N-Terminal Disordered Domain of Saccharomyces cerevisiae Hop1 Protein Is Dispensable for DNA Binding, Bridging, and Synapsis of Double-Stranded DNA Molecules But Is Necessary for Spore Formation

The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Delta hop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination.

Analysis of Wrist Pulse Signals Using Spatial Features in Time Domain

Wrist pulse signal contains more important information about the health status of a person and pulse signal diagnosis has been employed in oriental medicine since very long time. In this paper we have used signal processing techniques to extract information from wrist pulse signals. For this purpose we have acquired radial artery pulse signals at wrist position noninvasively for different cases of interest. The wrist pulse waveforms have been analyzed using spatial features. Results have been obtained for the case of wrist pulse signals recorded for several subjects before exercise and after exercise. It is shown that the spatial features show statistically significant changes for the two cases and hence they are effective in distinguishing the changes taking place due to exercise. Support vector machine classifier is used to classify between the groups, and a high classification accuracy of 99.71% is achieved. Thus this paper demonstrates the utility of the spatial features in studying wrist pulse signals obtained under various recording conditions. The ability of the model to distinguish changes occurring under two different recording conditions can be potentially used for health care applications.

State Transition Based Embedding in Cepstrum Domain for Audio Copyright Protection

In this paper, we propose a new state transition based embedding (STBE) technique for audio watermarking with high fidelity. Furthermore, we propose a new correlation based encoding (CBE) scheme for binary logo image in order to enhance the payload capacity. The result of CBE is also compared with standard run-length encoding (RLE) compression and Huffman schemes. Most of the watermarking algorithms are based on modulating selected transform domain feature of an audio segment in order to embed given watermark bit. In the proposed STBE method instead of modulating feature of each and every segment to embed data, our aim is to retain the default value of this feature for most of the segments. Thus, a high quality of watermarked audio is maintained. Here, the difference between the mean values (Mdiff) of insignificant complex cepstrum transform (CCT) coefficients of down-sampled subsets is selected as a robust feature for embedding. Mdiff values of the frames are changed only when certain conditions are met. Hence, almost 50% of the times, segments are not changed and still STBE can convey watermark information at receiver side. STBE also exhibits a partial restoration feature by which the watermarked audio can be restored partially after extraction of the watermark at detector side. The psychoacoustic model analysis showed that the noise-masking ratio (NMR) of our system is less than -10dB. As amplitude scaling in time domain does not affect selected insignificant CCT coefficients, strong invariance towards amplitude scaling attacks is also proved theoretically. Experimental results reveal that the proposed watermarking scheme maintains high audio quality and are simultaneously robust to general attacks like MP3 compression, amplitude scaling, additive noise, re-quantization, etc.

Field induced domain switching as the origin of anomalous lattice strain along non-polar direction in rhombohedral BiScO3-PbTiO3 close to the morphotropic phase boundary

The lattice strain and domain switching behavior of xBiScO(3)-(1-x) PbTiO3 (x = 0.40) was investigated as a function of cyclic field and grain orientation by in situ X-ray diffraction during application of electric fields. The electric field induced 200 lattice strain was measured to be five times larger than the 111 lattice strain in pseudorhombohedral xBiScO(3)-(1-x) PbTiO3 (x = 0.40). It is shown that the anomalous 200 lattice strain is not an intrinsic phenomenon, but arises primarily due to stress associated with the reorientation of the 111 domains in dense polycrystalline ceramic. (C) 2015 AIP Publishing LLC.

A carboxy terminal domain of the L protein of rinderpest virus possesses RNA triphosphatase activity - The first enzyme in the viral mRNA capping pathway

