA 3147T strain to investigate whether a Ca2+ response is activated in rhizobia upon perception of plant root exudates. We find that M. loti cells respond to environmental and symbiotic cues through transient elevations in intracellular free Ca2+ concentration. Only root exudates from the homologous host Lotus japonicus induce Ca2+ signalling and downstream activation of nodulation genes. The extracellular Ca2+ chelator EGTA inhibits both transient intracellular Ca2+ increase and inducible nod gene expression, while not affecting the expression of other genes, either constitutively expressed or inducible. Conclusion These findings indicate a newly described early event in the molecular dialogue between plants and rhizobia and highlight the use of aequorin-expressing bacterial strains as a promising novel approach for research in legume symbiosis. PMID:19775463

The cingulo-opercular network provides word-recognition benefit.

PubMed

Vaden, Kenneth I; Kuchinsky, Stefanie E; Cute, Stephanie L; Ahlstrom, Jayne B; Dubno, Judy R; Eckert, Mark A

2013-11-27

Recognizing speech in difficult listening conditions requires considerable focus of attention that is often demonstrated by elevated activity in putative attention systems, including the cingulo-opercular network. We tested the prediction that elevated cingulo-opercular activity provides word-recognition benefit on a subsequent trial. Eighteen healthy, normal-hearing adults (10 females; aged 20-38 years) performed word recognition (120 trials) in multi-talker babble at +3 and +10 dB signal-to-noise ratios during a sparse sampling functional magnetic resonance imaging (fMRI) experiment. Blood oxygen level-dependent (BOLD) contrast was elevated in the anterior cingulate cortex, anterior insula, and frontal operculum in response to poorer speech intelligibility and response errors. These brain regions exhibited significantly greater correlated activity during word recognition compared with rest, supporting the premise that word-recognition demands increased the coherence of cingulo-opercular network activity. Consistent with an adaptive control network explanation, general linear mixed model analyses demonstrated that increased magnitude and extent of cingulo-opercular network activity was significantly associated with correct word recognition on subsequent trials. These results indicate that elevated cingulo-opercular network activity is not simply a reflection of poor performance or error but also supports word recognition in difficult listening conditions.

Bacterial communications in implant infections: a target for an intelligence war.

PubMed

Costerton, J W; Montanaro, L; Arciola, C R

2007-09-01

The status of population density is communicated among bacteria by specific secreted molecules, called pheromones or autoinducers, and the control mechanism is called "quorum-sensing". Quorum-sensing systems regulate the expression of a panel of genes, allowing bacteria to adapt to modified environmental conditions at a high density of population. The two known different quorum systems are described as the LuxR-LuxI system in gram-negative bacteria, which uses an N-acyl-homoserine lactone (AHL) as signal, and the agr system in gram-positive bacteria, which uses a peptide-tiolactone as signal and the RNAIII as effector molecules. Both in gram-negative and in gram-positive bacteria, quorum-sensing systems regulate the expression of adhesion mechanisms (biofilm and adhesins) and virulence factors (toxins and exoenzymes) depending on population cell density. In gram-negative Pseudomonas aeruginosa, analogs of signaling molecules such as furanone analogs, are effective in attenuating bacterial virulence and controlling bacterial infections. In grampositive Staphylococcus aureus, the quorum-sensing RNAIII-inhibiting peptide (RIP), tested in vitro and in animal infection models, has been proved to inhibit virulence and prevent infections. Attenuation of bacterial virulence by quorum-sensing inhibitors, rather than by bactericidal or bacteriostatic drugs, is a highly attractive concept because these antibacterial agents are less likely to induce the development of bacterial resistance.

Double-Windows-Based Motion Recognition in Multi-Floor Buildings Assisted by a Built-In Barometer.

PubMed

Liu, Maolin; Li, Huaiyu; Wang, Yuan; Li, Fei; Chen, Xiuwan

2018-04-01

Accelerometers, gyroscopes and magnetometers in smartphones are often used to recognize human motions. Since it is difficult to distinguish between vertical motions and horizontal motions in the data provided by these built-in sensors, the vertical motion recognition accuracy is relatively low. The emergence of a built-in barometer in smartphones improves the accuracy of motion recognition in the vertical direction. However, there is a lack of quantitative analysis and modelling of the barometer signals, which is the basis of barometer's application to motion recognition, and a problem of imbalanced data also exists. This work focuses on using the barometers inside smartphones for vertical motion recognition in multi-floor buildings through modelling and feature extraction of pressure signals. A novel double-windows pressure feature extraction method, which adopts two sliding time windows of different length, is proposed to balance recognition accuracy and response time. Then, a random forest classifier correlation rule is further designed to weaken the impact of imbalanced data on recognition accuracy. The results demonstrate that the recognition accuracy can reach 95.05% when pressure features and the improved random forest classifier are adopted. Specifically, the recognition accuracy of the stair and elevator motions is significantly improved with enhanced response time. The proposed approach proves effective and accurate, providing a robust strategy for increasing accuracy of vertical motions.

Distributed Recognition of Natural Songs by European Starlings

ERIC Educational Resources Information Center

Knudsen, Daniel; Thompson, Jason V.; Gentner, Timothy Q.

2010-01-01

Individual vocal recognition behaviors in songbirds provide an excellent framework for the investigation of comparative psychological and neurobiological mechanisms that support the perception and cognition of complex acoustic communication signals. To this end, the complex songs of European starlings have been studied extensively. Yet, several…

Applications of sub-audible speech recognition based upon electromyographic signals

NASA Technical Reports Server (NTRS)

Jorgensen, C. Charles (Inventor); Betts, Bradley J. (Inventor)

2009-01-01

Method and system for generating electromyographic or sub-audible signals (''SAWPs'') and for transmitting and recognizing the SAWPs that represent the original words and/or phrases. The SAWPs may be generated in an environment that interferes excessively with normal speech or that requires stealth communications, and may be transmitted using encoded, enciphered or otherwise transformed signals that are less subject to signal distortion or degradation in the ambient environment.

The enzymes of bacterial census and censorship

PubMed Central

Fast, Walter; Tipton, Peter A.

