A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.

PubMed

Gupta, Amita; Shrivastava, Nimisha; Grover, Payal; Singh, Ajay; Mathur, Kapil; Verma, Vaishali; Kaur, Charanpreet; Chaudhary, Vijay K

2013-01-01

Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.

Selfish DNA in protein-coding genes of Rickettsia.

PubMed

Ogata, H; Audic, S; Barbe, V; Artiguenave, F; Fournier, P E; Raoult, D; Claverie, J M

2000-10-13

Rickettsia conorii, the aetiological agent of Mediterranean spotted fever, is an intracellular bacterium transmitted by ticks. Preliminary analyses of the nearly complete genome sequence of R. conorii have revealed 44 occurrences of a previously undescribed palindromic repeat (150 base pairs long) throughout the genome. Unexpectedly, this repeat was found inserted in-frame within 19 different R. conorii open reading frames likely to encode functional proteins. We found the same repeat in proteins of other Rickettsia species. The finding of a mobile element inserted in many unrelated genes suggests the potential role of selfish DNA in the creation of new protein sequences.

Facing the Sunrise: Cultural Worldview Underlying Intrinsic-Based Encoding of Absolute Frames of Reference in Aymara

ERIC Educational Resources Information Center

Nunez, Rafael E.; Cornejo, Carlos

2012-01-01

The Aymara of the Andes use absolute (cardinal) frames of reference for describing the relative position of ordinary objects. However, rather than encoding them in available absolute lexemes, they do it in lexemes that are intrinsic to the body: "nayra" ("front") and "qhipa" ("back"), denoting east and west,…

Frame prediction using recurrent convolutional encoder with residual learning

NASA Astrophysics Data System (ADS)

Yue, Boxuan; Liang, Jun

2018-05-01

The prediction for the frame of a video is difficult but in urgent need in auto-driving. Conventional methods can only predict some abstract trends of the region of interest. The boom of deep learning makes the prediction for frames possible. In this paper, we propose a novel recurrent convolutional encoder and DE convolutional decoder structure to predict frames. We introduce the residual learning in the convolution encoder structure to solve the gradient issues. The residual learning can transform the gradient back propagation to an identity mapping. It can reserve the whole gradient information and overcome the gradient issues in Recurrent Neural Networks (RNN) and Convolutional Neural Networks (CNN). Besides, compared with the branches in CNNs and the gated structures in RNNs, the residual learning can save the training time significantly. In the experiments, we use UCF101 dataset to train our networks, the predictions are compared with some state-of-the-art methods. The results show that our networks can predict frames fast and efficiently. Furthermore, our networks are used for the driving video to verify the practicability.

Node synchronization schemes for the Big Viterbi Decoder

NASA Technical Reports Server (NTRS)

Cheung, K.-M.; Swanson, L.; Arnold, S.

1992-01-01

The Big Viterbi Decoder (BVD), currently under development for the DSN, includes three separate algorithms to acquire and maintain node and frame synchronization. The first measures the number of decoded bits between two consecutive renormalization operations (renorm rate), the second detects the presence of the frame marker in the decoded bit stream (bit correlation), while the third searches for an encoded version of the frame marker in the encoded input stream (symbol correlation). A detailed account of the operation is given, as well as performance comparison, of the three methods.

Delay-Encoded Harmonic Imaging (DE-HI) in Multiplane-Wave Compounding.

PubMed

Gong, Ping; Song, Pengfei; Chen, Shigao

2017-04-01

The development of ultrafast ultrasound imaging brings great opportunities to improve imaging technologies such as shear wave elastography and ultrafast Doppler imaging. In ultrafast imaging, several tilted plane or diverging wave images are coherently combined to form a compounded image, leading to trade-offs among image signal-to-noise ratio (SNR), resolution, and post-compounded frame rate. Multiplane wave (MW) imaging is proposed to solve this trade-off by encoding multiple plane waves with Hadamard matrix during one transmission event (i.e. pulse-echo event), to improve image SNR without sacrificing the resolution or frame rate. However, it suffers from stronger reverberation artifacts in B-mode images compared to standard plane wave compounding due to longer transmitted pulses. If harmonic imaging can be combined with MW imaging, the reverberation artifacts and other clutter noises such as sidelobes and multipath scattering clutters should be suppressed. The challenge, however, is that the Hadamard codes used in MW imaging cannot encode the 2 nd harmonic component by inversing the pulse polarity. In this paper, we propose a delay-encoded harmonic imaging (DE-HI) technique to encode the 2 nd harmonic with a one quarter period delay calculated at the transmit center frequency, rather than reversing the pulse polarity during multiplane wave emissions. Received DE-HI signals can then be decoded in the frequency domain to recover the signals as in single plane wave emissions, but mainly with improved SNR at the 2 nd harmonic component instead of the fundamental component. DE-HI was tested experimentally with a point target, a B-mode imaging phantom, and in-vivo human liver imaging. Improvements in image contrast-to-noise ratio (CNR), spatial resolution, and lesion-signal-to-noise ratio ( l SNR) have been achieved compared to standard plane wave compounding, MW imaging, and standard harmonic imaging (maximal improvement of 116% on CNR and 115% on l SNR as compared to standard HI around 55 mm depth in the B-mode imaging phantom study). The potential high frame rate and the stability of encoding and decoding processes of DE-HI were also demonstrated, which made DE-HI promising for a wide spectrum of imaging applications.

Study of statistical coding for digital TV

NASA Technical Reports Server (NTRS)

Gardenhire, L. W.

1972-01-01

The results are presented for a detailed study to determine a pseudo-optimum statistical code to be installed in a digital TV demonstration test set. Studies of source encoding were undertaken, using redundancy removal techniques in which the picture is reproduced within a preset tolerance. A method of source encoding, which preliminary studies show to be encouraging, is statistical encoding. A pseudo-optimum code was defined and the associated performance of the code was determined. The format was fixed at 525 lines per frame, 30 frames per second, as per commercial standards.

Multi-volumetric registration and mosaicking using swept-source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography

NASA Astrophysics Data System (ADS)

Bozic, Ivan; El-Haddad, Mohamed T.; Malone, Joseph D.; Joos, Karen M.; Patel, Shriji N.; Tao, Yuankai K.

2017-02-01

Ophthalmic diagnostic imaging using optical coherence tomography (OCT) is limited by bulk eye motions and a fundamental trade-off between field-of-view (FOV) and sampling density. Here, we introduced a novel multi-volumetric registration and mosaicking method using our previously described multimodal swept-source spectrally encoded scanning laser ophthalmoscopy and OCT (SS-SESLO-OCT) system. Our SS-SESLO-OCT acquires an entire en face fundus SESLO image simultaneously with every OCT cross-section at 200 frames-per-second. In vivo human retinal imaging was performed in a healthy volunteer, and three volumetric datasets were acquired with the volunteer moving freely and refixating between each acquisition. In post-processing, SESLO frames were used to estimate en face rotational and translational motions by registering every frame in all three volumetric datasets to the first frame in the first volume. OCT cross-sections were contrast-normalized and registered axially and rotationally across all volumes. Rotational and translational motions calculated from SESLO frames were applied to corresponding OCT B-scans to compensate for interand intra-B-scan bulk motions, and the three registered volumes were combined into a single interpolated multi-volumetric mosaic. Using complementary information from SESLO and OCT over serially acquired volumes, we demonstrated multivolumetric registration and mosaicking to recover regions of missing data resulting from blinks, saccades, and ocular drifts. We believe our registration method can be directly applied for multi-volumetric motion compensation, averaging, widefield mosaicking, and vascular mapping with potential applications in ophthalmic clinical diagnostics, handheld imaging, and intraoperative guidance.

Draft Genome Sequence of Marinobacter sp. Strain ANT_B65, Isolated from Antarctic Marine Sponge.

PubMed

de França, Paula; Camilo, Esther; Fantinatti-Garboginni, Fabiana

2018-01-04

Marinobacter sp. strain ANT_B65 was isolated from sponge collected in King George Island, Antarctica. The draft genome of 4,173,840 bp encodes 3,743 protein-coding open reading frames. The genome will provide insights into the strain's potential use in the production of natural products. Copyright © 2018 de França et al.

Variable disparity-motion estimation based fast three-view video coding

NASA Astrophysics Data System (ADS)

Bae, Kyung-Hoon; Kim, Seung-Cheol; Hwang, Yong Seok; Kim, Eun-Soo

2009-02-01

In this paper, variable disparity-motion estimation (VDME) based 3-view video coding is proposed. In the encoding, key-frame coding (KFC) based motion estimation and variable disparity estimation (VDE) for effectively fast three-view video encoding are processed. These proposed algorithms enhance the performance of 3-D video encoding/decoding system in terms of accuracy of disparity estimation and computational overhead. From some experiments, stereo sequences of 'Pot Plant' and 'IVO', it is shown that the proposed algorithm's PSNRs is 37.66 and 40.55 dB, and the processing time is 0.139 and 0.124 sec/frame, respectively.

General Solution for Theoretical Packet Data Loss Rate

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin; Schlesinger, Adam

2006-01-01

Communications systems which transfer blocks ("frames") of data must use a marker ("frame synchronization pattern") for identifying where a block begins. A technique ("frame synchronization strategy") is used to locate the start of each frame and maintain synchronization as additional blocks are processed. A device which strips out the frame synchronization pattern [FSP] and provides an "end of frame" pulse is called a frame synchronizer. As clock and data errors are introduced into the system, the start-of-block marker becomes displaced and/or corrupted. The capability of the frame synchronizer to stay locked to the pattern under these conditions is a figure of merit for the frame synchronization strategy. It is important to select a strategy which will stay locked nearly all the time at bit error rates where the data is usable. ("Bit error rate" [BER] is the fraction of binary bits which are inverted by passage through a communication system.) The fraction of frames that are discarded because the frame synchronizer is not locked is called "Percent Data Loss" or "Packet Data Loss rate" [PDL]. A general approach for accurately predicting PDL given BER was developed in Theoretical Percent Data Loss Calculation and Measurement Accuracy, T. P. Kelly, LESC-30554, December 1992. Kelly gave a solution in terms of matrix equations, and only addressed "level" channel encoding. This paper goes on to give a closed-form polynomial solution for the most common class of frame synchronizer strategies, and will also address "mark" and "space" (differential) channel encoding, and burst error environments. The paper is divided into four sections and follows a logically ordered presentation, with results developed before they are evaluated. However, most readers will derive the greatest benefit from this paper by treating the results as reference material. The result developed for differential encoding can be extended to other applications (like block codes) where the probability is needed that a block contains only a certain number of errors.

Schemes for efficient transmission of encoded video streams on high-speed networks

NASA Astrophysics Data System (ADS)

Ramanathan, Srinivas; Vin, Harrick M.; Rangan, P. Venkat

1994-04-01

In this paper, we argue that significant performance benefits can accrue if integrated networks implement application-specific mechanisms that account for the diversities in media compression schemes. Towards this end, we propose a simple, yet effective, strategy called Frame Induced Packet Discarding (FIPD), in which, upon detection of loss of a threshold number (determined by an application's video encoding scheme) of packets belonging to a video frame, the network attempts to discard all the remaining packets of that frame. In order to analytically quantify the performance of FIPD so as to obtain fractional frame losses that can be guaranteed to video channels, we develop a finite state, discrete time markov chain model of the FIPD strategy. The fractional frame loss thus computed can serve as the criterion for admission control at the network. Performance evaluations demonstrate the utility of the FIPD strategy.

Radial k-t SPIRiT: autocalibrated parallel imaging for generalized phase-contrast MRI.

PubMed

Santelli, Claudio; Schaeffter, Tobias; Kozerke, Sebastian

2014-11-01

To extend SPIRiT to additionally exploit temporal correlations for highly accelerated generalized phase-contrast MRI and to compare the performance of the proposed radial k-t SPIRiT method relative to frame-by-frame SPIRiT and radial k-t GRAPPA reconstruction for velocity and turbulence mapping in the aortic arch. Free-breathing navigator-gated two-dimensional radial cine imaging with three-directional multi-point velocity encoding was implemented and fully sampled data were obtained in the aortic arch of healthy volunteers. Velocities were encoded with three different first gradient moments per axis to permit quantification of mean velocity and turbulent kinetic energy. Velocity and turbulent kinetic energy maps from up to 14-fold undersampled data were compared for k-t SPIRiT, frame-by-frame SPIRiT, and k-t GRAPPA relative to the fully sampled reference. Using k-t SPIRiT, improvements in magnitude and velocity reconstruction accuracy were found. Temporally resolved magnitude profiles revealed a reduction in spatial blurring with k-t SPIRiT compared with frame-by-frame SPIRiT and k-t GRAPPA for all velocity encodings, leading to improved estimates of turbulent kinetic energy. k-t SPIRiT offers improved reconstruction accuracy at high radial undersampling factors and hence facilitates the use of generalized phase-contrast MRI for routine use. Copyright © 2013 Wiley Periodicals, Inc.

Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins.

PubMed

Plant, Ewan P; Rakauskaite, Rasa; Taylor, Deborah R; Dinman, Jonathan D

2010-05-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

Transcriptionally active PCR for antigen identification and vaccine development: in vitro genome-wide screening and in vivo immunogenicity

PubMed Central

Regis, David P.; Dobaño, Carlota; Quiñones-Olson, Paola; Liang, Xiaowu; Graber, Norma L.; Stefaniak, Maureen E.; Campo, Joseph J.; Carucci, Daniel J.; Roth, David A.; He, Huaping; Felgner, Philip L.; Doolan, Denise L.

2009-01-01

We have evaluated a technology called Transcriptionally Active PCR (TAP) for high throughput identification and prioritization of novel target antigens from genomic sequence data using the Plasmodium parasite, the causative agent of malaria, as a model. First, we adapted the TAP technology for the highly AT-rich Plasmodium genome, using well-characterized P. falciparum and P. yoelii antigens and a small panel of uncharacterized open reading frames from the P. falciparum genome sequence database. We demonstrated that TAP fragments encoding six well-characterized P. falciparum antigens and five well-characterized P. yoelii antigens could be amplified in an equivalent manner from both plasmid DNA and genomic DNA templates, and that uncharacterized open reading frames could also be amplified from genomic DNA template. Second, we showed that the in vitro expression of the TAP fragments was equivalent or superior to that of supercoiled plasmid DNA encoding the same antigen. Third, we evaluated the in vivo immunogenicity of TAP fragments encoding a subset of the model P. falciparum and P. yoelii antigens. We found that antigen-specific antibody and cellular immune responses induced by the TAP fragments in mice were equivalent or superior to those induced by the corresponding plasmid DNA vaccines. Finally, we developed and demonstrated proof-of-principle for an in vitro humoral immunoscreening assay for down-selection of novel target antigens. These data support the potential of a TAP approach for rapid high throughput functional screening and identification of potential candidate vaccine antigens from genomic sequence data. PMID:18164079

Transcriptionally active PCR for antigen identification and vaccine development: in vitro genome-wide screening and in vivo immunogenicity.

PubMed

Regis, David P; Dobaño, Carlota; Quiñones-Olson, Paola; Liang, Xiaowu; Graber, Norma L; Stefaniak, Maureen E; Campo, Joseph J; Carucci, Daniel J; Roth, David A; He, Huaping; Felgner, Philip L; Doolan, Denise L

2008-03-01

We have evaluated a technology called transcriptionally active PCR (TAP) for high throughput identification and prioritization of novel target antigens from genomic sequence data using the Plasmodium parasite, the causative agent of malaria, as a model. First, we adapted the TAP technology for the highly AT-rich Plasmodium genome, using well-characterized P. falciparum and P. yoelii antigens and a small panel of uncharacterized open reading frames from the P. falciparum genome sequence database. We demonstrated that TAP fragments encoding six well-characterized P. falciparum antigens and five well-characterized P. yoelii antigens could be amplified in an equivalent manner from both plasmid DNA and genomic DNA templates, and that uncharacterized open reading frames could also be amplified from genomic DNA template. Second, we showed that the in vitro expression of the TAP fragments was equivalent or superior to that of supercoiled plasmid DNA encoding the same antigen. Third, we evaluated the in vivo immunogenicity of TAP fragments encoding a subset of the model P. falciparum and P. yoelii antigens. We found that antigen-specific antibody and cellular immune responses induced by the TAP fragments in mice were equivalent or superior to those induced by the corresponding plasmid DNA vaccines. Finally, we developed and demonstrated proof-of-principle for an in vitro humoral immunoscreening assay for down-selection of novel target antigens. These data support the potential of a TAP approach for rapid high throughput functional screening and identification of potential candidate vaccine antigens from genomic sequence data.

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins▿

PubMed Central

Plant, Ewan P.; Rakauskaitė, Rasa; Taylor, Deborah R.; Dinman, Jonathan D.

2010-01-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed −1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the −1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a “golden mean” model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins. PMID:20164235

Cloning and sequence analysis of complementary DNA encoding an aberrantly rearranged human T-cell gamma chain.

PubMed Central

Dialynas, D P; Murre, C; Quertermous, T; Boss, J M; Leiden, J M; Seidman, J G; Strominger, J L

1986-01-01

Complementary DNA (cDNA) encoding a human T-cell gamma chain has been cloned and sequenced. At the junction of the variable and joining regions, there is an apparent deletion of two nucleotides in the human cDNA sequence relative to the murine gamma-chain cDNA sequence, resulting simultaneously in the generation of an in-frame stop codon and in a translational frameshift. For this reason, the sequence presented here encodes an aberrantly rearranged human T-cell gamma chain. There are several surprising differences between the deduced human and murine gamma-chain amino acid sequences. These include poor homology in the variable region, poor homology in a discrete segment of the constant region precisely bounded by the expected junctions of exon CII, and the presence in the human sequence of five potential sites for N-linked glycosylation. Images PMID:3458221

A novel frame-level constant-distortion bit allocation for smooth H.264/AVC video quality

NASA Astrophysics Data System (ADS)

Liu, Li; Zhuang, Xinhua

2009-01-01

It is known that quality fluctuation has a major negative effect on visual perception. In previous work, we introduced a constant-distortion bit allocation method [1] for H.263+ encoder. However, the method in [1] can not be adapted to the newest H.264/AVC encoder directly as the well-known chicken-egg dilemma resulted from the rate-distortion optimization (RDO) decision process. To solve this problem, we propose a new two stage constant-distortion bit allocation (CDBA) algorithm with enhanced rate control for H.264/AVC encoder. In stage-1, the algorithm performs RD optimization process with a constant quantization QP. Based on prediction residual signals from stage-1 and target distortion for smooth video quality purpose, the frame-level bit target is allocated by using a close-form approximations of ratedistortion relationship similar to [1], and a fast stage-2 encoding process is performed with enhanced basic unit rate control. Experimental results show that, compared with original rate control algorithm provided by H.264/AVC reference software JM12.1, the proposed constant-distortion frame-level bit allocation scheme reduces quality fluctuation and delivers much smoother PSNR on all testing sequences.

Ipsilateral wrist-ankle movements in the sagittal plane encoded in extrinsic reference frame.

PubMed

Muraoka, Tetsuro; Ishida, Yuki; Obu, Takashi; Crawshaw, Larry; Kanosue, Kazuyuki

2013-04-01

When performing oscillatory movements of two joints in the sagittal plane, there is a directional constraint for performing such movements. Previous studies could not distinguish whether the directional constraint reflected movement direction encoded in the extrinsic (outside the body) reference frame or in the intrinsic (the participants' torso/head) reference frame since participants performed coordinated movements in a sitting position where the torso/head was stationary relative to the external world. In order to discern the reference frame in the present study, participants performed paced oscillatory movements of the ipsilateral wrist and ankle in the sagittal plane in a standing position so that the torso/head moved relative to the external world. The coordinated movements were performed in one of two modes of coordination, moving the hand upward concomitant with either ankle plantarflexion or ankle dorsiflexion. The same directional mode relative to extrinsic space was more stable and accurate as compared with the opposite directional mode. When forearm position was changed from the pronated position to the supinated position, similar results were obtained, indicating that the results were independent of a particular coupling of muscles. These findings suggest that the directional constraint on ipsilateral joints movements in the sagittal plane reflects movement direction encoded in the extrinsic reference frame. Copyright © 2013 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.

PubMed

Macreadie, I G; Scott, R M; Zinn, A R; Butow, R A

1985-06-01

The optional 1143 bp intron in the yeast mitochondrial 21S rRNA gene (omega +) is nearly quantitatively inserted in genetic crosses into 21S rRNA alleles that lack it (omega -). The intron contains an open reading frame that can encode a protein of 235 amino acids, but no function has been ascribed to this sequence. We previously found an in vivo double-strand break in omega - DNA at or close to the intron insertion site only in zygotes of omega + X omega - crosses that appears with the same kinetics as intron insertion. We now show that mutations in the intron open reading frame that would alter the translation product simultaneously inhibit nonreciprocal omega recombination and the in vivo double-strand break in omega - DNA. These results provide evidence that the open reading frame encodes a protein required for intron transposition and support the role of the double-strand break in the process.

Classical and quantum communication without a shared reference frame.

PubMed

Bartlett, Stephen D; Rudolph, Terry; Spekkens, Robert W

2003-07-11

We show that communication without a shared reference frame is possible using entangled states. Both classical and quantum information can be communicated with perfect fidelity without a shared reference frame at a rate that asymptotically approaches one classical bit or one encoded qubit per transmitted qubit. We present an optical scheme to communicate classical bits without a shared reference frame using entangled photon pairs and linear optical Bell state measurements.

The type II pullulanase of Thermococcus hydrothermalis: molecular characterization of the gene and expression of the catalytic domain.

PubMed

Erra-Pujada, M; Debeire, P; Duchiron, F; O'Donohue, M J

1999-05-01

The gene encoding a hyperthermostable type II pullulanase produced by Thermococcus hydrothermalis (Th-Apu) has been isolated. Analysis of a total of 5.2 kb of genomic DNA has revealed the presence of three open reading frames, one of which (apuA) encodes the pullulanase. This enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. In addition to a typical N-terminal signal peptide, Th-Apu possesses a catalytic domain, a domain bearing S-layer homology-like motifs, a Thr-rich region, and a potential C-terminal transmembrane domain. The presence of these noncatalytic domains suggests that Th-Apu may be anchored to the cell surface and be O glycosylated.

The Type II Pullulanase of Thermococcus hydrothermalis: Molecular Characterization of the Gene and Expression of the Catalytic Domain

PubMed Central

Erra-Pujada, Marta; Debeire, Philippe; Duchiron, Francis; O’Donohue, Michael J.

1999-01-01

The gene encoding a hyperthermostable type II pullulanase produced by Thermococcus hydrothermalis (Th-Apu) has been isolated. Analysis of a total of 5.2 kb of genomic DNA has revealed the presence of three open reading frames, one of which (apuA) encodes the pullulanase. This enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. In addition to a typical N-terminal signal peptide, Th-Apu possesses a catalytic domain, a domain bearing S-layer homology-like motifs, a Thr-rich region, and a potential C-terminal transmembrane domain. The presence of these noncatalytic domains suggests that Th-Apu may be anchored to the cell surface and be O glycosylated. PMID:10322035

Structure and strategy in encoding simplified graphs

NASA Technical Reports Server (NTRS)

Schiano, Diane J.; Tversky, Barbara

1992-01-01

Tversky and Schiano (1989) found a systematic bias toward the 45-deg line in memory for the slopes of identical lines when embedded in graphs, but not in maps, suggesting the use of a cognitive reference frame specifically for encoding meaningful graphs. The present experiments explore this issue further using the linear configurations alone as stimuli. Experiments 1 and 2 demonstrate that perception and immediate memory for the slope of a test line within orthogonal 'axes' are predictable from purely structural considerations. In Experiments 3 and 4, subjects were instructed to use a diagonal-reference strategy in viewing the stimuli, which were described as 'graphs' only in Experiment 3. Results for both studies showed the diagonal bias previously found only for graphs. This pattern provides converging evidence for the diagonal as a cognitive reference frame in encoding linear graphs, and demonstrates that even in highly simplified displays, strategic factors can produce encoding biases not predictable solely from stimulus structure alone.

JPEG XS-based frame buffer compression inside HEVC for power-aware video compression

NASA Astrophysics Data System (ADS)

Willème, Alexandre; Descampe, Antonin; Rouvroy, Gaël.; Pellegrin, Pascal; Macq, Benoit

2017-09-01

With the emergence of Ultra-High Definition video, reference frame buffers (FBs) inside HEVC-like encoders and decoders have to sustain huge bandwidth. The power consumed by these external memory accesses accounts for a significant share of the codec's total consumption. This paper describes a solution to significantly decrease the FB's bandwidth, making HEVC encoder more suitable for use in power-aware applications. The proposed prototype consists in integrating an embedded lightweight, low-latency and visually lossless codec at the FB interface inside HEVC in order to store each reference frame as several compressed bitstreams. As opposed to previous works, our solution compresses large picture areas (ranging from a CTU to a frame stripe) independently in order to better exploit the spatial redundancy found in the reference frame. This work investigates two data reuse schemes namely Level-C and Level-D. Our approach is made possible thanks to simplified motion estimation mechanisms further reducing the FB's bandwidth and inducing very low quality degradation. In this work, we integrated JPEG XS, the upcoming standard for lightweight low-latency video compression, inside HEVC. In practice, the proposed implementation is based on HM 16.8 and on XSM 1.1.2 (JPEG XS Test Model). Through this paper, the architecture of our HEVC with JPEG XS-based frame buffer compression is described. Then its performance is compared to HM encoder. Compared to previous works, our prototype provides significant external memory bandwidth reduction. Depending on the reuse scheme, one can expect bandwidth and FB size reduction ranging from 50% to 83.3% without significant quality degradation.

Transcriptional analysis of the bglP gene from Streptococcus mutans.

PubMed

Cote, Christopher K; Honeyman, Allen L

2006-04-21

An open reading frame encoding a putative antiterminator protein, LicT, was identified in the genomic sequence of Streptococcus mutans. A potential ribonucleic antitermination (RAT) site to which the LicT protein would potentially bind has been identified immediately adjacent to this open reading frame. The licT gene and RAT site are both located 5' to a beta-glucoside PTS regulon previously described in S. mutans that is responsible for esculin utilization in the presence of glucose. It was hypothesized that antitermination is the regulatory mechanism that is responsible for the control of the bglP gene expression, which encodes an esculin-specific PTS enzyme II. To localize the promoter activity associated with the bglP locus, a series of transcriptional lacZ gene fusions was formed on a reporter shuttle vector using various DNA fragments from the bglP promoter region. Subsequent beta-galactosidase assays in S. mutans localized the bglP promoter region and identified putative -35 and -10 promoter elements. Primer extension analysis identified the bglP transcriptional start site. In addition, a terminated bglP transcript formed by transcriptional termination was identified via transcript mapping experiments. The physical location of these genetic elements, the RAT site and the promoter regions, and the identification of a short terminated mRNA support the hypothesis that antitermination regulates the bglP transcript.

Transcriptional analysis of the bglP gene from Streptococcus mutans

PubMed Central

Cote, Christopher K; Honeyman, Allen L

2006-01-01

Background An open reading frame encoding a putative antiterminator protein, LicT, was identified in the genomic sequence of Streptococcus mutans. A potential ribonucleic antitermination (RAT) site to which the LicT protein would potentially bind has been identified immediately adjacent to this open reading frame. The licT gene and RAT site are both located 5' to a beta-glucoside PTS regulon previously described in S. mutans that is responsible for esculin utilization in the presence of glucose. It was hypothesized that antitermination is the regulatory mechanism that is responsible for the control of the bglP gene expression, which encodes an esculin-specific PTS enzyme II. Results To localize the promoter activity associated with the bglP locus, a series of transcriptional lacZ gene fusions was formed on a reporter shuttle vector using various DNA fragments from the bglP promoter region. Subsequent beta-galactosidase assays in S. mutans localized the bglP promoter region and identified putative -35 and -10 promoter elements. Primer extension analysis identified the bglP transcriptional start site. In addition, a terminated bglP transcript formed by transcriptional termination was identified via transcript mapping experiments. Conclusion The physical location of these genetic elements, the RAT site and the promoter regions, and the identification of a short terminated mRNA support the hypothesis that antitermination regulates the bglP transcript. PMID:16630357

Identification of a Linked Set of Genes in Serpulina hyodysenteriae (B204) Predicted To Encode Closely Related 39-Kilodalton Extracytoplasmic Proteins

PubMed Central

Gabe, Jeffrey D.; Dragon, Elizabeth; Chang, Ray-Jen; McCaman, Michael T.

1998-01-01

A tandem pair of nearly identical genes from Serpulina hyodysenteriae (B204) were cloned and sequenced. The full open reading frame of one gene and the partial open reading frame of the neighboring gene appear to encode secreted proteins which are homologous to, yet distinct from, the 39-kDa extracytoplasmic protein purified from the membrane fraction of S. hyodysenteriae. We have designated these newly identified genes vspA and vspB (for variable surface protein). PMID:9440540

Method and System for Temporal Filtering in Video Compression Systems

NASA Technical Reports Server (NTRS)

Lu, Ligang; He, Drake; Jagmohan, Ashish; Sheinin, Vadim

2011-01-01

Three related innovations combine improved non-linear motion estimation, video coding, and video compression. The first system comprises a method in which side information is generated using an adaptive, non-linear motion model. This method enables extrapolating and interpolating a visual signal, including determining the first motion vector between the first pixel position in a first image to a second pixel position in a second image; determining a second motion vector between the second pixel position in the second image and a third pixel position in a third image; determining a third motion vector between the first pixel position in the first image and the second pixel position in the second image, the second pixel position in the second image, and the third pixel position in the third image using a non-linear model; and determining a position of the fourth pixel in a fourth image based upon the third motion vector. For the video compression element, the video encoder has low computational complexity and high compression efficiency. The disclosed system comprises a video encoder and a decoder. The encoder converts the source frame into a space-frequency representation, estimates the conditional statistics of at least one vector of space-frequency coefficients with similar frequencies, and is conditioned on previously encoded data. It estimates an encoding rate based on the conditional statistics and applies a Slepian-Wolf code with the computed encoding rate. The method for decoding includes generating a side-information vector of frequency coefficients based on previously decoded source data and encoder statistics and previous reconstructions of the source frequency vector. It also performs Slepian-Wolf decoding of a source frequency vector based on the generated side-information and the Slepian-Wolf code bits. The video coding element includes receiving a first reference frame having a first pixel value at a first pixel position, a second reference frame having a second pixel value at a second pixel position, and a third reference frame having a third pixel value at a third pixel position. It determines a first motion vector between the first pixel position and the second pixel position, a second motion vector between the second pixel position and the third pixel position, and a fourth pixel value for a fourth frame based upon a linear or nonlinear combination of the first pixel value, the second pixel value, and the third pixel value. A stationary filtering process determines the estimated pixel values. The parameters of the filter may be predetermined constants.

Pathobiologic Roles of Epstein–Barr Virus-Encoded MicroRNAs in Human Lymphomas

PubMed Central

Navari, Mohsen; Etebari, Maryam; Ibrahimi, Mostafa; Leoncini, Lorenzo

2018-01-01

Epstein–Barr virus (EBV) is a human γ-herpesvirus implicated in several human malignancies, including a wide range of lymphomas. Several molecules encoded by EBV in its latent state are believed to be related to EBV-induced lymphomagenesis, among which microRNAs—small RNAs with a posttranscriptional regulating role—are of great importance. The genome of EBV encodes 44 mature microRNAs belonging to two different classes, including BamHI-A rightward transcript (BART) and Bam HI fragment H rightward open reading frame 1 (BHRF1), with different expression levels in different EBV latency types. These microRNAs might contribute to the pathogenetic effects exerted by EBV through targeting self mRNAs and host mRNAs and interfering with several important cellular mechanisms such as immunosurveillance, cell proliferation, and apoptosis. In addition, EBV microRNAs can regulate the surrounding microenvironment of the infected cells through exosomal transportation. Moreover, these small molecules could be potentially used as molecular markers. In this review, we try to present an updated and extensive view of the role of EBV-encoded miRNAs in human lymphomas. PMID:29649101

Robust 3D DFT video watermarking

NASA Astrophysics Data System (ADS)

Deguillaume, Frederic; Csurka, Gabriela; O'Ruanaidh, Joseph J.; Pun, Thierry

1999-04-01

This paper proposes a new approach for digital watermarking and secure copyright protection of videos, the principal aim being to discourage illicit copying and distribution of copyrighted material. The method presented here is based on the discrete Fourier transform (DFT) of three dimensional chunks of video scene, in contrast with previous works on video watermarking where each video frame was marked separately, or where only intra-frame or motion compensation parameters were marked in MPEG compressed videos. Two kinds of information are hidden in the video: a watermark and a template. Both are encoded using an owner key to ensure the system security and are embedded in the 3D DFT magnitude of video chunks. The watermark is a copyright information encoded in the form of a spread spectrum signal. The template is a key based grid and is used to detect and invert the effect of frame-rate changes, aspect-ratio modification and rescaling of frames. The template search and matching is performed in the log-log-log map of the 3D DFT magnitude. The performance of the presented technique is evaluated experimentally and compared with a frame-by-frame 2D DFT watermarking approach.

Gravity Influences the Visual Representation of Object Tilt in Parietal Cortex

PubMed Central

Angelaki, Dora E.

2014-01-01

Sensory systems encode the environment in egocentric (e.g., eye, head, or body) reference frames, creating inherently unstable representations that shift and rotate as we move. However, it is widely speculated that the brain transforms these signals into an allocentric, gravity-centered representation of the world that is stable and independent of the observer's spatial pose. Where and how this representation may be achieved is currently unknown. Here we demonstrate that a subpopulation of neurons in the macaque caudal intraparietal area (CIP) visually encodes object tilt in nonegocentric coordinates defined relative to the gravitational vector. Neuronal responses to the tilt of a visually presented planar surface were measured with the monkey in different spatial orientations (upright and rolled left/right ear down) and then compared. This revealed a continuum of representations in which planar tilt was encoded in a gravity-centered reference frame in approximately one-tenth of the comparisons, intermediate reference frames ranging between gravity-centered and egocentric in approximately two-tenths of the comparisons, and in an egocentric reference frame in less than half of the comparisons. Altogether, almost half of the comparisons revealed a shift in the preferred tilt and/or a gain change consistent with encoding object orientation in nonegocentric coordinates. Through neural network modeling, we further show that a purely gravity-centered representation of object tilt can be achieved directly from the population activity of CIP-like units. These results suggest that area CIP may play a key role in creating a stable, allocentric representation of the environment defined relative to an “earth-vertical” direction. PMID:25339732

The Protein Phosphatases of Synechocystis sp. Strain PCC 6803: Open Reading Frames sll1033 and sll1387 Encode Enzymes That Exhibit both Protein-Serine and Protein-Tyrosine Phosphatase Activity In Vitro.

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

Li, Ruiliang; Potters, M B.; Shi, Liang

2005-09-01

The open reading frames (ORFs) encoding two potential protein-serine/threonine phosphatases from the cyanobacterium Synechocystis sp. strain PCC 6803 were cloned and their protein products expressed in Escherichia coli cells. The product of ORF sll1033, SynPPM3, is a homologue of the PPM family of protein-serine/threonine phosphatases found in all eukaryotes as well as many members of the Bacteria. Surprisingly, the recombinant protein phosphatase dephosphorylated phosphotyrosine- as well as phosphoserine-containing proteins in vitro. While kinetic analyses indicate that the enzyme was more efficient at dephosphorylating the latter, replacement of Asp(608) by asparagine enhanced activity toward a phosphotyrosine-containing protein fourfold. The product ofmore » ORF sll1387, SynPPP1, is the sole homolog of the PPP family of protein phosphatases encoded by the genome of Synechocystis sp. strain PCC 6803. Like many other bacterial PPPs, the enzyme dephosphorylated phosphoserine- and phosphotyrosine-containing proteins with comparable efficiencies. However, while previously described PPPs from prokaryotic organisms required the addition of exogenous metal ion cofactors, such as Mg(2+) or Mn(2+), for activity, recombinantly produced SynPPP1 displayed near-maximal activity in the absence of added metals. Inductively coupled plasma mass spectrometry indicated that recombinant SynPPP1 contained significant quantities, 0.32 to 0.44 mol/mole total, of Mg and Mn. In this respect, the cyanobacterial enzyme resembled eukaryotic members of the PPP family, which are metalloproteins. mRNA encoding SynPPP1 or SynPPM3 could be detected in cells grown under many, but not all, environmental conditions.« less

Transient replication of BPV-1 requires two viral polypeptides encoded by the E1 and E2 open reading frames.

PubMed

Ustav, M; Stenlund, A

1991-02-01

Bovine papillomavirus (BPV) DNA is maintained as an episome with a constant copy number in transformed cells and is stably inherited. To study BPV replication we have developed a transient replication assay based on a highly efficient electroporation procedure. Using this assay we have determined that in the context of the viral genome two of the viral open reading frames, E1 and E2, are required for replication. Furthermore we show that when produced from expression vectors in the absence of other viral gene products, the full length E2 transactivator polypeptide and a 72 kd polypeptide encoded by the E1 open reading frame in its entirety, are both necessary and sufficient for replication BPV in C127 cells.

Cloning, characterization, expression analysis and inhibition studies of a novel gene encoding Bowman-Birk type protease inhibitor from rice bean

USDA-ARS?s Scientific Manuscript database

This paper presents the first study describing the isolation, cloning and characterization of a full length gene encoding Bowman-Birk protease inhibitor (RbTI) from rice bean (Vigna umbellata). A full-length protease inhibitor gene with complete open reading frame of 327bp encoding 109 amino acids w...

Visual tracking using neuromorphic asynchronous event-based cameras.

PubMed

Ni, Zhenjiang; Ieng, Sio-Hoi; Posch, Christoph; Régnier, Stéphane; Benosman, Ryad

2015-04-01

This letter presents a novel computationally efficient and robust pattern tracking method based on a time-encoded, frame-free visual data. Recent interdisciplinary developments, combining inputs from engineering and biology, have yielded a novel type of camera that encodes visual information into a continuous stream of asynchronous, temporal events. These events encode temporal contrast and intensity locally in space and time. We show that the sparse yet accurately timed information is well suited as a computational input for object tracking. In this letter, visual data processing is performed for each incoming event at the time it arrives. The method provides a continuous and iterative estimation of the geometric transformation between the model and the events representing the tracked object. It can handle isometry, similarities, and affine distortions and allows for unprecedented real-time performance at equivalent frame rates in the kilohertz range on a standard PC. Furthermore, by using the dimension of time that is currently underexploited by most artificial vision systems, the method we present is able to solve ambiguous cases of object occlusions that classical frame-based techniques handle poorly.

Quetzal: a transposon of the Tc1 family in the mosquito Anopheles albimanus.

PubMed

Ke, Z; Grossman, G L; Cornel, A J; Collins, F H

1996-10-01

A member of the Tc1 family of transposable elements has been identified in the Central and South American mosquito Anopheles albimanus. The full-length Quetzal element is 1680 base pairs (bp) in length, possesses 236 bp inverted terminal repeats (ITRs), and has a single open reading frame (ORF) with the potential of encoding a 341-amino-acid (aa) protein that is similar to the transposases of other members of the Tc1 family, particularly elements described from three different Drosophila species. The approximately 10-12 copies per genome of Quetzal are found in the euchromatin of all three chromosomes of A. albimanus. One full-length clone, Que27, appears capable of encoding a complete transposase and may represent a functional copy of this element.

Role of sleep for encoding of emotional memory.

PubMed

Kaida, Kosuke; Niki, Kazuhisa; Born, Jan

2015-05-01

Total sleep deprivation (TSD) has been consistently found to impair encoding of information during ensuing wakefulness, probably through suppressing NonREM (non-rapid eye movement) sleep. However, a possible contribution of missing REM sleep to this encoding impairment after TSD has so far not been systematically examined in humans, although such contribution might be suspected in particular for emotional information. Here, in two separate experiments in young healthy men, we compared effects of TSD and of selective REM sleep deprivation (REMD), relative to respective control conditions of undisturbed sleep, on the subsequent encoding of neutral and emotional pictures. The pictures were presented in conjunction with colored frames to also assess related source memory. REMD was achieved by tones presented contingently upon initial signs of REM sleep. Encoding capabilities were examined in the evening (18:00h) after the experimental nights, by a picture recognition test right after encoding. TSD significantly decreased both the rate of correctly recognized pictures and of recalled frames associated with the pictures. The TSD effect was robust and translated into an impaired long term memory formation, as it was likewise observed on a second recognition testing one week after the encoding phase. Contrary to our expectation, REMD did not affect encoding in general, or particularly of emotional pictures. Also, REMD did not affect valence ratings of the encoded pictures. However, like TSD, REMD distinctly impaired vigilance at the time of encoding. Altogether, these findings indicate an importance of NonREM rather than REM sleep for the encoding of information that is independent of the emotionality of the materials. Copyright © 2015 Elsevier Inc. All rights reserved.

Space-time encoding for high frame rate ultrasound imaging.

PubMed

Misaridis, Thanassis X; Jensen, Jørgen A

2002-05-01

Frame rate in ultrasound imaging can be dramatically increased by using sparse synthetic transmit aperture (STA) beamforming techniques. The two main drawbacks of the method are the low signal-to-noise ratio (SNR) and the motion artifacts, that degrade the image quality. In this paper we propose a spatio-temporal encoding for STA imaging based on simultaneous transmission of two quasi-orthogonal tapered linear FM signals. The excitation signals are an up- and a down-chirp with frequency division and a cross-talk of -55 dB. The received signals are first cross-correlated with the appropriate code, then spatially decoded and finally beamformed for each code, yielding two images per emission. The spatial encoding is a Hadamard encoding previously suggested by Chiao et al. [in: Proceedings of the IEEE Ultrasonics Symposium, 1997, p. 1679]. The Hadamard matrix has half the size of the transmit element groups, due to the orthogonality of the temporal encoded wavefronts. Thus, with this method, the frame rate is doubled compared to previous systems. Another advantage is the utilization of temporal codes which are more robust to attenuation. With the proposed technique it is possible to obtain images dynamically focused in both transmit and receive with only two firings. This reduces the problem of motion artifacts. The method has been tested with extensive simulations using Field II. Resolution and SNR are compared with uncoded STA imaging and conventional phased-array imaging. The range resolution remains the same for coded STA imaging with four emissions and is slightly degraded for STA imaging with two emissions due to the -55 dB cross-talk between the signals. The additional proposed temporal encoding adds more than 15 dB on the SNR gain, yielding a SNR at the same order as in phased-array imaging.

Real-time motion-based H.263+ frame rate control

NASA Astrophysics Data System (ADS)

Song, Hwangjun; Kim, JongWon; Kuo, C.-C. Jay

1998-12-01

Most existing H.263+ rate control algorithms, e.g. the one adopted in the test model of the near-term (TMN8), focus on the macroblock layer rate control and low latency under the assumptions of with a constant frame rate and through a constant bit rate (CBR) channel. These algorithms do not accommodate the transmission bandwidth fluctuation efficiently, and the resulting video quality can be degraded. In this work, we propose a new H.263+ rate control scheme which supports the variable bit rate (VBR) channel through the adjustment of the encoding frame rate and quantization parameter. A fast algorithm for the encoding frame rate control based on the inherent motion information within a sliding window in the underlying video is developed to efficiently pursue a good tradeoff between spatial and temporal quality. The proposed rate control algorithm also takes the time-varying bandwidth characteristic of the Internet into account and is able to accommodate the change accordingly. Experimental results are provided to demonstrate the superior performance of the proposed scheme.