The large protein L of negative-sense RNA viruses is a multifunctional protein involved in transcription and replication of genomic RNA. It also possesses enzymatic activities involved in capping and methylation of viral mRNAs. The pathway for mRNA capping followed by the L protein of the viruses in the Morbillivirus genus has not been established, although it has been speculated that these viruses may follow the unconventional capping pathway as has been shown for some viruses of Rhabdoviridae family. We had earlier shown that the large protein L of Rinderpest virus expressed as recombinant L-P complex in insect cells as well as the ribonucleoprotein complex from purified virus possesses RNA triphosphatase (RTPase) and guanylyltransferase activities, in addition to RNA dependent RNA polymerase activity. In the present work, we demonstrate that RTPase as well as nucleoside triphosphatase (NTPase) activities are exhibited by a subdomain of the L protein in the C terminal region (a.a. 1640 1840). The RTPase activity depends absolutely on a divalent cation, either magnesium or manganese. Both the RTPase and NTPase activities of the protein show dual metal specificity. Two mutant proteins having alanine mutations in the glutamic acid residues in motif-A of the RTPase domain did not show RTPase activity, while exhibiting reduced NTPase activity suggesting overlapping active sites for the two enzymatic functions. The RTPase and NTPase activities of the L subdomain resemble those of the Vaccinia capping enzyme D1 and the baculovirus LEF4 proteins. (C) 2015 Elsevier Inc. All rights reserved.

Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein

The survival protein SurE from Salmonella typhimurium (StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of beta-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167 degrees. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11 degrees between the B chains upon superposition of the A chains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.

Human action recognition in H.264/AVC compressed domain using meta-cognitive radial basis function network

In this paper, we propose a H.264/AVC compressed domain human action recognition system with projection based metacognitive learning classifier (PBL-McRBFN). The features are extracted from the quantization parameters and the motion vectors of the compressed video stream for a time window and used as input to the classifier. Since compressed domain analysis is done with noisy, sparse compression parameters, it is a huge challenge to achieve performance comparable to pixel domain analysis. On the positive side, compressed domain allows rapid analysis of videos compared to pixel level analysis. The classification results are analyzed for different values of Group of Pictures (GOP) parameter, time window including full videos. The functional relationship between the features and action labels are established using PBL-McRBFN with a cognitive and meta-cognitive component. The cognitive component is a radial basis function, while the meta-cognitive component employs self-regulation to achieve better performance in subject independent action recognition task. The proposed approach is faster and shows comparable performance with respect to the state-of-the-art pixel domain counterparts. It employs partial decoding, which rules out the complexity of full decoding, and minimizes computational load and memory usage. This results in reduced hardware utilization and increased speed of classification. The results are compared with two benchmark datasets and show more than 90% accuracy using the PBL-McRBFN. The performance for various GOP parameters and group of frames are obtained with twenty random trials and compared with other well-known classifiers in machine learning literature. (C) 2015 Elsevier B.V. All rights reserved.

Optimum Parameter Selection in Sparse Reconstruction of Frequency-Domain Optical-Coherence Tomography Signals

For a multilayered specimen, the back-scattered signal in frequency-domain optical-coherence tomography (FDOCT) is expressible as a sum of cosines, each corresponding to a change of refractive index in the specimen. Each of the cosines represent a peak in the reconstructed tomogram. We consider a truncated cosine series representation of the signal, with the constraint that the coefficients in the basis expansion be sparse. An l(2) (sum of squared errors) data error is considered with an l(1) (summation of absolute values) constraint on the coefficients. The optimization problem is solved using Weiszfeld's iteratively reweighted least squares (IRLS) algorithm. On real FDOCT data, improved results are obtained over the standard reconstruction technique with lower levels of background measurement noise and artifacts due to a strong l(1) penalty. The previous sparse tomogram reconstruction techniques in the literature proposed collecting sparse samples, necessitating a change in the data capturing process conventionally used in FDOCT. The IRLS-based method proposed in this paper does not suffer from this drawback.

Compressed domain human action recognition in H.264/AVC video streams

This paper discusses a novel high-speed approach for human action recognition in H.264/AVC compressed domain. The proposed algorithm utilizes cues from quantization parameters and motion vectors extracted from the compressed video sequence for feature extraction and further classification using Support Vector Machines (SVM). The ultimate goal of the proposed work is to portray a much faster algorithm than pixel domain counterparts, with comparable accuracy, utilizing only the sparse information from compressed video. Partial decoding rules out the complexity of full decoding, and minimizes computational load and memory usage, which can result in reduced hardware utilization and faster recognition results. The proposed approach can handle illumination changes, scale, and appearance variations, and is robust to outdoor as well as indoor testing scenarios. We have evaluated the performance of the proposed method on two benchmark action datasets and achieved more than 85 % accuracy. The proposed algorithm classifies actions with speed (> 2,000 fps) approximately 100 times faster than existing state-of-the-art pixel-domain algorithms.