2011-01-01

N-Acyl-l-homoserine lactones (AHLs) are a major class of quorum sensing signals used by Gram-negative bacteria to regulate gene expression in a population-dependent manner, thereby enabling group behavior. Enzymes capable of generating and catabolizing AHL signals are of significant interest for the study of microbial ecology and quorum-sensing pathways, for understanding the systems that bacteria have evolved to interact with small molecule signals, and for their possible use in therapeutic and industrial applications. The recent structural and functional studies reviewed here provide detailed insight into the chemistry and enzymology of bacterial communication. PMID:22099187

Structural Basis of Differential Ligand Recognition by Two Classes of bis-(3-5)-cyclic Dimeric Guanosine Monophosphate-binding Riboswitches

DOE Office of Scientific and Technical Information (OSTI.GOV)

K Smith; C Shanahan; E Moore

2011-12-31

The bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) signaling pathway regulates biofilm formation, virulence, and other processes in many bacterial species and is critical for their survival. Two classes of c-di-GMP-binding riboswitches have been discovered that bind this second messenger with high affinity and regulate diverse downstream genes, underscoring the importance of RNA receptors in this pathway. We have solved the structure of a c-di-GMP-II riboswitch, which reveals that the ligand is bound as part of a triplex formed with a pseudoknot. The structure also shows that the guanine bases of c-di-GMP are recognized through noncanonical pairings and that the phosphodiester backbonemore » is not contacted by the RNA. Recognition is quite different from that observed in the c-di-GMP-I riboswitch, demonstrating that at least two independent solutions for RNA second messenger binding have evolved. We exploited these differences to design a c-di-GMP analog that selectively binds the c-di-GMP-II aptamer over the c-di-GMP-I RNA. There are several bacterial species that contain both types of riboswitches, and this approach holds promise as an important tool for targeting one riboswitch, and thus one gene, over another in a selective fashion.« less

Optical character recognition of camera-captured images based on phase features

NASA Astrophysics Data System (ADS)

Diaz-Escobar, Julia; Kober, Vitaly

2015-09-01

Nowadays most of digital information is obtained using mobile devices specially smartphones. In particular, it brings the opportunity for optical character recognition in camera-captured images. For this reason many recognition applications have been recently developed such as recognition of license plates, business cards, receipts and street signal; document classification, augmented reality, language translator and so on. Camera-captured images are usually affected by geometric distortions, nonuniform illumination, shadow, noise, which make difficult the recognition task with existing systems. It is well known that the Fourier phase contains a lot of important information regardless of the Fourier magnitude. So, in this work we propose a phase-based recognition system exploiting phase-congruency features for illumination/scale invariance. The performance of the proposed system is tested in terms of miss classifications and false alarms with the help of computer simulation.

Primary Stability Recognition of the Newly Designed Cementless Femoral Stem Using Digital Signal Processing

PubMed Central

Salleh, Sh-Hussain; Hamedi, Mahyar; Zulkifly, Ahmad Hafiz; Lee, Muhammad Hisyam; Mohd Noor, Alias; Harris, Arief Ruhullah A.; Abdul Majid, Norazman

2014-01-01

Stress shielding and micromotion are two major issues which determine the success of newly designed cementless femoral stems. The correlation of experimental validation with finite element analysis (FEA) is commonly used to evaluate the stress distribution and fixation stability of the stem within the femoral canal. This paper focused on the applications of feature extraction and pattern recognition using support vector machine (SVM) to determine the primary stability of the implant. We measured strain with triaxial rosette at the metaphyseal region and micromotion with linear variable direct transducer proximally and distally using composite femora. The root mean squares technique is used to feed the classifier which provides maximum likelihood estimation of amplitude, and radial basis function is used as the kernel parameter which mapped the datasets into separable hyperplanes. The results showed 100% pattern recognition accuracy using SVM for both strain and micromotion. This indicates that DSP could be applied in determining the femoral stem primary stability with high pattern recognition accuracy in biomechanical testing. PMID:24800230

Primary stability recognition of the newly designed cementless femoral stem using digital signal processing.

PubMed

Baharuddin, Mohd Yusof; Salleh, Sh-Hussain; Hamedi, Mahyar; Zulkifly, Ahmad Hafiz; Lee, Muhammad Hisyam; Mohd Noor, Alias; Harris, Arief Ruhullah A; Abdul Majid, Norazman

2014-01-01

Stress shielding and micromotion are two major issues which determine the success of newly designed cementless femoral stems. The correlation of experimental validation with finite element analysis (FEA) is commonly used to evaluate the stress distribution and fixation stability of the stem within the femoral canal. This paper focused on the applications of feature extraction and pattern recognition using support vector machine (SVM) to determine the primary stability of the implant. We measured strain with triaxial rosette at the metaphyseal region and micromotion with linear variable direct transducer proximally and distally using composite femora. The root mean squares technique is used to feed the classifier which provides maximum likelihood estimation of amplitude, and radial basis function is used as the kernel parameter which mapped the datasets into separable hyperplanes. The results showed 100% pattern recognition accuracy using SVM for both strain and micromotion. This indicates that DSP could be applied in determining the femoral stem primary stability with high pattern recognition accuracy in biomechanical testing.

Aseptic and Bacterial Meningitis: Evaluation, Treatment, and Prevention.

PubMed

Mount, Hillary R; Boyle, Sean D

2017-09-01

The etiologies of meningitis range in severity from benign and self-limited to life-threatening with potentially severe morbidity. Bacterial meningitis is a medical emergency that requires prompt recognition and treatment. Mortality remains high despite the introduction of vaccinations for common pathogens that have reduced the incidence of meningitis worldwide. Aseptic meningitis is the most common form of meningitis with an annual incidence of 7.6 per 100,000 adults. Most cases of aseptic meningitis are viral and require supportive care. Viral meningitis is generally self-limited with a good prognosis. Examination maneuvers such as Kernig sign or Brudzinski sign may not be useful to differentiate bacterial from aseptic meningitis because of variable sensitivity and specificity. Because clinical findings are also unreliable, the diagnosis relies on the examination of cerebrospinal fluid obtained from lumbar puncture. Delayed initiation of antibiotics can worsen mortality. Treatment should be started promptly in cases where transfer, imaging, or lumbar puncture may slow a definitive diagnosis. Empiric antibiotics should be directed toward the most likely pathogens and should be adjusted by patient age and risk factors. Dexamethasone should be administered to children and adults with suspected bacterial meningitis before or at the time of initiation of antibiotics. Vaccination against the most common pathogens that cause bacterial meningitis is recommended. Chemoprophylaxis of close contacts is helpful in preventing additional infections.