Nucleotide sequencing and characterization of the genes encoding benzene oxidation enzymes of Pseudomonas putida.

PubMed Central

Irie, S; Doi, S; Yorifuji, T; Takagi, M; Yano, K

1987-01-01

The nucleotide sequence of the genes from Pseudomonas putida encoding oxidation of benzene to catechol was determined. Five open reading frames were found in the sequence. Four corresponding protein molecules were detected by a DNA-directed in vitro translation system. Escherichia coli cells containing the fragment with the four open reading frames transformed benzene to cis-benzene glycol, which is an intermediate of the oxidation of benzene to catechol. The relation between the product of each cistron and the components of the benzene oxidation enzyme system is discussed. Images PMID:3667527

Wavelength-encoded tomography based on optical temporal Fourier transform

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

Zhang, Chi; Wong, Kenneth K. Y., E-mail: kywong@eee.hku.hk

We propose and demonstrate a technique called wavelength-encoded tomography (WET) for non-invasive optical cross-sectional imaging, particularly beneficial in biological system. The WET utilizes time-lens to perform the optical Fourier transform, and the time-to-wavelength conversion generates a wavelength-encoded image of optical scattering from internal microstructures, analogous to the interferometery-based imaging such as optical coherence tomography. Optical Fourier transform, in principle, comes with twice as good axial resolution over the electrical Fourier transform, and will greatly simplify the digital signal processing after the data acquisition. As a proof-of-principle demonstration, a 150 -μm (ideally 36 μm) resolution is achieved based on a 7.5-nm bandwidth swept-pump,more » using a conventional optical spectrum analyzer. This approach can potentially achieve up to 100-MHz or even higher frame rate with some proven ultrafast spectrum analyzer. We believe that this technique is innovative towards the next-generation ultrafast optical tomographic imaging application.« less

Language supports young children’s use of spatial relations to remember locations

PubMed Central

Miller, Hilary E.; Patterson, Rebecca; Simmering, Vanessa R.

2016-01-01

Two experiments investigated the role of language in children’s spatial recall performance. In particular, we assessed whether selecting an intrinsic reference frame could be improved through verbal encoding. Selecting an intrinsic reference frame requires remembering locations relative to nearby objects independent of one’s body (egocentric) or distal environmental (allocentric) cues, and does not reliably occur in children under 5 years of age (Nardini, Burgess, Breckenridge, & Atkinson, 2006). The current studies tested the relation between spatial language and 4-year-olds’ selection of an intrinsic reference frame in spatial recall. Experiment 1 showed that providing 4-year-olds with location-descriptive cues during (Exp. 1a) or before (Exp. 1b) the recall task improved performance both overall and specifically on trials relying most on an intrinsic reference frame. Additionally, children’s recall performance was predicted by their verbal descriptions of the task space (Exp. 1a control condition). Non-verbally highlighting relations among objects during the recall task (Exp. 2) supported children’s performance relative to the control condition, but significantly less than the location-descriptive cues. These results suggest that the ability to verbally represent relations is a potential mechanism that could account for developmental changes in the selection of an intrinsic reference frame during spatial recall. PMID:26896902

Language supports young children's use of spatial relations to remember locations.

PubMed

Miller, Hilary E; Patterson, Rebecca; Simmering, Vanessa R

2016-05-01

Two experiments investigated the role of language in children's spatial recall performance. In particular, we assessed whether selecting an intrinsic reference frame could be improved through verbal encoding. Selecting an intrinsic reference frame requires remembering locations relative to nearby objects independent of one's body (egocentric) or distal environmental (allocentric) cues, and does not reliably occur in children under 5 years of age (Nardini, Burgess, Breckenridge, & Atkinson, 2006). The current studies tested the relation between spatial language and 4-year-olds' selection of an intrinsic reference frame in spatial recall. Experiment 1 showed that providing 4-year-olds with location-descriptive cues during (Exp. 1a) or before (Exp. 1b) the recall task improved performance both overall and specifically on trials relying most on an intrinsic reference frame. Additionally, children's recall performance was predicted by their verbal descriptions of the task space (Exp. 1a control condition). Non-verbally highlighting relations among objects during the recall task (Exp. 2) supported children's performance relative to the control condition, but significantly less than the location-descriptive cues. These results suggest that the ability to verbally represent relations is a potential mechanism that could account for developmental changes in the selection of an intrinsic reference frame during spatial recall. Copyright © 2016 Elsevier B.V. All rights reserved.

Cerebellar re-encoding of self-generated head movements

PubMed Central

Dugué, Guillaume P; Tihy, Matthieu; Gourévitch, Boris; Léna, Clément

2017-01-01

Head movements are primarily sensed in a reference frame tied to the head, yet they are used to calculate self-orientation relative to the world. This requires to re-encode head kinematic signals into a reference frame anchored to earth-centered landmarks such as gravity, through computations whose neuronal substrate remains to be determined. Here, we studied the encoding of self-generated head movements in the rat caudal cerebellar vermis, an area essential for graviceptive functions. We found that, contrarily to peripheral vestibular inputs, most Purkinje cells exhibited a mixed sensitivity to head rotational and gravitational information and were differentially modulated by active and passive movements. In a subpopulation of cells, this mixed sensitivity underlay a tuning to rotations about an axis defined relative to gravity. Therefore, we show that the caudal vermis hosts a re-encoded, gravitationally polarized representation of self-generated head kinematics in freely moving rats. DOI: http://dx.doi.org/10.7554/eLife.26179.001 PMID:28608779

Transient replication of BPV-1 requires two viral polypeptides encoded by the E1 and E2 open reading frames.

PubMed Central

Ustav, M; Stenlund, A

1991-01-01

Bovine papillomavirus (BPV) DNA is maintained as an episome with a constant copy number in transformed cells and is stably inherited. To study BPV replication we have developed a transient replication assay based on a highly efficient electroporation procedure. Using this assay we have determined that in the context of the viral genome two of the viral open reading frames, E1 and E2, are required for replication. Furthermore we show that when produced from expression vectors in the absence of other viral gene products, the full length E2 transactivator polypeptide and a 72 kd polypeptide encoded by the E1 open reading frame in its entirety, are both necessary and sufficient for replication BPV in C127 cells. Images PMID:1846806

Ameliorating pathogenesis by removing an exon containing a missense mutation: a potential exon-skipping therapy for laminopathies.

PubMed

Scharner, J; Figeac, N; Ellis, J A; Zammit, P S

2015-06-01

Exon skipping, as a therapy to restore a reading frame or switch protein isoforms, is under clinical trial. We hypothesised that removing an in-frame exon containing a mutation could also improve pathogenic phenotypes. Our model is laminopathies: incurable tissue-specific degenerative diseases associated with LMNA mutations. LMNA encodes A-type lamins, that together with B-type lamins, form the nuclear lamina. Lamins contain an alpha-helical central rod domain composed of multiple heptad repeats. Eliminating LMNA exon 3 or 5 removes six heptad repeats, so shortens, but should not otherwise significantly alter, the alpha-helix. Human Lamin A or Lamin C with a deletion corresponding to amino acids encoded by exon 5 (Lamin A/C-Δ5) localised normally in murine lmna-null cells, rescuing both nuclear shape and endogenous Lamin B1/emerin distribution. However, Lamin A carrying pathogenic mutations in exon 3 or 5, or Lamin A/C-Δ3, did not. Furthermore, Lamin A/C-Δ5 was not deleterious to wild-type cells, unlike the other Lamin A mutants including Lamin A/C-Δ3. Thus Lamin A/C-Δ5 function as effectively as wild-type Lamin A/C and better than mutant versions. Antisense oligonucleotides skipped LMNA exon 5 in human cells, demonstrating the possibility of treating certain laminopathies with this approach. This proof-of-concept is the first to report the therapeutic potential of exon skipping for diseases arising from missense mutations.

Overlapping reading frames at the LYS5 locus in the yeast Yarrowia lipolytica.

PubMed Central

Xuan, J W; Fournier, P; Declerck, N; Chasles, M; Gaillardin, C

1990-01-01

Mutants affected at the LYS5 locus of Yarrowia lipolytica lack detectable dehydrogenase (SDH) activity. The LYS5 gene has previously been cloned, and we present here the sequence of the 2.5-kilobase-pair (kb) DNA fragment complementing the lys5 mutation. Two large antiparallel open reading frames (ORF1 and ORF2) were observed, flanked by potential transcription signals. Both ORFs appear to be transcribed, but several lines of evidence suggest that only ORF2 is translated and encodes SDH. (i) The global amino acid compositions of Saccharomyces cerevisiae SDH and of the putative ORF2 product are similar and that of ORF1 is dissimilar. (ii) An in-frame translational fusion of ORF2 with the Escherichia coli lacZ gene was introduced into yeast cells and resulted in a beta-galactosidase activity regulated similarly to SDH; no beta-galactosidase activity was obtained with an in-frame fusion of ORF1 with lacZ. (iii) The introduction of a stop codon at the beginning of ORF2 prevented SDH expression in yeast cells, whereas no phenotypic effect was observed when ORF1 translation was blocked. Images PMID:2388625

Gravity influences the visual representation of object tilt in parietal cortex.

PubMed

Rosenberg, Ari; Angelaki, Dora E

2014-10-22

Sensory systems encode the environment in egocentric (e.g., eye, head, or body) reference frames, creating inherently unstable representations that shift and rotate as we move. However, it is widely speculated that the brain transforms these signals into an allocentric, gravity-centered representation of the world that is stable and independent of the observer's spatial pose. Where and how this representation may be achieved is currently unknown. Here we demonstrate that a subpopulation of neurons in the macaque caudal intraparietal area (CIP) visually encodes object tilt in nonegocentric coordinates defined relative to the gravitational vector. Neuronal responses to the tilt of a visually presented planar surface were measured with the monkey in different spatial orientations (upright and rolled left/right ear down) and then compared. This revealed a continuum of representations in which planar tilt was encoded in a gravity-centered reference frame in approximately one-tenth of the comparisons, intermediate reference frames ranging between gravity-centered and egocentric in approximately two-tenths of the comparisons, and in an egocentric reference frame in less than half of the comparisons. Altogether, almost half of the comparisons revealed a shift in the preferred tilt and/or a gain change consistent with encoding object orientation in nonegocentric coordinates. Through neural network modeling, we further show that a purely gravity-centered representation of object tilt can be achieved directly from the population activity of CIP-like units. These results suggest that area CIP may play a key role in creating a stable, allocentric representation of the environment defined relative to an "earth-vertical" direction. Copyright © 2014 the authors 0270-6474/14/3414170-11$15.00/0.

Quantifying the effect of disruptions to temporal coherence on the intelligibility of compressed American Sign Language video

NASA Astrophysics Data System (ADS)

Ciaramello, Frank M.; Hemami, Sheila S.

2009-02-01

Communication of American Sign Language (ASL) over mobile phones would be very beneficial to the Deaf community. ASL video encoded to achieve the rates provided by current cellular networks must be heavily compressed and appropriate assessment techniques are required to analyze the intelligibility of the compressed video. As an extension to a purely spatial measure of intelligibility, this paper quantifies the effect of temporal compression artifacts on sign language intelligibility. These artifacts can be the result of motion-compensation errors that distract the observer or frame rate reductions. They reduce the the perception of smooth motion and disrupt the temporal coherence of the video. Motion-compensation errors that affect temporal coherence are identified by measuring the block-level correlation between co-located macroblocks in adjacent frames. The impact of frame rate reductions was quantified through experimental testing. A subjective study was performed in which fluent ASL participants rated the intelligibility of sequences encoded at a range of 5 different frame rates and with 3 different levels of distortion. The subjective data is used to parameterize an objective intelligibility measure which is highly correlated with subjective ratings at multiple frame rates.

Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity.

PubMed

Harper, B; McClain, S; Ganko, E W

2012-08-01

Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence. Copyright © 2012 Elsevier Inc. All rights reserved.

Cellular Selenoprotein mRNA Tethering via Antisense Interactions with Ebola and HIV-1 mRNAs May Impact Host Selenium Biochemistry.

PubMed

Taylor, Ethan Will; Ruzicka, Jan A; Premadasa, Lakmini; Zhao, Lijun

2016-01-01

Regulation of protein expression by non-coding RNAs typically involves effects on mRNA degradation and/or ribosomal translation. The possibility of virus-host mRNA-mRNA antisense tethering interactions (ATI) as a gain-of-function strategy, via the capture of functional RNA motifs, has not been hitherto considered. We present evidence that ATIs may be exploited by certain RNA viruses in order to tether the mRNAs of host selenoproteins, potentially exploiting the proximity of a captured host selenocysteine insertion sequence (SECIS) element to enable the expression of virally-encoded selenoprotein modules, via translation of in-frame UGA stop codons as selenocysteine. Computational analysis predicts thermodynamically stable ATIs between several widely expressed mammalian selenoprotein mRNAs (e.g., isoforms of thioredoxin reductase) and specific Ebola virus mRNAs, and HIV-1 mRNA, which we demonstrate via DNA gel shift assays. The probable functional significance of these ATIs is further supported by the observation that, in both viruses, they are located in close proximity to highly conserved in-frame UGA stop codons at the 3' end of open reading frames that encode essential viral proteins (the HIV-1 nef protein and the Ebola nucleoprotein). Significantly, in HIV/AIDS patients, an inverse correlation between serum selenium and mortality has been repeatedly documented, and clinical benefits of selenium in the context of multi-micronutrient supplementation have been demonstrated in several well-controlled clinical trials. Hence, in the light of our findings, the possibility of a similar role for selenium in Ebola pathogenesis and treatment merits serious investigation.

Analysis of the DNA sequence of a 15,500 bp fragment near the left telomere of chromosome XV from Saccharomyces cerevisiae reveals a putative sugar transporter, a carboxypeptidase homologue and two new open reading frames.

PubMed

Gamo, F J; Lafuente, M J; Casamayor, A; Ariño, J; Aldea, M; Casas, C; Herrero, E; Gancedo, C

1996-06-15

We report the sequence of a 15.5 kb DNA segment located near the left telomere of chromosome XV of Saccharomyces cerevisiae. The sequence contains nine open reading frames (ORFs) longer than 300 bp. Three of them are internal to other ones. One corresponds to the gene LGT3 that encodes a putative sugar transporter. Three adjacent ORFs were separated by two stop codons in frame. These ORFs presented homology with the gene CPS1 that encodes carboxypeptidase S. The stop codons were not found in the same sequence derived from another yeast strain. Two other ORFs without significant homology in databases were also found. One of them, O0420, is very rich in serine and threonine and presents a series of repeated or similar amino acid stretches along the sequence.

DNA sequence analysis of a 10 624 bp fragment of the left arm of chromosome XV from Saccharomyces cerevisiae reveals a RNA binding protein, a mitochondrial protein, two ribosomal proteins and two new open reading frames.

PubMed

Lafuente, M J; Gamo, F J; Gancedo, C

1996-09-01

We have determined the sequence of a 10624 bp DNA segment located in the left arm of chromosome XV of Saccharomyces cerevisiae. The sequence contains eight open reading frames (ORFs) longer than 100 amino acids. Two of them do not present significant homology with sequences found in the databases. The product of ORF o0553 is identical to the protein encoded by the gene SMF1. Internal to it there is another ORF, o0555 that is apparently expressed. The proteins encoded by ORFs o0559 and o0565 are identical to ribosomal proteins S19.e and L18 respectively. ORF o0550 encodes a protein with an RNA binding signature including RNP motifs and stretches rich in asparagine, glutamine and arginine.

Robust video transmission with distributed source coded auxiliary channel.

PubMed

Wang, Jiajun; Majumdar, Abhik; Ramchandran, Kannan

2009-12-01

We propose a novel solution to the problem of robust, low-latency video transmission over lossy channels. Predictive video codecs, such as MPEG and H.26x, are very susceptible to prediction mismatch between encoder and decoder or "drift" when there are packet losses. These mismatches lead to a significant degradation in the decoded quality. To address this problem, we propose an auxiliary codec system that sends additional information alongside an MPEG or H.26x compressed video stream to correct for errors in decoded frames and mitigate drift. The proposed system is based on the principles of distributed source coding and uses the (possibly erroneous) MPEG/H.26x decoder reconstruction as side information at the auxiliary decoder. The distributed source coding framework depends upon knowing the statistical dependency (or correlation) between the source and the side information. We propose a recursive algorithm to analytically track the correlation between the original source frame and the erroneous MPEG/H.26x decoded frame. Finally, we propose a rate-distortion optimization scheme to allocate the rate used by the auxiliary encoder among the encoding blocks within a video frame. We implement the proposed system and present extensive simulation results that demonstrate significant gains in performance both visually and objectively (on the order of 2 dB in PSNR over forward error correction based solutions and 1.5 dB in PSNR over intrarefresh based solutions for typical scenarios) under tight latency constraints.

cDNA encoding a polypeptide including a hevein sequence

DOEpatents

Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.

1993-02-16

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

NUCLEOTIDE SEQUENCING AND TRANSCRIPTIONAL MAPPING OF THE GENES ENCODING BIPHENYL DIOXYGENASE, A MULTICOMPONENT POLYCHLORINATED-BIPHENYL-DEGRADING ENZYME IN PSEUDOMONAS STRAIN LB400

EPA Science Inventory

The DNA region encoding biphenyl dioxygenase, the first enzyme in the biphenyl-polychlorinated biphenyl degradation pathway of Pseudomonas species strain LB400, was sequenced. ix open reading frames were identified, four of which are, homologous to the components of toluene dioxy...

Edwardsiella ictaluri Encodes an Acid Activated Urease that is Required for Intracellular Replication in Channel Catfish Ictalurus punctatus Macrophages

USDA-ARS?s Scientific Manuscript database

Genomic analysis indicated that Edwardsiella ictaluri encodes a putative ureasepathogenicity island containing 9 open reading frames, including urea and ammonium transporters. In vitro studies with the wild-type E. ictaluri and a ureG::kan urease mutant strain indicated that E. ictaluri is significa...

Single-Frame Terrain Mapping Software for Robotic Vehicles

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.

2011-01-01

This software is a component in an unmanned ground vehicle (UGV) perception system that builds compact, single-frame terrain maps for distribution to other systems, such as a world model or an operator control unit, over a local area network (LAN). Each cell in the map encodes an elevation value, terrain classification, object classification, terrain traversability, terrain roughness, and a confidence value into four bytes of memory. The input to this software component is a range image (from a lidar or stereo vision system), and optionally a terrain classification image and an object classification image, both registered to the range image. The single-frame terrain map generates estimates of the support surface elevation, ground cover elevation, and minimum canopy elevation; generates terrain traversability cost; detects low overhangs and high-density obstacles; and can perform geometry-based terrain classification (ground, ground cover, unknown). A new origin is automatically selected for each single-frame terrain map in global coordinates such that it coincides with the corner of a world map cell. That way, single-frame terrain maps correctly line up with the world map, facilitating the merging of map data into the world map. Instead of using 32 bits to store the floating-point elevation for a map cell, the vehicle elevation is assigned to the map origin elevation and reports the change in elevation (from the origin elevation) in terms of the number of discrete steps. The single-frame terrain map elevation resolution is 2 cm. At that resolution, terrain elevation from 20.5 to 20.5 m (with respect to the vehicle's elevation) is encoded into 11 bits. For each four-byte map cell, bits are assigned to encode elevation, terrain roughness, terrain classification, object classification, terrain traversability cost, and a confidence value. The vehicle s current position and orientation, the map origin, and the map cell resolution are all included in a header for each map. The map is compressed into a vector prior to delivery to another system.

Novel transcripts of the estrogen receptor α gene in channel catfish

USGS Publications Warehouse

Patino, Reynaldo; Xia, Zhenfang; Gale, William L.; Wu, Chunfa; Maule, Alec G.; Chang, Xiaotian

2000-01-01

Complementary DNA libraries from liver and ovary of an immature female channel catfish were screened with a homologous ERα cDNA probe. The hepatic library yielded two new channel catfish ER cDNAs that encode N-terminal ERα variants of different sizes. Relative to the catfish ERα (medium size; 581 residues) previously reported, these new cDNAs encode Long-ERα (36 residues longer) and Short-ERα (389 residues shorter). The 5′-end of Long-ERα cDNA is identical to that of Medium-ERα but has an additional 503-bp segment with an upstream, in-frame translation-start codon. Recombinant Long-ERα binds estrogen with high affinity (Kd = 3.4 nM), similar to that previously reported for Medium-ERα but lower than reported for catfish ERβ. Short-ERα cDNA encodes a protein that lacks most of the receptor protein and does not bind estrogen. Northern hybridization confirmed the existence of multiple hepatic ERα RNAs that include the size range of the ERα cDNAs obtained from the libraries as well as additional sizes. Using primers for RT-PCR that target locations internal to the protein-coding sequence, we also established the presence of several ERα cDNA variants with in-frame insertions in the ligand-binding and DNA-binding domains and in-frame or out-of-frame deletions in the ligand-binding domain. These internal variants showed patterns of expression that differed between the ovary and liver. Further, the ovarian library yielded a full-length, ERα antisense cDNA containing a poly(A) signal and tail. A limited survey of histological preparations from juvenile catfish by in situ hybridization using directionally synthesized cRNA probes also suggested the expression of ERα antisense RNA in a tissue-specific manner. In conclusion, channel catfish seemingly have three broad classes of ERα mRNA variants: those encoding N-terminal truncated variants, those encoding internal variants (including C-terminal truncated variants), and antisense mRNA. The sense variants may encode functional ERα or related proteins that modulate ERα or ERβ activity. The existence of ER antisense mRNA is reported in this study for the first time. Its role may be to participate in the regulation of ER gene expression.

An approach to instrument qualified visual range

NASA Astrophysics Data System (ADS)

Courtade, Benoît; Bonnet, Jordan; Woodruff, Chris; Larson, Josiah; Giles, Andrew; Sonde, Nikhil; Moore, C. J.; Schimon, David; Harris, David Money; Pond, Duane; Way, Scott

2008-04-01

This paper describes a system that calculates aircraft visual range with instrumentation alone. A unique message is encoded using modified binary phase shift keying and continuously flashed at high speed by ALSF-II runway approach lights. The message is sampled at 400 frames per second by an aircraft borne high-speed camera. The encoding is designed to avoid visible flicker and minimize frame rate. Instrument qualified visual range is identified as the largest distance at which the aircraft system can acquire and verify the correct, runway-specific signal. Scaled testing indicates that if the system were implemented on one full ALSF-II fixture, instrument qualified range could be established at 5 miles in clear weather conditions.

The open reading frames in the 3' long terminal repeats of several mouse mammary tumor virus integrants encode V beta 3-specific superantigens

PubMed Central

1992-01-01

Mice expressing the minor lymphocyte stimulation antigens, Mls-1a, -2a, or -3a, singly on the B10.BR background have been generated. Mls phenotypes correlate with the integration of mouse mammary tumor viruses (MTV) in the mouse genome. The open reading frames within the 3' long terminal repeats of the integrated MTVs 1, 3, 6, and 13 encode V beta 3-specific superantigens. Sequence data for these viral superantigens is presented, indicating that it is the COOH-terminal portion of the viral superantigen that interacts with the T cell receptor V beta element. PMID:1309854

A Survey of Protein Structures from Archaeal Viruses

PubMed Central

Dellas, Nikki; Lawrence, C. Martin; Young, Mark J.

2013-01-01

Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs) whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%). This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight. PMID:25371334

A large-scale video codec comparison of x264, x265 and libvpx for practical VOD applications

NASA Astrophysics Data System (ADS)

De Cock, Jan; Mavlankar, Aditya; Moorthy, Anush; Aaron, Anne

2016-09-01

Over the last years, we have seen exciting improvements in video compression technology, due to the introduction of HEVC and royalty-free coding specifications such as VP9. The potential compression gains of HEVC over H.264/AVC have been demonstrated in different studies, and are usually based on the HM reference software. For VP9, substantial gains over H.264/AVC have been reported in some publications, whereas others reported less optimistic results. Differences in configurations between these publications make it more difficult to assess the true potential of VP9. Practical open-source encoder implementations such as x265 and libvpx (VP9) have matured, and are now showing high compression gains over x264. In this paper, we demonstrate the potential of these encoder imple- mentations, with settings optimized for non-real-time random access, as used in a video-on-demand encoding pipeline. We report results from a large-scale video codec comparison test, which includes x264, x265 and libvpx. A test set consisting of a variety of titles with varying spatio-temporal characteristics from our catalog is used, resulting in tens of millions of encoded frames, hence larger than test sets previously used in the literature. Re- sults are reported in terms of PSNR, SSIM, MS-SSIM, VIF and the recently introduced VMAF quality metric. BD-rate calculations show that using x265 and libvpx vs. x264 can lead to significant bitrate savings for the same quality. x265 outperforms libvpx in most cases, but the performance gap narrows (or even reverses) at the higher resolutions.

Mining for Micropeptides.

PubMed

Makarewich, Catherine A; Olson, Eric N

2017-09-01

Advances in computational biology and large-scale transcriptome analyses have revealed that a much larger portion of the genome is transcribed than was previously recognized, resulting in the production of a diverse population of RNA molecules with both protein-coding and noncoding potential. Emerging evidence indicates that several RNA molecules have been mis-annotated as noncoding and in fact harbor short open reading frames (sORFs) that encode functional peptides and that have evaded detection until now due to their small size. sORF-encoded peptides (SEPs), or micropeptides, have been shown to have important roles in fundamental biological processes and in the maintenance of cellular homeostasis. These small proteins can act independently, for example as ligands or signaling molecules, or they can exert their biological functions by engaging with and modulating larger regulatory proteins. Given their small size, micropeptides may be uniquely suited to fine-tune complex biological systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

NUCLEOTIDE SEQUENCING AND TRANSCRIPTIONAL MAPPING OF THE GENES ENCODING BIPHENYL DIOXYGENASE, A MULTICOM- PONENT POLYCHLORINATED-BIPHENYL-DEGRADING ENZYME IN PSEUDOMONAS STRAIN LB400

EPA Science Inventory

The DNA region encoding biphenyl dioxygenase, the first enzyme in the biphenyl-polychlorinated biphenyl degradation pathway of Pseudomonas species strain LB400, was sequenced. Six open reading frames were identified, four of which are homologous to the components of toluene dioxy...

ERP Subsequent Memory Effects Differ between Inter-Item and Unitization Encoding Tasks

PubMed Central

Kamp, Siri-Maria; Bader, Regine; Mecklinger, Axel

2017-01-01

The “subsequent memory paradigm” is an analysis tool to identify brain activity elicited during episodic encoding that is associated with successful subsequent retrieval. Two commonly observed event-related potential “subsequent memory effects” (SMEs) are the parietal SME in the P300 time window and the frontal slow wave SME, but to date a clear characterization of the circumstances under which each SME is observed is missing. To test the hypothesis that the parietal SME occurs when aspects of an experience are unitized into a single item representation, while inter-item associative encoding is reflected in the frontal slow wave effect, participants were assigned to one of two conditions that emphasized one of the encoding types under otherwise matched study phases of a recognition memory experiment. Word pairs were presented either in the context of a definition that allowed to combine the word pairs into a new concept (unitization or item encoding) or together with a sentence frame (inter-item encoding). Performance on the recognition test did not differ between the groups. The parietal SME was only found in the definition group, supporting the idea that this SME occurs when the components of an association are integrated in a unitized item representation. An early prefrontal negativity also exhibited an SME only in this group, suggesting that the formation of novel units occurs through interactions of multiple brain areas. The frontal slow wave SME was pronounced in both groups and may thus reflect processes generally involved in encoding of associations. Our results provide evidence for a partial dissociation of the eliciting conditions of the two types of SMEs and therefore provide a tool for future studies to characterize the different types of episodic encoding. PMID:28194105

ERP Subsequent Memory Effects Differ between Inter-Item and Unitization Encoding Tasks.

PubMed

Kamp, Siri-Maria; Bader, Regine; Mecklinger, Axel

2017-01-01

The "subsequent memory paradigm" is an analysis tool to identify brain activity elicited during episodic encoding that is associated with successful subsequent retrieval. Two commonly observed event-related potential "subsequent memory effects" (SMEs) are the parietal SME in the P300 time window and the frontal slow wave SME, but to date a clear characterization of the circumstances under which each SME is observed is missing. To test the hypothesis that the parietal SME occurs when aspects of an experience are unitized into a single item representation, while inter-item associative encoding is reflected in the frontal slow wave effect, participants were assigned to one of two conditions that emphasized one of the encoding types under otherwise matched study phases of a recognition memory experiment. Word pairs were presented either in the context of a definition that allowed to combine the word pairs into a new concept (unitization or item encoding) or together with a sentence frame (inter-item encoding). Performance on the recognition test did not differ between the groups. The parietal SME was only found in the definition group, supporting the idea that this SME occurs when the components of an association are integrated in a unitized item representation. An early prefrontal negativity also exhibited an SME only in this group, suggesting that the formation of novel units occurs through interactions of multiple brain areas. The frontal slow wave SME was pronounced in both groups and may thus reflect processes generally involved in encoding of associations. Our results provide evidence for a partial dissociation of the eliciting conditions of the two types of SMEs and therefore provide a tool for future studies to characterize the different types of episodic encoding.

Cellular Selenoprotein mRNA Tethering via Antisense Interactions with Ebola and HIV-1 mRNAs May Impact Host Selenium Biochemistry

PubMed Central

Taylor, Ethan Will; Ruzicka, Jan A.; Premadasa, Lakmini; Zhao, Lijun

2016-01-01

Regulation of protein expression by non-coding RNAs typically involves effects on mRNA degradation and/or ribosomal translation. The possibility of virus-host mRNA-mRNA antisense tethering interactions (ATI) as a gain-of-function strategy, via the capture of functional RNA motifs, has not been hitherto considered. We present evidence that ATIs may be exploited by certain RNA viruses in order to tether the mRNAs of host selenoproteins, potentially exploiting the proximity of a captured host selenocysteine insertion sequence (SECIS) element to enable the expression of virally-encoded selenoprotein modules, via translation of in-frame UGA stop codons as selenocysteine. Computational analysis predicts thermodynamically stable ATIs between several widely expressed mammalian selenoprotein mRNAs (e.g., isoforms of thioredoxin reductase) and specific Ebola virus mRNAs, and HIV-1 mRNA, which we demonstrate via DNA gel shift assays. The probable functional significance of these ATIs is further supported by the observation that, in both viruses, they are located in close proximity to highly conserved in-frame UGA stop codons at the 3′ end of open reading frames that encode essential viral proteins (the HIV-1 nef protein and the Ebola nucleoprotein). Significantly, in HIV/AIDS patients, an inverse correlation between serum selenium and mortality has been repeatedly documented, and clinical benefits of selenium in the context of multi-micronutrient supplementation have been demonstrated in several well-controlled clinical trials. Hence, in the light of our findings, the possibility of a similar role for selenium in Ebola pathogenesis and treatment merits serious investigation. PMID:26369818

Genetic Manipulation of Lactococcus lactis by Using Targeted Group II Introns: Generation of Stable Insertions without Selection

PubMed Central

Frazier, Courtney L.; San Filippo, Joseph; Lambowitz, Alan M.; Mills, David A.

2003-01-01

Despite their commercial importance, there are relatively few facile methods for genomic manipulation of the lactic acid bacteria. Here, the lactococcal group II intron, Ll.ltrB, was targeted to insert efficiently into genes encoding malate decarboxylase (mleS) and tetracycline resistance (tetM) within the Lactococcus lactis genome. Integrants were readily identified and maintained in the absence of a selectable marker. Since splicing of the Ll.ltrB intron depends on the intron-encoded protein, targeted invasion with an intron lacking the intron open reading frame disrupted TetM and MleS function, and MleS activity could be partially restored by expressing the intron-encoded protein in trans. Restoration of splicing from intron variants lacking the intron-encoded protein illustrates how targeted group II introns could be used for conditional expression of any gene. Furthermore, the modified Ll.ltrB intron was used to separately deliver a phage resistance gene (abiD) and a tetracycline resistance marker (tetM) into mleS, without the need for selection to drive the integration or to maintain the integrant. Our findings demonstrate the utility of targeted group II introns as a potential food-grade mechanism for delivery of industrially important traits into the genomes of lactococci. PMID:12571038

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs.

PubMed

Fozo, Elizabeth M; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S; Jones, Kristi L; Ocampo, Alejandro; Rudd, Kenneth E; Storz, Gisela

2008-12-01

The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, although the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five-sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18- to 19-amino-acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by coexpression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell.

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

PubMed Central

Fozo, Elizabeth M.; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S.; Jones, Kristi L.; Ocampo, Alejandro; Rudd, Kenneth E.; Storz, Gisela

2008-01-01

Summary The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, though the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18–19 amino acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by co-expression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell. PMID:18710431

Identification of the initiation site of poliovirus polyprotein synthesis

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

Dorner, A.J.; Dorner, L.F.; Larsen, G.R.

1982-06-01

The complete nucleotide sequence of poliovirus RNA has a long open reading frame capable of encoding the precursor polyprotein NCVPOO. The first AUG codon in this reading frame is located 743 nucleotides from the 5' end of the RNA and is preceded by eight AUG codons in all three reading frames. Because all proteins that map at the amino terminus of the polyprotein (P1-1a, VPO, and VP4) are blocked at their amino termini and previous studies of ribosome binding have been inconclusive, direct identification of the initiation site of protein synthesis was difficult. We separated and identified all of themore » tryptic peptides of capsid protein VP4 and correlated these peptides with the amino acid sequence predicted to follow the AUG codon at nucleotide 743. Our data indicate that VP4 begins with a blocked glycine that is encoded immediately after the AUG codon at nucleotide 743. An S1 nuclease analysis of poliovirus mRNA failed to reveal a splice in the 5' region. We concluded that synthesis of poliovirus polyprotein is initiated at nucleotide 743, the first AUG codon in the long open reading frame.« less

Identification and Cloning of gusA, Encoding a New β-Glucuronidase from Lactobacillus gasseri ADH†

PubMed Central

Russell, W. M.; Klaenhammer, T. R.

2001-01-01

The gusA gene, encoding a new β-glucuronidase enzyme, has been cloned from Lactobacillus gasseri ADH. This is the first report of a β-glucuronidase gene cloned from a bacterial source other than Escherichia coli. A plasmid library of L. gasseri chromosomal DNA was screened for complementation of an E. coli gus mutant. Two overlapping clones that restored β-glucuronidase activity in the mutant strain were sequenced and revealed three complete and two partial open reading frames. The largest open reading frame, spanning 1,797 bp, encodes a 597-amino-acid protein that shows 39% identity to β-glucuronidase (GusA) of E. coli K-12 (EC 3.2.1.31). The other two complete open reading frames, which are arranged to be separately transcribed, encode a putative bile salt hydrolase and a putative protein of unknown function with similarities to MerR-type regulatory proteins. Overexpression of GusA was achieved in a β-glucuronidase-negative L. gasseri strain by expressing the gusA gene, subcloned onto a low-copy-number shuttle vector, from the strong Lactobacillus P6 promoter. GusA was also expressed in E. coli from a pET expression system. Preliminary characterization of the GusA protein from crude cell extracts revealed that the enzyme was active across an acidic pH range and a broad temperature range. An analysis of other lactobacilli identified β-glucuronidase activity and gusA homologs in other L. gasseri isolates but not in other Lactobacillus species tested. PMID:11229918

Identification of a second PAD1 in Brettanomyces bruxellensis LAMAP2480.

PubMed

González, Camila; Godoy, Liliana; Ganga, Ma Angélica

2017-02-01

Volatile phenols are aromatic compounds produced by some yeasts of the genus Brettanomyces as defense against the toxicity of hydroxycinnamic acids (p-coumaric acid, ferulic acid and caffeic acid). The origin of these compounds in winemaking involves the sequential action of two enzymes: coumarate decarboxylase and vinylphenol reductase. The first one converts hydroxycinnamic acids into hydroxystyrenes, which are then reduced to ethyl derivatives by vinylphenol reductase. Volatile phenols derived from p-coumaric acid (4-vinylphenol and 4-ethylphenol) have been described as the major contributors to self-defeating aromas associated with stable, gouache, wet mouse, etc., which generates large economic losses in the wine industry. The gene responsible for the production of 4-vinylphenol from p-coumaric acid has been identified as PAD1, which encodes a phenylacrylic acid decarboxylase. PAD1 has been described for many species, among them Candida albicans, Candida dubliniensis, Debaryomyces hansenii and Pichia anomala. In Brettanomyces bruxellensis LAMAP2480, a 666 bp reading frame (DbPAD) encodes a coumarate decarboxylase. Recent studies have reported the existence of a new reading frame belonging to DbPAD called DbPAD2 of 531 bp, which could encode a protein with similar enzymatic activity to PAD1. The present study confirmed that the transformation of Saccharomyces cerevisiae strain BY4722 with reading frame DbPAD2 under the control of the B. bruxellensis ACT1 promoter, encodes an enzyme with coumarate decarboxylase activity. This work has provided deeper insight into the origin of aroma defects in wine due to contamination by Brettanomyces spp.

Adaptive Distributed Video Coding with Correlation Estimation using Expectation Propagation

PubMed Central

Cui, Lijuan; Wang, Shuang; Jiang, Xiaoqian; Cheng, Samuel

2013-01-01

Distributed video coding (DVC) is rapidly increasing in popularity by the way of shifting the complexity from encoder to decoder, whereas no compression performance degrades, at least in theory. In contrast with conventional video codecs, the inter-frame correlation in DVC is explored at decoder based on the received syndromes of Wyner-Ziv (WZ) frame and side information (SI) frame generated from other frames available only at decoder. However, the ultimate decoding performances of DVC are based on the assumption that the perfect knowledge of correlation statistic between WZ and SI frames should be available at decoder. Therefore, the ability of obtaining a good statistical correlation estimate is becoming increasingly important in practical DVC implementations. Generally, the existing correlation estimation methods in DVC can be classified into two main types: pre-estimation where estimation starts before decoding and on-the-fly (OTF) estimation where estimation can be refined iteratively during decoding. As potential changes between frames might be unpredictable or dynamical, OTF estimation methods usually outperforms pre-estimation techniques with the cost of increased decoding complexity (e.g., sampling methods). In this paper, we propose a low complexity adaptive DVC scheme using expectation propagation (EP), where correlation estimation is performed OTF as it is carried out jointly with decoding of the factor graph-based DVC code. Among different approximate inference methods, EP generally offers better tradeoff between accuracy and complexity. Experimental results show that our proposed scheme outperforms the benchmark state-of-the-art DISCOVER codec and other cases without correlation tracking, and achieves comparable decoding performance but with significantly low complexity comparing with sampling method. PMID:23750314

Adaptive distributed video coding with correlation estimation using expectation propagation

NASA Astrophysics Data System (ADS)

Cui, Lijuan; Wang, Shuang; Jiang, Xiaoqian; Cheng, Samuel

2012-10-01

Distributed video coding (DVC) is rapidly increasing in popularity by the way of shifting the complexity from encoder to decoder, whereas no compression performance degrades, at least in theory. In contrast with conventional video codecs, the inter-frame correlation in DVC is explored at decoder based on the received syndromes of Wyner-Ziv (WZ) frame and side information (SI) frame generated from other frames available only at decoder. However, the ultimate decoding performances of DVC are based on the assumption that the perfect knowledge of correlation statistic between WZ and SI frames should be available at decoder. Therefore, the ability of obtaining a good statistical correlation estimate is becoming increasingly important in practical DVC implementations. Generally, the existing correlation estimation methods in DVC can be classified into two main types: pre-estimation where estimation starts before decoding and on-the-fly (OTF) estimation where estimation can be refined iteratively during decoding. As potential changes between frames might be unpredictable or dynamical, OTF estimation methods usually outperforms pre-estimation techniques with the cost of increased decoding complexity (e.g., sampling methods). In this paper, we propose a low complexity adaptive DVC scheme using expectation propagation (EP), where correlation estimation is performed OTF as it is carried out jointly with decoding of the factor graph-based DVC code. Among different approximate inference methods, EP generally offers better tradeoff between accuracy and complexity. Experimental results show that our proposed scheme outperforms the benchmark state-of-the-art DISCOVER codec and other cases without correlation tracking, and achieves comparable decoding performance but with significantly low complexity comparing with sampling method.

Adaptive Distributed Video Coding with Correlation Estimation using Expectation Propagation.

PubMed

Cui, Lijuan; Wang, Shuang; Jiang, Xiaoqian; Cheng, Samuel

2012-10-15

Distributed video coding (DVC) is rapidly increasing in popularity by the way of shifting the complexity from encoder to decoder, whereas no compression performance degrades, at least in theory. In contrast with conventional video codecs, the inter-frame correlation in DVC is explored at decoder based on the received syndromes of Wyner-Ziv (WZ) frame and side information (SI) frame generated from other frames available only at decoder. However, the ultimate decoding performances of DVC are based on the assumption that the perfect knowledge of correlation statistic between WZ and SI frames should be available at decoder. Therefore, the ability of obtaining a good statistical correlation estimate is becoming increasingly important in practical DVC implementations. Generally, the existing correlation estimation methods in DVC can be classified into two main types: pre-estimation where estimation starts before decoding and on-the-fly (OTF) estimation where estimation can be refined iteratively during decoding. As potential changes between frames might be unpredictable or dynamical, OTF estimation methods usually outperforms pre-estimation techniques with the cost of increased decoding complexity (e.g., sampling methods). In this paper, we propose a low complexity adaptive DVC scheme using expectation propagation (EP), where correlation estimation is performed OTF as it is carried out jointly with decoding of the factor graph-based DVC code. Among different approximate inference methods, EP generally offers better tradeoff between accuracy and complexity. Experimental results show that our proposed scheme outperforms the benchmark state-of-the-art DISCOVER codec and other cases without correlation tracking, and achieves comparable decoding performance but with significantly low complexity comparing with sampling method.

Marek’s Disease Virus Encoded Ribonucleotide Reductase Large Subunit is not Essential for In Vitro Replication

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus (MDV) infected cells express a viral ribonucleotide reductase (RR) that is distinguishable from that present in uninfected cells by monoclonal antibody T81. Open reading frames UL39 and UL40 of the MDV genome encode the large (RR1) and small (RR2) subunits of RR enzyme, respe...

The effect of interference on delta modulation encoded video signals

NASA Technical Reports Server (NTRS)

Schilling, D. L.

1979-01-01

The results of a study on the use of the delta modulator as a digital encoder of television signals are presented. The computer simulation was studied of different delta modulators in order to find a satisfactory delta modulator. After finding a suitable delta modulator algorithm via computer simulation, the results are analyzed and then implemented in hardware to study the ability to encode real time motion pictures from an NTSC format television camera. The effects were investigated of channel errors on the delta modulated video signal and several error correction algorithms were tested via computer simulation. A very high speed delta modulator was built (out of ECL logic), incorporating the most promising of the correction schemes, so that it could be tested on real time motion pictures. The final area of investigation concerned itself with finding delta modulators which could achieve significant bandwidth reduction without regard to complexity or speed. The first such scheme to be investigated was a real time frame to frame encoding scheme which required the assembly of fourteen, 131,000 bit long shift registers as well as a high speed delta modulator. The other schemes involved two dimensional delta modulator algorithms.