Study of wrist pulse signals using time domain spatial features

Blood travels throughout the body and thus its flow is modulated by changes in body condition. As a consequence, the wrist pulse signal contains important information about the status of the human body. In this work we have employed signal processing techniques to extract important information from these signals. Radial artery pulse pressure signals are acquired at wrist position noninvasively for several subjects for two cases of interest, viz. before and after exercise, and before and after lunch. Further analysis is performed by fitting a bi-modal Gaussian model to the data and extracting spatial features from the fit. The spatial features show statistically significant (p < 0.001) changes between the groups for both the cases, which indicates that they are effective in distinguishing the changes taking place due to exercise or food intake. Recursive cluster elimination based support vector machine classifier is used to classify between the groups. A high classification accuracy of 99.71% is achieved for the exercise case and 99.94% is achieved for the lunch case. This paper demonstrates the utility of certain spatial features in studying wrist pulse signals obtained under various experimental conditions. The ability of the spatial features in distinguishing changing body conditions can be potentially used for various healthcare applications. (C) 2015 Elsevier Ltd. All rights reserved.

PERIODIC CONTROLS IN AN OSCILLATING DOMAIN: CONTROLS VIA UNFOLDING AND HOMOGENIZATION

An optimal control problem in a two-dimensional domain with a rapidly oscillating boundary is considered. The main features of this article are on two points, namely, we consider periodic controls in the thin periodic slabs of period epsilon > 0, a small parameter, and height O(1) in the oscillatory part, and the controls are characterized using unfolding operators. We then do a homogenization analysis of the optimal control problems as epsilon -> 0 with L-2 as well as Dirichlet (gradient-type) cost functionals.

First Structural View of a Peptide Interacting with the Nucleotide Binding Domain of Heat Shock Protein 90

The involvement of Hsp90 in progression of diseases like cancer, neurological disorders and several pathogen related conditions is well established. Hsp90, therefore, has emerged as an attractive drug target for many of these diseases. Several small molecule inhibitors of Hsp90, such as geldanamycin derivatives, that display antitumor activity, have been developed and are under clinical trials. However, none of these tested inhibitors or drugs are peptide-based compounds. Here we report the first crystal structure of a peptide bound at the ATP binding site of the N-terminal domain of Hsp90. The peptide makes several specific interactions with the binding site residues, which are comparable to those made by the nucleotide and geldanamycin. A modified peptide was designed based on these interactions. Inhibition of ATPase activity of Hsp90 was observed in the presence of the modified peptide. This study provides an alternative approach and a lead peptide molecule for the rational design of effective inhibitors of Hsp90 function.

Evidence for N-7 guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus

Post-transcriptional modification of viral mRNA is essential for the translation of viral proteins by cellular translation machinery. Due to the cytoplasmic replication of Paramyxoviruses, the viral-encoded RNA-dependent RNA polymerase (RdRP) is thought to possess all activities required for mRNA capping and methylation. In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Further, we show that a recombinant C-terminal fragment (1717-2183 aa) of L protein is capable of methylating capped mRNA, suggesting that the various post-transcriptional activities of the L protein are located in independently folding domains.

Ultrafast Chemical Dynamics in Time Domain Through Fluorescence Spectroscopy

While absorption and emission spectroscopy have always been used to detect and characterize molecules and molecular complexes, the availability of ultrashort laser pulses and associated computer-aided optical detection techniques allowed study of chemical processes directly in the time domain at unprecedented time scales, through appearance and disappearance of fluorescence from participating chemical species. Application of such techniques to chemical dynamics in liquids, where many processes occur with picosecond and femtosecond time scales lead to the discovery of a host of new phenomena that in turn led to the development of many new theories. Experiment and theory together provided new and valuable insight into many fundamental chemical processes, like isomerization dynamics, electron and proton transfer reactions, vibrational energy and phase relaxation, photosynthesis, to name just a few. In this article, we shall review a few of such discoveries in attempt to provide a glimpse of the fascinating research employing fluorescence spectroscopy that changed the field of chemical dynamics forever.