Simulation of Biomimetic Recognition between Polymers and Surfaces

NASA Astrophysics Data System (ADS)

Golumbfskie, Aaron J.; Pande, Vijay S.; Chakraborty, Arup K.

1999-10-01

Many biological processes, such as transmembrane signaling and pathogen-host interactions, are initiated by a protein recognizing a specific pattern of binding sites on part of a membrane or cell surface. By recognition, we imply that the polymer quickly finds and then adsorbs strongly on the pattern-matched region and not on others. The development of synthetic systems that can mimic such recognition between polymers and surfaces could have significant impact on advanced applications such as the development of sensors, molecular-scale separation processes, and synthetic viral inhibition agents. Attempting to affect recognition in synthetic systems by copying the detailed chemistries to which nature has been led over millenia of evolution does not seem practical for most applications. This leads us to the following question: Are there any universal strategies that can affect recognition between polymers and surfaces? Such generic strategies may be easier to implement in abiotic applications. We describe results that suggest that biomimetic recognition between synthetic polymers and surfaces is possible by exploiting certain generic strategies, and we elucidate the kinetic mechanisms by which this occurs. Our results suggest convenient model systems for experimental studies of dynamics in free energy landscapes characteristic of frustrated systems.

Detection of and Response to Signals Involved in Host-Microbe Interactions by Plant-Associated Bacteria

PubMed Central

Brencic, Anja; Winans, Stephen C.

2005-01-01

Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described. PMID:15755957

Discrete-State and Continuous Models of Recognition Memory: Testing Core Properties under Minimal Assumptions

ERIC Educational Resources Information Center

Kellen, David; Klauer, Karl Christoph

2014-01-01

A classic discussion in the recognition-memory literature concerns the question of whether recognition judgments are better described by continuous or discrete processes. These two hypotheses are instantiated by the signal detection theory model (SDT) and the 2-high-threshold model, respectively. Their comparison has almost invariably relied on…

Bacterial hybrid histidine kinases in plant-bacteria interactions.

PubMed

Borland, Stéphanie; Prigent-Combaret, Claire; Wisniewski-Dyé, Florence

2016-10-01

Two-component signal transduction systems are essential for many bacteria to maintain homeostasis and adapt to environmental changes. Two-component signal transduction systems typically involve a membrane-bound histidine kinase that senses stimuli, autophosphorylates in the transmitter region and then transfers the phosphoryl group to the receiver domain of a cytoplasmic response regulator that mediates appropriate changes in bacterial physiology. Although usually found on distinct proteins, the transmitter and receiver modules are sometimes fused into a so-called hybrid histidine kinase (HyHK). Such structure results in multiple phosphate transfers that are believed to provide extra-fine-tuning mechanisms and more regulatory checkpoints than classical phosphotransfers. HyHK-based regulation may be crucial for finely tuning gene expression in a heterogeneous environment such as the rhizosphere, where intricate plant-bacteria interactions occur. In this review, we focus on roles fulfilled by bacterial HyHKs in plant-associated bacteria, providing recent findings on the mechanistic of their signalling properties. Recent insights into understanding additive regulatory properties fulfilled by the tethered receiver domain of HyHKs are also addressed.

Bacterial Quorum Sensing and Microbial Community Interactions

PubMed Central

2018-01-01

ABSTRACT Many bacteria use a cell-cell communication system called quorum sensing to coordinate population density-dependent changes in behavior. Quorum sensing involves production of and response to diffusible or secreted signals, which can vary substantially across different types of bacteria. In many species, quorum sensing modulates virulence functions and is important for pathogenesis. Over the past half-century, there has been a significant accumulation of knowledge of the molecular mechanisms, signal structures, gene regulons, and behavioral responses associated with quorum-sensing systems in diverse bacteria. More recent studies have focused on understanding quorum sensing in the context of bacterial sociality. Studies of the role of quorum sensing in cooperative and competitive microbial interactions have revealed how quorum sensing coordinates interactions both within a species and between species. Such studies of quorum sensing as a social behavior have relied on the development of “synthetic ecological” models that use nonclonal bacterial populations. In this review, we discuss some of these models and recent advances in understanding how microbes might interact with one another using quorum sensing. The knowledge gained from these lines of investigation has the potential to guide studies of microbial sociality in natural settings and the design of new medicines and therapies to treat bacterial infections. PMID:29789364

Chemical recognition of gases and gas mixtures with terahertz waves.

PubMed

Jacobsen, R H; Mittleman, D M; Nuss, M C

1996-12-15

A time-domain chemical-recognition system for classifying gases and analyzing gas mixtures is presented. We analyze the free induction decay exhibited by gases excited by far-infrared (terahertz) pulses in the time domain, using digital signal-processing techniques. A simple geometric picture is used for the classif ication of the waveforms measured for unknown gas species. We demonstrate how the recognition system can be used to determine the partial pressures of an ammonia-water gas mixture.

Chemical recognition of gases and gas mixtures with terahertz waves

NASA Astrophysics Data System (ADS)

Jacobsen, R. H.; Mittleman, D. M.; Nuss, M. C.

1996-12-01

A time-domain chemical-recognition system for classifying gases and analyzing gas mixtures is presented. We analyze the free induction decay exhibited by gases excited by far-infrared (terahertz) pulses in the time domain, using digital signal-processing techniques. A simple geometric picture is used for the classification of the waveforms measured for unknown gas species. We demonstrate how the recognition system can be used to determine the partial pressures of an ammonia-water gas mixture.

Activation of RIG-I-like Receptor Signal Transduction

PubMed Central

Bruns, Annie; Horvath, Curt M.