Spatial cognition and navigation

NASA Technical Reports Server (NTRS)

Aretz, Anthony J.

1989-01-01

An experiment that provides data for the development of a cognitive model of pilot flight navigation is described. The experiment characterizes navigational awareness as the mental alignment of two frames of reference: (1) the ego centered reference frame that is established by the forward view out of the cockpit and (2) the world centered reference frame that is established by the aircraft's location on a map. The data support a model involving at least two components: (1) the perceptual encoding of the navigational landmarks and (2) the mental rotation of the map's world reference frame into alignment with the ego centered reference frame. The quantitative relationships of these two factors are provided as possible inputs for a computational model of spatial cognition during flight navigation.

Method and system for efficient video compression with low-complexity encoder

NASA Technical Reports Server (NTRS)

Chen, Jun (Inventor); He, Dake (Inventor); Sheinin, Vadim (Inventor); Jagmohan, Ashish (Inventor); Lu, Ligang (Inventor)

2012-01-01

Disclosed are a method and system for video compression, wherein the video encoder has low computational complexity and high compression efficiency. The disclosed system comprises a video encoder and a video decoder, wherein the method for encoding includes the steps of converting a source frame into a space-frequency representation; estimating conditional statistics of at least one vector of space-frequency coefficients; estimating encoding rates based on the said conditional statistics; and applying Slepian-Wolf codes with the said computed encoding rates. The preferred method for decoding includes the steps of; generating a side-information vector of frequency coefficients based on previously decoded source data, encoder statistics, and previous reconstructions of the source frequency vector; and performing Slepian-Wolf decoding of at least one source frequency vector based on the generated side-information, the Slepian-Wolf code bits and the encoder statistics.

Frameshifting in alphaviruses: a diversity of 3' stimulatory structures.

PubMed

Chung, Betty Y-W; Firth, Andrew E; Atkins, John F

2010-03-26

Programmed ribosomal frameshifting allows the synthesis of alternative, N-terminally coincident, C-terminally distinct proteins from the same RNA. Many viruses utilize frameshifting to optimize the coding potential of compact genomes, to circumvent the host cell's canonical rule of one functional protein per mRNA, or to express alternative proteins in a fixed ratio. Programmed frameshifting is also used in the decoding of a small number of cellular genes. Recently, specific ribosomal -1 frameshifting was discovered at a conserved U_UUU_UUA motif within the sequence encoding the alphavirus 6K protein. In this case, frameshifting results in the synthesis of an additional protein, termed TF (TransFrame). This new case of frameshifting is unusual in that the -1 frame ORF is very short and completely embedded within the sequence encoding the overlapping polyprotein. The present work shows that there is remarkable diversity in the 3' sequences that are functionally important for efficient frameshifting at the U_UUU_UUA motif. While many alphavirus species utilize a 3' RNA structure such as a hairpin or pseudoknot, some species (such as Semliki Forest virus) apparently lack any intra-mRNA stimulatory structure, yet just 20 nt 3'-adjacent to the shift site stimulates up to 10% frameshifting. The analysis, both experimental and bioinformatic, significantly expands the known repertoire of -1 frameshifting stimulators in mammalian and insect systems.

Simple scheme to implement decoy-state reference-frame-independent quantum key distribution

NASA Astrophysics Data System (ADS)

Zhang, Chunmei; Zhu, Jianrong; Wang, Qin

2018-06-01

We propose a simple scheme to implement decoy-state reference-frame-independent quantum key distribution (RFI-QKD), where signal states are prepared in Z, X, and Y bases, decoy states are prepared in X and Y bases, and vacuum states are set to no bases. Different from the original decoy-state RFI-QKD scheme whose decoy states are prepared in Z, X and Y bases, in our scheme decoy states are only prepared in X and Y bases, which avoids the redundancy of decoy states in Z basis, saves the random number consumption, simplifies the encoding device of practical RFI-QKD systems, and makes the most of the finite pulses in a short time. Numerical simulations show that, considering the finite size effect with reasonable number of pulses in practical scenarios, our simple decoy-state RFI-QKD scheme exhibits at least comparable or even better performance than that of the original decoy-state RFI-QKD scheme. Especially, in terms of the resistance to the relative rotation of reference frames, our proposed scheme behaves much better than the original scheme, which has great potential to be adopted in current QKD systems.

The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

PubMed Central

Grohmann, L; Brennicke, A; Schuster, W

1992-01-01

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed. Images PMID:1454526

Cloning and expression of clt genes encoding milk-clotting proteases from Myxococcus xanthus 422.

PubMed

Poza, M; Prieto-Alcedo, M; Sieiro, C; Villa, T G

2004-10-01

The screening of a gene library of the milk-clotting strain Myxococcus xanthus 422 constructed in Escherichia coli allowed the description of eight positive clones containing 26 open reading frames. Only three of them (cltA, cltB, and cltC) encoded proteins that exhibited intracellular milk-clotting ability in E. coli, Saccharomyces cerevisiae, and Pichia pastoris expression systems.

Wireless live streaming video of laparoscopic surgery: a bandwidth analysis for handheld computers.

PubMed

Gandsas, Alex; McIntire, Katherine; George, Ivan M; Witzke, Wayne; Hoskins, James D; Park, Adrian

2002-01-01

Over the last six years, streaming media has emerged as a powerful tool for delivering multimedia content over networks. Concurrently, wireless technology has evolved, freeing users from desktop boundaries and wired infrastructures. At the University of Kentucky Medical Center, we have integrated these technologies to develop a system that can wirelessly transmit live surgery from the operating room to a handheld computer. This study establishes the feasibility of using our system to view surgeries and describes the effect of bandwidth on image quality. A live laparoscopic ventral hernia repair was transmitted to a single handheld computer using five encoding speeds at a constant frame rate, and the quality of the resulting streaming images was evaluated. No video images were rendered when video data were encoded at 28.8 kilobytes per second (Kbps), the slowest encoding bitrate studied. The highest quality images were rendered at encoding speeds greater than or equal to 150 Kbps. Of note, a 15 second transmission delay was experienced using all four encoding schemes that rendered video images. We believe that the wireless transmission of streaming video to handheld computers has tremendous potential to enhance surgical education. For medical students and residents, the ability to view live surgeries, lectures, courses and seminars on handheld computers means a larger number of learning opportunities. In addition, we envision that wireless enabled devices may be used to telemonitor surgical procedures. However, bandwidth availability and streaming delay are major issues that must be addressed before wireless telementoring becomes a reality.

Frame-Insensitive Expression Cloning of Fluorescent Protein from Scolionema suvaense.

PubMed

Horiuchi, Yuki; Laskaratou, Danai; Sliwa, Michel; Ruckebusch, Cyril; Hatori, Kuniyuki; Mizuno, Hideaki; Hotta, Jun-Ichi

2018-01-26

Expression cloning from cDNA is an important technique for acquiring genes encoding novel fluorescent proteins. However, the probability of in-frame cDNA insertion following the first start codon of the vector is normally only 1/3, which is a cause of low cloning efficiency. To overcome this issue, we developed a new expression plasmid vector, pRSET-TriEX, in which transcriptional slippage was induced by introducing a DNA sequence of (dT) 14 next to the first start codon of pRSET. The effectiveness of frame-insensitive cloning was validated by inserting the gene encoding eGFP with all three possible frames to the vector. After transformation with one of these plasmids, E. coli cells expressed eGFP with no significant difference in the expression level. The pRSET-TriEX vector was then used for expression cloning of a novel fluorescent protein from Scolionema suvaense . We screened 3658 E. coli colonies transformed with pRSET-TriEX containing Scolionema suvaense cDNA, and found one colony expressing a novel green fluorescent protein, ScSuFP. The highest score in protein sequence similarity was 42% with the chain c of multi-domain green fluorescent protein like protein "ember" from Anthoathecata sp. Variations in the N- and/or C-terminal sequence of ScSuFP compared to other fluorescent proteins indicate that the expression cloning, rather than the sequence similarity-based methods, was crucial for acquiring the gene encoding ScSuFP. The absorption maximum was at 498 nm, with an extinction efficiency of 1.17 × 10⁵ M -1 ·cm -1 . The emission maximum was at 511 nm and the fluorescence quantum yield was determined to be 0.6. Pseudo-native gel electrophoresis showed that the protein forms obligatory homodimers.

Drosophila Nora virus capsid proteins differ from those of other picorna-like viruses.

PubMed

Ekström, Jens-Ola; Habayeb, Mazen S; Srivastava, Vaibhav; Kieselbach, Thomas; Wingsle, Gunnar; Hultmark, Dan

2011-09-01

The recently discovered Nora virus from Drosophila melanogaster is a single-stranded RNA virus. Its published genomic sequence encodes a typical picorna-like cassette of replicative enzymes, but no capsid proteins similar to those in other picorna-like viruses. We have now done additional sequencing at the termini of the viral genome, extending it by 455 nucleotides at the 5' end, but no more coding sequence was found. The completeness of the final 12,333-nucleotide sequence was verified by the production of infectious virus from the cloned genome. To identify the capsid proteins, we purified Nora virus particles and analyzed their proteins by mass spectrometry. Our results show that the capsid is built from three major proteins, VP4A, B and C, encoded in the fourth open reading frame of the viral genome. The viral particles also contain traces of a protein from the third open reading frame, VP3. VP4A and B are not closely related to other picorna-like virus capsid proteins in sequence, but may form similar jelly roll folds. VP4C differs from the others and is predicted to have an essentially α-helical conformation. In a related virus, identified from EST database sequences from Nasonia parasitoid wasps, VP4C is encoded in a separate open reading frame, separated from VP4A and B by a frame-shift. This opens a possibility that VP4C is produced in non-equimolar quantities. Altogether, our results suggest that the Nora virus capsid has a different protein organization compared to the order Picornavirales. Copyright © 2011 Elsevier B.V. All rights reserved.

Video compression of coronary angiograms based on discrete wavelet transform with block classification.

PubMed

Ho, B T; Tsai, M J; Wei, J; Ma, M; Saipetch, P

1996-01-01

A new method of video compression for angiographic images has been developed to achieve high compression ratio (~20:1) while eliminating block artifacts which leads to loss of diagnostic accuracy. This method adopts motion picture experts group's (MPEGs) motion compensated prediction to takes advantage of frame to frame correlation. However, in contrast to MPEG, the error images arising from mismatches in the motion estimation are encoded by discrete wavelet transform (DWT) rather than block discrete cosine transform (DCT). Furthermore, the authors developed a classification scheme which label each block in an image as intra, error, or background type and encode it accordingly. This hybrid coding can significantly improve the compression efficiency in certain eases. This method can be generalized for any dynamic image sequences applications sensitive to block artifacts.

Cloning and sequencing of a gene encoding the 69-kDa extracellular chitinase of Janthinobacterium lividum.

PubMed

Gleave, A P; Taylor, R K; Morris, B A; Greenwood, D R

1995-09-15

Janthinobacterium lividum secretes a major 56-kDa chitinase and a minor 69-kDa chitinase. A chitinase gene was defined on a 3-kb fragment of clone pRKT10, by virtue of fluorescent colonies in the presence of 4-methylumbelliferyl-beta-D-N,N',N"-chitotrioside. Nucleotide sequencing revealed an 1998-bp open reading frame with the potential to encode a 69,716-Da protein with amino acid sequences similar to those in other chitinases, suggesting it encodes the minor chitinase (Chi69). Chitinase activity of Escherichia coli (pRKT10) lysates was detected mainly in the periplasmic fraction and immunoblotting detected a 70-kDa protein in this fraction. Chi69 has an N-terminal secretory leader peptide preceding two probable chitin-binding domains and a catalytic domain. These functional domains are separated by linker regions of proline-threonine repeats. Amino acid sequencing of cyanogen bromide cleavage-derived peptides from the major 56-kDa chitinase suggested that Chi69 may be a precursor of Chi56. In addition, an N-terminally truncated version of Chi69 retained chitinase activity as expected if in vivo processing of Chi69 generates Chi56.

An Out-of-frame Overlapping Reading Frame in the Ataxin-1 Coding Sequence Encodes a Novel Ataxin-1 Interacting Protein*

PubMed Central

Bergeron, Danny; Lapointe, Catherine; Bissonnette, Cyntia; Tremblay, Guillaume; Motard, Julie; Roucou, Xavier

2013-01-01

Spinocerebellar ataxia type 1 is an autosomal dominant cerebellar ataxia associated with the expansion of a polyglutamine tract within the ataxin-1 (ATXN1) protein. Recent studies suggest that understanding the normal function of ATXN1 in cellular processes is essential to decipher the pathogenesis mechanisms in spinocerebellar ataxia type 1. We found an alternative translation initiation ATG codon in the +3 reading frame of human ATXN1 starting 30 nucleotides downstream of the initiation codon for ATXN1 and ending at nucleotide 587. This novel overlapping open reading frame (ORF) encodes a 21-kDa polypeptide termed Alt-ATXN1 (Alternative ATXN1) with a completely different amino acid sequence from ATXN1. We introduced a hemagglutinin tag in-frame with Alt-ATXN1 in ATXN1 cDNA and showed in cell culture the co-expression of both ATXN1 and Alt-ATXN1. Remarkably, Alt-ATXN1 colocalized and interacted with ATXN1 in nuclear inclusions. In contrast, in the absence of ATXN1 expression, Alt-ATXN1 displays a homogenous nucleoplasmic distribution. Alt-ATXN1 interacts with poly(A)+ RNA, and its nuclear localization is dependent on RNA transcription. Polyclonal antibodies raised against Alt-ATXN1 confirmed the expression of Alt-ATXN1 in human cerebellum expressing ATXN1. These results demonstrate that human ATXN1 gene is a dual coding sequence and that ATXN1 interacts with and controls the subcellular distribution of Alt-ATXN1. PMID:23760502

Genetic analysis of the agrocinopine catabolic region of Agrobacterium tumefaciens Ti plasmid pTiC58, which encodes genes required for opine and agrocin 84 transport.

PubMed Central

Hayman, G T; Beck von Bodman, S; Kim, H; Jiang, P; Farrand, S K

1993-01-01

The acc region, subcloned from pTiC58 of classical nopaline and agrocinopine A and B Agrobacterium tumefaciens C58, allowed agrobacteria to grow using agrocinopine B as the sole source of carbon and energy. acc is approximately 6 kb in size. It consists of at least five genes, accA through accE, as defined by complementation analysis using subcloned fragments and transposon insertion mutations of acc carried on different plasmids within the same cell. All five regions are required for agrocin 84 sensitivity, and at least four are required for agrocinopine and agrocin 84 uptake. The complementation results are consistent with the hypothesis that each of the five regions is separately transcribed. Maxicell experiments showed that the first of these genes, accA, encodes a 60-kDa protein. Analysis of osmotic shock fractions showed this protein to be located in the periplasm. The DNA sequence of the accA region revealed an open reading frame encoding a predicted polypeptide of 59,147 Da. The amino acid sequence encoded by this open reading frame is similar to the periplasmic binding proteins OppA and DppA of Escherichia coli and Salmonella typhimurium and OppA of Bacillus subtilis. Images PMID:8366042

Citrus psorosis virus RNA 1 is of negative polarity and potentially encodes in its complementary strand a 24K protein of unknown function and 280K putative RNA dependent RNA polymerase.

PubMed

Naum-Onganía, Gabriela; Gago-Zachert, Selma; Peña, Eduardo; Grau, Oscar; Garcia, Maria Laura

2003-10-01

Citrus psorosis virus (CPsV), the type member of genus Ophiovirus, has three genomic RNAs. Complete sequencing of CPsV RNA 1 revealed a size of 8184 nucleotides and Northern blot hybridization with chain specific probes showed that its non-coding strand is preferentially encapsidated. The complementary strand of RNA 1 contains two open reading frames (ORFs) separated by a 109-nt intergenic region, one located near the 5'-end potentially encoding a 24K protein of unknown function, and another of 280K containing the core polymerase motifs characteristic of viral RNA-dependent RNA polymerases (RdRp). Comparison of the core RdRp motifs of negative-stranded RNA viruses, supports grouping CPsV, Ranunculus white mottle virus (RWMV) and Mirafiori lettuce virus (MiLV) within the same genus (Ophiovirus), constituting a monophyletic group separated from all other negative-stranded RNA viruses. Furthermore, RNAs 1 of MiLV, CPsV and RWMV are similar in size and those of MiLV and CPsV also in genomic organization and sequence.

Molecular cloning of a putative gene encoding isopentenyltransferase from pingyitiancha (Malus hupehensis) and characterization of its response to nitrate.

PubMed

Peng, Jing; Peng, Futian; Zhu, Chunfu; Wei, Shaochong

2008-06-01

A putative isopentenyltransferase (IPT) encoding gene was identified from a pingyitiancha (Malus hupehensis Rehd.) expressed sequence tag database, and the full-length gene was cloned by RACE. Based on expression profile and sequence alignment, the nucleotide sequence of the clone, named MhIPT3, was most similar to AtIPT3, an IPT gene in Arabidopsis. The full-length cDNA contained a 963-bp open reading frame encoding a protein of 321 amino acids with a molecular mass of 37.3 kDa. Sequence analysis of genomic DNA revealed the absence of introns in the frame. Quantitative real-time PCR analysis demonstrated that the gene was expressed in roots, stems and leaves. Application of nitrate to roots of nitrogen-deprived seedlings strongly induced expression of MhIPT3 and was accompanied by the accumulation of cytokinins, whereas MhIPT3 expression was little affected by ammonium application to roots of nitrogen-deprived seedlings. Application of nitrate to leaves also up-regulated the expression of MhIPT3 and corresponded closely with the accumulation of isopentyladenine and isopentyladenosine in leaves.

Investigation of television transmission using adaptive delta modulation principles

NASA Technical Reports Server (NTRS)

Schilling, D. L.

1976-01-01

The results are presented of a study on the use of the delta modulator as a digital encoder of television signals. The computer simulation of different delta modulators was studied in order to find a satisfactory delta modulator. After finding a suitable delta modulator algorithm via computer simulation, the results were analyzed and then implemented in hardware to study its ability to encode real time motion pictures from an NTSC format television camera. The effects of channel errors on the delta modulated video signal were tested along with several error correction algorithms via computer simulation. A very high speed delta modulator was built (out of ECL logic), incorporating the most promising of the correction schemes, so that it could be tested on real time motion pictures. Delta modulators were investigated which could achieve significant bandwidth reduction without regard to complexity or speed. The first scheme investigated was a real time frame to frame encoding scheme which required the assembly of fourteen, 131,000 bit long shift registers as well as a high speed delta modulator. The other schemes involved the computer simulation of two dimensional delta modulator algorithms.

Frames and knowledge in mixed media: how activation changes information intake.

PubMed

Veenstra, Aaron S; Sayre, Ben; Shah, Dhavan V; McLeod, Douglas M

2008-08-01

Many people consider strategic framing, the journalistic tendency to reduce politics to a game or competition focused on the tactical maneuvers of political actors, to be harmful to democracy because it erodes citizen interest in the democratic process. Our results demonstrate that this is not always the case. Testing the effects of textual strategic frames and video processing in a digital environment, we show that strategic frames may also provide a context that is more conducive to learning in mixed media news environments than that provided by value frames, those focused on the value conflict between principled policy opponents. Further analysis reveals that this effect is most clearly seen among people who read political blogs (i.e., those who are already active and interested in politics). Our data suggest that for individuals with cognitive networks built around ideological concerns, such as blog readers, value-framed messages provide cues to stop encoding new information, while strategically framed messages lead people to continue absorbing and learning in mixed media environments.

Construction and Screening of a Lentiviral Secretome Library.

PubMed

Liu, Tao; Jia, Panpan; Ma, Huailei; Reed, Sean A; Luo, Xiaozhou; Larman, H Benjamin; Schultz, Peter G

2017-06-22

Over 2,000 human proteins are predicted to be secreted, but the biological function of the many of these proteins is still unknown. Moreover, a number of these proteins may act as new therapeutic agents or be targets for the development of therapeutic antibodies. To further explore the extracellular proteome, we have developed a secretome-enriched open reading frame (ORF) library that can be readily screened for autocrine activity in cell-based phenotypic or reporter assays. Next-generation sequencing (NGS) and database analysis predict that the library contains approximately 900 ORFs encoding known secreted proteins (accounting for 77.8% of the library), as well as genes encoding potentially unknown secreted proteins. In a proof-of-principle study, human TF-1 cells were screened for proliferative factors, and the known cytokine GMCSF was identified as a dominant hit. This library offers a relatively low-cost and straightforward approach for functional autocrine screens of secreted proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metadata management and semantics in microarray repositories.

PubMed

Kocabaş, F; Can, T; Baykal, N

2011-12-01

The number of microarray and other high-throughput experiments on primary repositories keeps increasing as do the size and complexity of the results in response to biomedical investigations. Initiatives have been started on standardization of content, object model, exchange format and ontology. However, there are backlogs and inability to exchange data between microarray repositories, which indicate that there is a great need for a standard format and data management. We have introduced a metadata framework that includes a metadata card and semantic nets that make experimental results visible, understandable and usable. These are encoded in syntax encoding schemes and represented in RDF (Resource Description Frame-word), can be integrated with other metadata cards and semantic nets, and can be exchanged, shared and queried. We demonstrated the performance and potential benefits through a case study on a selected microarray repository. We concluded that the backlogs can be reduced and that exchange of information and asking of knowledge discovery questions can become possible with the use of this metadata framework.

Oil Palm Defensin: A Thermal Stable Peptide that Restricts the Mycelial Growth of Ganoderma boninense.

PubMed

Tan, Yung-Chie; Ang, Cheng-Liang; Wong, Mui-Yun; Ho, Chai-Ling

2016-01-01

Plant defensins are plant defence peptides that have many different biological activities, including antifungal, antimicrobial, and insecticidal activities. A cDNA (EgDFS) encoding defensin was isolated from Elaeis guineensis. The open reading frame of EgDFS contained 231 nucleotides encoding a 71-amino acid protein with a predicted molecular weight at 8.69 kDa, and a potential signal peptide. The eight highly conserved cysteine sites in plant defensins were also conserved in EgDFS. The EgDFS sequence lacking 30 amino acid residues at its N-terminus (EgDFSm) was cloned into Escherichia coli BL21 (DE3) pLysS and successfully expressed as a soluble recombinant protein. The recombinant EgDFSm was found to be a thermal stable peptide which demonstrated inhibitory activity against the growth of G. boninense possibly by inhibiting starch assimilation. The role of EgDFSm in oil palm defence system against the infection of pathogen G. boninense was discussed.

The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more?

PubMed

Akhter, Yusuf; Ehebauer, Matthias T; Mukhopadhyay, Sangita; Hasnain, Seyed E

2012-01-01

The PE/PPE multigene family codes for approximately 10% of the Mycobacterium tuberculosis proteome and is encoded by 176 open reading frames. These proteins possess, and have been named after, the conserved proline-glutamate (PE) or proline-proline-glutamate (PPE) motifs at their N-terminus. Their genes have a conserved structure and repeat motifs that could be a potential source of antigenic variation in M. tuberculosis. PE/PPE genes are scattered throughout the genome and PE/PPE pairs are usually encoded in bicistronic operons although this is not universally so. This gene family has evolved by specific gene duplication events. PE/PPE proteins are either secreted or localized to the cell surface. Several are thought to be virulence factors, which participate in evasion of the host immune response. This review summarizes the current knowledge about the gene family in order to better understand its biological function. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Nucleotide sequence of the Saccharomyces cerevisiae PUT4 proline-permease-encoding gene: similarities between CAN1, HIP1 and PUT4 permeases.

PubMed

Vandenbol, M; Jauniaux, J C; Grenson, M

1989-11-15

The complete nucleotide (nt) sequence of the PUT4 gene, whose product is required for high-affinity proline active transport in the yeast Saccharomyces cerevisiae, is presented. The sequence contains a single long open reading frame of 1881 nt, encoding a polypeptide with a calculated Mr of 68,795. The predicted protein is strongly hydrophobic and exhibits six potential glycosylation sites. Its hydropathy profile suggests the presence of twelve membrane-spanning regions flanked by hydrophilic N- and C-terminal domains. The N terminus does not resemble signal sequences found in secreted proteins. These features are characteristic of integral membrane proteins catalyzing translocation of ligands across cellular membranes. Protein sequence comparisons indicate strong resemblance to the arginine and histidine permeases of S. cerevisiae, but no marked sequence similarity to the proline permease of Escherichia coli or to other known prokaryotic or eukaryotic transport proteins. The strong similarity between the three yeast amino acid permeases suggests a common ancestor for the three proteins.

Novel methods of imaging and analysis for the thermoregulatory sweat test.

PubMed

Carroll, Michael Sean; Reed, David W; Kuntz, Nancy L; Weese-Mayer, Debra Ellyn

2018-06-07

The thermoregulatory sweat test (TST) can be central to the identification and management of disorders affecting sudomotor function and small sensory and autonomic nerve fibers, but the cumbersome nature of the standard testing protocol has prevented its widespread adoption. A high resolution, quantitative, clean and simple assay of sweating could significantly improve identification and management of these disorders. Images from 89 clinical TSTs were analyzed retrospectively using two novel techniques. First, using the standard indicator powder, skin surface sweat distributions were determined algorithmically for each patient. Second, a fundamentally novel method using thermal imaging of forced evaporative cooling was evaluated through comparison with the standard technique. Correlation and receiver operating characteristic analyses were used to determine the degree of match between these methods, and the potential limits of thermal imaging were examined through cumulative analysis of all studied patients. Algorithmic encoding of sweating and non-sweating regions produces a more objective analysis for clinical decision making. Additionally, results from the forced cooling method correspond well with those from indicator powder imaging, with a correlation across spatial regions of -0.78 (CI: -0.84 to -0.71). The method works similarly across body regions, and frame-by-frame analysis suggests the ability to identify sweating regions within about 1 second of imaging. While algorithmic encoding can enhance the standard sweat testing protocol, thermal imaging with forced evaporative cooling can dramatically improve the TST by making it less time-consuming and more patient-friendly than the current approach.

Interaction Analysis through Proteomic Phage Display

PubMed Central

2014-01-01

Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs), or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance. PMID:25295249

Ultrafast Synthetic Transmit Aperture Imaging Using Hadamard-Encoded Virtual Sources With Overlapping Sub-Apertures.

PubMed

Ping Gong; Pengfei Song; Shigao Chen

2017-06-01

The development of ultrafast ultrasound imaging offers great opportunities to improve imaging technologies, such as shear wave elastography and ultrafast Doppler imaging. In ultrafast imaging, there are tradeoffs among image signal-to-noise ratio (SNR), resolution, and post-compounded frame rate. Various approaches have been proposed to solve this tradeoff, such as multiplane wave imaging or the attempts of implementing synthetic transmit aperture imaging. In this paper, we propose an ultrafast synthetic transmit aperture (USTA) imaging technique using Hadamard-encoded virtual sources with overlapping sub-apertures to enhance both image SNR and resolution without sacrificing frame rate. This method includes three steps: 1) create virtual sources using sub-apertures; 2) encode virtual sources using Hadamard matrix; and 3) add short time intervals (a few microseconds) between transmissions of different virtual sources to allow overlapping sub-apertures. The USTA was tested experimentally with a point target, a B-mode phantom, and in vivo human kidney micro-vessel imaging. Compared with standard coherent diverging wave compounding with the same frame rate, improvements on image SNR, lateral resolution (+33%, with B-mode phantom imaging), and contrast ratio (+3.8 dB, with in vivo human kidney micro-vessel imaging) have been achieved. The f-number of virtual sources, the number of virtual sources used, and the number of elements used in each sub-aperture can be flexibly adjusted to enhance resolution and SNR. This allows very flexible optimization of USTA for different applications.

An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.

PubMed

Durand, Pierre M; Oelofse, Andries J; Coetzer, Theresa L

2006-11-04

The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far--over 90% in some regions. In comparison, P. y. yoelii is approximately 77% and P. vivax is approximately 55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in Plasmodium has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three Plasmodium species. Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in P. vivax, eight in P. y. yoelii and only six in P. falciparum. Further investigation of the six open reading frames in P. falciparum revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in P. y. yoelii and P. falciparum. One of the P. vivax open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene. There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the P. falciparum genome.

Multicore-based 3D-DWT video encoder

NASA Astrophysics Data System (ADS)

Galiano, Vicente; López-Granado, Otoniel; Malumbres, Manuel P.; Migallón, Hector

2013-12-01

Three-dimensional wavelet transform (3D-DWT) encoders are good candidates for applications like professional video editing, video surveillance, multi-spectral satellite imaging, etc. where a frame must be reconstructed as quickly as possible. In this paper, we present a new 3D-DWT video encoder based on a fast run-length coding engine. Furthermore, we present several multicore optimizations to speed-up the 3D-DWT computation. An exhaustive evaluation of the proposed encoder (3D-GOP-RL) has been performed, and we have compared the evaluation results with other video encoders in terms of rate/distortion (R/D), coding/decoding delay, and memory consumption. Results show that the proposed encoder obtains good R/D results for high-resolution video sequences with nearly in-place computation using only the memory needed to store a group of pictures. After applying the multicore optimization strategies over the 3D DWT, the proposed encoder is able to compress a full high-definition video sequence in real-time.

Common sense reasoning about petroleum flow

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

Rosenberg, S.

1981-02-01

This paper describes an expert system for understanding and Reasoning in a petroleum resources domain. A basic model is implemented in FRL (Frame Representation Language). Expertise is encoded as rule frames. The model consists of a set of episodic contexts which are sequentially generated over time. Reasoning occurs in separate reasoning contexts consisting of a buffer frame and packets of rules. These function similar to small production systems. reasoning is linked to the model through an interface of Sentinels (instance driven demons) which notice anomalous conditions. Heuristics and metaknowledge are used through the creation of further reasoning contexts which overlaymore » the simpler ones.« less

Identification, cloning, and sequencing of a fragment of Amsacta moorei entomopoxvirus DNA containing the spheroidin gene and three vaccinia virus-related open reading frames.

PubMed Central

Hall, R L; Moyer, R W

1991-01-01

Entomopoxvirus virions are frequently contained within crystalline occlusion bodies, which are composed of primarily a single protein, spheroidin, which is analogous to the polyhedrin protein of baculovirus. The spheroidin gene of Amsacta moorei entomopoxvirus was identified following the microsequencing of polypeptides generated from cyanogen bromide treatment of spheroidin and the subsequent synthesis of oligonucleotide hybridization probes. DNA sequencing of a 6.8-kb region of DNA containing the spheroidin gene showed that the spheroidin protein is derived from a 3.0-kb open reading frame potentially encoding a protein of 115 kDa. Three copies of the heptanucleotide, TTTTTNT, a sequence associated with early gene transcription in the vertebrate poxviruses, and four in-frame translational termination signals were found within 60 bp upstream of the putative spheroidin gene promoter (TAAATG). The spheroidin gene promoter region contains the sequence TAAATG, which is found in many late promoters of the vertebrate poxviruses and which serves as the site of transcriptional initiation, as shown by primer extension. Primer extension experiments also showed that spheroidin gene transcripts contain 5' poly(A) sequences typical of vertebrate poxvirus late transcripts. The 92 bases upstream of the initiating TAAATG are unusually A + T rich and contain only 7 G or C residues. An analysis of open reading frames around the spheroidin gene suggests that the colinear core of "essential genes" typical of the vertebrate poxviruses is absent in A. moorei entomopoxvirus. Images PMID:1942245

Novel Integration of Frame Rate Up Conversion and HEVC Coding Based on Rate-Distortion Optimization.

PubMed

Guo Lu; Xiaoyun Zhang; Li Chen; Zhiyong Gao

2018-02-01

Frame rate up conversion (FRUC) can improve the visual quality by interpolating new intermediate frames. However, high frame rate videos by FRUC are confronted with more bitrate consumption or annoying artifacts of interpolated frames. In this paper, a novel integration framework of FRUC and high efficiency video coding (HEVC) is proposed based on rate-distortion optimization, and the interpolated frames can be reconstructed at encoder side with low bitrate cost and high visual quality. First, joint motion estimation (JME) algorithm is proposed to obtain robust motion vectors, which are shared between FRUC and video coding. What's more, JME is embedded into the coding loop and employs the original motion search strategy in HEVC coding. Then, the frame interpolation is formulated as a rate-distortion optimization problem, where both the coding bitrate consumption and visual quality are taken into account. Due to the absence of original frames, the distortion model for interpolated frames is established according to the motion vector reliability and coding quantization error. Experimental results demonstrate that the proposed framework can achieve 21% ~ 42% reduction in BDBR, when compared with the traditional methods of FRUC cascaded with coding.

On the time course of lexical stress priming in speech production: Behavioral and ERPs evidence from a free-stress language.

PubMed

Sulpizio, Simone; Vespignani, Francesco; Job, Remo

2016-10-01

The goal of the present research was to study the time course of lexical stress encoding in a free-stress language with unpredictable stress. To this aim we measured event-related brain potentials (ERPs) during lexical priming. Participants named pictures bearing either the dominant or non-dominant stress pattern, and preceded by either a congruent or an incongruent word prime (e.g., CInema-FRAgola'cinema-strawberry' vs. benZIna-FRAgola'petrol-strawberry'). Behavioral results show that participants were slower in naming targets that had the same stress pattern as the prime, and were also faster in producing words with the dominant stress pattern in the language. The electrophysiological results show that both the effects are compatible with the time course of phonological encoding in speech production. Surprisingly, a dominant stress effect occurred in the ERPs elicited by the primes, with a larger positivity for non-dominant stress words in a 150-250ms time-window. The pattern of results indicates that during speech production: a) the system is sensitive to the stress patterns distribution; b) the automatic pre-activation of a metrical frame may interfere with the phonological encoding of a to-be-uttered word. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular cloning of an inducible serine esterase gene from human cytotoxic lymphocytes.

PubMed Central

Trapani, J A; Klein, J L; White, P C; Dupont, B

1988-01-01

A cDNA clone encoding a human serine esterase gene was isolated from a library constructed from poly(A)+ RNA of allogeneically stimulated, interleukin 2-expanded peripheral blood mononuclear cells. The clone, designated HSE26.1, represents a full-length copy of a 0.9-kilobase mRNA present in human cytotoxic cells but absent from a wide variety of noncytotoxic cell lines. Clone HSE26.1 contains an 892-base-pair sequence, including a single 741-base-pair open reading frame encoding a putative 247-residue polypeptide. The first 20 amino acids of the polypeptide form a leader sequence. The mature protein is predicted to have an unglycosylated Mr of approximately equal to 26,000 and contains a single potential site for N-linked glycosylation. The nucleotide and predicted amino acid sequences of clone HSE26.1 are homologous with all murine and human serine esterases cloned thus far but are most similar to mouse granzyme B (70% nucleotide and 68% amino acid identity). HSE26.1 protein is expressed weakly in unstimulated peripheral blood mononuclear cells but is strongly induced within 6-hr incubation in medium containing phytohemagglutinin. The data suggest that the protein encoded by HSE26.1 plays a role in cell-mediated cytotoxicity. Images PMID:3261871

Real-time video compressing under DSP/BIOS

NASA Astrophysics Data System (ADS)

Chen, Qiu-ping; Li, Gui-ju

2009-10-01

This paper presents real-time MPEG-4 Simple Profile video compressing based on the DSP processor. The programming framework of video compressing is constructed using TMS320C6416 Microprocessor, TDS510 simulator and PC. It uses embedded real-time operating system DSP/BIOS and the API functions to build periodic function, tasks and interruptions etcs. Realize real-time video compressing. To the questions of data transferring among the system. Based on the architecture of the C64x DSP, utilized double buffer switched and EDMA data transfer controller to transit data from external memory to internal, and realize data transition and processing at the same time; the architecture level optimizations are used to improve software pipeline. The system used DSP/BIOS to realize multi-thread scheduling. The whole system realizes high speed transition of a great deal of data. Experimental results show the encoder can realize real-time encoding of 768*576, 25 frame/s video images.

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333

PubMed Central

Nishimura, Yuki; Kamikawa, Ryoma; Hashimoto, Tetsuo; Inagaki, Yuji

2014-01-01

Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames. PMID:25054084

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

PubMed Central

Vanderperre, Benoît; Lucier, Jean-François; Bissonnette, Cyntia; Motard, Julie; Tremblay, Guillaume; Vanderperre, Solène; Wisztorski, Maxence; Salzet, Michel; Boisvert, François-Michel; Roucou, Xavier

2013-01-01

A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome. PMID:23950983

The Nostoc punctiforme Genome

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

John C. Meeks

2001-12-31

Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9more » Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.« less

Self-Supervised Video Hashing With Hierarchical Binary Auto-Encoder.

PubMed

Song, Jingkuan; Zhang, Hanwang; Li, Xiangpeng; Gao, Lianli; Wang, Meng; Hong, Richang

2018-07-01

Existing video hash functions are built on three isolated stages: frame pooling, relaxed learning, and binarization, which have not adequately explored the temporal order of video frames in a joint binary optimization model, resulting in severe information loss. In this paper, we propose a novel unsupervised video hashing framework dubbed self-supervised video hashing (SSVH), which is able to capture the temporal nature of videos in an end-to-end learning to hash fashion. We specifically address two central problems: 1) how to design an encoder-decoder architecture to generate binary codes for videos and 2) how to equip the binary codes with the ability of accurate video retrieval. We design a hierarchical binary auto-encoder to model the temporal dependencies in videos with multiple granularities, and embed the videos into binary codes with less computations than the stacked architecture. Then, we encourage the binary codes to simultaneously reconstruct the visual content and neighborhood structure of the videos. Experiments on two real-world data sets show that our SSVH method can significantly outperform the state-of-the-art methods and achieve the current best performance on the task of unsupervised video retrieval.

Deletion of a Single-Copy Trna Affects Microtubule Function in Saccharomyces Cerevisiae

PubMed Central

Reijo, R. A.; Cho, D. S.; Huffaker, T. C.

1993-01-01

rts1-1 was identified as an extragenic suppressor of tub2-104, a cold-sensitive allele of the sole gene encoding β-tubulin in the yeast, Saccharomyces cerevisiae. In addition, rts1-1 cells are heat sensitive and resistant to the microtubule-destabilizing drug, benomyl. The rts1-1 mutation is a deletion of approximately 5 kb of genomic DNA on chromosome X that includes one open reading frame and three tRNA genes. Dissection of this region shows that heat sensitivity is due to deletion of the open reading frame (HIT1). Suppression and benomyl resistance are caused by deletion of the gene encoding a tRNA(AGG)(Arg) (HSX1). Northern analysis of rts1-1 cells indicates that HSX1 is the only gene encoding this tRNA. Deletion of HSX1 does not suppress the tub2-104 mutation by misreading at the AGG codons in TUB2. It also does not suppress by interfering with the protein arginylation that targets certain proteins for degradation. These results leave open the prospect that this tRNA(AGG)(Arg) plays a novel role in the cell. PMID:8307335

All Frames Are Not Created Equal: A Typology and Critical Analysis of Framing Effects.

PubMed

Levin; Schneider; Gaeth

1998-11-01

Accentuate the positive or accentuate the negative? The literature has been mixed as to how the alternative framing of information in positive or negative terms affects judgments and decisions. We argue that this is because different studies have employed different operational definitions of framing and thus have tapped different underlying processes. We develop a typology to distinguish between three different kinds of valence framing effects. First we discuss the standard risky choice framing effect introduced by Tversky and Kahneman (1981) to illustrate how valence affects willingness to take a risk. Then we discuss attribute framing, which affects the evaluation of object or event characteristics, and goal framing, which affects the persuasiveness of a communication. We describe the distinctions, provide a number of examples of each type, and discuss likely theoretical mechanisms underlying each type of framing effect. Our typology helps explain and resolve apparent confusions in the literature, ties together studies with common underlying mechanisms, and serves as a guide to future research and theory development. We conclude that a broader perspective, focused on the cognitive and motivational consequences of valence-based encoding, opens the door to a deeper understanding of the causes and consequences of framing effects. Copyright 1998 Academic Press.

Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages.

PubMed Central

Vasala, A; Dupont, L; Baumann, M; Ritzenthaler, P; Alatossava, T

1993-01-01

Virulent phage LL-H and temperate phage mv4 are two related bacteriophages of Lactobacillus delbrueckii. The gene clusters encoding structural proteins of these two phages have been sequenced and further analyzed. Six open reading frames (ORF-1 to ORF-6) were detected. Protein sequencing and Western immunoblotting experiments confirmed that ORF-3 (g34) encoded the main capsid protein Gp34. The presence of a putative late promoter in front of the phage LL-H g34 gene was suggested by primer extension experiments. Comparative sequence analysis between phage LL-H and phage mv4 revealed striking similarities in the structure and organization of this gene cluster, suggesting that the genes encoding phage structural proteins belong to a highly conservative module. Images PMID:8497043

Pulse Code Modulation (PCM) encoder handbook for Aydin Vector MMP-900 series system

NASA Technical Reports Server (NTRS)

Raphael, David

1995-01-01

This handbook explicates the hardware and software properties of a time division multiplex system. This system is used to sample analog and digital data. The data is then merged with frame synchronization information to produce a serial pulse coded modulation (PCM) bit stream. Information in this handbook is required by users to design congruous interface and attest effective utilization of this encoder system. Aydin Vector provides all of the components for these systems to Goddard Space Flight Center/Wallops Flight Facility.

Identification and Characterization of Three Differentially Expressed Genes, Encoding S-Adenosylhomocysteine Hydrolase, Methionine Aminopeptidase, and a Histone-Like Protein, in the Toxic Dinoflagellate Alexandrium fundyense†

PubMed Central

Taroncher-Oldenburg, Gaspar; Anderson, Donald M.