2011-01-01

Mammalian cells have the ability to recognize virus infection and mount a powerful antiviral response. Pattern recognition receptor proteins detect molecular signatures of virus infection and activate antiviral signaling cascades. The RIG-I-like receptors are cytoplasmic DExD/H box proteins that can specifically recognize virus-derived RNA species as a molecular feature discriminating the pathogen from the host. The RIG-I-like receptor family is composed of three homologous proteins, RIG-I, MDA5, and LGP2. All of these proteins can bind double-stranded RNA species with varying affinities via their conserved DExD/H box RNA helicase domains and C-terminal regulatory domains. The recognition of foreign RNA by the RLRs activates enzymatic functions and initiates signal transduction pathways resulting in the production of antiviral cytokines and the establishment of a broadly effective cellular antiviral state that protects neighboring cells from infection and triggers innate and adaptive immune systems. The propagation of this signal via the interferon antiviral system has been studied extensively, while the precise roles for enzymatic activities of the RNA helicase domain in antiviral responses are only beginning to be elucidated. Here, current models for RLR ligand recognition and signaling are reviewed. PMID:22066529

Structural Basis for the Recognition of Tyrosine-based Sorting Signals by the μ3A Subunit of the AP-3 Adaptor Complex*

PubMed Central

Mardones, Gonzalo A.; Burgos, Patricia V.; Lin, Yimo; Kloer, Daniel P.; Magadán, Javier G.; Hurley, James H.; Bonifacino, Juan S.

2013-01-01

Tyrosine-based signals fitting the YXXØ motif mediate sorting of transmembrane proteins to endosomes, lysosomes, the basolateral plasma membrane of polarized epithelial cells, and the somatodendritic domain of neurons through interactions with the homologous μ1, μ2, μ3, and μ4 subunits of the corresponding AP-1, AP-2, AP-3, and AP-4 complexes. Previous x-ray crystallographic analyses identified distinct binding sites for YXXØ signals on μ2 and μ4, which were located on opposite faces of the proteins. To elucidate the mode of recognition of YXXØ signals by other members of the μ family, we solved the crystal structure at 1.85 Å resolution of the C-terminal domain of the μ3 subunit of AP-3 (isoform A) in complex with a peptide encoding a YXXØ signal (SDYQRL) from the trans-Golgi network protein TGN38. The μ3A C-terminal domain consists of an immunoglobulin-like β-sandwich organized into two subdomains, A and B. The YXXØ signal binds in an extended conformation to a site on μ3A subdomain A, at a location similar to the YXXØ-binding site on μ2 but not μ4. The binding sites on μ3A and μ2 exhibit similarities and differences that account for the ability of both proteins to bind distinct sets of YXXØ signals. Biochemical analyses confirm the identification of the μ3A site and show that this protein binds YXXØ signals with 14–19 μm affinity. The surface electrostatic potential of μ3A is less basic than that of μ2, in part explaining the association of AP-3 with intracellular membranes having less acidic phosphoinositides. PMID:23404500

Structural basis for the recognition of tyrosine-based sorting signals by the μ3A subunit of the AP-3 adaptor complex.

PubMed

Mardones, Gonzalo A; Burgos, Patricia V; Lin, Yimo; Kloer, Daniel P; Magadán, Javier G; Hurley, James H; Bonifacino, Juan S

2013-03-29

Tyrosine-based signals fitting the YXXØ motif mediate sorting of transmembrane proteins to endosomes, lysosomes, the basolateral plasma membrane of polarized epithelial cells, and the somatodendritic domain of neurons through interactions with the homologous μ1, μ2, μ3, and μ4 subunits of the corresponding AP-1, AP-2, AP-3, and AP-4 complexes. Previous x-ray crystallographic analyses identified distinct binding sites for YXXØ signals on μ2 and μ4, which were located on opposite faces of the proteins. To elucidate the mode of recognition of YXXØ signals by other members of the μ family, we solved the crystal structure at 1.85 Å resolution of the C-terminal domain of the μ3 subunit of AP-3 (isoform A) in complex with a peptide encoding a YXXØ signal (SDYQRL) from the trans-Golgi network protein TGN38. The μ3A C-terminal domain consists of an immunoglobulin-like β-sandwich organized into two subdomains, A and B. The YXXØ signal binds in an extended conformation to a site on μ3A subdomain A, at a location similar to the YXXØ-binding site on μ2 but not μ4. The binding sites on μ3A and μ2 exhibit similarities and differences that account for the ability of both proteins to bind distinct sets of YXXØ signals. Biochemical analyses confirm the identification of the μ3A site and show that this protein binds YXXØ signals with 14-19 μm affinity. The surface electrostatic potential of μ3A is less basic than that of μ2, in part explaining the association of AP-3 with intracellular membranes having less acidic phosphoinositides.

Speech Recognition Using Multiple Features and Multiple Recognizers

DTIC Science & Technology

1991-12-03

6 2.1 Introduction ............................................... 6 2.2 Human Speech Communication Process...119 How to Setup ASRT.......................................... 119 How to Use Interactive Menus .................................. 120...recognize a word from an acoustic signal. The human ear and brain perform this type of recognition with incredible speed and precision. Even though

Sub-Audible Speech Recognition Based upon Electromyographic Signals

NASA Technical Reports Server (NTRS)

Jorgensen, Charles C. (Inventor); Agabon, Shane T. (Inventor); Lee, Diana D. (Inventor)

2012-01-01

Method and system for processing and identifying a sub-audible signal formed by a source of sub-audible sounds. Sequences of samples of sub-audible sound patterns ("SASPs") for known words/phrases in a selected database are received for overlapping time intervals, and Signal Processing Transforms ("SPTs") are formed for each sample, as part of a matrix of entry values. The matrix is decomposed into contiguous, non-overlapping two-dimensional cells of entries, and neural net analysis is applied to estimate reference sets of weight coefficients that provide sums with optimal matches to reference sets of values. The reference sets of weight coefficients are used to determine a correspondence between a new (unknown) word/phrase and a word/phrase in the database.

Human Action Recognition Using Wireless Wearable In-Ear Microphone

NASA Astrophysics Data System (ADS)

Nishimura, Jun; Kuroda, Tadahiro

To realize the ubiquitous eating habits monitoring, we proposed the use of sounds sensed by an in-ear placed wireless wearable microphone. A prototype of wireless wearable in-ear microphone was developed by utilizing a common Bluetooth headset. We proposed a robust chewing action recognition algorithm which consists of two recognition stages: “chew-like” signal detection and chewing sound verification stages. We also provide empirical results on other action recognition using in-ear sound including swallowing, cough, belch, and etc. The average chewing number counting error rate of 1.93% is achieved. Lastly, chewing sound mapping is proposed as a new prototypical approach to provide an additional intuitive feedback on food groups to be able to infer the eating habits in their daily life context.

PHYSICAL MODEL FOR RECOGNITION TUNNELING

PubMed Central

Krstić, Predrag; Ashcroft, Brian; Lindsay, Stuart

2015-01-01

Recognition tunneling (RT) identifies target molecules trapped between tunneling electrodes functionalized with recognition molecules that serve as specific chemical linkages between the metal electrodes and the trapped target molecule. Possible applications include single molecule DNA and protein sequencing. This paper addresses several fundamental aspects of RT by multiscale theory, applying both all-atom and coarse-grained DNA models: (1) We show that the magnitude of the observed currents are consistent with the results of non-equilibrium Green's function calculations carried out on a solvated all-atom model. (2) Brownian fluctuations in hydrogen bond-lengths lead to current spikes that are similar to what is observed experimentally. (3) The frequency characteristics of these fluctuations can be used to identify the trapped molecules with a machine-learning algorithm, giving a theoretical underpinning to this new method of identifying single molecule signals. PMID:25650375

[Surface electromyography signal classification using gray system theory].

PubMed

Xie, Hongbo; Ma, Congbin; Wang, Zhizhong; Huang, Hai

2004-12-01

A new method based on gray correlation was introduced to improve the identification rate in artificial limb. The electromyography (EMG) signal was first transformed into time-frequency domain by wavelet transform. Singular value decomposition (SVD) was then used to extract feature vector from the wavelet coefficient for pattern recognition. The decision was made according to the maximum gray correlation coefficient. Compared with neural network recognition, this robust method has an almost equivalent recognition rate but much lower computation costs and less training samples.

Pattern recognition of the targets with help of polarization properties of the signal

NASA Astrophysics Data System (ADS)

Ponomaryov, Volodymyr I.; de Rivera, Luis N.; Castellanos, Aldo B.; Popov, Anatoly V.

1999-10-01

We proposed to use the possibility of recognition of the targets on background of the scattering from the surface, weather objects with the help of polarimetric 3-cm radar. It has been investigated such polarization characteristics: the amplitudes of the polarization matrix elements; an anisotropy coefficient; depolarization coefficient; asymmetry coefficient; the energy section was less than 1 dB at ranges up to 15 km and less than 1.5 dB at ranges up to 100 km. During the experiments urban objects and 6 various ships of small displacement having the closest values of the backscattering cross-section were used. The analysis has shown: the factor of the polarization selection for anisotropy objects and weather objects had the values about 0.02-0.08 Isotropy had the values of polarimetric correlation factor for hydrometers about 0.7-0.8, for earth surface about 0.8-0.9, for sea surface - from 0.33 to 0.7. The results of the work of recognition algorithm of a class 'concrete objects', and 'metal objects' are submitted as example in the paper. The result of experiments have shown that the probability of correct recognition of the identified objects was in the limits from 0.93 to 0.97.

Extracting time-frequency feature of single-channel vastus medialis EMG signals for knee exercise pattern recognition.

PubMed

Zhang, Yi; Li, Peiyang; Zhu, Xuyang; Su, Steven W; Guo, Qing; Xu, Peng; Yao, Dezhong

2017-01-01

The EMG signal indicates the electrophysiological response to daily living of activities, particularly to lower-limb knee exercises. Literature reports have shown numerous benefits of the Wavelet analysis in EMG feature extraction for pattern recognition. However, its application to typical knee exercises when using only a single EMG channel is limited. In this study, three types of knee exercises, i.e., flexion of the leg up (standing), hip extension from a sitting position (sitting) and gait (walking) are investigated from 14 healthy untrained subjects, while EMG signals from the muscle group of vastus medialis and the goniometer on the knee joint of the detected leg are synchronously monitored and recorded. Four types of lower-limb motions including standing, sitting, stance phase of walking, and swing phase of walking, are segmented. The Wavelet Transform (WT) based Singular Value Decomposition (SVD) approach is proposed for the classification of four lower-limb motions using a single-channel EMG signal from the muscle group of vastus medialis. Based on lower-limb motions from all subjects, the combination of five-level wavelet decomposition and SVD is used to comprise the feature vector. The Support Vector Machine (SVM) is then configured to build a multiple-subject classifier for which the subject independent accuracy will be given across all subjects for the classification of four types of lower-limb motions. In order to effectively indicate the classification performance, EMG features from time-domain (e.g., Mean Absolute Value (MAV), Root-Mean-Square (RMS), integrated EMG (iEMG), Zero Crossing (ZC)) and frequency-domain (e.g., Mean Frequency (MNF) and Median Frequency (MDF)) are also used to classify lower-limb motions. The five-fold cross validation is performed and it repeats fifty times in order to acquire the robust subject independent accuracy. Results show that the proposed WT-based SVD approach has the classification accuracy of 91.85%±0.88% which

Estimation of muscle strength during motion recognition using multichannel surface EMG signals.

PubMed

Nagata, Kentaro; Nakano, Takemi; Magatani, Kazushige; Yamada, Masafumi

2008-01-01

The use of kinesiological electromyography is established as an evaluation tool for various kinds of applied research, and surface electromyogram (SEMG) has been widely used as a control source for human interfaces such as in a myoelectric prosthetic hand (we call them 'SEMG interfaces'). It is desirable to be able to control the SEMG interfaces with the same feeling as body movement. The existing SEMG interface mainly focuses on how to achieve accurate recognition of the intended movement. However, detecting muscular strength and reduced number of electrodes are also an important factor in controlling them. Therefore, our objective in this study is the development of and the estimation method for muscular strength that maintains the accuracy of hand motion recognition to reflect the result of measured power in a controlled object. Although the muscular strength can be evaluated by various methods, in this study a grasp force index was applied to evaluate the muscular strength. In order to achieve our objective, we directed our attention to measuring all valuable information for SEMG. This work proposes an application method of two simple linear models, and the selection method of an optimal electrode configuration to use them effectively. Our system required four SEMG measurement electrodes in which locations differed for every subject depending on the individual's characteristics, and those were selected from a 96ch multi electrode using the Monte Carlo method. From the experimental results, the performance in six normal subjects indicated that the recognition rate of four motions were perfect and the grasp force estimated result fit well with the actual measurement result.