2000-01-01

Genes showing differential expression related to the early G1 phase of the cell cycle during synchronized circadian growth of the toxic dinoflagellate Alexandrium fundyense were identified and characterized by differential display (DD). The determination in our previous work that toxin production in Alexandrium is relegated to a narrow time frame in early G1 led to the hypothesis that transcriptionally up- or downregulated genes during this subphase of the cell cycle might be related to toxin biosynthesis. Three genes, encoding S-adenosylhomocysteine hydrolase (Sahh), methionine aminopeptidase (Map), and a histone-like protein (HAf), were isolated. Sahh was downregulated, while Map and HAf were upregulated, during the early G1 phase of the cell cycle. Sahh and Map encoded amino acid sequences with about 90 and 70% similarity to those encoded by several eukaryotic and prokaryotic Sahh and Map genes, respectively. The partial Map sequence also contained three cobalt binding motifs characteristic of all Map genes. HAf encoded an amino acid sequence with 60% similarity to those of two histone-like proteins from the dinoflagellate Crypthecodinium cohnii Biecheler. This study documents the potential of applying DD to the identification of genes that are related to physiological processes or cell cycle events in phytoplankton under conditions where small sample volumes represent an experimental constraint. The identification of an additional 21 genes with various cell cycle-related DD patterns also provides evidence for the importance of pretranslational or transcriptional regulation in dinoflagellates, contrary to previous reports suggesting the possibility that translational mechanisms are the primary means of circadian regulation in this group of organisms. PMID:10788388

A Secure and Robust Compressed Domain Video Steganography for Intra- and Inter-Frames Using Embedding-Based Byte Differencing (EBBD) Scheme

PubMed Central

Idbeaa, Tarik; Abdul Samad, Salina; Husain, Hafizah

2016-01-01

This paper presents a novel secure and robust steganographic technique in the compressed video domain namely embedding-based byte differencing (EBBD). Unlike most of the current video steganographic techniques which take into account only the intra frames for data embedding, the proposed EBBD technique aims to hide information in both intra and inter frames. The information is embedded into a compressed video by simultaneously manipulating the quantized AC coefficients (AC-QTCs) of luminance components of the frames during MPEG-2 encoding process. Later, during the decoding process, the embedded information can be detected and extracted completely. Furthermore, the EBBD basically deals with two security concepts: data encryption and data concealing. Hence, during the embedding process, secret data is encrypted using the simplified data encryption standard (S-DES) algorithm to provide better security to the implemented system. The security of the method lies in selecting candidate AC-QTCs within each non-overlapping 8 × 8 sub-block using a pseudo random key. Basic performance of this steganographic technique verified through experiments on various existing MPEG-2 encoded videos over a wide range of embedded payload rates. Overall, the experimental results verify the excellent performance of the proposed EBBD with a better trade-off in terms of imperceptibility and payload, as compared with previous techniques while at the same time ensuring minimal bitrate increase and negligible degradation of PSNR values. PMID:26963093

A Secure and Robust Compressed Domain Video Steganography for Intra- and Inter-Frames Using Embedding-Based Byte Differencing (EBBD) Scheme.

PubMed

Idbeaa, Tarik; Abdul Samad, Salina; Husain, Hafizah

2016-01-01

This paper presents a novel secure and robust steganographic technique in the compressed video domain namely embedding-based byte differencing (EBBD). Unlike most of the current video steganographic techniques which take into account only the intra frames for data embedding, the proposed EBBD technique aims to hide information in both intra and inter frames. The information is embedded into a compressed video by simultaneously manipulating the quantized AC coefficients (AC-QTCs) of luminance components of the frames during MPEG-2 encoding process. Later, during the decoding process, the embedded information can be detected and extracted completely. Furthermore, the EBBD basically deals with two security concepts: data encryption and data concealing. Hence, during the embedding process, secret data is encrypted using the simplified data encryption standard (S-DES) algorithm to provide better security to the implemented system. The security of the method lies in selecting candidate AC-QTCs within each non-overlapping 8 × 8 sub-block using a pseudo random key. Basic performance of this steganographic technique verified through experiments on various existing MPEG-2 encoded videos over a wide range of embedded payload rates. Overall, the experimental results verify the excellent performance of the proposed EBBD with a better trade-off in terms of imperceptibility and payload, as compared with previous techniques while at the same time ensuring minimal bitrate increase and negligible degradation of PSNR values.

Molecular cloing and bioinformatics analysis of lactate dehydrogenase from Taenia multiceps.

PubMed

Guo, Cheng; Wang, Yu; Huang, Xing; Wang, Ning; Yan, Ming; He, Ran; Gu, Xiaobin; Xie, Yue; Lai, Weimin; Jing, Bo; Peng, Xuerong; Yang, Guangyou

2017-10-01

Coenurus cerebralis, the larval stage (metacestode or coenurus) of Taenia multiceps, parasitizes sheep, goats, and other ruminants and causes coenurosis. In this study, we isolated and characterized complementary DNAs that encode lactate dehydrogenase A (Tm-LDHA) and B (Tm-LDHB) from the transcriptome of T. multiceps and expressed recombinant Tm-LDHB (rTm-LDHB) in Escherichia coli. Bioinformatic analysis showed that both Tm-LDH genes (LDHA and LDHB) contain a 996-bp open reading frame and encode a protein of 331 amino acids. After determination of the immunogenicity of the recombinant Tm-LDHB, an indirect enzyme-linked immunosorbent assay (ELISA) was developed for preliminary evaluation of the serodiagnostic potential of rTm-LDHB in goats. However, the rTm-LDHB-based indirect ELISA developed here exhibited specificity of only 71.42% (10/14) and sensitivity of 1:3200 in detection of goats infected with T. multiceps in the field. This study is the first to describe LDHA and LDHB of T. multiceps; meanwhile, our results indicate that rTm-LDHB is not a specific antigen candidate for immunodiagnosis of T. multiceps infection in goats.

Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes.

PubMed

Schubert, Julian; Siekierska, Aleksandra; Langlois, Mélanie; May, Patrick; Huneau, Clément; Becker, Felicitas; Muhle, Hiltrud; Suls, Arvid; Lemke, Johannes R; de Kovel, Carolien G F; Thiele, Holger; Konrad, Kathryn; Kawalia, Amit; Toliat, Mohammad R; Sander, Thomas; Rüschendorf, Franz; Caliebe, Almuth; Nagel, Inga; Kohl, Bernard; Kecskés, Angela; Jacmin, Maxime; Hardies, Katia; Weckhuysen, Sarah; Riesch, Erik; Dorn, Thomas; Brilstra, Eva H; Baulac, Stephanie; Møller, Rikke S; Hjalgrim, Helle; Koeleman, Bobby P C; Jurkat-Rott, Karin; Lehman-Horn, Frank; Roach, Jared C; Glusman, Gustavo; Hood, Leroy; Galas, David J; Martin, Benoit; de Witte, Peter A M; Biskup, Saskia; De Jonghe, Peter; Helbig, Ingo; Balling, Rudi; Nürnberg, Peter; Crawford, Alexander D; Esguerra, Camila V; Weber, Yvonne G; Lerche, Holger

2014-12-01

Febrile seizures affect 2-4% of all children and have a strong genetic component. Recurrent mutations in three main genes (SCN1A, SCN1B and GABRG2) have been identified that cause febrile seizures with or without epilepsy. Here we report the identification of mutations in STX1B, encoding syntaxin-1B, that are associated with both febrile seizures and epilepsy. Whole-exome sequencing in independent large pedigrees identified cosegregating STX1B mutations predicted to cause an early truncation or an in-frame insertion or deletion. Three additional nonsense or missense mutations and a de novo microdeletion encompassing STX1B were then identified in 449 familial or sporadic cases. Video and local field potential analyses of zebrafish larvae with antisense knockdown of stx1b showed seizure-like behavior and epileptiform discharges that were highly sensitive to increased temperature. Wild-type human syntaxin-1B but not a mutated protein rescued the effects of stx1b knockdown in zebrafish. Our results thus implicate STX1B and the presynaptic release machinery in fever-associated epilepsy syndromes.

Functions and impact of tal-like genes in animals with regard to applied aspects.

PubMed

Zhu, Min; Hu, Xiaolong; Cao, Guangli; Xue, Renyu; Gong, Chengliang

2018-06-16

A large number of DNAs in eukaryote genomes can code for atypical transcripts, and their functions are controversial. It has been reported that the transcripts contain many small open reading frames (sORFs), which were originally considered as non-translatable RNAs. However, increasing evidence has suggested that some of these sORFs can encode for small peptides and some are conserved across large evolutionary distances. It has been reported that the small peptides have functions and may be involved in varieties of cellular processes, playing important roles in development, physiology, and metabolism. Among the sORFs, studies of the non-canonical gene polished rice/tarsal-less (pri/tal) in Drosophila and mille-pattes(mlpt) in Tribolium have been more thoroughly studied. The genes similar to pri/tal in other species have been defined as the tarsal-less-related gene family, tal-like gene. In this review, we described recent progress in the discovery and functional characterization of the small peptides encoded by the tal-like gene and their possible functional potentials.

Characterization of the Tupaia rhabdovirus genome reveals a long open reading frame overlapping with P and a novel gene encoding a small hydrophobic protein.

PubMed

Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

2005-06-01

Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses.

Characterization of the Tupaia Rhabdovirus Genome Reveals a Long Open Reading Frame Overlapping with P and a Novel Gene Encoding a Small Hydrophobic Protein

PubMed Central

Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

2005-01-01

Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses. PMID:15890917

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

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

Jackson, P.J.; Walthers, E.A.; Richmond, K.L.

1997-04-01

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats aremore » generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.« less

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

NASA Astrophysics Data System (ADS)

Tian, Ye; Wang, Tong; Liu, Wenyan; Xin, Huolin L.; Li, Huilin; Ke, Yonggang; Shih, William M.; Gang, Oleg

2015-07-01

Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we report a strategy for assembling three-dimensional nanoparticle clusters that uses a molecular frame designed with encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA frame and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be assembled with designed particle arrangements.

Fast Kinetics of Calcium Signaling and Sensor Design

PubMed Central

Tang, Shen; Reddish, Florence; Zhuo, You; Yang, Jenny J.

2015-01-01

Fast calcium signaling is regulated by numerous calcium channels exhibiting high spatiotemporal profiles which are currently measured by fluorescent calcium sensors. There is still a strong need to improve the kinetics of genetically encoded calcium indicators (sensors) to capture calcium dynamics in the millisecond time frame. In this review, we summarize several major fast calcium signaling pathways and discuss the recent developments and application of genetically encoded calcium indicators to detect these pathways. A new class of genetically encoded calcium indicators designed with site-directed mutagenesis on the surface of beta-barrel fluorescent proteins to form a pentagonal bipyramidal-like calcium binding domain dramatically accelerates calcium binding kinetics. Furthermore, novel genetically encoded calcium indicators with significantly increased fluorescent lifetime change are advantageous in deep-field imaging with high light-scattering and notable morphology change. PMID:26151819

Molecular characterization and expression of the M6 gene of grass carp hemorrhage virus (GCHV), an aquareovirus.

PubMed

Qiu, T; Lu, R H; Zhang, J; Zhu, Z Y

2001-07-01

The complete nucleotide sequence of M6 gene of grass carp hemorrhage virus (GCHV) was determined. It is 2039 nucleotides in length and contains a single large open reading frame that could encode a protein of 648 amino acids with predicted molecular mass of 68.7 kDa. Amino acid sequence comparison revealed that the protein encoded by GCHV M6 is closely related to the protein mu1 of mammalian reovirus. The M6 gene, encoding the major outer-capsid protein, was expressed using the pET fusion protein vector in Escherichia coli and detected by Western blotting using chicken anti-GCHV immunoglobulin (IgY). The result indicates that the protein encoded by M6 may share a putative Asn-42-Pro-43 proteolytic cleavage site with mu1.

Subversion of cytokine networks by virally encoded decoy receptors

PubMed Central

Epperson, Megan L.; Lee, Chung A.; Fremont, Daved H.

2012-01-01

Summary During the course of evolution, viruses have captured or created a diverse array of open reading frames that encode for proteins that serve to evade and sabotage the host innate and adaptive immune responses, which would otherwise lead to their elimination. These viral genomes are some of the best textbooks of immunology ever written. The established arsenal of immunomodulatory proteins encoded by viruses is large and growing and includes specificities for virtually all known inflammatory pathways and targets. The focus of this review is on herpes and poxvirus-encoded cytokine and chemokine binding proteins that serve to undermine the coordination of host immune surveillance. Structural and mechanistic studies of these decoy receptors have provided a wealth of information, not only about viral pathogenesis but also about the inner workings of cytokine signaling networks. PMID:23046131

Complete sequence of Tvv1, a family of Ty 1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking.

PubMed

Pelsy, F.; Merdinoglu, D.

2002-09-01

A chromosome-walking strategy was used to sequence and characterize retrotransposons in the grapevine genome. The reconstitution of a family of retroelements, named Tvv1, was achieved by six successive steps. These elements share a single, highly conserved open reading frame 4,153 nucleotides-long, putatively encoding the gag, pro, int, rt and rh proteins. Comparison of the Tvv1 open reading frame coding potential with those of drosophila copia and tobacco Tnt1, revealed that Tvv1 is closely related to Ty 1 copia-like retrotransposons. A highly variable untranslated leader region, upstream of the open reading frame, allowed us to differentiate Tvv1 variants, which represent a family of at least 28 copies, in varying sizes. This internal region is flanked by two long terminal repeats in direct orientation, sized between 149 and 157 bp. Among elements theoretically sized from 4,970 to 5,550 bp, we describe the full-length sequence of a reference element Tvv1-1, 5,343 nucleotides-long. The full-length sequence of Tvv1-1 compared to pea PDR1 shows a 53.3% identity. In addition, both elements contain long terminal repeats of nearly the same size in which the U5 region could be entirely absent. Therefore, we assume that Tvv1 and PDR1 could constitute a particular class of short LTRs retroelements.

Memory Metals (Marchon Eyewear)

NASA Technical Reports Server (NTRS)

1991-01-01

Another commercial application of memory metal technology is found in a "smart" eyeglass frame that remembers its shape and its wearer's fit. A patented "memory encoding process" makes this possible. Heat is not required to return the glasses to shape. A large commercial market is anticipated.

An Upstream Open Reading Frame Is Essential for Feedback Regulation of Ascorbate Biosynthesis in Arabidopsis

PubMed Central

Laing, William A.; Martínez-Sánchez, Marcela; Wright, Michele A.; Bulley, Sean M.; Brewster, Di; Dare, Andrew P.; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C.; Hellens, Roger P.

2015-01-01

Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. PMID:25724639

An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis.

PubMed

Laing, William A; Martínez-Sánchez, Marcela; Wright, Michele A; Bulley, Sean M; Brewster, Di; Dare, Andrew P; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C; Hellens, Roger P

2015-03-01

Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. © 2015 American Society of Plant Biologists. All rights reserved.

Production and pathogenicity of hepatitis C virus core gene products

PubMed Central

Li, Hui-Chun; Ma, Hsin-Chieh; Yang, Chee-Hing; Lo, Shih-Yen

2014-01-01

Hepatitis C virus (HCV) is a major cause of chronic liver diseases, including steatosis, cirrhosis and hepatocellular carcinoma, and its infection is also associated with insulin resistance and type 2 diabetes mellitus. HCV, belonging to the Flaviviridae family, is a small enveloped virus whose positive-stranded RNA genome encoding a polyprotein. The HCV core protein is cleaved first at residue 191 by the host signal peptidase and further cleaved by the host signal peptide peptidase at about residue 177 to generate the mature core protein (a.a. 1-177) and the cleaved peptide (a.a. 178-191). Core protein could induce insulin resistance, steatosis and even hepatocellular carcinoma through various mechanisms. The peptide (a.a. 178-191) may play a role in the immune response. The polymorphism of this peptide is associated with the cellular lipid drop accumulation, contributing to steatosis development. In addition to the conventional open reading frame (ORF), in the +1 frame, an ORF overlaps with the core protein-coding sequence and encodes the alternative reading frame proteins (ARFP or core+1). ARFP/core+1/F protein could enhance hepatocyte growth and may regulate iron metabolism. In this review, we briefly summarized the current knowledge regarding the production of different core gene products and their roles in viral pathogenesis. PMID:24966583

Dynamic frame resizing with convolutional neural network for efficient video compression

NASA Astrophysics Data System (ADS)

Kim, Jaehwan; Park, Youngo; Choi, Kwang Pyo; Lee, JongSeok; Jeon, Sunyoung; Park, JeongHoon

2017-09-01

In the past, video codecs such as vc-1 and H.263 used a technique to encode reduced-resolution video and restore original resolution from the decoder for improvement of coding efficiency. The techniques of vc-1 and H.263 Annex Q are called dynamic frame resizing and reduced-resolution update mode, respectively. However, these techniques have not been widely used due to limited performance improvements that operate well only under specific conditions. In this paper, video frame resizing (reduced/restore) technique based on machine learning is proposed for improvement of coding efficiency. The proposed method features video of low resolution made by convolutional neural network (CNN) in encoder and reconstruction of original resolution using CNN in decoder. The proposed method shows improved subjective performance over all the high resolution videos which are dominantly consumed recently. In order to assess subjective quality of the proposed method, Video Multi-method Assessment Fusion (VMAF) which showed high reliability among many subjective measurement tools was used as subjective metric. Moreover, to assess general performance, diverse bitrates are tested. Experimental results showed that BD-rate based on VMAF was improved by about 51% compare to conventional HEVC. Especially, VMAF values were significantly improved in low bitrate. Also, when the method is subjectively tested, it had better subjective visual quality in similar bit rate.

As the world turns: short-term human spatial memory in egocentric and allocentric coordinates.

PubMed

Banta Lavenex, Pamela; Lecci, Sandro; Prêtre, Vincent; Brandner, Catherine; Mazza, Christian; Pasquier, Jérôme; Lavenex, Pierre

2011-05-16

We aimed to determine whether human subjects' reliance on different sources of spatial information encoded in different frames of reference (i.e., egocentric versus allocentric) affects their performance, decision time and memory capacity in a short-term spatial memory task performed in the real world. Subjects were asked to play the Memory game (a.k.a. the Concentration game) without an opponent, in four different conditions that controlled for the subjects' reliance on egocentric and/or allocentric frames of reference for the elaboration of a spatial representation of the image locations enabling maximal efficiency. We report experimental data from young adult men and women, and describe a mathematical model to estimate human short-term spatial memory capacity. We found that short-term spatial memory capacity was greatest when an egocentric spatial frame of reference enabled subjects to encode and remember the image locations. However, when egocentric information was not reliable, short-term spatial memory capacity was greater and decision time shorter when an allocentric representation of the image locations with respect to distant objects in the surrounding environment was available, as compared to when only a spatial representation encoding the relationships between the individual images, independent of the surrounding environment, was available. Our findings thus further demonstrate that changes in viewpoint produced by the movement of images placed in front of a stationary subject is not equivalent to the movement of the subject around stationary images. We discuss possible limitations of classical neuropsychological and virtual reality experiments of spatial memory, which typically restrict the sensory information normally available to human subjects in the real world. Copyright © 2011 Elsevier B.V. All rights reserved.

Predicted secondary structure similarity in the absence of primary amino acid sequence homology: hepatitis B virus open reading frames.

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

Proteins that are related evolutionarily may have diverged at the level of primary amino acid sequence while maintaining similar secondary structures. Computer analysis has been used to compare the open reading frames of the hepatitis B virus to those of the woodchuck hepatitis virus at the level of amino acid sequence, and to predict the relative hydrophilic character and the secondary structure of putative polypeptides. Similarity is seen at the levels of relative hydrophilicity and secondary structure, in the absence of sequence homology. These data reinforce the proposal that these open reading frames encode viral proteins. Computer analysis of this type can be more generally used to establish structural similarities between proteins that do not share obvious sequence homology as well as to assess whether an open reading frame is fortuitous or codes for a protein. PMID:6585835

Newton-Cartan Gravity in Noninertial Reference Frames

NASA Astrophysics Data System (ADS)

Rodriguez, Leo; St. Germaine-Fuller, James; Wickramasekara, Sujeev

2015-03-01

We study Newton-Cartan gravity under transformations into all noninertial, nonrelativistic reference frames. These transformations form an infinite dimensional Lie group, called the Galilean line group, which contains as a subgroup the Galilei group. The fictitious forces of noninertial reference frames are encoded in the Cartan connection transformed under the Galilean line group. These fictitious forces, which are coordinate effects, do not contribute to the Ricci tensor. Only the 00-component of the Ricci tensor is non-zero and equals (4 π times) the matter density in all reference frames. While the Ricci field equation and Gauss' law are fulfilled by the physical matter density in inertial and linearly accelerating reference frames, in rotating reference frames Gauss' law holds for an effective mass density that differs from the physical matter density. This effective density has its origin in the simulated magnetic field of rotating frames, highlighting a striking difference between linearly and rotationally accelerating frames. The equations governing the simulated fields have the same form as Maxwell's equations, a surprising result given that these equations obey special relativity (and U (1) -gauge symmetry), rather than Galilean symmetry. This work was supported in part by the HHMI Undergraduate Science Education Award 52006298 and the Grinnell College Academic Affairs' CSFS and MAP programs.

Cloning and characterization of an inulinase gene from the marine yeast Candida membranifaciens subsp. flavinogenie W14-3 and its expression in Saccharomyces sp. W0 for ethanol production.

PubMed

Zhang, Lin-Lin; Tan, Mei-Juan; Liu, Guang-Lei; Chi, Zhe; Wang, Guang-Yuan; Chi, Zhen-Ming

2015-04-01

The INU1 gene encoding an exo-inulinase from the marine-derived yeast Candida membranifaciens subsp. flavinogenie W14-3 was cloned and characterized. It had an open reading frame of 1,536 bp long encoding an inulinase. The coding region of it was not interrupted by any intron. The cloned gene encoded 512 amino acid residues of a protein with a putative signal peptide of 23 amino acids and a calculated molecular mass of 57.8 kDa. The protein sequence deduced from the inulinase gene contained the inulinase consensus sequences (WMNDPNGL), (RDP), ECP FS and Q. The protein also had six conserved putative N-glycosylation sites. The deduced inulinase from the yeast strain W14-3 was found to be closely related to that from Candida kutaonensis sp. nov. KRF1, Kluyveromyces marxianus, and Cryptococcus aureus G7a. The inulinase gene with its signal peptide encoding sequence was subcloned into the pMIRSC11 expression vector and expressed in Saccharomyces sp. W0. The recombinant yeast strain W14-3-INU-112 obtained could produce 16.8 U/ml of inulinase activity and 12.5 % (v/v) ethanol from 250 g/l of inulin within 168 h. The monosaccharides were detected after the hydrolysis of inulin with the crude inulinase (the yeast culture). All the results indicated that the cloned gene and the recombinant yeast strain W14-3-INU-112 had potential applications in biotechnology.

Isolation and characterization of a cDNA encoding a heat shock protein 70 from a sterile mutant of Ulva pertusa (Ulvales, Chlorophyta).

PubMed

Tominaga, Hiroshi; Coury, Daniel Adam; Amano, Hideomi; Kakinuma, Makoto

2010-03-01

Synthesis and accumulation of molecular chaperones are universal responses found in all cellular organisms when exposed to a variety of unfavorable conditions. Heat shock protein 70 (Hsp70), which is one of the major classes of molecular chaperones, plays a particularly important role in cellular stress responses, and the Hsp70 system is the most intensely studied in higher plants and algae. Therefore, we isolated and characterized a cDNA clone encoding Hsp70 from a sterile strain of Ulva pertusa (Ulvales, Chlorophyta). The sterile U. pertusa Hsp70 (UpHsp70) cDNA consisted of 2,272 nucleotides and had an open reading frame encoding a polypeptide of 663 amino acid (AA) residues with a molecular mass of 71.7 kDa. Amino acid alignment and phylogenetic analysis of Hsp70s from other organisms showed that UpHsp70 was more similar to cytoplasmic Hsp70s from green algae and higher plants (> or =75%) than to those from other algae and microorganisms. Southern blot analysis indicated that the sterile U. pertusa genome had at least four cytoplasmic Hsp70-encoding genes. UpHsp70 mRNA levels were significantly affected by diurnal changes, rapidly increased by high-temperature stress, and gradually increased by exposure to copper, cadmium, and lead. These results suggest that UpHsp70 plays particularly important roles in adaptation to high-temperature conditions and diurnal changes, and is potentially involved in tolerance to heavy metal toxicity.

cDNA encoding a polypeptide including a hevein sequence

DOEpatents

Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

1993-02-16

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a pu GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

In Silico Pattern-Based Analysis of the Human Cytomegalovirus Genome

PubMed Central

Rigoutsos, Isidore; Novotny, Jiri; Huynh, Tien; Chin-Bow, Stephen T.; Parida, Laxmi; Platt, Daniel; Coleman, David; Shenk, Thomas

2003-01-01

More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze this set of putative viral genes. With the help of an objective annotation method that is based on the Bio-Dictionary, a comprehensive collection of amino acid patterns that describes the currently known natural sequence space of proteins, we have reannotated all of the previously reported putative genes of the human cytomegalovirus. Also, with the help of MUSCA, a pattern-based multiple sequence alignment algorithm, we have reexamined the original human cytomegalovirus gene family definitions. Our analysis of the genome shows that many of the coded proteins comprise amino acid combinations that are unique to either the human cytomegalovirus or the larger group of herpesviruses. We have confirmed that a surprisingly large portion of the analyzed ORFs encode membrane proteins, and we have discovered a significant number of previously uncharacterized proteins that are predicted to be G-protein-coupled receptor homologues. The analysis also indicates that many of the encoded proteins undergo posttranslational modifications such as hydroxylation, phosphorylation, and glycosylation. ORFs encoding proteins with similar functional behavior appear in neighboring regions of the human cytomegalovirus genome. All of the results of the present study can be found and interactively explored online (http://cbcsrv.watson.ibm.com/virus/). PMID:12634390

Molecular cloning and expression of gene encoding aromatic amino acid decarboxylase in 'Vidal blanc' grape berries.

PubMed

Pan, Qiu-Hong; Chen, Fang; Zhu, Bao-Qing; Ma, Li-Yan; Li, Li; Li, Jing-Ming

2012-04-01

The pleasantly fruity and floral 2-phenylethanol are a dominant aroma compound in post-ripening 'Vidal blanc' grapes. However, to date little has been reported about its synthetic pathway in grapevine. In the present study, a full-length cDNA of VvAADC (encoding aromatic amino acid decarboxylase) was firstly cloned from the berries of 'Vidal blanc', an interspecific hybrid variety of Vitis vinifera × Vitis riparia. This sequence encodes a complete open reading frame of 482 amino acids with a calculated molecular mass of 54 kDa and isoelectric point value (pI) of 5.73. The amino acid sequence deduced shared about 79% identity with that of aromatic L: -amino acid decarboxylases (AADCs) from tomato. Real-time PCR analysis indicated that VvAADC transcript abundance presented a small peak at 110 days after full bloom and then a continuous increase at the berry post-ripening stage, which was consistent with the accumulation of 2-phenylethanol, but did not correspond to the trends of two potential intermediates, phenethylamine and 2-phenylacetaldehyde. Furthermore, phenylalanine still exhibited a continuous increase even in post-ripening period. It is thus suggested that 2-phenylethanol biosynthetic pathway mediated by AADC exists in grape berries, but it has possibly little contribution to a considerable accumulation of 2-phenylethanol in post-ripening 'Vidal blanc' grapes.

In silico pattern-based analysis of the human cytomegalovirus genome.

PubMed

Rigoutsos, Isidore; Novotny, Jiri; Huynh, Tien; Chin-Bow, Stephen T; Parida, Laxmi; Platt, Daniel; Coleman, David; Shenk, Thomas

2003-04-01

More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze this set of putative viral genes. With the help of an objective annotation method that is based on the Bio-Dictionary, a comprehensive collection of amino acid patterns that describes the currently known natural sequence space of proteins, we have reannotated all of the previously reported putative genes of the human cytomegalovirus. Also, with the help of MUSCA, a pattern-based multiple sequence alignment algorithm, we have reexamined the original human cytomegalovirus gene family definitions. Our analysis of the genome shows that many of the coded proteins comprise amino acid combinations that are unique to either the human cytomegalovirus or the larger group of herpesviruses. We have confirmed that a surprisingly large portion of the analyzed ORFs encode membrane proteins, and we have discovered a significant number of previously uncharacterized proteins that are predicted to be G-protein-coupled receptor homologues. The analysis also indicates that many of the encoded proteins undergo posttranslational modifications such as hydroxylation, phosphorylation, and glycosylation. ORFs encoding proteins with similar functional behavior appear in neighboring regions of the human cytomegalovirus genome. All of the results of the present study can be found and interactively explored online (http://cbcsrv.watson.ibm.com/virus/).

Limitation to Communication of Fermionic System in Accelerated Frame

NASA Astrophysics Data System (ADS)

Chang, Jinho; Kwon, Younghun

2015-03-01

In this article, we investigate communication between an inertial observer and an accelerated observer, sharing fermionic system, when they use classical and quantum communication using single rail or dual rail encoding. The purpose of this work is to understand the limit to the communication between an inertial observer and an accelerated observer, with single rail or dual rail encoding of fermionic system. We observe that at the infinite acceleration, the coherent information of single(or double) rail quantum channel vanishes, but those of classical ones may have finite values. In addition, we see that even when considering a method beyond the single-mode approximation, for the communication between Alice and Bob, the dual rail entangled state seems to provide better information transfer than the single rail entangled state, when we take a fixed choice of the Unruh mode. Moreover, we find that the single-mode approximation may not be sufficient to analyze communication of fermionic system in an accelerated frame.

Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci.

PubMed

Mills, D A; McKay, L L; Dunny, G M

1996-06-01

Analysis of a region involved in the conjugative transfer of the lactococcal conjugative element pRS01 has revealed a bacteria] group II intron. Splicing of this lactococcal intron (designated Ll.ltrB) in vivo resulted in the ligation of two exon messages (ltrBE1 and ltrBE2) which encoded a putative conjugative relaxase essential for the transfer of pRS01. Like many group II introns, the Ll.ltrB intron possessed an open reading frame (ltrA) with homology to reverse transcriptases. Remarkably, sequence analysis of ltrA suggested a greater similarity to open reading frames encoded by eukaryotic mitochondrial group II introns than to those identified to date from other bacteria. Several insertional mutations within ltrA resulted in plasmids exhibiting a conjugative transfer-deficient phenotype. These results provide the first direct evidence for splicing of a prokaryotic group II intron in vivo and suggest that conjugative transfer is a mechanism for group II intron dissemination in bacteria.

Video time encoding machines.

PubMed

Lazar, Aurel A; Pnevmatikakis, Eftychios A

2011-03-01

We investigate architectures for time encoding and time decoding of visual stimuli such as natural and synthetic video streams (movies, animation). The architecture for time encoding is akin to models of the early visual system. It consists of a bank of filters in cascade with single-input multi-output neural circuits. Neuron firing is based on either a threshold-and-fire or an integrate-and-fire spiking mechanism with feedback. We show that analog information is represented by the neural circuits as projections on a set of band-limited functions determined by the spike sequence. Under Nyquist-type and frame conditions, the encoded signal can be recovered from these projections with arbitrary precision. For the video time encoding machine architecture, we demonstrate that band-limited video streams of finite energy can be faithfully recovered from the spike trains and provide a stable algorithm for perfect recovery. The key condition for recovery calls for the number of neurons in the population to be above a threshold value.

Video Time Encoding Machines

PubMed Central

Lazar, Aurel A.; Pnevmatikakis, Eftychios A.

2013-01-01

We investigate architectures for time encoding and time decoding of visual stimuli such as natural and synthetic video streams (movies, animation). The architecture for time encoding is akin to models of the early visual system. It consists of a bank of filters in cascade with single-input multi-output neural circuits. Neuron firing is based on either a threshold-and-fire or an integrate-and-fire spiking mechanism with feedback. We show that analog information is represented by the neural circuits as projections on a set of band-limited functions determined by the spike sequence. Under Nyquist-type and frame conditions, the encoded signal can be recovered from these projections with arbitrary precision. For the video time encoding machine architecture, we demonstrate that band-limited video streams of finite energy can be faithfully recovered from the spike trains and provide a stable algorithm for perfect recovery. The key condition for recovery calls for the number of neurons in the population to be above a threshold value. PMID:21296708

Plasmids encoding therapeutic agents

DOEpatents

Keener, William K [Idaho Falls, ID

2007-08-07

Plasmids encoding anti-HIV and anti-anthrax therapeutic agents are disclosed. Plasmid pWKK-500 encodes a fusion protein containing DP178 as a targeting moiety, the ricin A chain, an HIV protease cleavable linker, and a truncated ricin B chain. N-terminal extensions of the fusion protein include the maltose binding protein and a Factor Xa protease site. C-terminal extensions include a hydrophobic linker, an L domain motif peptide, a KDEL ER retention signal, another Factor Xa protease site, an out-of-frame buforin II coding sequence, the lacZ.alpha. peptide, and a polyhistidine tag. More than twenty derivatives of plasmid pWKK-500 are described. Plasmids pWKK-700 and pWKK-800 are similar to pWKK-500 wherein the DP178-encoding sequence is substituted by RANTES- and SDF-1-encoding sequences, respectively. Plasmid pWKK-900 is similar to pWKK-500 wherein the HIV protease cleavable linker is substituted by a lethal factor (LF) peptide-cleavable linker.

Complementary DNA sequences encoding the multimammate rat MHC class II DQ alpha and beta chains and cross-species sequence comparison in rodents.

PubMed

de Bellocq, J Goüy; Leirs, H

2009-09-01

Sequences of the complete open reading frame (ORF) for rodents major histocompatibility complex (MHC) class II genes are rare. Multimammate rat (Mastomys natalensis) complementary DNA (cDNA) encoding the alpha and beta chains of MHC class II DQ gene was cloned from a rapid amplifications of cDNA Emds (RACE) cDNA library. The ORFs consist of 801 and 771 bp encoding 266 and 256 amino acid residues for DQB and DQA, respectively. The genomic structure of Mana-DQ genes is globally analogous to that described for other rodents except for the insertion of a serine residue in the signal peptide of Mana-DQB, which is unique among known rodents.

Myocardial strain estimation from CT: towards computer-aided diagnosis on infarction identification

NASA Astrophysics Data System (ADS)

Wong, Ken C. L.; Tee, Michael; Chen, Marcus; Bluemke, David A.; Summers, Ronald M.; Yao, Jianhua

2015-03-01

Regional myocardial strains have the potential for early quantification and detection of cardiac dysfunctions. Although image modalities such as tagged and strain-encoded MRI can provide motion information of the myocardium, they are uncommon in clinical routine. In contrary, cardiac CT images are usually available, but they only provide motion information at salient features such as the cardiac boundaries. To estimate myocardial strains from a CT image sequence, we adopted a cardiac biomechanical model with hyperelastic material properties to relate the motion on the cardiac boundaries to the myocardial deformation. The frame-to-frame displacements of the cardiac boundaries are obtained using B-spline deformable image registration based on mutual information, which are enforced as boundary conditions to the biomechanical model. The system equation is solved by the finite element method to provide the dense displacement field of the myocardium, and the regional values of the three principal strains and the six strains in cylindrical coordinates are computed in terms of the American Heart Association nomenclature. To study the potential of the estimated regional strains on identifying myocardial infarction, experiments were performed on cardiac CT image sequences of ten canines with artificially induced myocardial infarctions. The leave-one-subject-out cross validations show that, by using the optimal strain magnitude thresholds computed from ROC curves, the radial strain and the first principal strain have the best performance.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.

PubMed

Powell, Bradford C; Hutchison, Clyde A

2006-01-19

Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene prediction. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

PubMed Central

Powell, Bradford C; Hutchison, Clyde A

2006-01-01

Background Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. Results "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene predicion. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Conclusion Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes. PMID:16423288

Transcriptional analysis of Penaeus stylirostris densovirus genes

USDA-ARS?s Scientific Manuscript database

Penaeus stylirostris densovirus (PstDNV) genome contains three open reading frames (ORFs), left, middle, and right, which encode a non-structural (NS) protein, an unknown protein, and a capsid protein (CP), respectively. Transcription mapping revealed that P2, P11 and P61 promoters transcribe the le...

Influencing Memory Performance in Learning Disabled Students through Semantic Processing.

ERIC Educational Resources Information Center

Walker, Stephen C.; Poteet, James A.

1989-01-01

Thirty learning-disabled and 30 nonhandicapped intermediate grade children were assessed on memory performance for stimulus words, which were presented with congruent and noncongruent rhyming words and semantically congruent and noncongruent sentence frames. Both groups performed significantly better on words encoded using deep level congruent…

An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene

PubMed Central

Sheshukova, Ekaterina V.; Komarova, Tatiana V.; Ershova, Natalia M.; Shindyapina, Anastasia V.; Dorokhov, Yuri L.

2017-01-01

Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP, a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is “matryoshka,” containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5′-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves. PMID:29312392

An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene.

PubMed

Sheshukova, Ekaterina V; Komarova, Tatiana V; Ershova, Natalia M; Shindyapina, Anastasia V; Dorokhov, Yuri L

2017-01-01

Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP , a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is "matryoshka," containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5'-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves.

Force encoding in stick insect legs delineates a reference frame for motor control

PubMed Central

Schmitz, Josef; Chaudhry, Sumaiya; Büschges, Ansgar

2012-01-01

The regulation of forces is integral to motor control. However, it is unclear how information from sense organs that detect forces at individual muscles or joints is incorporated into a frame of reference for motor control. Campaniform sensilla are receptors that monitor forces by cuticular strains. We studied how loads and muscle forces are encoded by trochanteral campaniform sensilla in stick insects. Forces were applied to the middle leg to emulate loading and/or muscle contractions. Selective sensory ablations limited activities recorded in the main leg nerve to specific receptor groups. The trochanteral campaniform sensilla consist of four discrete groups. We found that the dorsal groups (Groups 3 and 4) encoded force increases and decreases in the plane of movement of the coxo-trochanteral joint. Group 3 receptors discharged to increases in dorsal loading and decreases in ventral load. Group 4 showed the reverse directional sensitivities. Vigorous, directional responses also occurred to contractions of the trochanteral depressor muscle and to forces applied at the muscle insertion. All sensory discharges encoded the amplitude and rate of loading or muscle force. Stimulation of the receptors produced reflex effects in the depressor motoneurons that could reverse in sign during active movements. These data, in conjunction with findings of previous studies, support a model in which the trochanteral receptors function as an array that can detect forces in all directions relative to the intrinsic plane of leg movement. The array could provide requisite information about forces and simplify the control and adaptation of posture and walking. PMID:22673329

Virus versus Host Plant MicroRNAs: Who Determines the Outcome of the Interaction?

PubMed Central

Maghuly, Fatemeh; Ramkat, Rose C.; Laimer, Margit

2014-01-01

Considering the importance of microRNAs (miRNAs) in the regulation of essential processes in plant pathogen interactions, it is not surprising that, while plant miRNA sequences counteract viral attack via antiviral RNA silencing, viruses in turn have developed antihost defense mechanisms blocking these RNA silencing pathways and establish a counter-defense. In the current study, computational and stem-loop Reverse Transcription – Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5′/3′ harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. Different viral pre-miRNA hairpin sequences and viral miR/miR* length variants occurring as isomiRs were predicted in both viruses. These miRNAs were located in three Open Reading Frames (ORFs) and in the Intergenic Region (IR). Moreover, various target genes for miRNAs from both viruses were predicted and annotated in the host plant genomes indicating that they are involved in biotic response, metabolic pathways and transcription factors. Plant miRs/miRs* from conserved and highly expressed families were identified, which were shown to have potential targets in the genome of both begomoviruses, representing potential plant miRNAs mediating antiviral defense. This is the first assessment of predicted viral miRs/miRs* of ACMV and EACMV-UG and host plant miRNAs, providing a reference point for miRNA identification in pathogens and their hosts. These findings will improve the understanding of host- pathogen interaction pathways and the function of viral miRNAs in Euphorbiaceous crop plants. PMID:24896088

Loss tolerant speech decoder for telecommunications

NASA Technical Reports Server (NTRS)

Prieto, Jr., Jaime L. (Inventor)

1999-01-01

A method and device for extrapolating past signal-history data for insertion into missing data segments in order to conceal digital speech frame errors. The extrapolation method uses past-signal history that is stored in a buffer. The method is implemented with a device that utilizes a finite-impulse response (FIR) multi-layer feed-forward artificial neural network that is trained by back-propagation for one-step extrapolation of speech compression algorithm (SCA) parameters. Once a speech connection has been established, the speech compression algorithm device begins sending encoded speech frames. As the speech frames are received, they are decoded and converted back into speech signal voltages. During the normal decoding process, pre-processing of the required SCA parameters will occur and the results stored in the past-history buffer. If a speech frame is detected to be lost or in error, then extrapolation modules are executed and replacement SCA parameters are generated and sent as the parameters required by the SCA. In this way, the information transfer to the SCA is transparent, and the SCA processing continues as usual. The listener will not normally notice that a speech frame has been lost because of the smooth transition between the last-received, lost, and next-received speech frames.

Effects of the HN gene c-terminal extensions on the Newcastle disease virus virulence

USDA-ARS?s Scientific Manuscript database

The hemagglutinin-neuraminidase (HN) of Newcastle disease virus (NDV) is a multifunctional protein that has receptor recognition, neuraminidase and fusion promotion activities. Sequence analysis revealed that the HN gene of many extremely low virulence NDV strains encodes a larger open reading frame...

PRIMARY STRUCTURE OF THE P450 LANOSTEROL DEMETHYLASE GENE FROM SACCHAROMYCES CEREVISIAE

EPA Science Inventory

We have sequenced the structural gene and flanking regions for lanosterol 14 alpha-demethylase (14DM) from Saccharomyces cerevisiae. An open reading frame of 530 codons encodes a 60.7-kDa protein. When this gene is disrupted by integrative transformation, the resulting strain req...

Shared Semantic Representations for Coordinating Distributed Robot Teams

DTIC Science & Technology

2003-12-01

Encoding of Rules, Variables, and Dynamic Bindings Using Temporal Synchrony." Behavioral and Brain Sciences, 16:3 p. 417-494. 29 16. Marvin Minsky . "Plain...is limited. Minsky [16] also describes a proposal for c-lines, a frame implementation mechanism similar in spirit to role passing, although the details

High speed, long distance, data transmission multiplexing circuit

DOEpatents

Mariotti, Razvan

1991-01-01

A high speed serial data transmission multiplexing circuit, which is operable to accurately transmit data over long distances (up to 3 Km), and to multiplex, select and continuously display real time analog signals in a bandwidth from DC to 100 Khz. The circuit is made fault tolerant by use of a programmable flywheel algorithm, which enables the circuit to tolerate one transmission error before losing synchronization of the transmitted frames of data. A method of encoding and framing captured and transmitted data is used which has a low overhead and prevents some particular transmitted data patterns from locking an included detector/decoder circuit.

An MR/MRI compatible core holder with the RF probe immersed in the confining fluid.

PubMed

Shakerian, M; Balcom, B J

2018-01-01

An open frame RF probe for high pressure and high temperature MR/MRI measurements was designed, fabricated, and tested. The open frame RF probe was installed inside an MR/MRI compatible metallic core holder, withstanding a maximum pressure and temperature of 5000 psi and 80 °C. The open frame RF probe was tunable for both 1 H and 19 F resonance frequencies with a 0.2 T static magnetic field. The open frame structure was based on simple pillars of PEEK polymer upon which the RF probe was wound. The RF probe was immersed in the high pressure confining fluid during operation. The open frame structure simplified fabrication of the RF probe and significantly reduced the amount of polymeric materials in the core holder. This minimized the MR background signal detected. Phase encoding MRI methods were employed to map the spin density of a sulfur hexafluoride gas saturating a Berea core plug in the core holder. The SF 6 was imaged as a high pressure gas and as a supercritical fluid. Copyright © 2017 Elsevier Inc. All rights reserved.

The modular modality frame model: continuous body state estimation and plausibility-weighted information fusion.