A Versatile Embedded Platform for EMG Acquisition and Gesture Recognition.

PubMed

Benatti, Simone; Casamassima, Filippo; Milosevic, Bojan; Farella, Elisabetta; Schönle, Philipp; Fateh, Schekeb; Burger, Thomas; Huang, Qiuting; Benini, Luca

2015-10-01

Wearable devices offer interesting features, such as low cost and user friendliness, but their use for medical applications is an open research topic, given the limited hardware resources they provide. In this paper, we present an embedded solution for real-time EMG-based hand gesture recognition. The work focuses on the multi-level design of the system, integrating the hardware and software components to develop a wearable device capable of acquiring and processing EMG signals for real-time gesture recognition. The system combines the accuracy of a custom analog front end with the flexibility of a low power and high performance microcontroller for on-board processing. Our system achieves the same accuracy of high-end and more expensive active EMG sensors used in applications with strict requirements on signal quality. At the same time, due to its flexible configuration, it can be compared to the few wearable platforms designed for EMG gesture recognition available on market. We demonstrate that we reach similar or better performance while embedding the gesture recognition on board, with the benefit of cost reduction. To validate this approach, we collected a dataset of 7 gestures from 4 users, which were used to evaluate the impact of the number of EMG channels, the number of recognized gestures and the data rate on the recognition accuracy and on the computational demand of the classifier. As a result, we implemented a SVM recognition algorithm capable of real-time performance on the proposed wearable platform, achieving a classification rate of 90%, which is aligned with the state-of-the-art off-line results and a 29.7 mW power consumption, guaranteeing 44 hours of continuous operation with a 400 mAh battery.

The progesterone-induced enhancement of object recognition memory consolidation involves activation of the extracellular signal-regulated kinase (ERK) and mammalian target of rapamycin (mTOR) pathways in the dorsal hippocampus

PubMed Central

Orr, Patrick T.; Rubin, Amanda J.; Fan, Lu; Kent, Brianne A.; Frick, Karyn M.

2012-01-01

Although much recent work has elucidated the biochemical mechanisms underlying the modulation of memory by 17β-estradiol, little is known about the signaling events through which progesterone (P) regulates memory. We recently demonstrated that immediate post-training infusion of P into the dorsal hippocampus enhances object recognition memory consolidation in young ovariectomized female mice (Orr et al., 2009). The goal of the present study was to identify the biochemical alterations that might underlie this mnemonic enhancement. We hypothesized that the P-induced enhancement of object recognition would be dependent on activation of the ERK and mTOR pathways. In young ovariectomized mice, we found that bilateral dorsal hippocampal infusion of P significantly increased levels of phospho-p42 ERK and the mTOR substrate S6K in the dorsal hippocampus 5 minutes after infusion. Phospho-p42 ERK levels were downregulated 15 minutes after infusion and returned to baseline 30 minutes after infusion, suggesting a biphasic effect of P on ERK activation. Dorsal hippocampal ERK and mTOR activation were necessary for P to facilitate memory consolidation, as suggested by the fact that inhibitors of both pathways infused into the dorsal hippocampus immediately after training blocked the P-induced enhancement of object recognition. Collectively, these data provide the first demonstration that the ability of P to enhance memory consolidation depends on the rapid activation of cell signaling and protein synthesis pathways in the dorsal hippocampus. PMID:22265866

Recognition of Handwriting from Electromyography

PubMed Central

Linderman, Michael; Lebedev, Mikhail A.; Erlichman, Joseph S.

2009-01-01

Handwriting – one of the most important developments in human culture – is also a methodological tool in several scientific disciplines, most importantly handwriting recognition methods, graphology and medical diagnostics. Previous studies have relied largely on the analyses of handwritten traces or kinematic analysis of handwriting; whereas electromyographic (EMG) signals associated with handwriting have received little attention. Here we show for the first time, a method in which EMG signals generated by hand and forearm muscles during handwriting activity are reliably translated into both algorithm-generated handwriting traces and font characters using decoding algorithms. Our results demonstrate the feasibility of recreating handwriting solely from EMG signals – the finding that can be utilized in computer peripherals and myoelectric prosthetic devices. Moreover, this approach may provide a rapid and sensitive method for diagnosing a variety of neurogenerative diseases before other symptoms become clear. PMID:19707562

Striatal and Hippocampal Entropy and Recognition Signals in Category Learning: Simultaneous Processes Revealed by Model-Based fMRI

PubMed Central

Davis, Tyler; Love, Bradley C.; Preston, Alison R.

2012-01-01

Category learning is a complex phenomenon that engages multiple cognitive processes, many of which occur simultaneously and unfold dynamically over time. For example, as people encounter objects in the world, they simultaneously engage processes to determine their fit with current knowledge structures, gather new information about the objects, and adjust their representations to support behavior in future encounters. Many techniques that are available to understand the neural basis of category learning assume that the multiple processes that subserve it can be neatly separated between different trials of an experiment. Model-based functional magnetic resonance imaging offers a promising tool to separate multiple, simultaneously occurring processes and bring the analysis of neuroimaging data more in line with category learning’s dynamic and multifaceted nature. We use model-based imaging to explore the neural basis of recognition and entropy signals in the medial temporal lobe and striatum that are engaged while participants learn to categorize novel stimuli. Consistent with theories suggesting a role for the anterior hippocampus and ventral striatum in motivated learning in response to uncertainty, we find that activation in both regions correlates with a model-based measure of entropy. Simultaneously, separate subregions of the hippocampus and striatum exhibit activation correlated with a model-based recognition strength measure. Our results suggest that model-based analyses are exceptionally useful for extracting information about cognitive processes from neuroimaging data. Models provide a basis for identifying the multiple neural processes that contribute to behavior, and neuroimaging data can provide a powerful test bed for constraining and testing model predictions. PMID:22746951

Real-time object recognition in multidimensional images based on joined extended structural tensor and higher-order tensor decomposition methods

NASA Astrophysics Data System (ADS)

Cyganek, Boguslaw; Smolka, Bogdan

2015-02-01

In this paper a system for real-time recognition of objects in multidimensional video signals is proposed. Object recognition is done by pattern projection into the tensor subspaces obtained from the factorization of the signal tensors representing the input signal. However, instead of taking only the intensity signal the novelty of this paper is first to build the Extended Structural Tensor representation from the intensity signal that conveys information on signal intensities, as well as on higher-order statistics of the input signals. This way the higher-order input pattern tensors are built from the training samples. Then, the tensor subspaces are built based on the Higher-Order Singular Value Decomposition of the prototype pattern tensors. Finally, recognition relies on measurements of the distance of a test pattern projected into the tensor subspaces obtained from the training tensors. Due to high-dimensionality of the input data, tensor based methods require high memory and computational resources. However, recent achievements in the technology of the multi-core microprocessors and graphic cards allows real-time operation of the multidimensional methods as is shown and analyzed in this paper based on real examples of object detection in digital images.

Classification of EEG Signals Based on Pattern Recognition Approach

PubMed Central

Amin, Hafeez Ullah; Mumtaz, Wajid; Subhani, Ahmad Rauf; Saad, Mohamad Naufal Mohamad; Malik, Aamir Saeed

2017-01-01

Feature extraction is an important step in the process of electroencephalogram (EEG) signal classification. The authors propose a “pattern recognition” approach that discriminates EEG signals recorded during different cognitive conditions. Wavelet based feature extraction such as, multi-resolution decompositions into detailed and approximate coefficients as well as relative wavelet energy were computed. Extracted relative wavelet energy features were normalized to zero mean and unit variance and then optimized using Fisher's discriminant ratio (FDR) and principal component analysis (PCA). A high density EEG dataset validated the proposed method (128-channels) by identifying two classifications: (1) EEG signals recorded during complex cognitive tasks using Raven's Advance Progressive Metric (RAPM) test; (2) EEG signals recorded during a baseline task (eyes open). Classifiers such as, K-nearest neighbors (KNN), Support Vector Machine (SVM), Multi-layer Perceptron (MLP), and Naïve Bayes (NB) were then employed. Outcomes yielded 99.11% accuracy via SVM classifier for coefficient approximations (A5) of low frequencies ranging from 0 to 3.90 Hz. Accuracy rates for detailed coefficients were 98.57 and 98.39% for SVM and KNN, respectively; and for detailed coefficients (D5) deriving from the sub-band range (3.90–7.81 Hz). Accuracy rates for MLP and NB classifiers were comparable at 97.11–89.63% and 91.60–81.07% for A5 and D5 coefficients, respectively. In addition, the proposed approach was also applied on public dataset for classification of two cognitive tasks and achieved comparable classification results, i.e., 93.33% accuracy with KNN. The proposed scheme yielded significantly higher classification performances using machine learning classifiers compared to extant quantitative feature extraction. These results suggest the proposed feature extraction method reliably classifies EEG signals recorded during cognitive tasks with a higher degree of accuracy. PMID

A genome-wide screen of bacterial mutants that enhance dauer formation in C. elegans.

PubMed

Khanna, Amit; Kumar, Jitendra; Vargas, Misha A; Barrett, LaKisha; Katewa, Subhash; Li, Patrick; McCloskey, Tom; Sharma, Amit; Naudé, Nicole; Nelson, Christopher; Brem, Rachel; Killilea, David W; Mooney, Sean D; Gill, Matthew; Kapahi, Pankaj

2016-12-13

Molecular pathways involved in dauer formation, an alternate larval stage that allows Caenorhabditis elegans to survive adverse environmental conditions during development, also modulate longevity and metabolism. The decision to proceed with reproductive development or undergo diapause depends on food abundance, population density, and temperature. In recent years, the chemical identities of pheromone signals that modulate dauer entry have been characterized. However, signals derived from bacteria, the major source of nutrients for C. elegans, remain poorly characterized. To systematically identify bacterial components that influence dauer formation and aging in C. elegans, we utilized the individual gene deletion mutants in E. coli (K12). We identified 56 diverse E. coli deletion mutants that enhance dauer formation in an insulin-like receptor mutant (daf-2) background. We describe the mechanism of action of a bacterial mutant cyaA, that is defective in the production of cyclic AMP, which extends lifespan and enhances dauer formation through the modulation of TGF-β (daf-7) signaling in C. elegans. Our results demonstrate the importance of bacterial components in influencing developmental decisions and lifespan in C. elegans. Furthermore, we demonstrate that C. elegans is a useful model to study bacterial-host interactions.

M. tuberculosis-Initiated Human Mannose Receptor Signaling Regulates Macrophage Recognition and Vesicle Trafficking by FcRγ-Chain, Grb2, and SHP-1.

PubMed

Rajaram, Murugesan V S; Arnett, Eusondia; Azad, Abul K; Guirado, Evelyn; Ni, Bin; Gerberick, Abigail D; He, Li-Zhen; Keler, Tibor; Thomas, Lawrence J; Lafuse, William P; Schlesinger, Larry S

2017-10-03

Despite its prominent role as a C-type lectin (CTL) pattern recognition receptor, mannose receptor (MR, CD206)-specific signaling molecules and pathways are unknown. The MR is highly expressed on human macrophages, regulating endocytosis, phagocytosis, and immune responses and mediating Mycobacterium tuberculosis (M.tb) phagocytosis by human macrophages, thereby limiting phagosome-lysosome (P-L) fusion. We identified human MR-associated proteins using phosphorylated and non-phosphorylated MR cytoplasmic tail peptides. We found that MR binds FcRγ-chain, which is required for MR plasma membrane localization and M.tb cell association. Additionally, we discovered that MR-mediated M.tb association triggers immediate MR tyrosine residue phosphorylation and Grb2 recruitment, activating the Rac/Pak/Cdc-42 signaling cascade important for M.tb uptake. MR activation subsequently recruits SHP-1 to the M.tb-containing phagosome, where its activity limits PI(3)P generation at the phagosome and M.tb P-L fusion and promotes M.tb growth. In sum, we identify human MR signaling pathways that temporally regulate phagocytosis and P-L fusion during M.tb infection. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Bench-to-bedside review: Quorum sensing and the role of cell-to-cell communication during invasive bacterial infection

PubMed Central

Asad, Shadaba; Opal, Steven M

2008-01-01

Bacteria communicate extensively with each other and employ a communal approach to facilitate survival in hostile environments. A hierarchy of cell-to-cell signaling pathways regulates bacterial growth, metabolism, biofilm formation, virulence expression, and a myriad of other essential functions in bacterial populations. The notion that bacteria can signal each other and coordinate their assault patterns against susceptible hosts is now well established. These signaling networks represent a previously unrecognized survival strategy by which bacterial pathogens evade antimicrobial defenses and overwhelm the host. These quorum sensing communication signals can transgress species barriers and even kingdom barriers. Quorum sensing molecules can regulate human transcriptional programs to the advantage of the pathogen. Human stress hormones and cytokines can be detected by bacterial quorum sensing systems. By this mechanism, the pathogen can detect the physiologically stressed host, providing an opportunity to invade when the patient is most vulnerable. These rather sophisticated, microbial communication systems may prove to be a liability to pathogens as they make convenient targets for therapeutic intervention in our continuing struggle to control microbial pathogens. PMID:19040778

Pupil size changes during recognition memory.