PubMed

Ehrenfeld, Stephan; Butz, Martin V

2013-02-01

Humans show admirable capabilities in movement planning and execution. They can perform complex tasks in various contexts, using the available sensory information very effectively. Body models and continuous body state estimations appear necessary to realize such capabilities. We introduce the Modular Modality Frame (MMF) model, which maintains a highly distributed, modularized body model continuously updating, modularized probabilistic body state estimations over time. Modularization is realized with respect to modality frames, that is, sensory modalities in particular frames of reference and with respect to particular body parts. We evaluate MMF performance on a simulated, nine degree of freedom arm in 3D space. The results show that MMF is able to maintain accurate body state estimations despite high sensor and motor noise. Moreover, by comparing the sensory information available in different modality frames, MMF can identify faulty sensory measurements on the fly. In the near future, applications to lightweight robot control should be pursued. Moreover, MMF may be enhanced with neural encodings by introducing neural population codes and learning techniques. Finally, more dexterous goal-directed behavior should be realized by exploiting the available redundant state representations.

An MR/MRI compatible core holder with the RF probe immersed in the confining fluid

NASA Astrophysics Data System (ADS)

Shakerian, M.; Balcom, B. J.

2018-01-01

An open frame RF probe for high pressure and high temperature MR/MRI measurements was designed, fabricated, and tested. The open frame RF probe was installed inside an MR/MRI compatible metallic core holder, withstanding a maximum pressure and temperature of 5000 psi and 80 °C. The open frame RF probe was tunable for both 1H and 19F resonance frequencies with a 0.2 T static magnetic field. The open frame structure was based on simple pillars of PEEK polymer upon which the RF probe was wound. The RF probe was immersed in the high pressure confining fluid during operation. The open frame structure simplified fabrication of the RF probe and significantly reduced the amount of polymeric materials in the core holder. This minimized the MR background signal detected. Phase encoding MRI methods were employed to map the spin density of a sulfur hexafluoride gas saturating a Berea core plug in the core holder. The SF6 was imaged as a high pressure gas and as a supercritical fluid.

Single-cut genome editing restores dystrophin expression in a new mouse model of muscular dystrophy

PubMed Central

Amoasii, Leonela; Long, Chengzu; Li, Hui; Mireault, Alex A.; Shelton, John M.; Sanchez-Ortiz, Efrain; McAnally, John R.; Bhattacharyya, Samadrita; Schmidt, Florian; Grimm, Dirk; Hauschka, Stephen D.; Bassel-Duby, Rhonda; Olson, Eric N.

2017-01-01

Duchenne muscular dystrophy (DMD) is a severe, progressive muscle disease caused by mutations in the dystrophin gene. The majority of DMD mutations are deletions that prematurely terminate the dystrophin protein. Deletions of exon 50 of the dystrophin gene are among the most common single exon deletions causing DMD. Such mutations can be corrected by skipping exon 51, thereby restoring the dystrophin reading frame. Using clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9), we generated a DMD mouse model by deleting exon 50. These ΔEx50 mice displayed severe muscle dysfunction, which was corrected by systemic delivery of adeno-associated virus encoding CRISPR/Cas9 genome editing components. We optimized the method for dystrophin reading frame correction using a single guide RNA that created reframing mutations and allowed skipping of exon 51. In conjunction with muscle-specific expression of Cas9, this approach restored up to 90% of dystrophin protein expression throughout skeletal muscles and the heart of ΔEx50 mice. This method of permanently bypassing DMD mutations using a single cut in genomic DNA represents a step toward clinical correction of DMD mutations and potentially those of other neuromuscular disorders. PMID:29187645

Sequencing and phylogenetic analysis of tobacco virus 2, a polerovirus from Nicotiana tabacum.

PubMed

Zhou, Benguo; Wang, Fang; Zhang, Xuesong; Zhang, Lina; Lin, Huafeng

2017-07-01

The complete genome sequence of a new virus, provisionally named tobacco virus 2 (TV2), was determined and identified from leaves of tobacco (Nicotiana tabacum) exhibiting leaf mosaic, yellowing, and deformity, in Anhui Province, China. The genome sequence of TV2 comprises 5,979 nucleotides, with 87% nucleotide sequence identity to potato leafroll virus (PLRV). Its genome organization is similar to that of PLRV, containing six open reading frames (ORFs) that potentially encode proteins with putative functions in cell-to-cell movement and suppression of RNA silencing. Phylogenetic analysis of the nucleotide sequence placed TV2 alongside members of the genus Polerovirus in the family Luteoviridae. To the best our knowledge, this study is the first report of a complete genome sequence of a new polerovirus identified in tobacco.

The Saccharomyces cerevisiae LOS1 gene involved in pre-tRNA splicing encodes a nuclear protein that behaves as a component of the nuclear matrix.

PubMed

Shen, W C; Selvakumar, D; Stanford, D R; Hopper, A K

1993-09-15

Mutations of the Saccharomyces cerevisiae LOS1 gene cause the accumulation of end matured intron-containing pre-tRNAs at elevated temperatures. In an effort to decipher the role of the LOS1 protein in pre-tRNA splicing, we have analyzed the LOS1 gene and its protein product. The LOS1 gene is located on the left arm of chromosome XI and the order of genes in this area of the chromosome is .... URA1 ... SAC1 TRP3 UBA1 STE6 LOS1 .... FAS1..... The LOS1 open reading frame encodes a putative protein of 1100 amino acids that shows no significant homology to other genes. The LOS1 open reading frame was tagged with the influenza virus hemagglutinin epitope recognized by the 12CA5 antibody. The 12CA5 antibody recognizes an epitope-tagged protein of the size predicted by the LOS1 open reading frame. Using this antibody for indirect immunofluorescence and cell fractionation studies we show that the LOS1 protein is located in nuclei. Los1p cannot be extracted from nuclei by treatment with nucleases, salts, or Triton X-100. This insolubility suggests that Los1p is a component of the nucleoskeleton. We propose that LOS1 mutations may affect pre-tRNA processing via alteration of the nuclear matrix.

Quantum Communication without Alignment using Multiple-Qubit Single-Photon States

NASA Astrophysics Data System (ADS)

Aolita, L.; Walborn, S. P.

2007-03-01

We propose a scheme for encoding logical qubits in a subspace protected against collective rotations around the propagation axis using the polarization and transverse spatial degrees of freedom of single photons. This encoding allows for quantum key distribution without the need of a shared reference frame. We present methods to generate entangled states of two logical qubits using present day down-conversion sources and linear optics, and show that the application of these entangled logical states to quantum information schemes allows for alignment-free tests of Bell’s inequalities, quantum dense coding, and quantum teleportation.

Detection of hepatitis B virus X product using an open reading frame Escherichia coli expression vector.

PubMed Central

Elfassi, E; Haseltine, W A; Dienstag, J L

1986-01-01

The genome of the hepatitis B virus (HBV) contains a sequence, designated X, capable of encoding a protein of 154 amino acids. To determine whether the putative protein synthesized from this region is antigenic, we examined the sera of HBV-infected patients for the ability to react with a hybrid protein that contained 133 amino acids encoded by the X region and portions of the bacterial ompF and beta-galactosidase genes. Some HBV-positive sera tested contained antibodies that specifically recognized the hybrid protein. All sera were from patients diagnosed as suffering from chronic active hepatitis. We conclude that the X region of HBV encodes a protein and that this protein is antigenic in some patients. Images PMID:3515347

Theory of equilibria of elastic 2-braids with interstrand interaction

NASA Astrophysics Data System (ADS)

Starostin, E. L.; van der Heijden, G. H. M.

2014-03-01

Motivated by continuum models for DNA supercoiling we formulate a theory for equilibria of 2-braids, i.e., structures formed by two elastic rods winding around each other in continuous contact and subject to a local interstrand interaction. No assumption is made on the shape of the contact curve. The theory is developed in terms of a moving frame of directors attached to one of the strands. The other strand is tracked by including in this frame the normalised closest-approach chord connecting the two strands. The kinematic constant-distance constraint is formulated at strain level through the introduction of what we call braid strains. As a result the total potential energy involves arclength derivatives of these strains, thus giving rise to a second-order variational problem. The Euler-Lagrange equations for this problem give balance equations for the overall braid force and moment referred to the moving frame as well as differential equations that can be interpreted as effective constitutive relations encoding the effect that the second strand has on the first as the braid deforms under the action of end loads. Hard contact models are used to obtain the normal contact pressure between strands that has to be non-negative for a physically realisable solution without the need for external devices such as clamps or glue to keep the strands together. The theory is first illustrated by a number of problems that can be solved analytically and then applied to several new problems that have not hitherto been treated.

Modular neuron-based body estimation: maintaining consistency over different limbs, modalities, and frames of reference

PubMed Central

Ehrenfeld, Stephan; Herbort, Oliver; Butz, Martin V.

2013-01-01

This paper addresses the question of how the brain maintains a probabilistic body state estimate over time from a modeling perspective. The neural Modular Modality Frame (nMMF) model simulates such a body state estimation process by continuously integrating redundant, multimodal body state information sources. The body state estimate itself is distributed over separate, but bidirectionally interacting modules. nMMF compares the incoming sensory and present body state information across the interacting modules and fuses the information sources accordingly. At the same time, nMMF enforces body state estimation consistency across the modules. nMMF is able to detect conflicting sensory information and to consequently decrease the influence of implausible sensor sources on the fly. In contrast to the previously published Modular Modality Frame (MMF) model, nMMF offers a biologically plausible neural implementation based on distributed, probabilistic population codes. Besides its neural plausibility, the neural encoding has the advantage of enabling (a) additional probabilistic information flow across the separate body state estimation modules and (b) the representation of arbitrary probability distributions of a body state. The results show that the neural estimates can detect and decrease the impact of false sensory information, can propagate conflicting information across modules, and can improve overall estimation accuracy due to additional module interactions. Even bodily illusions, such as the rubber hand illusion, can be simulated with nMMF. We conclude with an outlook on the potential of modeling human data and of invoking goal-directed behavioral control. PMID:24191151

Translation, modification and cellular distribution of two AC4 variants of African cassava mosaic virus in yeast and their pathogenic potential in plants

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

Hipp, Katharina, E-mail: katharina.hipp@bio.uni-st

Plant infecting geminiviruses encode a small (A)C4 protein within the open reading frame of the replication-initiator protein. In African cassava mosaic virus, two in-frame start codons may be used for the translation of a longer and a shorter AC4 variant. Both were fused to green fluorescent protein or glutathione-S-transferase genes and expressed in fission yeast. The longer variant accumulated in discrete spots in the cytoplasm, whereas the shorter variant localized to the plasma membrane. A similar expression pattern was found in plants. A myristoylation motif may promote a targeting of the shorter variant to the plasma membrane. Mass spectrometry analysismore » of the yeast-expressed shorter variant detected the corresponding myristoylation. The biological relevance of the second start codon was confirmed using mutated infectious clones. Whereas mutating the first start codon had no effect on the infectivity in Nicotiana benthamiana plants, the second start codon proved to be essential. -- Highlights: •The ACMV AC4 may be translated from one or the other in-frame start codon. •Both AC4 variants are translated in fission yeast. •The long AC4 protein localizes to the cytoplasm, the short to the plasma membrane. •The short variant is myristoylated in yeast and may promote membrane localization. •Only the shorter AC4 variant has an impact on viral infections in plants.« less

Purification, characterization, and cDNA cloning of a novel acidic endoglycoceramidase from the jellyfish, Cyanea nozakii.

PubMed

Horibata, Y; Okino, N; Ichinose, S; Omori, A; Ito, M

2000-10-06

Endoglycoceramidase (EC ) is an enzyme capable of cleaving the glycosidic linkage between oligosaccharides and ceramides in various glycosphingolipids. We report here the purification, characterization, and cDNA cloning of a novel endoglycoceramidase from the jellyfish, Cyanea nozakii. The purified enzyme showed a single protein band estimated to be 51 kDa on SDS-polyacrylamide gel electrophoresis. The enzyme showed a pH optimum of 3.0 and was activated by Triton X-100 and Lubrol PX but not by sodium taurodeoxycholate. This enzyme preferentially hydrolyzed gangliosides, especially GT1b and GQ1b, whereas neutral glycosphingolipids were somewhat resistant to hydrolysis by the enzyme. A full-length cDNA encoding the enzyme was cloned by 5'- and 3'-rapid amplification of cDNA ends using a partial amino acid sequence of the purified enzyme. The open reading frame of 1509 nucleotides encoded a polypeptide of 503 amino acids including a signal sequence of 25 residues and six potential N-glycosylation sites. Interestingly, the Asn-Glu-Pro sequence, which is the putative active site of Rhodococcus endoglycoceramidase, was conserved in the deduced amino acid sequences. This is the first report of the cloning of an endoglycoceramidase from a eukaryote.

The Env-like open reading frame of the baculovirus-integrated retrotransposon TED encodes a retrovirus-like envelope protein.

PubMed

Ozers, M S; Friesen, P D

1996-12-15

TED is a 7.5-kbp member of the gypsy family of retrotransposons that was first identified by its integration within the baculovirus DNA genome. This lepidopteran (moth) transposon contains three retrovirus-like genes, including functional gag and pol that yield reverse transcriptase-containing virus-like particles. To identify and characterize the product(s) of the third env-like open reading frame, TED ORF3 was expressed in homologous lepidopteran cells by using a baculovirus vector, vENV. Immunoblots and immunoprecipitations with antiserum raised against a bacterial ORF3-fusion protein detected two ORF3-encoded proteins, p68env and gp75env. On the basis of selective incorporation of [3H]mannose and inhibition of modification by tunicamycin which blocks N-linked glycosylation, gp75env is a glycoprotein derived from core precursor p68env. As predicted by the presence of a transmembrane domain near the carboxyl terminus, both p68env and gp75env were associated with heavy membranes of vENV-infected cells. Thus, TED ORF3 encodes a membrane glycoprotein with properties characteristic of retroviral env proteins. These data are consistent with the hypothesis that TED is an invertebrate retrovirus. Moreover, TED integration within the baculovirus genome provides an example of retroelement-mediated acquisition of host genes that may contribute to virus evolution.

Profiling of EBV-Encoded microRNAs in EBV-Associated Hemophagocytic Lymphohistiocytosis.

PubMed

Zhou, Chen; Xie, Zhengde; Gao, Liwei; Liu, Chunyan; Ai, Junhong; Zhang, Li; Shen, Kunling

2015-10-01

Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis (EBV-HLH) is a life-threatening complication of EBV infection. MicroRNAs (miRNAs) were small non-coding RNA, and EBV could encode miRNAs that are involved in the progression of infection. However, the profiles of EBV-miRNAs in EBV-HLH were unknown. Here, we aimed to profile the expression of EBV-miRNAs in children with EBV-HLH by analyzing 44 known EBV-miRNAs, encoded within the BamHI fragment H rightward open reading frame 1 (BHRF1) and the BamHI-A region rightward transcript (BART), in plasma and cellular targets by real-time quantitative PCR. The study included 15 children with EBV-HLH, 15 children with infectious mononucleosis (IM), and 15 healthy controls. CD8(+) T cells were found to be the cellular target of EBV infection in EBV-HLH, while CD19(+) B cells were infected with EBV in IM. We also found the greater levels of several miRNAs encoded by BART in EBV-HLH, compared to those in IM and healthy controls, whereas the levels of BHRF1 miRNAs were lower than those in IM. The profile and pattern of EBV-miRNAs in EBV-HLH indicated that EBV could display type II latency in EBV-HLH. Importantly, the level of plasma miR-BART16-1 continued decreasing during the whole chemotherapy, suggesting that plasma miR-BART16-1 could be a potential biomarker for monitoring EBV-HLH progression. The pathogenesis of EBV-HLH might be attributed to the abundance of EBV-miRNAs in EBV-HLH. These findings help elucidate the roles of EBV miRNAs in EBV-HLH, enabling the understanding of the basis of this disease and providing clues for its treatment.

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

DOE PAGES

Tian, Ye; Wang, Tong; Liu, Wenyan; ...

2015-05-25

Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we report a strategy for assembling 3D nanoparticle clusters that uses a molecular frame designed with encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA framemore » and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be assembled that have designed particle arrangements.« less

Two-Stream Transformer Networks for Video-based Face Alignment.

PubMed

Liu, Hao; Lu, Jiwen; Feng, Jianjiang; Zhou, Jie

2017-08-01

In this paper, we propose a two-stream transformer networks (TSTN) approach for video-based face alignment. Unlike conventional image-based face alignment approaches which cannot explicitly model the temporal dependency in videos and motivated by the fact that consistent movements of facial landmarks usually occur across consecutive frames, our TSTN aims to capture the complementary information of both the spatial appearance on still frames and the temporal consistency information across frames. To achieve this, we develop a two-stream architecture, which decomposes the video-based face alignment into spatial and temporal streams accordingly. Specifically, the spatial stream aims to transform the facial image to the landmark positions by preserving the holistic facial shape structure. Accordingly, the temporal stream encodes the video input as active appearance codes, where the temporal consistency information across frames is captured to help shape refinements. Experimental results on the benchmarking video-based face alignment datasets show very competitive performance of our method in comparisons to the state-of-the-arts.

Examining reference frame interaction in spatial memory using a distribution analysis.

PubMed

Street, Whitney N; Wang, Ranxiao Frances

2016-02-01

Previous research showed competition among reference frames in spatial attention and language. The present studies developed a new distribution analysis to examine reference frame interactions in spatial memory. Participants viewed virtual arrays of colored pegs and were instructed to remember them either from their own perspective or from the perspective aligned with the rectangular floor. Then they made judgments of relative directions from their respective encoding orientation. Those taking the floor-axis perspective showed systematic bias in the signed errors toward their egocentric perspective, while those taking their own perspective showed no systematic bias, both for random and symmetrical object arrays. The bias toward the egocentric perspective was observed when learning a real symmetric regular object array with strong environmental cues for the aligned axis. These results indicate automatic processing of the self reference while taking the floor-axis perspective but not vice versa, and suggest that research on spatial memory needs to consider the implications of competition effects in reference frame use.

Implementation of MPEG-2 encoder to multiprocessor system using multiple MVPs (TMS320C80)

NASA Astrophysics Data System (ADS)

Kim, HyungSun; Boo, Kenny; Chung, SeokWoo; Choi, Geon Y.; Lee, YongJin; Jeon, JaeHo; Park, Hyun Wook

1997-05-01

This paper presents the efficient algorithm mapping for the real-time MPEG-2 encoding on the KAIST image computing system (KICS), which has a parallel architecture using five multimedia video processors (MVPs). The MVP is a general purpose digital signal processor (DSP) of Texas Instrument. It combines one floating-point processor and four fixed- point DSPs on a single chip. The KICS uses the MVP as a primary processing element (PE). Two PEs form a cluster, and there are two processing clusters in the KICS. Real-time MPEG-2 encoder is implemented through the spatial and the functional partitioning strategies. Encoding process of spatially partitioned half of the video input frame is assigned to ne processing cluster. Two PEs perform the functionally partitioned MPEG-2 encoding tasks in the pipelined operation mode. One PE of a cluster carries out the transform coding part and the other performs the predictive coding part of the MPEG-2 encoding algorithm. One MVP among five MVPs is used for system control and interface with host computer. This paper introduces an implementation of the MPEG-2 algorithm with a parallel processing architecture.

Fusagene vectors: a novel strategy for the expression of multiple genes from a single cistron.

PubMed

Gäken, J; Jiang, J; Daniel, K; van Berkel, E; Hughes, C; Kuiper, M; Darling, D; Tavassoli, M; Galea-Lauri, J; Ford, K; Kemeny, M; Russell, S; Farzaneh, F

2000-12-01

Transduction of cells with multiple genes, allowing their stable and co-ordinated expression, is difficult with the available methodologies. A method has been developed for expression of multiple gene products, as fusion proteins, from a single cistron. The encoded proteins are post-synthetically cleaved and processed into each of their constituent proteins as individual, biologically active factors. Specifically, linkers encoding cleavage sites for the Golgi expressed endoprotease, furin, have been incorporated between in-frame cDNA sequences encoding different secreted or membrane bound proteins. With this strategy we have developed expression vectors encoding multiple proteins (IL-2 and B7.1, IL-4 and B7.1, IL-4 and IL-2, IL-12 p40 and p35, and IL-12 p40, p35 and IL-2 ). Transduction and analysis of over 100 individual clones, derived from murine and human tumour cell lines, demonstrate the efficient expression and biological activity of each of the encoded proteins. Fusagene vectors enable the co-ordinated expression of multiple gene products from a single, monocistronic, expression cassette.

A plasmid toolkit for cloning chimeric cDNAs encoding customized fusion proteins into any Gateway destination expression vector

PubMed Central

2013-01-01

Background Valuable clone collections encoding the complete ORFeomes for some model organisms have been constructed following the completion of their genome sequencing projects. These libraries are based on Gateway cloning technology, which facilitates the study of protein function by simplifying the subcloning of open reading frames (ORF) into any suitable destination vector. The expression of proteins of interest as fusions with functional modules is a frequent approach in their initial functional characterization. A limited number of Gateway destination expression vectors allow the construction of fusion proteins from ORFeome-derived sequences, but they are restricted to the possibilities offered by their inbuilt functional modules and their pre-defined model organism-specificity. Thus, the availability of cloning systems that overcome these limitations would be highly advantageous. Results We present a versatile cloning toolkit for constructing fully-customizable three-part fusion proteins based on the MultiSite Gateway cloning system. The fusion protein components are encoded in the three plasmids integral to the kit. These can recombine with any purposely-engineered destination vector that uses a heterologous promoter external to the Gateway cassette, leading to the in-frame cloning of an ORF of interest flanked by two functional modules. In contrast to previous systems, a third part becomes available for peptide-encoding as it no longer needs to contain a promoter, resulting in an increased number of possible fusion combinations. We have constructed the kit’s component plasmids and demonstrate its functionality by providing proof-of-principle data on the expression of prototype fluorescent fusions in transiently-transfected cells. Conclusions We have developed a toolkit for creating fusion proteins with customized N- and C-term modules from Gateway entry clones encoding ORFs of interest. Importantly, our method allows entry clones obtained from ORFeome collections to be used without prior modifications. Using this technology, any existing Gateway destination expression vector with its model-specific properties could be easily adapted for expressing fusion proteins. PMID:23957834

A plasmid toolkit for cloning chimeric cDNAs encoding customized fusion proteins into any Gateway destination expression vector.

PubMed

Buj, Raquel; Iglesias, Noa; Planas, Anna M; Santalucía, Tomàs

2013-08-20

Valuable clone collections encoding the complete ORFeomes for some model organisms have been constructed following the completion of their genome sequencing projects. These libraries are based on Gateway cloning technology, which facilitates the study of protein function by simplifying the subcloning of open reading frames (ORF) into any suitable destination vector. The expression of proteins of interest as fusions with functional modules is a frequent approach in their initial functional characterization. A limited number of Gateway destination expression vectors allow the construction of fusion proteins from ORFeome-derived sequences, but they are restricted to the possibilities offered by their inbuilt functional modules and their pre-defined model organism-specificity. Thus, the availability of cloning systems that overcome these limitations would be highly advantageous. We present a versatile cloning toolkit for constructing fully-customizable three-part fusion proteins based on the MultiSite Gateway cloning system. The fusion protein components are encoded in the three plasmids integral to the kit. These can recombine with any purposely-engineered destination vector that uses a heterologous promoter external to the Gateway cassette, leading to the in-frame cloning of an ORF of interest flanked by two functional modules. In contrast to previous systems, a third part becomes available for peptide-encoding as it no longer needs to contain a promoter, resulting in an increased number of possible fusion combinations. We have constructed the kit's component plasmids and demonstrate its functionality by providing proof-of-principle data on the expression of prototype fluorescent fusions in transiently-transfected cells. We have developed a toolkit for creating fusion proteins with customized N- and C-term modules from Gateway entry clones encoding ORFs of interest. Importantly, our method allows entry clones obtained from ORFeome collections to be used without prior modifications. Using this technology, any existing Gateway destination expression vector with its model-specific properties could be easily adapted for expressing fusion proteins.

Temporal coding of reward-guided choice in the posterior parietal cortex

PubMed Central

Hawellek, David J.; Wong, Yan T.; Pesaran, Bijan

2016-01-01

Making a decision involves computations across distributed cortical and subcortical networks. How such distributed processing is performed remains unclear. We test how the encoding of choice in a key decision-making node, the posterior parietal cortex (PPC), depends on the temporal structure of the surrounding population activity. We recorded spiking and local field potential (LFP) activity in the PPC while two rhesus macaques performed a decision-making task. We quantified the mutual information that neurons carried about an upcoming choice and its dependence on LFP activity. The spiking of PPC neurons was correlated with LFP phases at three distinct time scales in the theta, beta, and gamma frequency bands. Importantly, activity at these time scales encoded upcoming decisions differently. Choice information contained in neural firing varied with the phase of beta and gamma activity. For gamma activity, maximum choice information occurred at the same phase as the maximum spike count. However, for beta activity, choice information and spike count were greatest at different phases. In contrast, theta activity did not modulate the encoding properties of PPC units directly but was correlated with beta and gamma activity through cross-frequency coupling. We propose that the relative timing of local spiking and choice information reveals temporal reference frames for computations in either local or large-scale decision networks. Differences between the timing of task information and activity patterns may be a general signature of distributed processing across large-scale networks. PMID:27821752

Genomic analysis of Staphylococcus phage Stau2 isolated from medical specimen.

PubMed

Hsieh, Sue-Er; Tseng, Yi-Hsiung; Lo, Hsueh-Hsia; Chen, Shui-Tu; Wu, Cheng-Nan

2016-02-01

Stau2 is a lytic myophage of Staphylococcus aureus isolated from medical specimen. Exhibiting a broad host range against S. aureus clinical isolates, Stau2 is potentially useful for topical phage therapy or as an additive in food preservation. In this study, Stau2 was firstly revealed to possess a circularly permuted linear genome of 133,798 bp, with low G + C content, containing 146 open reading frames, but encoding no tRNA. The genome is organized into several modules containing genes for packaging, structural proteins, replication/transcription and host-cell-lysis, with the structural proteins and DNA polymerase modules being organized similarly to that in Twort-like phages of Staphylococcus. With the encoded DNA replication genes, Stau2 can possibly use its own system for replication. In addition, analysis in silico found several introns in seven genes, including those involved in DNA metabolism, packaging, and structure, while one of them (helicase gene) is experimentally confirmed to undergo splicing. Furthermore, phylogenetic analysis suggested Stau2 to be most closely related to Staphylococcus phages SA11 and Remus, members of Twort-like phages. The results of sodium dodecyl sulfate polyacrylamide gel electrophoresis showed 14 structural proteins of Stau2 and N-terminal sequencing identified three of them. Importantly, this phage does not encode any proteins which are known or suspected to be involved in toxicity, pathogenicity, or antibiotic resistance. Therefore, further investigations of feasible therapeutic application of Stau2 are needed.

CYC2 encodes a factor involved in mitochondrial import of yeast cytochrome c.

PubMed Central

Dumont, M E; Schlichter, J B; Cardillo, T S; Hayes, M K; Bethlendy, G; Sherman, F

1993-01-01

The gene CYC2 from the yeast Saccharomyces cerevisiae was previously shown to affect levels of mitochondrial cytochrome c by acting at a posttranslational step in cytochrome c biosynthesis. We report here the cloning and identification of the CYC2 gene product as a protein involved in import of cytochrome c into mitochondria. CYC2 encodes a 168-amino-acid open reading frame with at least two potential transmembrane segments. Antibodies against a synthetic peptide corresponding to the carboxyl terminus of the predicted sequence were raised. These antibodies recognize multiple bands on immunoblots of mitochondrial extracts. The intensities of these bands vary according to the gene dosage of CYC2 in various isogenic strains. Immunoblotting of subcellular fractions suggests that the CYC2 gene product is a mitochondrial protein. Deletion of CYC2 leads to accumulation of apocytochrome c in the cytoplasm. However, strains with deletions of this gene still import low levels of cytochrome c into mitochondria. The effects of cyc2 mutations are more pronounced in rho- strains than in rho+ strains, even though rho- strains that are CYC2+ contain normal levels of holocytochrome c. cyc2 mutations affect levels of iso-1-cytochrome c more than they do levels of iso-2-cytochrome c, apparently because of the greater susceptibility of apo-iso-1-cytochrome c to degradation in the cytoplasm. We propose that CYC2 encodes a factor that increases the efficiency of cytochrome c import into mitochondria. Images PMID:8413243

Complete genome sequence of yam chlorotic necrosis virus, a novel macluravirus infecting yam

USDA-ARS?s Scientific Manuscript database

Complete genomic sequence of a novel member of the genus Macluravirus was determined from yam plants with chlorotic and necrotic symptoms in China. The genomic RNA consists of 8,261 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing one long open reading frame (ORF) encoding a larg...

Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses

USDA-ARS?s Scientific Manuscript database

Solenopsis invicta virus 2 is a single-stranded positive-sense picorna-like RNA virus with an unusual genome structure. The monopartite genome of approximately 11 kb contains four short open reading frames in its 5' one third, three of which encode proteins with homology to picornavirus-like jelly-r...

A NOVEL CADHERIN-LIKE GENE FROM WESTERN CORN ROOTWORM, DIABROTICA VIRGIFERA VIRGIFERA (COLEOPTERA: CHRYSOMELIDAE), LARVAL MIDGUT TISSUE

EPA Science Inventory

A cadherin-like gene and its mRNA were cloned from western corn rootworm (Diabrotica virgifera virgifera: Coleoptera), an economically important agricultural pest in North America and Europe. The full length cDNA (5371 bp in length) encodes an open reading frame for a 1688 amino ...

47 CFR Appendix - Technical Appendix 1

Code of Federal Regulations, 2010 CFR

2010-10-01

... display program material that has been encoded in any and all of the video formats contained in Table A3... frame rate of the transmitted video format. 2. Output Formats Equipment shall support 4:3 center cut-out... for composite video (yellow). Output shall produce video with ITU-R BT.500-11 quality scale of Grade 4...

Long interspersed element-1 protein expression is a hallmark of many human cancers.

PubMed

Rodić, Nemanja; Sharma, Reema; Sharma, Rajni; Zampella, John; Dai, Lixin; Taylor, Martin S; Hruban, Ralph H; Iacobuzio-Donahue, Christine A; Maitra, Anirban; Torbenson, Michael S; Goggins, Michael; Shih, Ie-Ming; Duffield, Amy S; Montgomery, Elizabeth A; Gabrielson, Edward; Netto, George J; Lotan, Tamara L; De Marzo, Angelo M; Westra, William; Binder, Zev A; Orr, Brent A; Gallia, Gary L; Eberhart, Charles G; Boeke, Jef D; Harris, Chris R; Burns, Kathleen H

2014-05-01

Cancers comprise a heterogeneous group of human diseases. Unifying characteristics include unchecked abilities of tumor cells to proliferate and spread anatomically, and the presence of clonal advantageous genetic changes. However, universal and highly specific tumor markers are unknown. Herein, we report widespread long interspersed element-1 (LINE-1) repeat expression in human cancers. We show that nearly half of all human cancers are immunoreactive for a LINE-1-encoded protein. LINE-1 protein expression is a common feature of many types of high-grade malignant cancers, is rarely detected in early stages of tumorigenesis, and is absent from normal somatic tissues. Studies have shown that LINE-1 contributes to genetic changes in cancers, with somatic LINE-1 insertions seen in selected types of human cancers, particularly colon cancer. We sought to correlate this observation with expression of the LINE-1-encoded protein, open reading frame 1 protein, and found that LINE-1 open reading frame 1 protein is a surprisingly broad, yet highly tumor-specific, antigen. Copyright © 2014 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Porcine parvovirus: DNA sequence and genome organization.

PubMed

Ranz, A I; Manclús, J J; Díaz-Aroca, E; Casal, J I

1989-10-01

We have determined the nucleotide sequence of an almost full-length clone of porcine parvovirus (PPV). The sequence is 4973 nucleotides (nt) long. The 3' end of virion DNA shows a Y-shaped configuration homologous to rodent parvoviruses. The 5' end of virion DNA shows a repetition of 127 nt at the carboxy terminus of the capsid proteins. The overall organization of the PPV genome is similar to those of other autonomous parvoviruses. There are two large open reading frames (ORFs) that almost entirely cover the genome, both located in the same frame of the complementary strand. The left ORF encodes the non-structural protein NS1 and the right ORF encodes the capsid proteins (VP1, VP2 and VP3). Promoter analysis, location of splicing sites and putative amino acid sequences for the viral proteins show a high homology of PPV with feline panleukopenia virus and canine parvoviruses (FPV and CPV) and rodent parvovirus. Therefore we conclude that PPV is related to the Kilham rat virus (KRV) group of autonomous parvoviruses formed by KRV, minute virus of mice, Lu III, H-1, FPV and CPV.

Backwards compatible high dynamic range video compression

NASA Astrophysics Data System (ADS)

Dolzhenko, Vladimir; Chesnokov, Vyacheslav; Edirisinghe, Eran A.

2014-02-01

This paper presents a two layer CODEC architecture for high dynamic range video compression. The base layer contains the tone mapped video stream encoded with 8 bits per component which can be decoded using conventional equipment. The base layer content is optimized for rendering on low dynamic range displays. The enhancement layer contains the image difference, in perceptually uniform color space, between the result of inverse tone mapped base layer content and the original video stream. Prediction of the high dynamic range content reduces the redundancy in the transmitted data while still preserves highlights and out-of-gamut colors. Perceptually uniform colorspace enables using standard ratedistortion optimization algorithms. We present techniques for efficient implementation and encoding of non-uniform tone mapping operators with low overhead in terms of bitstream size and number of operations. The transform representation is based on human vision system model and suitable for global and local tone mapping operators. The compression techniques include predicting the transform parameters from previously decoded frames and from already decoded data for current frame. Different video compression techniques are compared: backwards compatible and non-backwards compatible using AVC and HEVC codecs.

Pseudo-polyprotein translated from the full-length ORF1 of capillovirus is important for pathogenicity, but a truncated ORF1 protein without variable and CP regions is sufficient for replication.

PubMed

Hirata, Hisae; Yamaji, Yasuyuki; Komatsu, Ken; Kagiwada, Satoshi; Oshima, Kenro; Okano, Yukari; Takahashi, Shuichiro; Ugaki, Masashi; Namba, Shigetou

2010-09-01

The first open-reading frame (ORF) of the genus Capillovirus encodes an apparently chimeric polyprotein containing conserved regions for replicase (Rep) and coat protein (CP), while other viruses in the family Flexiviridae have separate ORFs encoding these proteins. To investigate the role of the full-length ORF1 polyprotein of capillovirus, we generated truncation mutants of ORF1 of apple stem grooving virus by inserting a termination codon into the variable region located between the putative Rep- and CP-coding regions. These mutants were capable of systemic infection, although their pathogenicity was attenuated. In vitro translation of ORF1 produced both the full-length polyprotein and the smaller Rep protein. The results of in vivo reporter assays suggested that the mechanism of this early termination is a ribosomal -1 frame-shift occurring downstream from the conserved Rep domains. The mechanism of capillovirus gene expression and the very close evolutionary relationship between the genera Capillovirus and Trichovirus are discussed. Copyright (c) 2010. Published by Elsevier B.V.

Image acquisition system using on sensor compressed sampling technique

NASA Astrophysics Data System (ADS)

Gupta, Pravir Singh; Choi, Gwan Seong

2018-01-01

Advances in CMOS technology have made high-resolution image sensors possible. These image sensors pose significant challenges in terms of the amount of raw data generated, energy efficiency, and frame rate. This paper presents a design methodology for an imaging system and a simplified image sensor pixel design to be used in the system so that the compressed sensing (CS) technique can be implemented easily at the sensor level. This results in significant energy savings as it not only cuts the raw data rate but also reduces transistor count per pixel; decreases pixel size; increases fill factor; simplifies analog-to-digital converter, JPEG encoder, and JPEG decoder design; decreases wiring; and reduces the decoder size by half. Thus, CS has the potential to increase the resolution of image sensors for a given technology and die size while significantly decreasing the power consumption and design complexity. We show that it has potential to reduce power consumption by about 23% to 65%.

Asynchronous accumulation of lettuce infectious yellows virus RNAs 1 and 2 and identification of an RNA 1 trans enhancer of RNA 2 accumulation.

PubMed

Yeh, H H; Tian, T; Rubio, L; Crawford, B; Falk, B W

2000-07-01

Time course and mutational analyses were used to examine the accumulation in protoplasts of progeny RNAs of the bipartite Crinivirus, Lettuce infectious yellow virus (LIYV; family Closteroviridae). Hybridization analyses showed that simultaneous inoculation of LIYV RNAs 1 and 2 resulted in asynchronous accumulation of progeny LIYV RNAs. LIYV RNA 1 progeny genomic and subgenomic RNAs could be detected in protoplasts as early as 12 h postinoculation (p.i.) and accumulated to high levels by 24 h p.i. The LIYV RNA 1 open reading frame 2 (ORF 2) subgenomic RNA was the most abundant of all LIYV RNAs detected. In contrast, RNA 2 progeny were not readily detected until ca. 36 h p.i. Mutational analyses showed that in-frame stop codons introduced into five of seven RNA 2 ORFs did not affect accumulation of progeny LIYV RNA 1 or RNA 2, confirming that RNA 2 does not encode proteins necessary for LIYV RNA replication. Mutational analyses also supported that LIYV RNA 1 encodes proteins necessary for replication of LIYV RNAs 1 and 2. A mutation introduced into the LIYV RNA 1 region encoding the overlapping ORF 1B and ORF 2 was lethal. However, mutations introduced into only LIYV RNA 1 ORF 2 resulted in accumulation of progeny RNA 1 near or equal to wild-type RNA 1. In contrast, the RNA 1 ORF 2 mutants did not efficiently support the trans accumulation of LIYV RNA 2. Three distinct RNA 1 ORF 2 mutants were analyzed and all exhibited a similar phenotype for progeny LIYV RNA accumulation. These data suggest that the LIYV RNA 1 ORF 2 encodes a trans enhancer for RNA 2 accumulation.

Asynchronous Accumulation of Lettuce Infectious Yellows Virus RNAs 1 and 2 and Identification of an RNA 1 trans Enhancer of RNA 2 Accumulation

PubMed Central

Yeh, Hsin-Hung; Tian, Tongyan; Rubio, Luis; Crawford, Brett; Falk, Bryce W.

2000-01-01

Time course and mutational analyses were used to examine the accumulation in protoplasts of progeny RNAs of the bipartite Crinivirus, Lettuce infectious yellow virus (LIYV; family Closteroviridae). Hybridization analyses showed that simultaneous inoculation of LIYV RNAs 1 and 2 resulted in asynchronous accumulation of progeny LIYV RNAs. LIYV RNA 1 progeny genomic and subgenomic RNAs could be detected in protoplasts as early as 12 h postinoculation (p.i.) and accumulated to high levels by 24 h p.i. The LIYV RNA 1 open reading frame 2 (ORF 2) subgenomic RNA was the most abundant of all LIYV RNAs detected. In contrast, RNA 2 progeny were not readily detected until ca. 36 h p.i. Mutational analyses showed that in-frame stop codons introduced into five of seven RNA 2 ORFs did not affect accumulation of progeny LIYV RNA 1 or RNA 2, confirming that RNA 2 does not encode proteins necessary for LIYV RNA replication. Mutational analyses also supported that LIYV RNA 1 encodes proteins necessary for replication of LIYV RNAs 1 and 2. A mutation introduced into the LIYV RNA 1 region encoding the overlapping ORF 1B and ORF 2 was lethal. However, mutations introduced into only LIYV RNA 1 ORF 2 resulted in accumulation of progeny RNA 1 near or equal to wild-type RNA 1. In contrast, the RNA 1 ORF 2 mutants did not efficiently support the trans accumulation of LIYV RNA 2. Three distinct RNA 1 ORF 2 mutants were analyzed and all exhibited a similar phenotype for progeny LIYV RNA accumulation. These data suggest that the LIYV RNA 1 ORF 2 encodes a trans enhancer for RNA 2 accumulation. PMID:10846054

Characterization of GM-CSF-inhibitory factor and Uracil DNA glycosylase encoding genes from camel pseudocowpoxvirus.

PubMed

Nagarajan, G; Swami, Shelesh Kumar; Dahiya, Shyam Singh; Narnaware, S D; Mehta, S C; Singh, P K; Singh, Raghvendar; Tuteja, F C; Patil, N V

2015-06-01

The present study describes the PCR amplification of GM-CSF-inhibitory factor (GIF) and Uracil DNA glycosylase (UDG) encoding genes of pseudocowpoxvirus (PCPV) from the Indian Dromedaries (Camelus dromedarius) infected with contagious ecthyma using the primers based on the corresponding gene sequences of human PCPV and reindeer PCPV, respectively. The length of GIF gene of PCPV obtained from camel is 795 bp and due to the addition of one cytosine residue at position 374 and one adenine residue at position 516, the open reading frame (ORF) got altered, resulting in the production of truncated polypeptide. The ORF of UDG encoding gene of camel PCPV is 696 bp encoding a polypeptide of 26.0 kDa. Comparison of amino acid sequence homologies of GIF and UDG of camel PCPV revealed that the camel PCPV is closer to ORFV and PCPV (reference stains of both human and reindeer), respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cloning and characterization of the ddc homolog encoding L-2,4-diaminobutyrate decarboxylase in Enterobacter aerogenes.

PubMed

Yamamoto, S; Mutoh, N; Tsuzuki, D; Ikai, H; Nakao, H; Shinoda, S; Narimatsu, S; Miyoshi, S I

2000-05-01

L-2,4-diaminobutyrate decarboxylase (DABA DC) catalyzes the formation of 1,3-diaminopropane (DAP) from DABA. In the present study, the ddc gene encoding DABA DC from Enterobacter aerogenes ATCC 13048 was cloned and characterized. Determination of the nucleotide sequence revealed an open reading frame of 1470 bp encoding a 53659-Da protein of 490 amino acids, whose deduced NH2-terminal sequence was identical to that of purified DABA DC from E. aerogenes. The deduced amino acid sequence was highly similar to those of Acinetobacter baumannii and Haemophilus influenzae DABA DCs encoded by the ddc genes. The lysine-307 of the E. aerogenes DABA DC was identified as the pyridoxal 5'-phosphate binding residue by site-directed mutagenesis. Furthermore, PCR analysis revealed the distribution of E. aerogenes ddc homologs in some other species of Enterobacteriaceae. Such a relatively wide occurrence of the ddc homologs implies biological significance of DABA DC and its product DAP.

JND measurements of the speech formants parameters and its implication in the LPC pole quantization

NASA Astrophysics Data System (ADS)

Orgad, Yaakov

1988-08-01

The inherent sensitivity of auditory perception is explicitly used with the objective of designing an efficient speech encoder. Speech can be modelled by a filter representing the vocal tract shape that is driven by an excitation signal representing glottal air flow. This work concentrates on the filter encoding problem, assuming that excitation signal encoding is optimal. Linear predictive coding (LPC) techniques were used to model a short speech segment by an all-pole filter; each pole was directly related to the speech formants. Measurements were made of the auditory just noticeable difference (JND) corresponding to the natural speech formants, with the LPC filter poles as the best candidates to represent the speech spectral envelope. The JND is the maximum precision required in speech quantization; it was defined on the basis of the shift of one pole parameter of a single frame of a speech segment, necessary to induce subjective perception of the distortion, with .75 probability. The average JND in LPC filter poles in natural speech was found to increase with increasing pole bandwidth and, to a lesser extent, frequency. The JND measurements showed a large spread of the residuals around the average values, indicating that inter-formant coupling and, perhaps, other, not yet fully understood, factors were not taken into account at this stage of the research. A future treatment should consider these factors. The average JNDs obtained in this work were used to design pole quantization tables for speech coding and provided a better bit-rate than the standard quantizer of reflection coefficient; a 30-bits-per-frame pole quantizer yielded a speech quality similar to that obtained with a standard 41-bits-per-frame reflection coefficient quantizer. Owing to the complexity of the numerical root extraction system, the practical implementation of the pole quantization approach remains to be proved.

A universal cue for grammatical categories in the input to children: Frequent frames.

PubMed

Moran, Steven; Blasi, Damián E; Schikowski, Robert; Küntay, Aylin C; Pfeiler, Barbara; Allen, Shanley; Stoll, Sabine

2018-06-01

How does a child map words to grammatical categories when words are not overtly marked either lexically or prosodically? Recent language acquisition theories have proposed that distributional information encoded in sequences of words or morphemes might play a central role in forming grammatical classes. To test this proposal, we analyze child-directed speech from seven typologically diverse languages to simulate maximum variation in the structures of the world's languages. We ask whether the input to children contains cues for assigning syntactic categories in frequent frames, which are frequently occurring nonadjacent sequences of words or morphemes. In accord with aggregated results from previous studies on individual languages, we find that frequent word frames do not provide a robust distributional pattern for accurately predicting grammatical categories. However, our results show that frames are extremely accurate cues cross-linguistically at the morpheme level. We theorize that the nonadjacent dependency pattern captured by frequent frames is a universal anchor point for learners on the morphological level to detect and categorize grammatical categories. Whether frames also play a role on higher linguistic levels such as words is determined by grammatical features of the individual language. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Cloning and characterization of the metE gene encoding S-adenosylmethionine synthetase from Bacillus subtilis.

PubMed Central

Yocum, R R; Perkins, J B; Howitt, C L; Pero, J

1996-01-01

The metE gene, encoding S-adenosylmethionine synthetase (EC 2.5.1.6) from Bacillus subtilis, was cloned in two steps by normal and inverse PCR. The DNA sequence of the metE gene contains an open reading frame which encodes a 400-amino-acid sequence that is homologous to other known S-adenosylmethionine synthetases. The cloned gene complements the metE1 mutation and integrates at or near the chromosomal site of metE1. Expression of S-adenosylmethionine synthetase is reduced by only a factor of about 2 by exogenous methioinine. Overproduction of S-adenosylmethionine synthetase from a strong constitutive promoter leads to methionine auxotrophy in B. subtilis, suggesting that S-adenosylmethionine is a corepressor of methionine biosynthesis in B. subtilis, as others have already shown for Escherichia coli. PMID:8755891

Cloning and characterization of the metE gene encoding S-adenosylmethionine synthetase from Bacillus subtilis.

PubMed

Yocum, R R; Perkins, J B; Howitt, C L; Pero, J

1996-08-01

The metE gene, encoding S-adenosylmethionine synthetase (EC 2.5.1.6) from Bacillus subtilis, was cloned in two steps by normal and inverse PCR. The DNA sequence of the metE gene contains an open reading frame which encodes a 400-amino-acid sequence that is homologous to other known S-adenosylmethionine synthetases. The cloned gene complements the metE1 mutation and integrates at or near the chromosomal site of metE1. Expression of S-adenosylmethionine synthetase is reduced by only a factor of about 2 by exogenous methioinine. Overproduction of S-adenosylmethionine synthetase from a strong constitutive promoter leads to methionine auxotrophy in B. subtilis, suggesting that S-adenosylmethionine is a corepressor of methionine biosynthesis in B. subtilis, as others have already shown for Escherichia coli.

The Status of Exon Skipping as a Therapeutic Approach to Duchenne Muscular Dystrophy

PubMed Central

Lu, Qi-Long; Yokota, Toshifumi; Takeda, Shin'ichi; Garcia, Luis; Muntoni, Francesco; Partridge, Terence

2011-01-01

Duchenne muscular dystrophy (DMD) is associated with mutations in the dystrophin gene that disrupt the open reading frame whereas the milder Becker's form is associated with mutations which leave an in-frame mRNA transcript that can be translated into a protein that includes the N- and C- terminal functional domains. It has been shown that by excluding specific exons at, or adjacent to, frame-shifting mutations, open reading frame can be restored to an out-of-frame mRNA, leading to the production of a partially functional Becker-like dystrophin protein. Such targeted exclusion can be achieved by administration of oligonucleotides that are complementary to sequences that are crucial to normal splicing of the exon into the transcript. This principle has been validated in mouse and canine models of DMD with a number of variants of oligonucleotide analogue chemistries and by transduction with adeno-associated virus (AAV)-small nuclear RNA (snRNA) reagents encoding the antisense sequence. Two different oligonucleotide agents are now being investigated in human trials for splicing out of exon 51 with some early indications of success at the biochemical level. PMID:20978473

Cas9 in Genetically Modified Food Is Unlikely to Cause Food Allergy.

PubMed

Nakajima, Osamu; Nishimaki-Mogami, Tomoko; Kondo, Kazunari

2016-01-01

Genome editing has undergone rapid development during the last three years. It is anticipated that genetically modified organisms (GMOs) for food purposes will be widely produced using the clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR)/Cas9 system in the near future. However, the Cas9 gene may then enter the genomes of GMOs for food if the breeding process is not strictly managed, which could lead to the Cas9 protein or associated peptides being produced within these organisms. A variety of peptides could theoretically be produced from the Cas9 gene by using open reading frames different from that of Cas9 in the GMOs. In this study, Cas9 and the peptides potentially encoded by Cas9 genes were studied regarding their immunogenicity, in terms of the digestibility of Cas9 and the homology of the peptides to food allergens. First, the digestibility and thermal stability of Cas9 were studied. Digestibility was tested with natural or heat-denatured Cas9 in simulated gastric fluid in vitro. The two types of Cas9 were digested rapidly. Cas9 was also gradually degraded during heat treatment. Second, the peptides potentially encoded by Cas9 genes were examined for their homology to food allergens. Specifically, an 8-mer exact match search and a sliding 80-mer window search were performed using allergen databases. One of the peptides was found to have homology with a food allergen.

Plasma viral microRNA profiles reveal potential biomarkers for chronic active Epstein-Barr virus infection.

PubMed

Kawano, Yoshihiko; Iwata, Seiko; Kawada, Jun-ichi; Gotoh, Kensei; Suzuki, Michio; Torii, Yuka; Kojima, Seiji; Kimura, Hiroshi; Ito, Yoshinori

2013-09-01

Chronic active Epstein-Barr virus (CAEBV) infection has high mortality and morbidity, and biomarkers for disease severity and prognosis are required. MicroRNAs (miRNAs) are small noncoding RNAs, and EBV encodes multiple miRNAs. Because plasma contains sufficiently stable miRNAs, circulating EBV-associated miRNA profiles were investigated as novel biomarkers in CAEBV infection. Plasma miRNA expression was assessed for 12 miRNAs encoded within 2 EBV open reading frames (BART and BHRF). Expression levels were investigated in 19 patients with CAEBV infection, 14 patients with infectious mononucleosis, and 11 healthy controls. Relative expression levels of plasma miRNAs were determined by TaqMan probe-based quantitative assay. Plasma miR-BART1-5p, 2-5p, 5, and 22 levels in patients with CAEBV infection were significantly greater than those in patients with infectious mononucleosis and in controls. Plasma miR-BART2-5p, 4, 7, 13, 15, and 22 levels were significantly elevated in patients with CAEBV infection with systemic symptoms, compared with levels in patients with no systemic symptoms. The levels of miR-BART2-5p, 13, and 15 showed clinical cutoff values associated with specific clinical conditions, in contrast to plasma EBV loads. Levels of specific plasma EBV miRNAs were elevated differentially in patients with CAEBV infection. Several EBV miRNAs, particularly miR-BART2-5p, 13, and 15, are potentially biomarkers of disease severity or prognosis.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

2008-06-24

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S; Cabantous, Stephanie

2013-02-12

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

2011-06-14

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S.; Cabantous, Stephanie

2013-04-16

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Video Encryption and Decryption on Quantum Computers

NASA Astrophysics Data System (ADS)

Yan, Fei; Iliyasu, Abdullah M.; Venegas-Andraca, Salvador E.; Yang, Huamin

2015-08-01

A method for video encryption and decryption on quantum computers is proposed based on color information transformations on each frame encoding the content of the encoding the content of the video. The proposed method provides a flexible operation to encrypt quantum video by means of the quantum measurement in order to enhance the security of the video. To validate the proposed approach, a tetris tile-matching puzzle game video is utilized in the experimental simulations. The results obtained suggest that the proposed method enhances the security and speed of quantum video encryption and decryption, both properties required for secure transmission and sharing of video content in quantum communication.

Egocentric and allocentric representations in auditory cortex

PubMed Central

Brimijoin, W. Owen; Bizley, Jennifer K.

2017-01-01

A key function of the brain is to provide a stable representation of an object’s location in the world. In hearing, sound azimuth and elevation are encoded by neurons throughout the auditory system, and auditory cortex is necessary for sound localization. However, the coordinate frame in which neurons represent sound space remains undefined: classical spatial receptive fields in head-fixed subjects can be explained either by sensitivity to sound source location relative to the head (egocentric) or relative to the world (allocentric encoding). This coordinate frame ambiguity can be resolved by studying freely moving subjects; here we recorded spatial receptive fields in the auditory cortex of freely moving ferrets. We found that most spatially tuned neurons represented sound source location relative to the head across changes in head position and direction. In addition, we also recorded a small number of neurons in which sound location was represented in a world-centered coordinate frame. We used measurements of spatial tuning across changes in head position and direction to explore the influence of sound source distance and speed of head movement on auditory cortical activity and spatial tuning. Modulation depth of spatial tuning increased with distance for egocentric but not allocentric units, whereas, for both populations, modulation was stronger at faster movement speeds. Our findings suggest that early auditory cortex primarily represents sound source location relative to ourselves but that a minority of cells can represent sound location in the world independent of our own position. PMID:28617796

Expression of Human Hemojuvelin (HJV) Is Tightly Regulated by Two Upstream Open Reading Frames in HJV mRNA That Respond to Iron Overload in Hepatic Cells

PubMed Central

Onofre, Cláudia; Tomé, Filipa; Barbosa, Cristina; Silva, Ana Luísa

2015-01-01

The gene encoding human hemojuvelin (HJV) is one of the genes that, when mutated, can cause juvenile hemochromatosis, an early-onset inherited disorder associated with iron overload. The 5′ untranslated region of the human HJV mRNA has two upstream open reading frames (uORFs), with 28 and 19 codons formed by two upstream AUGs (uAUGs) sharing the same in-frame stop codon. Here we show that these uORFs decrease the translational efficiency of the downstream main ORF in HeLa and HepG2 cells. Indeed, ribosomal access to the main AUG is conditioned by the strong uAUG context, which results in the first uORF being translated most frequently. The reach of the main ORF is then achieved by ribosomes that resume scanning after uORF translation. Furthermore, the amino acid sequences of the uORF-encoded peptides also reinforce the translational repression of the main ORF. Interestingly, when iron levels increase, translational repression is relieved specifically in hepatic cells. The upregulation of protein levels occurs along with phosphorylation of the eukaryotic initiation factor 2α. Nevertheless, our results support a model in which the increasing recognition of the main AUG is mediated by a tissue-specific factor that promotes uORF bypass. These results support a tight HJV translational regulation involved in iron homeostasis. PMID:25666510

Functional characterization of the triple gene block 1 (TGB1) gene of Pepino mosaic virus in tomato

USDA-ARS?s Scientific Manuscript database

Pepino mosaic virus (PepMV) has caused serious economic losses to many greenhouse tomato productions around the world. This potexvirus genome contains five major open reading frames (ORFs) encoding for a 164-kDa RNA-dependent RNA polymerase (RdRp), three triple gene block (TGB) proteins of 26, 14 an...

Complete genome sequence of Paris mosaic necrosis virus, a distinct member of the genus Potyvirus

USDA-ARS?s Scientific Manuscript database

The complete genomic sequence of a novel potyvirus was determined from Paris polyphylla var. yunnanensis. Its genomic RNA consists of 9,660 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing a single open reading frame (ORF) encoding a large polyprotein. The virus shares 52.1-69.7%...

Whole-genome sequence of “Candidatus Liberibacter solanacearum” strain R1 from California

USDA-ARS?s Scientific Manuscript database

The draft whole-genome sequence of “Candidatus Liberibacter solanacearum” strain R1, isolated from a tomato plant in California, United States, is reported. The R1 strain genome is 1,204,257 bp in size (G+C content of 35.3%), encoding 1,101 open reading frames and 57 RNA genes....

PRIMARY STRUCTURE OF THE CYTOCHROME P450 LANOSTEROL 14A-DEMETHYLASE GENE FROM CANDIDA TROPICALIS

EPA Science Inventory

We report the nucleotide sequence of the gene and flanking DNA for the cytochrome P450 lanosterol 14 alpha-demethylase (14DM) from the yeast Candida tropicalis ATCC750. An open reading frame (ORF) of 528 codons encoding a 60.9-kD protein is identified. This ORF includes a charact...

Expression and strain variation of the novel “Small Open Reading Frame” 3 (smorf) multigene family in Babesia bovis

USDA-ARS?s Scientific Manuscript database

Small open reading frame (smorf) genes comprise the second largest Babesia bovis multigene family. All known 44 variant smorf genes are located in close chromosomal proximity to ves1 genes, which encode proteins that mediate cytoadhesion and contribute to immune evasion. In this study, we characte...

Syntax "and" Semantics: A Teaching Model.

ERIC Educational Resources Information Center

Wolfe, Frank

In translating perception into written language, a child must learn an encoding process which is a continuation of the process of improving sensing of the world around him or her. To verbalize an object (a perception) we use frames which name a referent, locate the referent in space and time, identify its appearance and behavior, and define terms…

Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications

USDA-ARS?s Scientific Manuscript database

The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-based clones to expres...

A draft genome sequence of “Candidatus Liberibacter asiaticus” from California, USA

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain HHCA, collected from a lemon tree in California, USA, is reported. The HHCA strain has a genome size of 1,118,244 bp, with G+C content of 36.6%. The HHCA genome encodes 1,191 predicted open reading frames and 51 RNA genes....

LMOf2365_0442 encoding for a fructose specific PTS permease IIA may Be required for virulence in L. monocytogenes Strain F2365

USDA-ARS?s Scientific Manuscript database

Listeria monocytogenes is a foodborne pathogen that causes listeriosis, which is a major public health concern due to the high fatality rate. The Phosphotransferase Transport System (PTS) is responsible for sugar transport. In previous studies, in-frame deletion mutants of a putative fructose-spec...

Molecular Characterization of Mosquitocidal Toxin (Surface Layer Protein, SLP) from Bacillus cereus VCRC B540.

PubMed

Mani, Chinnasamy; Selvakumari, Jeyaperumal; Han, YeonSoo; Jo, YongHun; Thirugnanasambantham, Krishnaraj; Sundarapandian, Somaiah; Poopathi, Subbiah

2018-04-01

A marine Bacillus cereus (VCRC B540) with mosquitocidal effect was recently reported from red snapper fish (Lutjanus sanguineous) gut and surface layer protein (S-layer protein, SLP) was reported to be mosquito larvicidal factor. In this present study, the gene encoding the surface layer protein was amplified from the genomic DNA and functionally characterized. Amplification of SLP-encoding gene revealed 1,518 bp PCR product, and analysis of the sequence revealed the presence of 1482 bp open reading frame with coding capacity for a polypeptide of 493 amino acids. Phylogenetic analysis revealed with homology among closely related Bacillus cereus groups of organisms as well as Bacillus strains. Removal of nucleotides encoding signaling peptide revealed the functional cloning fragment of length 1398 bp. Theoretical molecular weight (51.7 kDa) and isoelectric point (5.99) of the deduced functional SLP protein were predicted using ProtParam. The amplified PCR product was cloned into a plasmid vector (pGEM-T), and the open reading frame free off signaling peptide was subsequently cloned inpET-28a(+) and expressed in Escherichia coli BL21 (DE3). The isopropyl-β-D-thiogalactopyranoside (IPTG)-induced recombinant SLP was confirmed using western blotting, and functional SLP revealed mosquito larvicidal property. Therefore, the major findings revealed that SLP is a factor responsible for mosquitocidal activity, and the molecular characterization of this toxin was extensively studied.

Open reading frame 5 (ORF5), encoding a ferredoxinlike protein, and nifQ are cotranscribed with nifE, nifN, nifX, and ORF4 in Rhodobacter capsulatus.

PubMed Central

Moreno-Vivian, C; Hennecke, S; Pühler, A; Klipp, W

1989-01-01

DNA sequence analysis of a 1,600-base-pair fragment located downstream of nifENX in nif region A of Rhodobacter capsulatus revealed two additional open reading frames (ORFs): ORF5, encoding a ferredoxinlike protein, and nifQ. The ferredoxinlike gene product contained two cysteine motifs, typical of ferredoxins coordinating two 4Fe-4S clusters, but the distance between these two motifs was unusual for low-molecular-weight ferredoxins. The R. capsulatus nifQ gene product shared a high degree of homology with Klebsiella pneumoniae and Azotobacter vinelandii NifQ, including a typical cysteine motif located in the C-terminal part. nifQ insertion mutants and also an ORF5-nifQ double deletion mutant showed normal diazotrophic growth only in the presence of high concentrations of molybdate. This demonstrated that the gene encoding the ferredoxinlike protein is not essential for nitrogen fixation. No NifA-activated consensus promoter could be found in the intergenic region between nifENX-ORF4 and ORF5-nifQ. Analyses of a nifQ-lacZYA fusion revealed that transcription of nifQ was initiated at a promoter in front of nifE. In contrast to other nitrogen-fixing organisms, R. capsulatus nifE, nifN, nifX, ORF4, ORF5, and nifQ were organized in one transcriptional unit. PMID:2708314

Characterisation of IS153, an IS3-family insertion sequence isolated from Lactobacillus sanfranciscensis and its use for strain differentiation.

PubMed

Ehrmann, M A; Vogel, R E

2001-11-01

An insertion sequence has been identified in the genome of Lactobacillus sanfranciscensis DSM 20451T as segment of 1351 nucleotides containing 37-bp imperfect terminal inverted repeats. The sequence of this element encodes two out of phase, overlapping open reading frames, orfA and orfB, from which three putative proteins are produced. OrfAB is a transframe protein produced by -1 translational frame shifting between orf A and orf B that is presumed to be the transposase. The large orfAB of this element encodes a 342 amino acid protein that displays similarities with transposases encoded by bacterial insertion sequences belonging to the IS3 family. In L. sanfranciscensis type strain DSM 20451T multiple truncated IS elements were identified. Inverse PCR was used to analyze target sites of four of these elements, but except of their highly AT rich character not any sequence specificity was identified so far. Moreover, no flanking direct repeats were identified. Multiple copies of IS153 were detected by hybridization in other strains of L. sanfranciscensis. Resulting hybridization patterns were shown to differentiate between organisms at strain level rather than a probe targeted against the 16S rDNA. With a PCR based approach IS153 or highly similar sequences were detected in L. acidophilus, L. casei, L. malefermentans, L. plantarum, L. hilgardii, L. collinoides L. farciminis L. sakei and L. salivarius, L. reuteri as well as in Enterococcus faecium, Pediococcus acidilactici and P. pentosaceus.

Efficient Encoding and Rendering of Time-Varying Volume Data

NASA Technical Reports Server (NTRS)

Ma, Kwan-Liu; Smith, Diann; Shih, Ming-Yun; Shen, Han-Wei

1998-01-01

Visualization of time-varying volumetric data sets, which may be obtained from numerical simulations or sensing instruments, provides scientists insights into the detailed dynamics of the phenomenon under study. This paper describes a coherent solution based on quantization, coupled with octree and difference encoding for visualizing time-varying volumetric data. Quantization is used to attain voxel-level compression and may have a significant influence on the performance of the subsequent encoding and visualization steps. Octree encoding is used for spatial domain compression, and difference encoding for temporal domain compression. In essence, neighboring voxels may be fused into macro voxels if they have similar values, and subtrees at consecutive time steps may be merged if they are identical. The software rendering process is tailored according to the tree structures and the volume visualization process. With the tree representation, selective rendering may be performed very efficiently. Additionally, the I/O costs are reduced. With these combined savings, a higher level of user interactivity is achieved. We have studied a variety of time-varying volume datasets, performed encoding based on data statistics, and optimized the rendering calculations wherever possible. Preliminary tests on workstations have shown in many cases tremendous reduction by as high as 90% in both storage space and inter-frame delay.

Identification of the cleavage sites of the RNA2-encoded polyproteins for two members of the genus Torradovirus by N-terminal sequencing of the virion capsid proteins.

PubMed

Ferriol, I; Silva Junior, D M; Nigg, J C; Zamora-Macorra, E J; Falk, B W

2016-11-01

Torradoviruses, family Secoviridae, are emergent bipartite RNA plant viruses. RNA1 is ca. 7kb and has one open reading frame (ORF) encoding for the protease, helicase and RNA-dependent RNA polymerase (RdRp). RNA2 is ca. 5kb and has two ORFs. RNA2-ORF1 encodes for a putative protein with unknown function(s). RNA2-ORF2 encodes for a putative movement protein and three capsid proteins. Little is known about the replication and polyprotein processing strategies of torradoviruses. Here, the cleavage sites in the RNA2-ORF2-encoded polyproteins of two torradoviruses, Tomato marchitez virus isolate M (ToMarV-M) and tomato chocolate spot virus, were determined by N-terminal sequencing, revealing that the amino acid (aa) at the -1 position of the cleavage sites is a glutamine. Multiple aa sequence comparison confirmed that this glutamine is conserved among other torradoviruses. Finally, site-directed mutagenesis of conserved aas in the ToMarV-M RdRp and protease prevented substantial accumulation of viral coat proteins or RNAs. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification and characterization of the gltK gene encoding a membrane-associated glucose transport protein of pseudomonas aeruginosa.

PubMed

Adewoye, L O; Worobec, E A

2000-08-08

The Pseudomonas aeruginosa oprB gene encodes the carbohydrate-selective OprB porin, which translocates substrate molecules across the outer membrane to the periplasmic glucose-binding protein. We identified and cloned two open reading frames (ORFs) flanking the oprB gene but are not in operonic arrangement with the oprB gene. The downstream ORF encodes a putative polypeptide homologous to members of a family of transcriptional repressors, whereas the oprB gene is preceded by an ORF encoding a putative product, which exhibits strong homology to several carbohydrate transport ATP-binding cassette (ABC) proteins. The genomic copy of the upstream ORF was mutagenized by homologous recombination. Analysis of the deletion mutant in comparison with the wild type revealed a significant reduction in [14C] glucose transport activity in the mutant strain, suggesting that this ORF likely encodes the inner membrane component of the glucose ABC transporter. It is thus designated gltK gene to reflect its homology to the Pseudomona fluorescens mtlK and its involvement in the high-affinity glucose transport system. Multiple alignment analysis revealed that the P. aeruginosa gltK gene product is a member of the MalK subfamily of ABC proteins.

Reengineering a transmembrane protein to treat muscular dystrophy using exon skipping.

PubMed

Gao, Quan Q; Wyatt, Eugene; Goldstein, Jeff A; LoPresti, Peter; Castillo, Lisa M; Gazda, Alec; Petrossian, Natalie; Earley, Judy U; Hadhazy, Michele; Barefield, David Y; Demonbreun, Alexis R; Bönnemann, Carsten; Wolf, Matthew; McNally, Elizabeth M

2015-11-02

Exon skipping uses antisense oligonucleotides as a treatment for genetic diseases. The antisense oligonucleotides used for exon skipping are designed to bypass premature stop codons in the target RNA and restore reading frame disruption. Exon skipping is currently being tested in humans with dystrophin gene mutations who have Duchenne muscular dystrophy. For Duchenne muscular dystrophy, the rationale for exon skipping derived from observations in patients with naturally occurring dystrophin gene mutations that generated internally deleted but partially functional dystrophin proteins. We have now expanded the potential for exon skipping by testing whether an internal, in-frame truncation of a transmembrane protein γ-sarcoglycan is functional. We generated an internally truncated γ-sarcoglycan protein that we have termed Mini-Gamma by deleting a large portion of the extracellular domain. Mini-Gamma provided functional and pathological benefits to correct the loss of γ-sarcoglycan in a Drosophila model, in heterologous cell expression studies, and in transgenic mice lacking γ-sarcoglycan. We generated a cellular model of human muscle disease and showed that multiple exon skipping could be induced in RNA that encodes a mutant human γ-sarcoglycan. Since Mini-Gamma represents removal of 4 of the 7 coding exons in γ-sarcoglycan, this approach provides a viable strategy to treat the majority of patients with γ-sarcoglycan gene mutations.

Reengineering a transmembrane protein to treat muscular dystrophy using exon skipping

PubMed Central

Gao, Quan Q.; Wyatt, Eugene; Goldstein, Jeff A.; LoPresti, Peter; Castillo, Lisa M.; Gazda, Alec; Petrossian, Natalie; Earley, Judy U.; Hadhazy, Michele; Barefield, David Y.; Demonbreun, Alexis R.; Bönnemann, Carsten; Wolf, Matthew; McNally, Elizabeth M.

2015-01-01

Exon skipping uses antisense oligonucleotides as a treatment for genetic diseases. The antisense oligonucleotides used for exon skipping are designed to bypass premature stop codons in the target RNA and restore reading frame disruption. Exon skipping is currently being tested in humans with dystrophin gene mutations who have Duchenne muscular dystrophy. For Duchenne muscular dystrophy, the rationale for exon skipping derived from observations in patients with naturally occurring dystrophin gene mutations that generated internally deleted but partially functional dystrophin proteins. We have now expanded the potential for exon skipping by testing whether an internal, in-frame truncation of a transmembrane protein γ-sarcoglycan is functional. We generated an internally truncated γ-sarcoglycan protein that we have termed Mini-Gamma by deleting a large portion of the extracellular domain. Mini-Gamma provided functional and pathological benefits to correct the loss of γ-sarcoglycan in a Drosophila model, in heterologous cell expression studies, and in transgenic mice lacking γ-sarcoglycan. We generated a cellular model of human muscle disease and showed that multiple exon skipping could be induced in RNA that encodes a mutant human γ-sarcoglycan. Since Mini-Gamma represents removal of 4 of the 7 coding exons in γ-sarcoglycan, this approach provides a viable strategy to treat the majority of patients with γ-sarcoglycan gene mutations. PMID:26457733

Equilibrium theory for braided elastic filaments

NASA Astrophysics Data System (ADS)

van der Heijden, Gert

Motivated by supercoiling of DNA and other filamentous structures, we formulate a theory for equilibria of 2-braids, i.e., structures formed by two elastic rods winding around each other in continuous contact and subject to a local interstrand interaction. Unlike in previous work no assumption is made on the shape of the contact curve. Rather, this shape is found as part of the solution. The theory is developed in terms of a moving frame of directors attached to one of the strands with one of the directors pointing to the position of the other strand. The constant-distance constraint is automatically satisfied by the introduction of what we call braid strains. The price we pay is that the potential energy involves arclength derivatives of these strains, thus giving rise to a second-order variational problem. The Euler-Lagrange equations for this problem give balance equations for the overall braid force and moment referred to the moving frame as well as differential equations that can be interpreted as effective constitutive relations encoding the effect that the second strand has on the first as the braid deforms under the action of end loads. Simple analytical cases are discussed first and used as starting solutions in parameter continuation studies to compute classes of both open and closed (linked or knotted) braid solutions.

Theory of equilibria of elastic braids with applications to DNA supercoiling

NASA Astrophysics Data System (ADS)

van der Heijden, Gert; Starostin, Eugene

2014-03-01

Motivated by supercoiling of DNA and other filamentous structures, we formulate a new theory for equilibria of 2-braids, i.e., structures formed by two elastic rods winding around each other in continuous contact and subject to a local interstrand interaction. Unlike in previous work no assumption is made on the shape of the contact curve. Rather, this shape is solved for. The theory is developed in terms of a moving frame of directors attached to one of the strands with one of the directors pointing to the position of the other strand. The constant-distance constraint is automatically satisfied by the introduction of what we call braid strains. The price we pay is that the potential energy involves arclength derivatives of these strains, thus giving rise to a second-order variational problem. The Euler-Lagrange equations for this problem give balance equations for the overall braid force and moment referred to the moving frame as well as differential equations that can be interpreted as effective constitutive relations encoding the effect that the second strand has on the first as the braid deforms under the action of end loads. Both open braid and closed braid solutions (links and knots) are computed and current applications to DNA supercoiling are discussed. Research supported by EPSRC and HFSP.

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius.

PubMed

Johnston, Christopher D; Bannantine, John P; Govender, Rodney; Endersen, Lorraine; Pletzer, Daniel; Weingart, Helge; Coffey, Aidan; O'Mahony, Jim; Sleator, Roy D

2014-01-01

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease.

An electrophysiological investigation of memory encoding, depth of processing, and word frequency in humans.

PubMed

Guo, Chunyan; Zhu, Ying; Ding, Jinhong; Fan, Silu; Paller, Ken A

2004-02-12

Memory encoding can be studied by monitoring brain activity correlated with subsequent remembering. To understand brain potentials associated with encoding, we compared multiple factors known to affect encoding. Depth of processing was manipulated by requiring subjects to detect animal names (deep encoding) or boldface (shallow encoding) in a series of Chinese words. Recognition was more accurate with deep than shallow encoding, and for low- compared to high-frequency words. Potentials were generally more positive for subsequently recognized versus forgotten words; for deep compared to shallow processing; and, for remembered words only, for low- than for high-frequency words. Latency and topographic differences between these potentials suggested that several factors influence the effectiveness of encoding and can be distinguished using these methods, even with Chinese logographic symbols.

The complete nucleotide sequence and genome organization of a novel betaflexivirus infecting Citrullus lanatus.

PubMed

Xin, Min; Zhang, Peipei; Liu, Wenwen; Ren, Yingdang; Cao, Mengji; Wang, Xifeng

2017-10-01

The complete nucleotide sequence of a novel positive single-stranded (+ss) RNA virus, tentatively named watermelon virus A (WVA), was determined using a combination of three methods: RNA sequencing, small RNA sequencing, and Sanger sequencing. The full genome of WVA is comprised of 8,372 nucleotides (nt), excluding the poly (A) tail, and contains four open reading frames (ORFs). The largest ORF, ORF1 encodes a putative replication-associated polyprotein (RP) with three conserved domains. ORF2 and ORF4 encode a movement protein (MP) and coat protein (CP), respectively. The putative product encoded by ORF3, of an estimated molecular mass of 25 kDa, has no significant similarity with other proteins. Identity and phylogenetic analysis indicate that WVA is a new virus, closely related to members of the family Betaflexiviridae. However, the final taxonomic allocation of WVA within the family is yet to be determined.

Molecular cloning and characterization of an SRCAP chromatin remodeling homologue in Toxoplasma gondii.

PubMed

Sullivan, William J; Monroy, M Alexandra; Bohne, Wolfgang; Nallani, Karuna C; Chrivia, John; Yaciuk, Peter; Smith, Charles K; Queener, Sherry F

2003-05-01

We have identified and mapped a gene in Toxoplasma gondii that encodes a homologue of SRCAP (Snf2-related CBP activator protein), a member of the SNF/SWI family of chromatin remodeling factors. The genomic locus (TgSRCAP) is present as a single copy and contains 16 introns. The predicted cDNA contains an open reading frame of 8,775 bp and encodes a protein of 2,924 amino acids. We have identified additional SRCAP-like sequences in Apicomplexa for comparison by screening genomic databases. An analysis of SRCAP homologues between species reveals signature features that may be indicative of SRCAP members. Expression of mRNA encoding TgSRCAP is upregulated when tachyzoite (invasive form) parasites are induced to differentiate into bradyzoites (encysted form) in vitro. Recombinant TgSRCAP protein is functionally equivalent to the human homologue, being capable of increasing transcription mediated by CREB.

Deep hierarchical attention network for video description

NASA Astrophysics Data System (ADS)

Li, Shuohao; Tang, Min; Zhang, Jun

2018-03-01

Pairing video to natural language description remains a challenge in computer vision and machine translation. Inspired by image description, which uses an encoder-decoder model for reducing visual scene into a single sentence, we propose a deep hierarchical attention network for video description. The proposed model uses convolutional neural network (CNN) and bidirectional LSTM network as encoders while a hierarchical attention network is used as the decoder. Compared to encoder-decoder models used in video description, the bidirectional LSTM network can capture the temporal structure among video frames. Moreover, the hierarchical attention network has an advantage over single-layer attention network on global context modeling. To make a fair comparison with other methods, we evaluate the proposed architecture with different types of CNN structures and decoders. Experimental results on the standard datasets show that our model has a more superior performance than the state-of-the-art techniques.

Spatial reference frames of visual, vestibular, and multimodal heading signals in the dorsal subdivision of the medial superior temporal area.

PubMed

Fetsch, Christopher R; Wang, Sentao; Gu, Yong; Deangelis, Gregory C; Angelaki, Dora E

2007-01-17

Heading perception is a complex task that generally requires the integration of visual and vestibular cues. This sensory integration is complicated by the fact that these two modalities encode motion in distinct spatial reference frames (visual, eye-centered; vestibular, head-centered). Visual and vestibular heading signals converge in the primate dorsal subdivision of the medial superior temporal area (MSTd), a region thought to contribute to heading perception, but the reference frames of these signals remain unknown. We measured the heading tuning of MSTd neurons by presenting optic flow (visual condition), inertial motion (vestibular condition), or a congruent combination of both cues (combined condition). Static eye position was varied from trial to trial to determine the reference frame of tuning (eye-centered, head-centered, or intermediate). We found that tuning for optic flow was predominantly eye-centered, whereas tuning for inertial motion was intermediate but closer to head-centered. Reference frames in the two unimodal conditions were rarely matched in single neurons and uncorrelated across the population. Notably, reference frames in the combined condition varied as a function of the relative strength and spatial congruency of visual and vestibular tuning. This represents the first investigation of spatial reference frames in a naturalistic, multimodal condition in which cues may be integrated to improve perceptual performance. Our results compare favorably with the predictions of a recent neural network model that uses a recurrent architecture to perform optimal cue integration, suggesting that the brain could use a similar computational strategy to integrate sensory signals expressed in distinct frames of reference.

Processing Interrogative Sentence Mood at the Semantic-Syntactic Interface: An Electrophysiological Research in Chinese, German, and Polish

PubMed Central

Kao, Chung-Shan; Dietrich, Rainer; Sommer, Werner

2010-01-01

Background Languages differ in the marking of the sentence mood of a polar interrogative (yes/no question). For instance, the interrogative mood is marked at the beginning of the surface structure in Polish, whereas the marker appears at the end in Chinese. In order to generate the corresponding sentence frame, the syntactic specification of the interrogative mood is early in Polish and late in Chinese. In this respect, German belongs to an interesting intermediate class. The yes/no question is expressed by a shift of the finite verb from its final position in the underlying structure into the utterance initial position, a move affecting, hence, both the sentence's final and the sentence's initial constituents. The present study aimed to investigate whether during generation of the semantic structure of a polar interrogative, i.e., the processing preceding the grammatical formulation, the interrogative mood is encoded according to its position in the syntactic structure at distinctive time points in Chinese, German, and Polish. Methodology/Principal Findings In a two-choice go/nogo experimental design, native speakers of the three languages responded to pictures by pressing buttons and producing utterances in their native language while their brain potentials were recorded. The emergence and latency of lateralized readiness potentials (LRP) in nogo conditions, in which speakers asked a yes/no question, should indicate the time point of processing the interrogative mood. The results revealed that Chinese, German, and Polish native speakers did not differ from each other in the electrophysiological indicator. Conclusions/Significance The findings suggest that the semantic encoding of the interrogative mood is temporally consistent across languages despite its disparate syntactic specification. The consistent encoding may be ascribed to economic processing of interrogative moods at various sentential positions of the syntactic structures in languages or, more generally, to the overarching status of sentence mood in the semantic structure. PMID:20927373

System and method for forward error correction

NASA Technical Reports Server (NTRS)

Cole, Robert M. (Inventor); Bishop, James E. (Inventor)

2006-01-01

A system and method are provided for transferring a packet across a data link. The packet may include a stream of data symbols which is delimited by one or more framing symbols. Corruptions of the framing symbol which result in valid data symbols may be mapped to invalid symbols. If it is desired to transfer one of the valid data symbols that has been mapped to an invalid symbol, the data symbol may be replaced with an unused symbol. At the receiving end, these unused symbols are replaced with the corresponding valid data symbols. The data stream of the packet may be encoded with forward error correction information to detect and correct errors in the data stream.

System and method for transferring data on a data link

NASA Technical Reports Server (NTRS)

Cole, Robert M. (Inventor); Bishop, James E. (Inventor)

2007-01-01

A system and method are provided for transferring a packet across a data link. The packet may include a stream of data symbols which is delimited by one or more framing symbols. Corruptions of the framing symbol which result in valid data symbols may be mapped to invalid symbols. If it is desired to transfer one of the valid data symbols that has been mapped to an invalid symbol, the data symbol may be replaced with an unused symbol. At the receiving end, these unused symbols are replaced with the corresponding valid data symbols. The data stream of the packet may be encoded with forward error correction information to detect and correct errors in the data stream.

The bag-of-frames approach: A not so sufficient model for urban soundscapes.

PubMed

Lagrange, Mathieu; Lafay, Grégoire; Défréville, Boris; Aucouturier, Jean-Julien

2015-11-01

The "bag-of-frames" (BOF) approach, which encodes audio signals as the long-term statistical distribution of short-term spectral features, is commonly regarded as an effective and sufficient way to represent environmental sound recordings (soundscapes). The present paper describes a conceptual replication of a use of the BOF approach in a seminal article using several other soundscape datasets, with results strongly questioning the adequacy of the BOF approach for the task. As demonstrated in this paper, the good accuracy originally reported with BOF likely resulted from a particularly permissive dataset with low within-class variability. Soundscape modeling, therefore, may not be the closed case it was once thought to be.

LMOf2365_0442 Encoding for a Fructose Specific PTS Permease IIA May Be Required for Virulence in L. monocytogenes Strain F2365

PubMed Central

Liu, Yanhong; Yoo, Brian B.; Hwang, Cheng-An; Suo, Yujuan; Sheen, Shiowshuh; Khosravi, Parvaneh; Huang, Lihan

2017-01-01

Listeria monocytogenes is a foodborne pathogen that causes listeriosis, which is a major public health concern due to the high fatality rate. LMOf2365_0442, 0443, and 0444 encode for fructose-specific EIIABC components of phosphotransferase transport system (PTS) permease that is responsible for sugar transport. In previous studies, in-frame deletion mutants of a putative fructose-specific PTS permease (LMOf2365_0442, 0443, and 0444) were constructed and analyzed. However, the virulence potential of these deletion mutants has not been studied. In this study, two in vitro methods were used to analyze the virulence potential of these L. monocytogenes deletion mutants. First, invasion assays were used to measure the invasion efficiencies to host cells using the human HT-29 cell line. Second, plaque forming assays were used to measure cell-to-cell spread in host cells. Our results showed that the deletion mutant ΔLMOf2365_0442 had reduced invasion and cell-to-cell spread efficiencies in human cell line compared to the parental strain LMOf2365, indicating that LMOf2365_0442 encoding for a fructose specific PTS permease IIA may be required for virulence in L. monocytogenes strain F2365. In addition, the gene expression levels of 15 virulence and stress-related genes were analyzed in the stationary phase cells of the deletion mutants using RT-PCR assays. Virulence-related gene expression levels were elevated in the deletion mutants ΔLMOf2365_0442-0444 compared to the wild type parental strain LMOf2365, indicating the down-regulation of virulence genes by this PTS permease in L. monocytogenes. Finally, stress-related gene clpC expression levels were also increased in all of the deletion mutants, suggesting the involvement of this PTS permease in stress response. Furthermore, these deletion mutants displayed the same pressure tolerance and the same capacity for biofilm formation compared to the wild-type parental strain LMOf2365. In summary, our findings suggest that the LMOf2365_0442 gene can be used as a potential target to develop inhibitors for new therapeutic and pathogen control strategies for public health. PMID:28900418

Plasmid-Encoded MCP Is Involved in Virulence, Motility, and Biofilm Formation of Cronobacter sakazakii ATCC 29544

PubMed Central

Choi, Younho; Kim, Seongok; Hwang, Hyelyeon; Kim, Kwang-Pyo; Kang, Dong-Hyun

2014-01-01

The aim of this study was to elucidate the function of the plasmid-borne mcp (methyl-accepting chemotaxis protein) gene, which plays pleiotropic roles in Cronobacter sakazakii ATCC 29544. By searching for virulence factors using a random transposon insertion mutant library, we identified and sequenced a new plasmid, pCSA2, in C. sakazakii ATCC 29544. An in silico analysis of pCSA2 revealed that it included six putative open reading frames, and one of them was mcp. The mcp mutant was defective for invasion into and adhesion to epithelial cells, and the virulence of the mcp mutant was attenuated in rat pups. In addition, we demonstrated that putative MCP regulates the motility of C. sakazakii, and the expression of the flagellar genes was enhanced in the absence of a functional mcp gene. Furthermore, a lack of the mcp gene also impaired the ability of C. sakazakii to form a biofilm. Our results demonstrate a regulatory role for MCP in diverse biological processes, including the virulence of C. sakazakii ATCC 29544. To the best of our knowledge, this study is the first to elucidate a potential function of a plasmid-encoded MCP homolog in the C. sakazakii sequence type 8 (ST8) lineage. PMID:25332122

Molecular Characterization of Lactobacillus plantarum Genes for β-Ketoacyl-Acyl Carrier Protein Synthase III (fabH) and Acetyl Coenzyme A Carboxylase (accBCDA), Which Are Essential for Fatty Acid Biosynthesis

PubMed Central

Kiatpapan, Pornpimon; Kobayashi, Hajime; Sakaguchi, Maki; Ono, Hisayo; Yamashita, Mitsuo; Kaneko, Yoshinobu; Murooka, Yoshikatsu

2001-01-01

Genes for subunits of acetyl coenzyme A carboxylase (ACC), which is the enzyme that catalyzes the first step in the synthesis of fatty acids in Lactobacillus plantarum L137, were cloned and characterized. We identified six potential open reading frames, namely, manB, fabH, accB, accC, accD, and accA, in that order. Nucleotide sequence analysis suggested that fabH encoded β-ketoacyl-acyl carrier protein synthase III, that the accB, accC, accD, and accA genes encoded biotin carboxyl carrier protein, biotin carboxylase, and the β and α subunits of carboxyltransferase, respectively, and that these genes were clustered. The organization of acc genes was different from that reported for Escherichia coli, for Bacillus subtilis, and for Pseudomonas aeruginosa. E. coli accB and accD mutations were complemented by the L. plantarum accB and accD genes, respectively. The predicted products of all five genes were confirmed by using the T7 expression system in E. coli. The gene product of accB was biotinylated in E. coli. Northern and primer extension analyses demonstrated that the five genes in L. plantarum were regulated polycistronically in an acc operon. PMID:11133475

Molecular cloning and characterization of novel phytocystatin gene from turmeric, Curcuma longa.