PubMed

Otero, Samantha C; Weekes, Brendan S; Hutton, Samuel B

2011-10-01

Pupils dilate to a greater extent when participants view old compared to new items during recognition memory tests. We report three experiments investigating the cognitive processes associated with this pupil old/new effect. Using a remember/know procedure, we found that the effect occurred for old items that were both remembered and known at recognition, although it was attenuated for known compared to remembered items. In Experiment 2, the pupil old/new effect was observed when items were presented acoustically, suggesting the effect does not depend on low-level visual processes. The pupil old/new effect was also greater for items encoded under deep compared to shallow orienting instructions, suggesting it may reflect the strength of the underlying memory trace. Finally, the pupil old/new effect was also found when participants falsely recognized items as being old. We propose that pupils respond to a strength-of-memory signal and suggest that pupillometry provides a useful technique for exploring the underlying mechanisms of recognition memory. Copyright © 2011 Society for Psychophysiological Research.

Transcriptome landscape of a bacterial pathogen under plant immunity.

PubMed

Nobori, Tatsuya; Velásquez, André C; Wu, Jingni; Kvitko, Brian H; Kremer, James M; Wang, Yiming; He, Sheng Yang; Tsuda, Kenichi

2018-03-27

Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes in planta and determined high-resolution transcriptome patterns of the foliar bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana with a total of 27 combinations of plant immunity mutants and bacterial strains. Bacterial transcriptomes were analyzed at 6 h post infection to capture early effects of plant immunity on bacterial processes and to avoid secondary effects caused by different bacterial population densities in planta We identified specific "immune-responsive" bacterial genes and processes, including those that are activated in susceptible plants and suppressed by plant immune activation. Expression patterns of immune-responsive bacterial genes at the early time point were tightly linked to later bacterial growth levels in different host genotypes. Moreover, we found that a bacterial iron acquisition pathway is commonly suppressed by multiple plant immune-signaling pathways. Overexpression of a P. syringae sigma factor gene involved in iron regulation and other processes partially countered bacterial growth restriction during the plant immune response triggered by AvrRpt2. Collectively, this study defines the effects of plant immunity on the transcriptome of a bacterial pathogen and sheds light on the enigmatic mechanisms of bacterial growth inhibition during the plant immune response.

Overview of radar intra-pulse modulation recognition

NASA Astrophysics Data System (ADS)

Zang, Hanlin; Li, Yanling

2018-05-01

This paper introduces the current radar intra-pulse modulation method, describes the status quo and development direction of the intentional modulation and unintentional modulation in the pulse, and summarizes the existing problems and prospects for the future. Looking forward to the future, and providing a reference direction for the research on radar signal recognition in the next step.

Functional microdomains in bacterial membranes.

PubMed

López, Daniel; Kolter, Roberto

2010-09-01

The membranes of eukaryotic cells harbor microdomains known as lipid rafts that contain a variety of signaling and transport proteins. Here we show that bacterial membranes contain microdomains functionally similar to those of eukaryotic cells. These membrane microdomains from diverse bacteria harbor homologs of Flotillin-1, a eukaryotic protein found exclusively in lipid rafts, along with proteins involved in signaling and transport. Inhibition of lipid raft formation through the action of zaragozic acid--a known inhibitor of squalene synthases--impaired biofilm formation and protein secretion but not cell viability. The orchestration of physiological processes in microdomains may be a more widespread feature of membranes than previously appreciated.

Saturation of recognition elements blocks evolution of new tRNA identities

PubMed Central

Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D.; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A.; Ribas de Pouplana, Lluís

2016-01-01

Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. PMID:27386510

Transcriptome of American oysters, Crassostrea virginica, in response to bacterial challenge: insights into potential mechanisms of disease resistance.

PubMed

McDowell, Ian C; Nikapitiya, Chamilani; Aguiar, Derek; Lane, Christopher E; Istrail, Sorin; Gomez-Chiarri, Marta

2014-01-01

The American oyster Crassostrea virginica, an ecologically and economically important estuarine organism, can suffer high mortalities in areas in the Northeast United States due to Roseovarius Oyster Disease (ROD), caused by the gram-negative bacterial pathogen Roseovarius crassostreae. The goals of this research were to provide insights into: 1) the responses of American oysters to R. crassostreae, and 2) potential mechanisms of resistance or susceptibility to ROD. The responses of oysters to bacterial challenge were characterized by exposing oysters from ROD-resistant and susceptible families to R. crassostreae, followed by high-throughput sequencing of cDNA samples from various timepoints after disease challenge. Sequence data was assembled into a reference transcriptome and analyzed through differential gene expression and functional enrichment to uncover genes and processes potentially involved in responses to ROD in the American oyster. While susceptible oysters experienced constant levels of mortality when challenged with R. crassostreae, resistant oysters showed levels of mortality similar to non-challenged oysters. Oysters exposed to R. crassostreae showed differential expression of transcripts involved in immune recognition, signaling, protease inhibition, detoxification, and apoptosis. Transcripts involved in metabolism were enriched in susceptible oysters, suggesting that bacterial infection places a large metabolic demand on these oysters. Transcripts differentially expressed in resistant oysters in response to infection included the immune modulators IL-17 and arginase, as well as several genes involved in extracellular matrix remodeling. The identification of potential genes and processes responsible for defense against R. crassostreae in the American oyster provides insights into potential mechanisms of disease resistance.