PubMed

Chan, Seow-Neng; Abu Bakar, Norliza; Mahmood, Maziah; Ho, Chai-Ling; Shaharuddin, Noor Azmi

2014-01-01

Phytocystatin, a type of protease inhibitor (PI), plays major roles in plant defense mechanisms and has been reported to show antipathogenic properties and plant stress tolerance. Recombinant plant PIs are gaining popularity as potential candidates in engineering of crop protection and in synthesizing medicine. It is therefore crucial to identify PI from novel sources like Curcuma longa as it is more effective in combating against pathogens due to its novelty. In this study, a novel cDNA fragment encoding phytocystatin was isolated using degenerate PCR primers, designed from consensus regions of phytocystatin from other plant species. A full-length cDNA of the phytocystatin gene, designated CypCl, was acquired using 5'/3' rapid amplification of cDNA ends method and it has been deposited in NCBI database (accession number KF545954.1). It has a 687 bp long open reading frame (ORF) which encodes 228 amino acids. BLAST result indicated that CypCl is similar to cystatin protease inhibitor from Cucumis sativus with 74% max identity. Sequence analysis showed that CypCl contains most of the motifs found in a cystatin, including a G residue, LARFAV-, QxVxG sequence, PW dipeptide, and SNSL sequence at C-terminal extension. Phylogenetic studies also showed that CypCl is related to phytocystatin from Elaeis guineensis.

Plasmid-encoded MCP is involved in virulence, motility, and biofilm formation of Cronobacter sakazakii ATCC 29544.

PubMed

Choi, Younho; Kim, Seongok; Hwang, Hyelyeon; Kim, Kwang-Pyo; Kang, Dong-Hyun; Ryu, Sangryeol

2015-01-01

The aim of this study was to elucidate the function of the plasmid-borne mcp (methyl-accepting chemotaxis protein) gene, which plays pleiotropic roles in Cronobacter sakazakii ATCC 29544. By searching for virulence factors using a random transposon insertion mutant library, we identified and sequenced a new plasmid, pCSA2, in C. sakazakii ATCC 29544. An in silico analysis of pCSA2 revealed that it included six putative open reading frames, and one of them was mcp. The mcp mutant was defective for invasion into and adhesion to epithelial cells, and the virulence of the mcp mutant was attenuated in rat pups. In addition, we demonstrated that putative MCP regulates the motility of C. sakazakii, and the expression of the flagellar genes was enhanced in the absence of a functional mcp gene. Furthermore, a lack of the mcp gene also impaired the ability of C. sakazakii to form a biofilm. Our results demonstrate a regulatory role for MCP in diverse biological processes, including the virulence of C. sakazakii ATCC 29544. To the best of our knowledge, this study is the first to elucidate a potential function of a plasmid-encoded MCP homolog in the C. sakazakii sequence type 8 (ST8) lineage. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Identification and characterization of a phospholipid scramblase encoded by planarian Dugesia japonica.

PubMed

Han, Yu; Li, Ao; Gao, Lili; Wu, Weiwei; Deng, Hongkuan; Hu, Wenjing; Li, Na; Sun, Shimin; Zhang, Xiufang; Zhao, Bosheng; Liu, Baohua; Pang, Qiuxiang

2017-02-20

Phospholipid scramblases (PLSCRs) are the conserved calcium-binding, type II transmembrane proteins synthesized in all eukaryotic organisms. In mammals, these proteins play essential roles in various physiological processes, especially in the immune responses. However, the existence of PLSCRs and their biological functions in planarian are still unknown at present. In this study, a new member of PLSCRs was identified in planarian Dugesia japonica (D. japonica), named DjPLSCR. The sequence analysis revealed that it contains an opening reading frame consisting of 726bp encoding a putative protein of 241 amino acids with a predicted molecular mass of ~28.7kDa and an isoelectric point of 6.21. Whole-mount in situ hybridization showed that mRNAs of DjPLSCR are predominantly expressed in adult and regenerative pharynx which is an important organ of immune system in planarians. Importantly, we found that the transcription level of DjPLSCR was significantly upregulated when planarians were stimulated with the pathogen-associated molecular patterns [polyinosinic-polycytidylic acid, lipopolysaccharide, peptidoglycan and β-glucan], suggesting that DjPLSCR is involved in the immune response upon pathogen invasion. Our findings provide the first experimental insights into the characteristics and potential functions of PLSCR in planarians. Copyright © 2016 Elsevier B.V. All rights reserved.

Nucleotide sequence and phylogenetic analysis of Cucurbit yellow stunting disorder virus RNA 2.

PubMed

Livieratos, Ioannis C; Coutts, Robert H A

2002-06-01

The complete nucleotide sequence of Cucurbit yellow stunting disorder virus (CYSDV) RNA 2, a whitefly (Bemisia tabaci)-transmitted closterovirus with a bi-partite genome, is reported. CYSDV RNA 2 is 7,281 nucleotides long and contains the closterovirus hallmark gene array with a similar arrangement to the prototype member of the genus Crinivirus, Lettuce infectious yellows virus (LIYV). CYSDV RNA 2 contains open reading frames (ORFs) potentially encoding in a 5' to 3' direction for proteins of 5 kDa (ORF 1; hydrophobic protein), 62 kDa (ORF 2; heat shock protein 70 homolog, HSP70h), 59 kDa (ORF 3; protein of unknown function), 9 kDa (ORF 4; protein of unknown function), 28.5 kDa (ORF 5; coat protein, CP), 53 kDa (ORF 6; coat protein minor, CPm), and 26.5 kDa (ORF 7; protein of unknown function). Pairwise comparisons of CYSDV RNA 2-encoded proteins (HSP70h, p59 and CPm) among the closteroviruses showed that CYSDV is closely related to LIYV. Phylogenetic analysis based on the amino acid sequence of the HSP70h, indicated that CYSDV clusters with other members of the genus Crinivirus, and it is related to Little cherry virus-1 (LChV-1), but is distinct from the aphid- or mealybug-transmitted closteroviruses.

Molecular Cloning and Characterization of Novel Phytocystatin Gene from Turmeric, Curcuma longa

PubMed Central

Chan, Seow-Neng; Abu Bakar, Norliza; Mahmood, Maziah; Ho, Chai-Ling

2014-01-01

Phytocystatin, a type of protease inhibitor (PI), plays major roles in plant defense mechanisms and has been reported to show antipathogenic properties and plant stress tolerance. Recombinant plant PIs are gaining popularity as potential candidates in engineering of crop protection and in synthesizing medicine. It is therefore crucial to identify PI from novel sources like Curcuma longa as it is more effective in combating against pathogens due to its novelty. In this study, a novel cDNA fragment encoding phytocystatin was isolated using degenerate PCR primers, designed from consensus regions of phytocystatin from other plant species. A full-length cDNA of the phytocystatin gene, designated CypCl, was acquired using 5′/3′ rapid amplification of cDNA ends method and it has been deposited in NCBI database (accession number KF545954.1). It has a 687 bp long open reading frame (ORF) which encodes 228 amino acids. BLAST result indicated that CypCl is similar to cystatin protease inhibitor from Cucumis sativus with 74% max identity. Sequence analysis showed that CypCl contains most of the motifs found in a cystatin, including a G residue, LARFAV-, QxVxG sequence, PW dipeptide, and SNSL sequence at C-terminal extension. Phylogenetic studies also showed that CypCl is related to phytocystatin from Elaeis guineensis. PMID:25853138

Open Reading Frame E3-10.9K of Subspecies B1 Human Adenoviruses Encodes a Family of Late Orthologous Proteins That Vary in Their Predicted Structural Features and Subcellular Localization ▿

PubMed Central

Frietze, Kathryn M.; Campos, Samuel K.; Kajon, Adriana E.

2010-01-01

Subspecies B1 human adenoviruses (HAdV-B1s) are important causative agents of acute respiratory disease, but the molecular bases of their distinct pathobiology are still poorly understood. Marked differences in genetic content between HAdV-B1s and the well-characterized HAdV-Cs that may contribute to distinct pathogenic properties map to the E3 region. Between the highly conserved E3-19K and E3-10.4K/RIDα open reading frames (ORFs), and in the same location as the HAdV-C ADP/E3-11.6K ORF, HAdV-B1s carry ORFs E3-20.1K and E3-20.5K and a polymorphic third ORF, designated E3-10.9K, that varies in the size of its predicted product among HAdV-B1 serotypes and genomic variants. As an initial effort to define the function of the E3-10.9K ORF, we carried out a biochemical characterization of E3-10.9K-encoded orthologous proteins and investigated their expression in infected cells. Sequence-based predictions suggested that E3-10.9K orthologs with a hydrophobic domain are integral membrane proteins. Ectopically expressed, C-terminally tagged (with enhanced green fluorescent protein [EGFP]) E3-10.9K and E3-9K localized primarily to the plasma membrane, while E3-7.7K localized primarily to a juxtanuclear compartment that could not be identified. EGFP fusion proteins with a hydrophobic domain were N and O glycosylated. EGFP-tagged E3-4.8K, which lacked the hydrophobic domain, displayed diffuse cellular localization similar to that of the EGFP control. E3-10.9K transcripts from the major late promoter were detected at late time points postinfection. A C-terminally hemagglutinin-tagged version of E3-9K was detected by immunoprecipitation at late times postinfection in the membrane fraction of mutant virus-infected cells. These data suggest a role for ORF E3-10.9K-encoded proteins at late stages of HAdV-B1 replication, with potentially important functional implications for the documented ORF polymorphism. PMID:20739542

Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

PubMed

Youssef, Noha H; Blainey, Paul C; Quake, Stephen R; Elshahed, Mostafa S

2011-11-01

Members of candidate division OP11 are widely distributed in terrestrial and marine ecosystems, yet little information regarding their metabolic capabilities and ecological role within such habitats is currently available. Here, we report on the microfluidic isolation, multiple-displacement-amplification, pyrosequencing, and genomic analysis of a single cell (ZG1) belonging to candidate division OP11. Genome analysis of the ∼270-kb partial genome assembly obtained showed that it had no particular similarity to a specific phylum. Four hundred twenty-three open reading frames were identified, 46% of which had no function prediction. In-depth analysis revealed a heterotrophic lifestyle, with genes encoding endoglucanase, amylopullulanase, and laccase enzymes, suggesting a capacity for utilization of cellulose, starch, and, potentially, lignin, respectively. Genes encoding several glycolysis enzymes as well as formate utilization were identified, but no evidence for an electron transport chain was found. The presence of genes encoding various components of lipopolysaccharide biosynthesis indicates a Gram-negative bacterial cell wall. The partial genome also provides evidence for antibiotic resistance (β-lactamase, aminoglycoside phosphotransferase), as well as antibiotic production (bacteriocin) and extracellular bactericidal peptidases. Multiple mechanisms for stress response were identified, as were elements of type I and type IV secretion systems. Finally, housekeeping genes identified within the partial genome were used to demonstrate the OP11 affiliation of multiple hitherto unclassified genomic fragments from multiple database-deposited metagenomic data sets. These results provide the first glimpse into the lifestyle of a member of a ubiquitous, yet poorly understood bacterial candidate division.

Sequencing and diversity analyses reveal extensive similarities between some epsilon-toxin-encoding plasmids and the pCPF5603 Clostridium perfringens enterotoxin plasmid.

PubMed

Miyamoto, Kazuaki; Li, Jihong; Sayeed, Sameera; Akimoto, Shigeru; McClane, Bruce A

2008-11-01

Clostridium perfringens type B and D isolates produce epsilon-toxin, the third most potent clostridial toxin. The epsilon-toxin gene (etx) is plasmid borne in type D isolates, but etx genetics have been poorly studied in type B isolates. This study reports the first sequencing of any etx plasmid, i.e., pCP8533etx, from type B strain NCTC8533. This etx plasmid is 64.7 kb, carries tcp conjugative transfer genes, and encodes additional potential virulence factors including beta2-toxin, sortase, and collagen adhesin but not beta-toxin. Interestingly, nearly 80% of pCP8533etx open reading frames (ORFs) are also present on pCPF5603, an enterotoxin-encoding plasmid from type A isolate F5603. Pulsed-field gel electrophoresis and overlapping PCR indicated that a pCP8533etx-like etx plasmid is also present in most, if not all, other type B isolates and some beta2-toxin-positive, cpe-negative type D isolates, while other type D isolates carry different etx plasmids. Sequences upstream of the etx gene vary between type B isolates and some type D isolates that do not carry a pCP8533etx-like etx plasmid. However, nearly all type B and D isolates have an etx locus with an upstream IS1151, and those etx loci typically reside near a dcm ORF. These results suggest that pCPF5603 and pCP8533etx evolved from insertion of mobile genetic elements carrying enterotoxin or etx genes, respectively, onto a common progenitor plasmid.

A draft whole genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351 from Asian citrus psyllids in Texas, USA

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351 collected from ACP in South Texas has been determined. The TX2351 genome is 1,252,043 bp in size with a 36.5% G+C content, encoding 1,184 predicted open reading frames and 51 RNA genes....

The ferredoxin-thioredoxin reductase variable subunit gene from Anacystis nidulans.

PubMed

Szekeres, M; Droux, M; Buchanan, B B

1991-03-01

The ferredoxin-thioredoxin reductase variable subunit gene of Anacystis nidulans was cloned, and its nucleotide sequence was determined. A single-copy 219-bp open reading frame encoded a protein of 73 amino acid residues, with a calculated Mr of 8,400. The monocistronic transcripts were represented in a 400-base and a less abundant 300-base mRNA form.

Motion Encoding in Russian and English: Moving beyond Talmy's Typology

ERIC Educational Resources Information Center

Pavlenko, Aneta; Volynsky, Maria

2015-01-01

The aim of the present study is twofold. One, we will show that Talmy's (1985, 1991, 2000) motion typology that groups Russian and English together as satellite-framed languages may be justified on linguistic grounds but is inadequate from a psycholinguistic point of view. Two, we will argue that the shortcomings of the typology may account…

Deletion of Marek’s disease virus large subunit of ribonucleotide reductase (RR) impairs virus growth in vitro and in vivo

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus (MDV), a highly cell-associated lymphotropic alphaherpesvirus, is the causative agent of a neoplastic disease in domestic chickens, called Marek’s disease (MD). In the unique long region of the MDV genome, open reading frames UL39 and UL40 encode the large and small subunits o...

Design and construction of a first-generation high-throughput integrated molecular biology platform for production of optimized synthetic genes and improved industrial strains

USDA-ARS?s Scientific Manuscript database

The molecular biological techniques for plasmid-based assembly and cloning of synthetic assembled gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-bas...

The virion glycoproteins of Ebola viruses are encoded in two reading frames and are expressed through transcriptional editing.

PubMed Central

Sanchez, A; Trappier, S G; Mahy, B W; Peters, C J; Nichol, S T

1996-01-01

In late 1994 and early 1995, Ebola (EBO) virus dramatically reemerged in Africa, causing human disease in the Ivory Coast and Zaire. Analysis of the entire glycoprotein genes of these viruses and those of other EBO virus subtypes has shown that the virion glycoprotein (130 kDa) is encoded in two reading frames, which are linked by transcriptional editing. This editing results in the addition of an extra nontemplated adenosine within a run of seven adenosines near the middle of the coding region. The primary gene product is a smaller (50-70 kDa), nonstructural, secreted glycoprotein, which is produced in large amounts and has an unknown function. Phylogenetic analysis indicates that EBO virus subtypes are genetically diverse and that the recent Ivory Coast isolate represents a new (fourth) subtype of EBO virus. In contrast, the EBO virus isolate from the 1995 outbreak in Kikwit, Zaire, is virtually identical to the virus that caused a similar epidemic in Yambuku, Zaire, almost 20 years earlier. This genetic stability may indicate that EBO viruses have coevolved with their natural reservoirs and do not change appreciably in the wild. Images Fig. 2 Fig. 3 PMID:8622982

Self-Supervised Video Hashing With Hierarchical Binary Auto-Encoder

NASA Astrophysics Data System (ADS)

Song, Jingkuan; Zhang, Hanwang; Li, Xiangpeng; Gao, Lianli; Wang, Meng; Hong, Richang

2018-07-01

Existing video hash functions are built on three isolated stages: frame pooling, relaxed learning, and binarization, which have not adequately explored the temporal order of video frames in a joint binary optimization model, resulting in severe information loss. In this paper, we propose a novel unsupervised video hashing framework dubbed Self-Supervised Video Hashing (SSVH), that is able to capture the temporal nature of videos in an end-to-end learning-to-hash fashion. We specifically address two central problems: 1) how to design an encoder-decoder architecture to generate binary codes for videos; and 2) how to equip the binary codes with the ability of accurate video retrieval. We design a hierarchical binary autoencoder to model the temporal dependencies in videos with multiple granularities, and embed the videos into binary codes with less computations than the stacked architecture. Then, we encourage the binary codes to simultaneously reconstruct the visual content and neighborhood structure of the videos. Experiments on two real-world datasets (FCVID and YFCC) show that our SSVH method can significantly outperform the state-of-the-art methods and achieve the currently best performance on the task of unsupervised video retrieval.

An adaptive DPCM algorithm for predicting contours in NTSC composite video signals

NASA Astrophysics Data System (ADS)

Cox, N. R.

An adaptive DPCM algorithm is proposed for encoding digitized National Television Systems Committee (NTSC) color video signals. This algorithm essentially predicts picture contours in the composite signal without resorting to component separation. The contour parameters (slope thresholds) are optimized using four 'typical' television frames that have been sampled at three times the color subcarrier frequency. Three variations of the basic predictor are simulated and compared quantitatively with three non-adaptive predictors of similar complexity. By incorporating a dual-word-length coder and buffer memory, high quality color pictures can be encoded at 4.0 bits/pel or 42.95 Mbit/s. The effect of channel error propagation is also investigated.

Complete genome sequence of keunjorong mosaic virus, a potyvirus from Cynanchum wilfordii.

PubMed

Nam, Moon; Lee, Joo-Hee; Choi, Hong Soo; Lim, Hyoun-Sub; Moon, Jae Sun; Lee, Su-Heon

2013-08-01

We have determined the complete genome sequence of keunjorong mosaic virus (KjMV). The KjMV genome is composed of 9,611 nucleotides, excluding the 3'-terminal poly(A) tail. It contains two open reading frames (ORFs), with the large one encoding a polyprotein of 3,070 amino acids and the small overlapping ORF encoding a PIPO protein of 81 amino acids. The KjMV genome shared the highest nucleotide sequence identity (57.5  %) with pepper mottle virus and freesia mosaic virus, two members of the genus Potyvirus. Based on the phylogenetic relatedness to known potyviruses, KjMV appears to be a member of a new species in the genus Potyvirus.

Cloning and expression analysis of FaPR-1 gene in strawberry

NASA Astrophysics Data System (ADS)

Mo, Fan; Luo, Ya; Ge, Cong; Mo, Qin; Ling, Yajie; Luo, Shu; Tang, Haoru

2018-04-01

The FaPR-1 gene was cloned by RT-PCR from `Benihoppe' strawberry and its bioinformatics analysis was conducted. The results showed that the open reading frame was 483 bp encoding encoding l60 amino acids which protein molecular weight and theoretical isoelectricity were 17854.17 and 8.72 respectively. Subcellular localization prediction shows that this gene is located extracellularly. By comparing strawberry FaPR-l and other plant Pathogenesis-related protein, homology and phylogenetic tree construction showed that the homology with grapes, peach is relatively close. In the treatments of ABA, sucrose and the mixture of the two, the expression of FaPR-1 in strawberry fruit were significantly increased.

Method of laser beam coding for control systems

NASA Astrophysics Data System (ADS)

Pałys, Tomasz; Arciuch, Artur; Walczak, Andrzej; Murawski, Krzysztof

2017-08-01

The article presents the method of encoding a laser beam for control systems. The experiments were performed using a red laser emitting source with a wavelength of λ = 650 nm and a power of P ≍ 3 mW. The aim of the study was to develop methods of modulation and demodulation of the laser beam. Results of research, in which we determined the effect of selected camera parameters, such as image resolution, number of frames per second on the result of demodulation of optical signal, is also shown in the paper. The experiments showed that the adopted coding method provides sufficient information encoded in a single laser beam (36 codes with the effectiveness of decoding at 99.9%).

Efficient biprediction decision scheme for fast high efficiency video coding encoding

NASA Astrophysics Data System (ADS)

Park, Sang-hyo; Lee, Seung-ho; Jang, Euee S.; Jun, Dongsan; Kang, Jung-Won

2016-11-01

An efficient biprediction decision scheme of high efficiency video coding (HEVC) is proposed for fast-encoding applications. For low-delay video applications, bidirectional prediction can be used to increase compression performance efficiently with previous reference frames. However, at the same time, the computational complexity of the HEVC encoder is significantly increased due to the additional biprediction search. Although a some research has attempted to reduce this complexity, whether the prediction is strongly related to both motion complexity and prediction modes in a coding unit has not yet been investigated. A method that avoids most compression-inefficient search points is proposed so that the computational complexity of the motion estimation process can be dramatically decreased. To determine if biprediction is critical, the proposed method exploits the stochastic correlation of the context of prediction units (PUs): the direction of a PU and the accuracy of a motion vector. Through experimental results, the proposed method showed that the time complexity of biprediction can be reduced to 30% on average, outperforming existing methods in view of encoding time, number of function calls, and memory access.

Characterization of a cDNA encoding a protein involved in formation of the skeleton during development of the sea urchin Lytechinus pictus.

PubMed

Livingston, B T; Shaw, R; Bailey, A; Wilt, F

1991-12-01

In order to investigate the role of proteins in the formation of mineralized tissues during development, we have isolated a cDNA that encodes a protein that is a component of the organic matrix of the skeletal spicule of the sea urchin, Lytechinus pictus. The expression of the RNA encoding this protein is regulated over development and is localized to the descendents of the micromere lineage. Comparison of the sequence of this cDNA to homologous cDNAs from other species of urchin reveal that the protein is basic and contains three conserved structural motifs: a signal peptide, a proline-rich region, and an unusual region composed of a series of direct repeats. Studies on the protein encoded by this cDNA confirm the predicted reading frame deduced from the nucleotide sequence and show that the protein is secreted and not glycosylated. Comparison of the amino acid sequence to databases reveal that the repeat domain is similar to proteins that form a unique beta-spiral supersecondary structure.

k-t Acceleration in pure phase encode MRI to monitor dynamic flooding processes in rock core plugs

NASA Astrophysics Data System (ADS)

Xiao, Dan; Balcom, Bruce J.

2014-06-01

Monitoring the pore system in sedimentary rocks with MRI when fluids are introduced is very important in the study of petroleum reservoirs and enhanced oil recovery. However, the lengthy acquisition time of each image, with pure phase encode MRI, limits the temporal resolution. Spatiotemporal correlations can be exploited to undersample the k-t space data. The stacked frames/profiles can be well approximated by an image matrix with rank deficiency, which can be recovered by nonlinear nuclear norm minimization. Sparsity of the x-t image can also be exploited for nonlinear reconstruction. In this work the results of a low rank matrix completion technique were compared with k-t sparse compressed sensing. These methods are demonstrated with one dimensional SPRITE imaging of a Bentheimer rock core plug and SESPI imaging of a Berea rock core plug, but can be easily extended to higher dimensionality and/or other pure phase encode measurements. These ideas will enable higher dimensionality pure phase encode MRI studies of dynamic flooding processes in low magnetic field systems.

Consequences of germline variation disrupting the constitutional translational initiation codon start sites of MLH1 and BRCA2: use of potential alternative start sites and implications for predicting variant pathogenicity

PubMed Central

Parsons, Michael T.; Whiley, Phillip J.; Beesley, Jonathan; Drost, Mark; de Wind, Niels; Thompson, Bryony A.; Marquart, Louise; Hopper, John L.; Jenkins, Mark A.; Brown, Melissa A.; Tucker, Kathy; Warwick, Linda; Buchanan, Daniel D.; Spurdle, Amanda B.

2014-01-01

Variants that disrupt the translation initiation sequences in cancer predisposition genes are generally assumed to be deleterious. However few studies have validated these assumptions with functional and clinical data. Two cancer syndrome gene variants likely to affect native translation initiation were identified by clinical genetic testing: MLH1:c.1A>G p.(Met1?) and BRCA2:c.67+3A>G. In vitro GFP-reporter assays were conducted to assess the consequences of translation initiation disruption on alternative downstream initiation codon usage. Analysis of MLH1:c.1A>G p.(Met1?) showed that translation was mostly initiated at an in-frame position 103 nucleotides downstream, but also at two ATG sequences downstream. The protein product encoded by the in-frame transcript initiating from position c.103 showed loss of in vitro mismatch repair activity comparable to known pathogenic mutations. BRCA2:c.67+3A>G was shown by mRNA analysis to result in an aberrantly spliced transcript deleting exon 2 and the consensus ATG site. In the absence of exon 2, translation initiated mostly at an out-of-frame ATG 323 nucleotides downstream, and to a lesser extent at an in-frame ATG 370 nucleotides downstream. Initiation from any of the downstream alternative sites tested in both genes would lead to loss of protein function, but further clinical data is required to confirm if these variants are associated with a high cancer risk. Importantly, our results highlight the need for caution in interpreting the functional and clinical consequences of variation that leads to disruption of the initiation codon, since translation may not necessarily occur from the first downstream alternative start site, or from a single alternative start site. PMID:24302565

Open reading frames in a 4556 nucleotide sequence within MDV-1 BamHI-D DNA fragment: evidence for splicing of mRNA from a new viral glycoprotein gene.

PubMed

Becker, Y; Asher, Y; Tabor, E; Davidson, I; Malkinson, M

1994-01-01

A DNA segment of the MDV-1 BamHI-D fragment was sequenced, and the open reading frames (ORFs) present in the 4556 nucleotide fragment were analyzed by computer programs. Computer analysis identified 19 putative ORFs in the sequence ranging from a coding capacity of 37 amino acids (aa) (ORF-1a) to 684aa (ORF-1). The special properties of four ORFs (1a, 1, 2, and 3) were investigated. Two adjacent ORFs, ORF-1a and ORF-1, were found by computer analysis to have the properties of two introns encoding a glycoprotein: ORF-1a encodes an aa sequence with the properties of a signal peptide, and ORF-1 encodes a polypeptide with a membrane anchor domain and putative N-glycosylation sites in the aa sequence. ORF-1a and ORF-1 were found to be transcribed in MDV-1-infected cells. Two RNA transcripts were detected: a precursor RNA and its spliced form. Both are transcribed from a promoter located 5' to ORF-1a, and splice donor and acceptor sites are used to splice the mRNA after cleavage of a 71-nucleotide sequence. This finding suggest that ORF-1a and ORF-1 are two introns of a new MDV-1 glycoprotein gene. The DNA sequence containing ORF-1 was transiently expressed in COS-1 cells, and the viral protein produced in these cells was found to react with anti-MDV serotype-1 Antigen B-specific monoclonal antibodies. These studies indicate that the protein encoded by ORF-1 has antigenic properties resembling Antigen B of MDV-1. A gene homologous to ORF-1 was detected in the genome of both MDV-2(SB1) and MDV-3(HVT), which serve as commercial vaccine strains. Two additional ORFs were noted in the 4556 nucleotide sequence: ORF-2, which encodes a 333 aa polypeptide initiating in the UL and terminating in the TRL prior to the putative origin of replication, and ORF-3, which encodes a 155 aa polypeptide that is partly homologous to the phosphoprotein pp38 encoded by the BamHI-H sequence. The 65 N-terminal aa of the two gene products are identical, both being derived from the nucleotide sequences in the TRL and IRL, respectively. Additional homologous aa sequences are the hydrophobic aa domain in the middle of both proteins. The functions of ORF-2, ORF-3, and additional ORFs are under study.

Molecular cloning of Kazal-type proteinase inhibitor of the shrimp Fenneropenaeus chinensis.

PubMed

Kong, Hee Jeong; Cho, Hyun Kook; Park, Eun-Mi; Hong, Gyeong-Eun; Kim, Young-Ok; Nam, Bo-Hye; Kim, Woo-Jin; Lee, Sang-Jun; Han, Hyon Sob; Jang, In-Kwon; Lee, Chang Hoon; Cheong, Jaehun; Choi, Tae-Jin

2009-01-01

Proteinase inhibitors play important roles in host defence systems involving blood coagulation and pathogen digestion. We isolated and characterized a cDNA clone for a Kazal-type proteinase inhibitor (KPI) from a hemocyte cDNA library of the oriental white shrimp Fenneropenaeus chinensis. The KPI gene consists of three exons and two introns. KPI cDNA contains an open reading frame of 396 bp, a polyadenylation signal sequence AATAAA, and a poly (A) tail. KPI cDNA encodes a polypeptide of 131 amino acids with a putative signal peptide of 21 amino acids. The deduced amino acid sequence of KPI contains two homologous Kazal domains, each with six conserved cysteine residues. The mRNA of KPI is expressed in the hemocytes of healthy shrimp, and the higher expression of KPI transcript is observed in shrimp infected with the white spot syndrome virus (WSSV), suggesting a potential role for KPI in host defence mechanisms.

Ribosomal protein S14 transcripts are edited in Oenothera mitochondria.

PubMed Central

Schuster, W; Unseld, M; Wissinger, B; Brennicke, A

1990-01-01

The gene encoding ribosomal protein S14 (rps14) in Oenothera mitochondria is located upstream of the cytochrome b gene (cob). Sequence analysis of independently derived cDNA clones covering the entire rps14 coding region shows two nucleotides edited from the genomic DNA to the mRNA derived sequences by C to U modifications. A third editing event occurs four nucleotides upstream of the AUG initiation codon and improves a potential ribosome binding site. A CGG codon specifying arginine in a position conserved in evolution between chloroplasts and E. coli as a UGG tryptophan codon is not edited in any of the cDNAs analysed. An inverted repeat 3' of an unidentified open reading frame is located upstream of the rps14 gene. The inverted repeat sequence is highly conserved at analogous regions in other Oenothera mitochondrial loci. Images PMID:2326162

ORFeome Phage Display.

PubMed

Zantow, Jonas; Moreira, Gustavo Marçal Schmidt Garcia; Dübel, Stefan; Hust, Michael

2018-01-01

ORFeome phage display allows the efficient functional screening of entire proteomes or even metaproteomes to identify immunogenic proteins. For this purpose, randomly fragmented, whole genomes or metagenomes are cloned into a phage-display vector allowing positive selection for open reading frames (ORF) to improve the library quality. These libraries display all possible proteins encoded by a pathogen or a microbiome on the phage surface. Consequently, immunogenic proteins can be selected from these libraries using disease-related immunoglobulins from patient serum. ORFeome phage display in particular allows the identification of immunogenic proteins that are only expressed in the host-pathogen interaction but not in cultivation, as well as the detection of very low expressed and very small immunogens and immunogenic proteins of non-cultivable organisms. The identified immunogenic proteins are potential biomarkers for the development of diagnostic assays or vaccines. These articles will give an introduction to ORFeome phage-display technology and give detailed protocols to identify immunogenic proteins by phage display.

yadBC of Yersinia pestis, a new virulence determinant for bubonic plague.

PubMed

Forman, Stanislav; Wulff, Christine R; Myers-Morales, Tanya; Cowan, Clarissa; Perry, Robert D; Straley, Susan C

2008-02-01

In all Yersinia pestis strains examined, the adhesin/invasin yadA gene is a pseudogene, yet Y. pestis is invasive for epithelial cells. To identify potential surface proteins that are structurally and functionally similar to YadA, we searched the Y. pestis genome for open reading frames with homology to yadA and found three: the bicistronic operon yadBC (YPO1387 and YPO1388 of Y. pestis CO92; y2786 and y2785 of Y. pestis KIM5), which encodes two putative surface proteins, and YPO0902, which lacks a signal sequence and likely is nonfunctional. In this study we characterized yadBC regulation and tested the importance of this operon for Y. pestis adherence, invasion, and virulence. We found that loss of yadBC caused a modest loss of invasiveness for epithelioid cells and a large decrease in virulence for bubonic plague but not for pneumonic plague in mice.

Strategies and Challenges in Identifying Function for Thousands of sORF-Encoded Peptides in Meiosis.

PubMed

Hollerer, Ina; Higdon, Andrea; Brar, Gloria A

2017-09-20

Recent genomic analyses have revealed pervasive translation from formerly unrecognized short open reading frames (sORFs) during yeast meiosis. Despite their short length, which has caused these regions to be systematically overlooked by traditional gene annotation approaches, meiotic sORFs share many features with classical genes, implying the potential for similar types of cellular functions. We found that sORF expression accounts for approximately 10-20% of the cellular translation capacity in yeast during meiotic differentiation and occurs within well-defined time windows, suggesting the production of relatively abundant peptides with stage-specific meiotic roles from these regions. Here, we provide arguments supporting this hypothesis and discuss sORF similarities and differences, as a group, to traditional protein coding regions, as well as challenges in defining their specific functions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Decoding sORF translation - from small proteins to gene regulation.

PubMed

Cabrera-Quio, Luis Enrique; Herberg, Sarah; Pauli, Andrea

2016-11-01

Translation is best known as the fundamental mechanism by which the ribosome converts a sequence of nucleotides into a string of amino acids. Extensive research over many years has elucidated the key principles of translation, and the majority of translated regions were thought to be known. The recent discovery of wide-spread translation outside of annotated protein-coding open reading frames (ORFs) came therefore as a surprise, raising the intriguing possibility that these newly discovered translated regions might have unrecognized protein-coding or gene-regulatory functions. Here, we highlight recent findings that provide evidence that some of these newly discovered translated short ORFs (sORFs) encode functional, previously missed small proteins, while others have regulatory roles. Based on known examples we will also speculate about putative additional roles and the potentially much wider impact that these translated regions might have on cellular homeostasis and gene regulation.

Influence of negative emotion on the framing effect: evidence from event-related potentials.

PubMed

Ma, Qingguo; Pei, Guanxiong; Wang, Kai

2015-04-15

The framing effect is the phenomenon in which different descriptions of an identical problem can result in different choices. The influence of negative emotions on the framing effect and its neurocognitive basis are important issues, especially in the domain of saving lives, which is essential and highly risky. In each trial of our experiment, the emotion stimulus is presented to the participants, followed by the decision-making stimulus, which comprises certain and risky options with the same expected value. Each pair of options is positively or negatively framed. The behavioral results indicate a significant interactive effect between negative emotion and frame; thus, the risk preference under the positive frame can be enhanced by negative emotions, whereas this finding is not true under the negative frame. The event-related potential analysis indicates that choosing certain options under the positive frame with negative emotion priming generates smaller P2 and P3 amplitudes and a larger N2 amplitude than with neutral emotion priming. The event-related potential findings indicate that individuals can detect risk faster and experience more conflict and increased decision difficulty if they choose certain options under the positive frame with negative priming compared with neutral priming.

Frames of Reference: A Metaphor for Analyzing and Interpreting Attitudes of Environmental Policy Makers and Policy Influencers

PubMed

Swaffield

1998-07-01

/ The concept of frame of reference offers a potentially useful analytical metaphor in environmental management. This is illustrated by a case study in which attitudes of individuals involved in the management of trees in the New Zealand high country are classified into seven distinctive frames of reference. Some practical and theoretical implications of the use of the frame metaphor are explored, including its potential contribution to the emerg- ing field of communicative planning. KEY WORDS: Frames of reference; Environmental policy analysis; Metaphor; New Zealand high country

Multimodal integration in rostral fastigial nucleus provides an estimate of body movement

PubMed Central

Brooks, Jessica X.; Cullen, Kathleen E.

2012-01-01

The ability to accurately control posture and perceive self motion and spatial orientation requires knowledge of both the motion of the head and body. However, while the vestibular sensors and nuclei directly encode head motion, no sensors directly encode body motion. Instead, the convergence of vestibular and neck proprioceptive inputs during self-motion is generally believed to underlie the ability to compute body motion. Here, we provide evidence that the brain explicitly computes an internal estimate of body motion at the level of single cerebellar neurons. Neuronal responses were recorded from the rostral fastigial nucleus, the most medial of the deep cerebellar nuclei, during whole-body, body-under-head, and head-on-body rotations. We found that approximately half of the neurons encoded the motion of the body-in-space, while the other half encoded the motion of the head-in-space in a manner similar to neurons in the vestibular nuclei. Notably, neurons encoding body motion responded to both vestibular and proprioceptive stimulation (accordingly termed bimodal neurons). In contrast, neurons encoding head motion were only sensitive to vestibular inputs (accordingly termed unimodal neurons). Comparison of the proprioceptive and vestibular responses of bimodal neurons further revealed similar tuning in response to changes in head-on-body position. We propose that the similarity in nonlinear processing of vestibular and proprioceptive signals underlies the accurate computation of body motion. Furthermore, the same neurons that encode body motion (i.e., bimodal neurons) most likely encode vestibular signals in a body referenced coordinate frame, since the integration of proprioceptive and vestibular information is required for both computations. PMID:19710303

Identification of 9α-Hydroxy-17-Oxo-1,2,3,4,10,19-Hexanorandrostan-5-Oic Acid in Steroid Degradation by Comamonas testosteroni TA441 and Its Conversion to the Corresponding 6-En-5-Oyl Coenzyme A (CoA) Involving Open Reading Frame 28 (ORF28)- and ORF30-Encoded Acyl-CoA Dehydrogenases

PubMed Central

Hayashi, Toshiaki; Koshino, Hiroyuki; Malon, Michal; Hirota, Hiroshi; Kudo, Toshiaki

2014-01-01

Comamonas testosteroni TA441 degrades steroids via aromatization and meta-cleavage of the A ring, followed by hydrolysis, and produces 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid as an intermediate compound. Herein, we identify a new intermediate compound, 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid. Open reading frame 28 (ORF28)- and ORF30-encoded acyl coenzyme A (acyl-CoA) dehydrogenase was shown to convert the CoA ester of 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid to the CoA ester of 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrost-6-en-5-oic acid. A homology search of the deduced amino acid sequences suggested that the ORF30-encoded protein is a member of the acyl-CoA dehydrogenase_fadE6_17_26 family, whereas the deduced amino acid sequence of ORF28 showed no significant similarity to specific acyl-CoA dehydrogenase family proteins. Possible steroid degradation gene clusters similar to the cluster of TA441 appear in bacterial genome analysis data. In these clusters, ORFs similar to ORFs 28 and 30 are often found side by side and ordered in the same manner as ORFs 28 and 30. PMID:25092028

Understanding Immersivity: Image Generation and Transformation Processes in 3D Immersive Environments

PubMed Central

Kozhevnikov, Maria; Dhond, Rupali P.

2012-01-01

Most research on three-dimensional (3D) visual-spatial processing has been conducted using traditional non-immersive 2D displays. Here we investigated how individuals generate and transform mental images within 3D immersive (3DI) virtual environments, in which the viewers perceive themselves as being surrounded by a 3D world. In Experiment 1, we compared participants’ performance on the Shepard and Metzler (1971) mental rotation (MR) task across the following three types of visual presentation environments; traditional 2D non-immersive (2DNI), 3D non-immersive (3DNI – anaglyphic glasses), and 3DI (head mounted display with position and head orientation tracking). In Experiment 2, we examined how the use of different backgrounds affected MR processes within the 3DI environment. In Experiment 3, we compared electroencephalogram data recorded while participants were mentally rotating visual-spatial images presented in 3DI vs. 2DNI environments. Overall, the findings of the three experiments suggest that visual-spatial processing is different in immersive and non-immersive environments, and that immersive environments may require different image encoding and transformation strategies than the two other non-immersive environments. Specifically, in a non-immersive environment, participants may utilize a scene-based frame of reference and allocentric encoding whereas immersive environments may encourage the use of a viewer-centered frame of reference and egocentric encoding. These findings also suggest that MR performed in laboratory conditions using a traditional 2D computer screen may not reflect spatial processing as it would occur in the real world. PMID:22908003

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

Tzeng, W.-P.; Frey, Teryl K.

Rubella virus (RUB) replicons are derivatives of the RUB infectious cDNA clone that retain the nonstructural open reading frame (NS-ORF) that encodes the replicase proteins but not the structural protein ORF (SP-ORF) that encodes the virion proteins. RUB defective interfering (DI) RNAs contain deletions within the SP-ORF and thus resemble replicons. DI RNAs often retain the 5' end of the capsid protein (C) gene that has been shown to modulate virus-specific RNA synthesis. However, when replicons either with or without the C gene were passaged serially in the presence of wt RUB as a source of the virion proteins, itmore » was found that neither replicon was maintained and DI RNAs were generated. The majority DI RNA species contained in-frame deletions in the SP-ORF leading to a fusion between the 5' end of the C gene and the 3' end of the E1 glycoprotein gene. DI infectious cDNA clones were constructed and transcripts from these DI infectious cDNA clones were maintained during serial passage with wt RUB. The C-E1 fusion protein encoded by the DI RNAs was synthesized and was required for maintenance of the DI RNA during serial passage. This is the first report of a functional novel gene product resulting from deletion during DI RNA generation. Thus far, the role of the C-E1 fusion protein in maintenance of DI RNAs during serial passage remained elusive as it was found that the fusion protein diminished rather than enhanced DI RNA synthesis and was not incorporated into virus particles.« less

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

Claus, Claudia; Tzeng, W.-P.; Liebert, Uwe Gerd

During serial passaging of rubella virus (RUB) in cell culture, the dominant species of defective-interfering RNA (DI) generated contains an in-frame deletion between the capsid protein (C) gene and E1 glycoprotein gene resulting in production of a C-E1 fusion protein that is necessary for the maintenance of the DI [Tzeng, W.P., Frey, T.K. (2006). C-E1 fusion protein synthesized by rubella virus DI RNAs maintained during serial passage. Virology 356 198-207.]. A BHK cell line stably expressing the RUB structural proteins was established which was used to package DIs into virus particles following transfection with in vitro transcripts from DI infectiousmore » cDNA constructs. Packaging of a DI encoding an in-frame C-GFP-E1 reporter fusion protein corresponding to the C-E1 fusion protein expressed in a native DI was only marginally more efficient than packaging of a DI encoding GFP, indicating that the C-E1 fusion protein did not function by enhancing packaging. However, infection with the DI encoding the C-GFP-E1 fusion protein (in the absence of wt RUB helper virus) resulted in formation of clusters of GFP-positive cells and the percentage of GFP-positive cells in the culture following infection remained relatively constant. In contrast, a DI encoding GFP did not form GFP-positive clusters and the percentage of GFP-positive cells declined by roughly half from 2 to 4 days post-infection. Cluster formation and sustaining the percentage of infected (GFP-positive) cells required the C part of the fusion protein, including the downstream but not the upstream of two arginine clusters (both of which are associated with RNA binding and association with mitochondrial p32 protein) and the E1 part through the transmembrane sequence, but not the C-terminal cytoplasmic tail. Among a collection of mutant DI constructs, cluster formation and sustaining infected cell percentage correlated with maintenance during serial passage with wt RUB. We hypothesize that cluster formation and sustaining infected cell percentage increase the likelihood of co-infection by a DI and wt RUB during serial passage thus enhancing maintenance of the DI. Cluster formation and sustaining infected cell percentage were found to be due to a combination of attenuated cytopathogenicity of DIs that express the C-E1 fusion protein and cell-to-cell movement of the DI. In infected cells, the C-GFP-E1 fusion protein was localized to potentially novel vesicular structures that appear to originate from ER-Golgi transport vacuoles. This species of DI expressing a C-E1 fusion protein that exhibits attenuated cytopathogenicity and the ability to increase the number of infected cells through cell-to-cell movement could be the basis for development of an attractive vaccine vector.« less

Biochemical characterization of the bifunctional enzyme dihydrofolate reductase-thymidylate synthase from Leishmania (Viannia) and its evaluation as a drug target.

PubMed

Osorio, Edison; Aguilera, Carolina; Naranjo, Nelson; Marín, Marcel; Muskus, Carlos

2013-01-01

Dihydrofolate reductase (DHFR) has been used successfully as a drug target in the area of anti-bacterial, anti-cancer and anti-malarial therapy. Although this bifunctional enzyme is also a potential drug target for treatment of leishmaniasis, there have been no reports on its efficacy against Leishmania (Viannia) species. The gene encoding the bifunctional DHFR and thymidylate synthase (TS) of Le. (V.) braziliensis was isolated and expressed in E. coli. The enzyme was purified and characterized. The inhibitory effects of antifolates and four aporphine alkaloids on its activity were evaluated. The full-length gene consists of a 1560-bp open reading frame encoding a 58 kDa translated peptide containing DHFR and TS domains linked together in a single polypeptide chain. The recombinant DHFR-TS enzyme revealed Km and Vmax values of 55.35 ± 4.02 µ M (mean ± SE) and 0.02 ± 5.34 x 10 -4 µ M/min respectively for dihydrofolic acid (H₂F). The Le. braziliensis rDHFR-TS have Ki values for antimicrobial antifolates in the µM range. Methotrexate (MTX) was a more-potent inhibitor of enzymatic activity (Ki = 22.0 µM) than trimethoprim (Ki = 33 µM) and pyrimethamine (Ki = 68 µM). These Ki values are significantly lower than those obtained for the aporphine alkaloids. The results of the study show the inhibitory effect of antifolate drugs on enzymatic activity, indicating that Le. braziliensis rDHFR-TS could be a model to studying antifolate compounds as potential antiprotozoal drugs.

Molecular cloning and transcriptional analysis of a NPY receptor-like in common Chinese cuttlefish Sepiella japonica

NASA Astrophysics Data System (ADS)

Yang, Jingwen; Xu, Yuchao; Xu, Ke; Ping, Hongling; Shi, Huilai; Lü, Zhenming; Wu, Changwen; Wang, Tianming

2017-08-01

Neuropeptide Y (NPY) has a pivotal role in the regulation of many physiological processes. In this study, the gene encoding a NPY receptor-like from the common Chinese cuttlefish Sepiella japonica (SjNPYR-like) was identified and characterized. The full-length SjNPYR-like cDNA was cloned containing a 492-bp of 5' untranslated region (UTR), 1 182 bp open reading frame (ORF) encoding a protein of 393 amino acid residues, and 228 bp of 3' UTR. The putative protein was predicted to have a molecular weight of 45.54 kDa and an isoelectric point (pI) of 8.13. By informatic analyses, SjNPYR-like was identified as belonging to the class A G protein coupled receptor (GPCR) family (the rhodopsin-type). The amino acid sequence contained 12 potential phosphorylation sites and five predicted N-linked glycosylation sites. Multiple sequence alignment and 3D structure modeling were conducted to clarify SjNPYR bioinformatics characteristics. Phylogenetic analysis identifies it as an NPYR with identity of 33% to Lymnaea stagnalis NPFR. Transmembrane properties of SjNPYR-like were demonstrated in vitro using HEK293 cells and the pEGFP-N1 plasmid. Relative quantification of SjNPYR-like mRNA level confirmed a high level expression and broad distribution of SjNPYR - like in various tissues of female S. japonica. In addition, the transcriptional profile of SjNPYR - like in the brain, liver, and ovary during gonadal development was analyzed. The results provide basic understanding on the molecular characteristics of SjNPYR-like and its potentially physical functions.

Novel Protease-Resistant Exochitinase (Echi47) from Pig Fecal Environment DNA with Application Potentials in the Food and Feed Industries.

PubMed

Liu, Yuchun; Yan, Qiaojuan; Yang, Shaoqing; Jiang, Zhengqiang

2015-07-15

A novel exochitinase gene (Echi47) was directly cloned from the pig fecal environment DNA using the genomic walking PCR technique and expressed in Escherichia coli BL21 (DE3). Echi47 has an open reading frame (ORF) of 1,161 bp encoding 386 amino acids. The amino acid sequence of Echi47 showed 36% identity with that of chitinase from Coprinellus congregatus. The recombinant exochitinase was purified with specific activity toward colloidal chitin of 6.84 U/mg. Echi47 was optimally active at pH 5.0 and 40 °C, respectively. When colloidal chitin was used as substrate, N-acetylchitobiose [(GlcNAc)2] was mostly produced at the initial stage, suggesting that it is an exochitinase. Echi47 exhibited excellent resistance to pepsin, trypsin, proteinase K, and flavor protease. Under simulated alimentary tract conditions, Echi47 was stable and active, releasing 21.1 mg of N-acetylchitooligosaccharides from 80 mg of colloidal chitin. These properties make Echi47 a potential additive in the food and feed industries.

Biarsenical labeling of vesicular stomatitis virus encoding tetracysteine-tagged m protein allows dynamic imaging of m protein and virus uncoating in infected cells.

PubMed

Das, Subash C; Panda, Debasis; Nayak, Debasis; Pattnaik, Asit K

2009-03-01

A recombinant vesicular stomatitis virus (VSV-PeGFP-M-MmRFP) encoding enhanced green fluorescent protein fused in frame with P (PeGFP) in place of P and a fusion matrix protein (monomeric red fluorescent protein fused in frame at the carboxy terminus of M [MmRFP]) at the G-L gene junction, in addition to wild-type (wt) M protein in its normal location, was recovered, but the MmRFP was not incorporated into the virions. Subsequently, we generated recombinant viruses (VSV-PeGFP-DeltaM-Mtc and VSV-DeltaM-Mtc) encoding M protein with a carboxy-terminal tetracysteine tag (Mtc) in place of the M protein. These recombinant viruses incorporated Mtc at levels similar to M in wt VSV, demonstrating recovery of infectious rhabdoviruses encoding and incorporating a tagged M protein. Virions released from cells infected with VSV-PeGFP-DeltaM-Mtc and labeled with the biarsenical red dye (ReAsH) were dually fluorescent, fluorescing green due to incorporation of PeGFP in the nucleocapsids and red due to incorporation of ReAsH-labeled Mtc in the viral envelope. Transport and subsequent association of M protein with the plasma membrane were shown to be independent of microtubules. Sequential labeling of VSV-DeltaM-Mtc-infected cells with the biarsenical dyes ReAsH and FlAsH (green) revealed that newly synthesized M protein reaches the plasma membrane in less than 30 min and continues to accumulate there for up to 2 1/2 hours. Using dually fluorescent VSV, we determined that following adsorption at the plasma membrane, the time taken by one-half of the virus particles to enter cells and to uncoat their nucleocapsids in the cytoplasm is approximately 28 min.

Sequence characterization of cDNA sequence of encoding of an antimicrobial Peptide with no disulfide bridge from the Iranian mesobuthus eupeus venomous glands.

PubMed

Farajzadeh-Sheikh, Ahmad; Jolodar, Abbas; Ghaemmaghami, Shamsedin

2013-01-01

Scorpion venom glands produce some antimicrobial peptides (AMP) that can rapidly kill a broad range of microbes and have additional activities that impact on the quality and effectiveness of innate responses and inflammation. In this study, we reported the identification of a cDNA sequence encoding cysteine-free antimicrobial peptides isolated from venomous glands of this species. Total RNA was extracted from the Iranian mesobuthus eupeus venom glands, and cDNA was synthesized by using the modified oligo (dT). The cDNA was used as the template for applying Semi-nested RT- PCR technique. PCR Products were used for direct nucleotide sequencing and the results were compared with Gen Bank database. A 213 BP cDNA fragment encoding the entire coding region of an antimicrobial toxin from the Iranian scorpion M. Eupeus venom glands were isolated. The full-length sequence of the coding region was 210 BP contained an open reading frame of 70 amino with a predicted molecular mass of 7970.48 Da and theoretical Pi of 9.10. The open reading frame consists of 210 BP encoding a precursor of 70 amino acid residues, including a signal peptide of 23 residues a propertied of 7 residues, and a mature peptide of 34 residues with no disulfide bridge. The peptide has detectable sequence identity to the Lesser Asian mesobuthus eupeus MeVAMP-2 (98%), MeVAMP-9 (60%) and several previously described AMPs from other scorpion venoms including mesobuthus martensii (94%) and buthus occitanus Israelis (82%). The secondary structure of the peptide mainly consisted of α-helical structure which was generally conserved by previously reported scorpion counterparts. The phylogenetic analysis showed that the Iranian MeAMP-like toxin was similar but not identical with that of venom antimicrobial peptides from lesser Asian scorpion mesobuthus eupeus.

Genome sequence variation in the constricta strain dramatically alters the protein interaction and localization map of Potato yellow dwarf virus

USDA-ARS?s Scientific Manuscript database

The genome sequence of the constricta strain of Potato yellow dwarf virus (CYDV) was determined to be 12,792 nucleotides long and organized into seven open reading frames with the gene order 3’-N-X-P-Y-M-G-L-5’, which encodes the nucleocapsid, phosphoprotein, movement, matrix, glycoprotein and RNA-d...

Preparation of a Burkholderia Mallei Vaccine

DTIC Science & Technology

2000-01-01

together with the indications of the portions of this data which are subject to such limitations, shall be included on any reproduction hereof which... on to apoptosis; hence, virulent mycobacteria will survive in those macrophages. To assess any similarity between Mycobacterium and Burkholderia...the presence of an open reading frame encoding for a type I polyketide synthase from Streptomyces species (data not 13 shown). We are currently

ORF43 of Maize rayado fino virus is dispensable for systemic infection of maize and transmission by leafhoppers

USDA-ARS?s Scientific Manuscript database

Maize rayado fino virus (MRFV) possesses an open reading frame (ORF) encoding a protein with predicted mass of 43 kDa (ORF43) that has been postulated to be a viral movement protein. Using a clone of MRFV (pMRFV-US) from which infectious RNA can be produced, point mutations were introduced to eithe...

Naturally occurring frame-shift mutations in the tvb receptor gene are responsible for decreased susceptibility to subgroups B, D, and E

USDA-ARS?s Scientific Manuscript database

The group of highly related avian leukosis viruses (ALVs) in chickens are thought to have evolved from a common retroviral ancestor into six subgroups, A to E and J. These ALV subgroups use diverse cellular proteins encoded by four genetic loci in chickens as receptors to gain entry into host cells....

The ferredoxin-thioredoxin reductase variable subunit gene from Anacystis nidulans.

PubMed Central

Szekeres, M; Droux, M; Buchanan, B B

1991-01-01

The ferredoxin-thioredoxin reductase variable subunit gene of Anacystis nidulans was cloned, and its nucleotide sequence was determined. A single-copy 219-bp open reading frame encoded a protein of 73 amino acid residues, with a calculated Mr of 8,400. The monocistronic transcripts were represented in a 400-base and a less abundant 300-base mRNA form. Images PMID:1705544

Draft Genome Sequence of the d-Xylose-Fermenting Yeast Spathaspora arborariae UFMG-HM19.1AT

PubMed Central

Lobo, Francisco P.; Gonçalves, Davi L.; Alves, Sergio L.; Gerber, Alexandra L.; de Vasconcelos, Ana Tereza R.; Basso, Luiz C.; Franco, Glória R.; Soares, Marco A.; Cadete, Raquel M.; Rosa, Carlos A.

2014-01-01

The draft genome sequence of the yeast Spathaspora arborariae UFMG-HM19.1AT (CBS 11463 = NRRL Y-48658) is presented here. The sequenced genome size is 12.7 Mb, consisting of 41 scaffolds containing a total of 5,625 predicted open reading frames, including many genes encoding enzymes and transporters involved in d-xylose fermentation. PMID:24435867

Impact of Molecular Hydrogen on Chalcopyrite Bioleaching by the Extremely Thermoacidophilic Archaeon Metallosphaera sedula▿

PubMed Central

Auernik, Kathryne S.; Kelly, Robert M.

2010-01-01

Hydrogen served as a competitive inorganic energy source, impacting the CuFeS2 bioleaching efficiency of the extremely thermoacidophilic archaeon Metallosphaera sedula. Open reading frames encoding key terminal oxidase and electron transport chain components were triggered by CuFeS2. Evidence of heterotrophic metabolism was noted after extended periods of bioleaching, presumably related to cell lysis. PMID:20190092

Molecular Characterization of a Novel Bovine Viral Diarrhea Virus Isolate SD-15

PubMed Central

Zhu, Lisai; Lu, Haibing; Cao, Yufeng; Gai, Xiaochun; Guo, Changming; Liu, Yajing; Liu, Jiaxu; Wang, Xinping

2016-01-01

As one of the major pathogens, bovine viral diarrhea virus caused a significant economic loss to the livestock industry worldwide. Although BVDV infections have increasingly been reported in China in recent years, the molecular aspects of those BVDV strains were barely characterized. In this study, we reported the identification and characterization of a novel BVDV isolate designated as SD-15 from cattle, which is associated with an outbreak characterized by severe hemorrhagic and mucous diarrhea with high morbidity and mortality in Shandong, China. SD-15 was revealed to be a noncytopathic BVDV, and has a complete genomic sequence of 12,285 nucleotides that contains a large open reading frame encoding 3900 amino acids. Alignment analysis showed that SD-15 has 93.8% nucleotide sequence identity with BVDV ZM-95 isolate, a previous BVDV strain isolated from pigs manifesting clinical signs and lesions resembling to classical swine fever. Phylogenetic analysis clustered SD-15 to a BVDV-1m subgenotype. Analysis of the deduced amino acid sequence of glycoproteins revealed that E2 has several highly conserved and variable regions within BVDV-1 genotypes. An additional N-glycosylation site (240NTT) was revealed exclusively in SD-15-encoded E2 in addition to four potential glycosylation sites (Asn-X-Ser/Thr) shared by all BVDV-1 genotypes. Furthermore, unique amino acid and linear epitope mutations were revealed in SD-15-encoded Erns glycoprotein compared with known BVDV-1 genotype. In conclusion, we have isolated a noncytopathic BVDV-1m strain that is associated with a disease characterized by high morbidity and mortality, revealed the complete genome sequence of the first BVDV-1m virus originated from cattle, and found a unique glycosylation site in E2 and a linear epitope mutation in Erns encoded by SD-15 strain. Those results will broaden the current understanding of BVDV infection and lay a basis for future investigation on SD-15-related pathogenesis. PMID:27764206

The Saccharomyces cerevisiae ETH1 Gene, an Inducible Homolog of Exonuclease III That Provides Resistance to DNA-Damaging Agents and Limits Spontaneous Mutagenesis

PubMed Central

Bennett, Richard A. O.

1999-01-01

The recently sequenced Saccharomyces cerevisiae genome was searched for a gene with homology to the gene encoding the major human AP endonuclease, a component of the highly conserved DNA base excision repair pathway. An open reading frame was found to encode a putative protein (34% identical to the Schizosaccharomyces pombe eth1+ [open reading frame SPBC3D6.10] gene product) with a 347-residue segment homologous to the exonuclease III family of AP endonucleases. Synthesis of mRNA from ETH1 in wild-type cells was induced sixfold relative to that in untreated cells after exposure to the alkylating agent methyl methanesulfonate (MMS). To investigate the function of ETH1, deletions of the open reading frame were made in a wild-type strain and a strain deficient in the known yeast AP endonuclease encoded by APN1. eth1 strains were not more sensitive to killing by MMS, hydrogen peroxide, or phleomycin D1, whereas apn1 strains were ∼3-fold more sensitive to MMS and ∼10-fold more sensitive to hydrogen peroxide than was the wild type. Double-mutant strains (apn1 eth1) were ∼15-fold more sensitive to MMS and ∼2- to 3-fold more sensitive to hydrogen peroxide and phleomycin D1 than were apn1 strains. Elimination of ETH1 in apn1 strains also increased spontaneous mutation rates 9- or 31-fold compared to the wild type as determined by reversion to adenine or lysine prototrophy, respectively. Transformation of apn1 eth1 cells with an expression vector containing ETH1 reversed the hypersensitivity to MMS and limited the rate of spontaneous mutagenesis. Expression of ETH1 in a dut-1 xthA3 Escherichia coli strain demonstrated that the gene product functionally complements the missing AP endonuclease activity. Thus, in apn1 cells where the major AP endonuclease activity is missing, ETH1 offers an alternate capacity for repair of spontaneous or induced damage to DNA that is normally repaired by Apn1 protein. PMID:10022867

All-optical framing photography based on hyperspectral imaging method

NASA Astrophysics Data System (ADS)

Liu, Shouxian; Li, Yu; Li, Zeren; Chen, Guanghua; Peng, Qixian; Lei, Jiangbo; Liu, Jun; Yuan, Shuyun

2017-02-01

We propose and experimentally demonstrate a new all optical-framing photography that uses hyperspectral imaging methods to record a chirped pulse's temporal-spatial information. This proposed method consists of three parts: (1) a chirped laser pulse encodes temporal phenomena onto wavelengths; (2) a lenslet array generates a series of integral pupil images;(3) a dispersive device disperses the integral images at void space of image sensor. Compared with Ultrafast All-Optical Framing Technology(Daniel Frayer,2013,2014) and Sequentially Time All-Optical Mapping Photography( Nakagawa 2014, 2015), our method is convenient to adjust the temporal resolution and to flexibly increase the numbers of frames. Theoretically, the temporal resolution of our scheme is limited by the amount of dispersion that is added to a Fourier transform limited femtosecond laser pulse. Correspondingly, the optimal number of frames is decided by the ratio of the observational time window to the temporal resolution, and the effective pixels of each frame are mostly limited by the dimensions M×N of the lenslet array. For example, if a 40fs Fourier transform limited femtosecond pulse is stretched to 10ps, a CCD camera with 2048×3072 pixels can record 15 framing images with temporal resolution of 650fs and image size of 100×100 pixels. As spectrometer structure, our recording part has another advantage that not only amplitude images but also frequency domain interferograms can be imaged. Therefore, it is comparatively easy to capture fast dynamics in the refractive index change of materials. A further dynamic experiment is being conducted.

Molecular cloning and nucleotide sequences of the genes for two essential proteins constituting a novel enzyme system for heptaprenyl diphosphate synthesis.

PubMed

Koike-Takeshita, A; Koyama, T; Obata, S; Ogura, K

1995-08-04

The genes encoding two dissociable components essential for Bacillus stearothermophilus heptaprenyl diphosphate synthase (all-trans-hexparenyl-diphosphate:isopentenyl-diphosphate hexaprenyl-trans-transferase, EC 2.5.1.30) were cloned, and their nucleotide sequences were determined. Sequence analyses revealed the presence of three open reading frames within 2,350 base pairs, designated as ORF-1, ORF-2, and ORF-3 in order of nucleotide sequence, which encode proteins of 220, 234, and 323 amino acids, respectively. Deletion experiments have shown that expression of the enzymatic activity requires the presence of ORF-1 and ORF-3, but ORF-2 is not essential. As a result, this enzyme was proved genetically to consist of two different protein compounds with molecular masses of 25 kDa (Component I) and 36 kDa (Component II), encoded by two of the three tandem genes. The protein encoded by ORF-1 has no similarity to any protein so far registered. However, the protein encoded by ORF-3 shows a 32% similarity to the farnesyl diphosphate synthase of the same bacterium and has seven highly conserved regions that have been shown typical in prenyltransferases (Koyama, T., Obata, S., Osabe, M., Takeshita, A., Yokoyama, K., Uchida, M., Nishino, T., and Ogura, K. (1993) J. Biochem. (Tokyo) 113, 355-363).

The bglA Gene of Aspergillus kawachii Encodes Both Extracellular and Cell Wall-Bound β-Glucosidases

PubMed Central

Iwashita, Kazuhiro; Nagahara, Tatsuya; Kimura, Hitoshi; Takano, Makoto; Shimoi, Hitoshi; Ito, Kiyoshi

1999-01-01

We cloned the genomic DNA and cDNA of bglA, which encodes β-glucosidase in Aspergillus kawachii, based on a partial amino acid sequence of purified cell wall-bound β-glucosidase CB-1. The nucleotide sequence of the cloned bglA gene revealed a 2,933-bp open reading frame with six introns that encodes an 860-amino-acid protein. Based on the deduced amino acid sequence, we concluded that the bglA gene encodes cell wall-bound β-glucosidase CB-1. The amino acid sequence exhibited high levels of homology with the amino acid sequences of fungal β-glucosidases classified in subfamily B. We expressed the bglA cDNA in Saccharomyces cerevisiae and detected the recombinant β-glucosidase in the periplasm fraction of the recombinant yeast. A. kawachii can produce two extracellular β-glucosidases (EX-1 and EX-2) in addition to the cell wall-bound β-glucosidase. A. kawachii in which the bglA gene was disrupted produced none of the three β-glucosidases, as determined by enzyme assays and a Western blot analysis. Thus, we concluded that the bglA gene encodes both extracellular and cell wall-bound β-glucosidases in A. kawachii. PMID:10584016

Pulse Code Modulation (PCM) data storage and analysis using a microcomputer

NASA Technical Reports Server (NTRS)

Massey, D. E.

1986-01-01

A PCM storage device/data analyzer is described. This instrument is a peripheral plug-in board especially built to enable a personal computer to store and analyze data from a PCM source. This board and custom written software turns a computer into a snapshot PCM decommutator. This instrument will take in and store many hundreds or thousands of PCM telemetry data frames, then sift through them over and over again. The data can be converted to any number base and displayed, examined for any bit dropouts or changes in particular words or frames, graphically plotted, or statistically analyzed. This device was designed and built for use on the NASA Sounding Rocket Program for PCM encoder configuration and testing.

Brain potentials associated with the outcome processing in framing effects.

PubMed

Ma, Qingguo; Feng, Yandong; Xu, Qing; Bian, Jun; Tang, Huixian

2012-10-24

Framing effect is a cognitive bias referring to the phenomenon that people respond differently to different but objectively equivalent descriptions of the same problem. By measuring event-related potentials, the present study aimed to investigate the neural mechanisms underlying the framing effect, especially how the negative and positive frames influence the outcome processing in our brain. Participants were presented directly with outcomes framed either positively in terms of lives saved or negatively in terms of lives lost in large and small group conditions, and were asked to rate the favorableness of each of them. The behavioral results showed that the framing effect occurred in both group size conditions, with more favorable evaluations associated with positive framing. Compared with outcomes in positive framing condition, a significant feedback-related negativity (FRN) effect was elicited by outcomes in negative framing condition, even though the outcomes in different conditions were objectively equivalent. The results are explained in terms of the associative model of attribute framing effect which states that attribute framing effect occurs as a result of a valence-based associative processing. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Subjective quality evaluation of low-bit-rate video

NASA Astrophysics Data System (ADS)

Masry, Mark; Hemami, Sheila S.; Osberger, Wilfried M.; Rohaly, Ann M.

2001-06-01

A subjective quality evaluation was performed to qualify vie4wre responses to visual defects that appear in low bit rate video at full and reduced frame rates. The stimuli were eight sequences compressed by three motion compensated encoders - Sorenson Video, H.263+ and a Wavelet based coder - operating at five bit/frame rate combinations. The stimulus sequences exhibited obvious coding artifacts whose nature differed across the three coders. The subjective evaluation was performed using the Single Stimulus Continuos Quality Evaluation method of UTI-R Rec. BT.500-8. Viewers watched concatenated coded test sequences and continuously registered the perceived quality using a slider device. Data form 19 viewers was colleted. An analysis of their responses to the presence of various artifacts across the range of possible coding conditions and content is presented. The effects of blockiness and blurriness on perceived quality are examined. The effects of changes in frame rate on perceived quality are found to be related to the nature of the motion in the sequence.

The nucleotide sequence of a segment of Trypanosoma brucei mitochondrial maxi-circle DNA that contains the gene for apocytochrome b and some unusual unassigned reading frames.

PubMed Central

Benne, R; De Vries, B F; Van den Burg, J; Klaver, B

1983-01-01

The nucleotide sequence of a 2.5-kb segment of the maxi-circle of Trypanosoma brucei mtDNA has been determined. The segment contains the gene for apocytochrome b, which displays about 25% homology at the amino acid level to the apocytochrome b gene from fungal and mammalian mtDNAs. Northern blot and S1 nuclease analyses have yielded accurate map positions of an RNA species in an area that coincides with the reading frame. The segment also contains two pairs of overlapping unassigned reading frames, which lack homology with any known mitochondrial gene or URF. The DNA sequence in these areas is AG-rich (70%), resulting in URFs with an unusually high level of glycine and charged amino acids (60%). They may not encode proteins, in spite of their size and the fact that abundant transcripts are mapped in these areas. Images PMID:6314266

High-performance software-only H.261 video compression on PC

NASA Astrophysics Data System (ADS)

Kasperovich, Leonid

1996-03-01

This paper describes an implementation of a software H.261 codec for PC, that takes an advantage of the fast computational algorithms for DCT-based video compression, which have been presented by the author at the February's 1995 SPIE/IS&T meeting. The motivation for developing the H.261 prototype system is to demonstrate a feasibility of real time software- only videoconferencing solution to operate across a wide range of network bandwidth, frame rate, and resolution of the input video. As the bandwidths of current network technology will be increased, the higher frame rate and resolution of video to be transmitted is allowed, that requires, in turn, a software codec to be able to compress pictures of CIF (352 X 288) resolution at up to 30 frame/sec. Running on Pentium 133 MHz PC the codec presented is capable to compress video in CIF format at 21 - 23 frame/sec. This result is comparable to the known hardware-based H.261 solutions, but it doesn't require any specific hardware. The methods to achieve high performance, the program optimization technique for Pentium microprocessor along with the performance profile, showing the actual contribution of the different encoding/decoding stages to the overall computational process, are presented.

Research on compression performance of ultrahigh-definition videos

NASA Astrophysics Data System (ADS)

Li, Xiangqun; He, Xiaohai; Qing, Linbo; Tao, Qingchuan; Wu, Di

2017-11-01

With the popularization of high-definition (HD) images and videos (1920×1080 pixels and above), there are even 4K (3840×2160) television signals and 8 K (8192×4320) ultrahigh-definition videos. The demand for HD images and videos is increasing continuously, along with the increasing data volume. The storage and transmission cannot be properly solved only by virtue of the expansion capacity of hard disks and the update and improvement of transmission devices. Based on the full use of the coding standard high-efficiency video coding (HEVC), super-resolution reconstruction technology, and the correlation between the intra- and the interprediction, we first put forward a "division-compensation"-based strategy to further improve the compression performance of a single image and frame I. Then, by making use of the above thought and HEVC encoder and decoder, a video compression coding frame is designed. HEVC is used inside the frame. Last, with the super-resolution reconstruction technology, the reconstructed video quality is further improved. The experiment shows that by the proposed compression method for a single image (frame I) and video sequence here, the performance is superior to that of HEVC in a low bit rate environment.

D{sub H} element reading frame selection is influenced by an Ig heavy chain transgene, but not by bcl-2

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

Tarlinton, D.; Strasser, A.; McLean, M.

1995-04-01

Mouse B cell precursors containing Ig D{sub H}J{sub H} junctions in one particular reading frame are selectively lost during B cell development. In this register, arbitrarily referred to as reading frame 2, D{sub H}J{sub H} junctions give rise to an open reading frame starting upstream of the D{sub H} element and including the D{sub H}J{sub H}-peptide fused to the constant region of IgM. Expression of this protein, called D{mu}, has been strongly implicated in the loss of B cell precursors containing reading frame 2 D{sub H}J{sub H} junctions. In an attempt to elucidate the means of D{mu} counterselection, we havemore » examined the reading frame distribution of D{sub H}J{sub H} junctions in peripheral B cells from mice transgenic for either the human bcl-2 oncogene or for a functionally rearranged Ig {mu} heavy chain. In bcl-2 transgenic mice, reading frame 2 accounted for < 5% of the D{sub H}J{sub H} junctions in peripheral B cells, a value not significantly different from controls. Reading frames 1 and 3 were equally represented among the remaining junctions. By contrast, the reading frame distribution of endogenous D{sub H}J{sub H} junctions in splenic B cells from Ig {mu} heavy chain transgenic mice showed no evidence of bias against D{mu} encoding D{sub H}J{sub H} junctions. Reading frames 2 and 3 accounted for 27% and 30% of the sequenced D{sub H}J{sub H} junctions, respectively, and the remaining 43% were reading frame 1. Thus although the presence of BCL-2 cannot prevent the selective loss of reading frame 2 D{sub H}J{sub H} B cells, a functional {mu} heavy chain can. These results suggest that D{mu}-expressing B cell precursors may be selectively lost because of the premature and inappropriate cessation of heavy chain gene rearrangement rather than because of the induction of an apoptotic process which can be blocked by BCL-2. 42 refs., 4 figs., 4 tabs.« less

Cloning and characterization of an abalone (Haliotis discus hannai) actin gene

NASA Astrophysics Data System (ADS)

Ma, Hongming; Xu, Wei; Mai, Kangsen; Liufu, Zhiguo; Chen, Hong

2004-10-01

An actin encoding gene was cloned by using RT-PCR, 3‧ RACE and 5‧ RACE from abalone Haliotis discus hannai. The full length of the gene is 1532 base pairs, which contains a long 3‧ untranslated region of 307 base pairs and 79 base pairs of 5‧ untranslated sequence. The open reading frame encodes 376 amino acid residues. Sequence comparison with those of human and other mollusks showed high conservation among species at amino acid level. The identities was 96%, 97% and 96% respectively compared with Aplysia californica, Biomphalaria glabrata and Homo sapience β-actin. It is also indicated that this actin is more similar to the human cytoplasmic actin (β-actin) than to human muscle actin.

Identification of herpes simplex virus type 1 proteins encoded within the first 1.5 kb of the latency-associated transcript.

PubMed

Henderson, Gail; Jaber, Tareq; Carpenter, Dale; Wechsler, Steven L; Jones, Clinton

2009-09-01

Expression of the first 1.5 kb of the latency-associated transcript (LAT) that is encoded by herpes simplex virus type 1 (HSV-1) is sufficient for wild-type (wt) levels of reactivation from latency in small animal models. Peptide-specific immunoglobulin G (IgG) was generated against open reading frames (ORFs) that are located within the first 1.5 kb of LAT coding sequences. Cells stably transfected with LAT or trigeminal ganglionic neurons of mice infected with a LAT expressing virus appeared to express the L2 or L8 ORF. Only L2 ORF expression was readily detected in trigeminal ganglionic neurons of latently infected mice.

CelF of Orpinomyces PC-2 has an intron and encodes a cellulase (CelF) containing a carbohydrate-binding module.

PubMed

Chen, Huizhong; Li, Xin-Liang; Blum, David L; Ximenes, Eduardo A; Ljungdahl, Lars G

2003-01-01

A cDNA, designated celF, encoding a cellulase (CelF) was isolated from the anaerobic fungus Orpinomyces PC-2. The open reading frame contains regions coding for a signal peptide, a carbohydrate-binding module (CBM), a linker, and a catalytic domain. The catalytic domain was homologous to those of CelA and CelC of the same fungus and to that of the Neocallimastix patriciarum CELA, but CelF lacks a docking domain, characteristic for enzymes of cellulosomes. It was also homologous to the cellobiohydrolase IIs and endoglucanases of aerobic organisms. The gene has a 111-bp intron, located within the CBM-coding region. Some biochemical properties of the purified recombinant enzyme are described.

Isolation and expression of a Bacillus cereus gene encoding benzil reductase.

PubMed

Maruyama, R; Nishizawa, M; Itoi, Y; Ito, S; Inoue, M

2001-12-20

Benzil was reduced stereospecifically to (S)-benzoin by Bacillus cereus strain Tim-r01. To isolate the gene responsible for asymmetric reduction, we constructed a library consisting of Escherichia coli clones that harbored plasmids expressing Bacillus cereus genes. The library was screened using the halo formation assay, and one clone showed benzil reduction to (S)-benzoin. Thus, this clone seemed to carry a plasmid encoding a Bacillus cereus benzil reductase. The deduced amino acid sequence had marked homologies to the Bacillus subtilis yueD protein (41% identity), the yeast open reading frame YIR036C protein (31%), and the mammalian sepiapterin reductases (28% to 30%), suggesting that benzil reductase is a novel short-chain de-hydrogenases/ reductase. Copyright 2001 John Wiley & Sons, Inc.

Molecular cloning and nucleotide sequence of CYP6BF1 from the diamondback moth, Plutella xylostella

PubMed Central

Li, Hongshan; Dai, Huaguo; Wei, Hui

2005-01-01

A novel cDNA clong encoding a cytochrome P450 was screened from the insecticide-susceptible strain of Plutella xylostella (L.) (Lepidoptera:Yponomeutidae). The nucleotide sequence of the clone, designated CYP6BF1, was determined. This is the first full-length sequence of the CYP6 family from Plutella xylostella (L.). The cDNA is 1661bp in length and contains an open reading frame from base pairs 26 to 1570, encoding a protein of 514 amino acid residues. It is similar to the other insect P450s in gene family 6, including CYP6AE1 from Depressaria pastinacella, (46%). The GenBank accession number is AY971374. PMID:17119627

Cloning and characterization of the human 5,10-methenyltetrahydrofolate synthetase-encoding cDNA.

PubMed

Dayan, A; Bertrand, R; Beauchemin, M; Chahla, D; Mamo, A; Filion, M; Skup, D; Massie, B; Jolivet, J

1995-11-20

Methenyltetrahydrofolate synthetase (MTHFS) catalyses the obligatory initial metabolic step in the intracellular conversion of 5-formyltetrahydrofolate to other reduced folates. We have isolated and sequenced a human MTHFS cDNA which is 872-bp long and codes for a 203-amino-acid protein of 23,229 Da. Escherichia coli BL21(DE3), transfected with pET11c plasmids containing an open reading frame encoding MTHFS, showed a 100-fold increase in MTHFS activity in bacterial extracts after IPTG induction. Northern blot studies of human tissues determined that the MTHFS mRNA was expressed preferentially in the liver and Southern blot analysis of human genomic DNA suggested the presence of a single-copy gene.

Simultaneous orthogonal plane imaging.

PubMed

Mickevicius, Nikolai J; Paulson, Eric S

2017-11-01

Intrafraction motion can result in a smearing of planned external beam radiation therapy dose distributions, resulting in an uncertainty in dose actually deposited in tissue. The purpose of this paper is to present a pulse sequence that is capable of imaging a moving target at a high frame rate in two orthogonal planes simultaneously for MR-guided radiotherapy. By balancing the zero gradient moment on all axes, slices in two orthogonal planes may be spatially encoded simultaneously. The orthogonal slice groups may be acquired with equal or nonequal echo times. A Cartesian spoiled gradient echo simultaneous orthogonal plane imaging (SOPI) sequence was tested in phantom and in vivo. Multiplexed SOPI acquisitions were performed in which two parallel slices were imaged along two orthogonal axes simultaneously. An autocalibrating phase-constrained 2D-SENSE-GRAPPA (generalized autocalibrating partially parallel acquisition) algorithm was implemented to reconstruct the multiplexed data. SOPI images without intraslice motion artifacts were reconstructed at a maximum frame rate of 8.16 Hz. The 2D-SENSE-GRAPPA reconstruction separated the parallel slices aliased along each orthogonal axis. The high spatiotemporal resolution provided by SOPI has the potential to be beneficial for intrafraction motion management during MR-guided radiation therapy or other MRI-guided interventions. Magn Reson Med 78:1700-1710, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

In planta expression of HIV-1 p24 protein using an RNA plant virus-based expression vector.

PubMed

Zhang, G; Leung, C; Murdin, L; Rovinski, B; White, K A

2000-02-01

Plant viruses show significant potential as expression vectors for the production of foreign proteins (e.g., antigens) in plants. The HIV-1 p24 nucleocapsid protein is an important early marker of HIV infection and has been used as an antigen in the development of HIV vaccines. Toward developing a plant-based expression system for the production of p24, we have investigated the use of a (positive)-strand RNA plant virus, tomato bushy stunt virus (TBSV), as an expression vector. The HIV p24 open reading frame (ORF) was introduced into a cloned cDNA copy of the TBSV genome as an in-frame fusion with a 5'-terminal portion of the TBSV coat protein ORF. In vitro-generated RNA transcripts corresponding to the engineered virus vector were infectious when inoculated into plant protoplasts; Northern and Western blot analyses verified the accumulation of a predicted p24-encoding viral subgenomic mRNA and the production of p24 fusion product. Whole-plant infections with the viral vector led to the accumulation of p24 fusion protein in inoculated leaves, which cross-reacted with p24-specific antibodies, thus confirming the maintenance of key antigenic determinants. This study is the first to demonstrate that TBSV can be engineered to express a complete foreign protein of clinical importance. Strategies for optimizing protein yield from this viral vector are discussed.

Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames.

PubMed

Liang, Xue-Hai; Shen, Wen; Crooke, Stanley T

2017-01-01

A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.

A novel strategy for the identification of antigens that are recognised by bovine MHC class I restricted cytotoxic T cells in a protozoan infection using reverse vaccinology.

PubMed

Graham, Simon P; Honda, Yoshikazu; Pellé, Roger; Mwangi, Duncan M; Glew, E Jane; de Villiers, Etienne P; Shah, Trushar; Bishop, Richard; van der Bruggen, Pierre; Nene, Vishvanath; Taracha, Evans L N

2007-02-09

Immunity against the bovine protozoan parasite Theileria parva has previously been shown to be mediated through lysis of parasite-infected cells by MHC class I restricted CD8+ cytotoxic T lymphocytes. It is hypothesized that identification of CTL target schizont antigens will aid the development of a sub-unit vaccine. We exploited the availability of the complete genome sequence data and bioinformatics tools to identify genes encoding secreted or membrane anchored proteins that may be processed and presented by the MHC class I molecules of infected cells to CTL. Of the 986 predicted open reading frames (ORFs) encoded by chromosome 1 of the T. parva genome, 55 were selected based on the presence of a signal peptide and/or a transmembrane helix domain. Thirty six selected ORFs were successfully cloned into a eukaryotic expression vector, transiently transfected into immortalized bovine skin fibroblasts and screened in vitro using T. parva-specific CTL. Recognition of gene products by CTL was assessed using an IFN-gamma ELISpot assay. A 525 base pair ORF encoding a 174 amino acid protein, designated Tp2, was identified by T. parva-specific CTL from 4 animals. These CTL recognized and lysed Tp2 transfected skin fibroblasts and recognized 4 distinct epitopes. Significantly, Tp2 specific CD8+ T cell responses were observed during the protective immune response against sporozoite challenge. The identification of an antigen containing multiple CTL epitopes and its apparent immunodominance during a protective anti-parasite response makes Tp2 an attractive candidate for evaluation of its vaccine potential.

Molecular biology of human herpesvirus 8: novel functions and virus-host interactions implicated in viral pathogenesis and replication.

PubMed

Cousins, Emily; Nicholas, John

2014-01-01

Human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus (KSHV), is the second identified human gammaherpesvirus. Like its relative Epstein-Barr virus, HHV-8 is linked to B-cell tumors, specifically primary effusion lymphoma and multicentric Castleman's disease, in addition to endothelial-derived KS. HHV-8 is unusual in its possession of a plethora of "accessory" genes and encoded proteins in addition to the core, conserved herpesvirus and gammaherpesvirus genes that are necessary for basic biological functions of these viruses. The HHV-8 accessory proteins specify not only activities deducible from their cellular protein homologies but also novel, unsuspected activities that have revealed new mechanisms of virus-host interaction that serve virus replication or latency and may contribute to the development and progression of virus-associated neoplasia. These proteins include viral interleukin-6 (vIL-6), viral chemokines (vCCLs), viral G protein-coupled receptor (vGPCR), viral interferon regulatory factors (vIRFs), and viral antiapoptotic proteins homologous to FLICE (FADD-like IL-1β converting enzyme)-inhibitory protein (FLIP) and survivin. Other HHV-8 proteins, such as signaling membrane receptors encoded by open reading frames K1 and K15, also interact with host mechanisms in unique ways and have been implicated in viral pathogenesis. Additionally, a set of micro-RNAs encoded by HHV-8 appear to modulate expression of multiple host proteins to provide conditions conducive to virus persistence within the host and could also contribute to HHV-8-induced neoplasia. Here, we review the molecular biology underlying these novel virus-host interactions and their potential roles in both virus biology and virus-associated disease.

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

2011-01-01

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

Molecular Cloning of an Immunogenic Protein of Baylisascaris procyonis and Expression in Escherichia coli for Use in Developing Improved Serodiagnostic Assays▿

PubMed Central

Dangoudoubiyam, Sriveny; Vemulapalli, Ramesh; Hancock, Kathy; Kazacos, Kevin R.

2010-01-01

Larva migrans caused by Baylisascaris procyonis is an important zoonotic disease. Current serological diagnostic assays for this disease depend on the use of the parasite's larval excretory-secretory (ES) antigens. In order to identify genes encoding ES antigens and to generate recombinant antigens for use in diagnostic assays, construction and immunoscreening of a B. procyonis third-stage larva cDNA expression library was performed and resulted in identification of a partial-length cDNA clone encoding an ES antigen, designated repeat antigen 1 (RAG1). The full-length rag1 cDNA contained a 753-bp open reading frame that encoded a protein of 250 amino acids with 12 tandem repeats of a 12-amino-acid long sequence. The rag1 genomic DNA revealed a single intron of 837 bp that separated the 753-bp coding sequence into two exons delimited by canonical splice sites. No nucleotide or amino acid sequences present in the GenBank databases had significant similarity with those of RAG1. We have cloned, expressed, and purified the recombinant RAG1 (rRAG1) and analyzed its diagnostic potential by enzyme-linked immunosorbent assay. Anti-Baylisascaris species-specific rabbit serum showed strong reactivity to rRAG1, while only minimal to no reactivity was observed with sera against the related ascarids Toxocara canis and Ascaris suum, strongly suggesting the specificity of rRAG1. On the basis of these results, the identified RAG1 appears to be a promising diagnostic antigen for the development of serological assays for specific detection of B. procyonis larva migrans. PMID:20926699

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

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

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott

2012-02-13

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF)more » CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.« less

Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis.

PubMed Central

Li, S J; Cronan, J E

1993-01-01

Acetyl coenzyme A (CoA) carboxylase catalyzes the synthesis of malonyl-CoA, the first intermediate of fatty acid synthesis. The Escherichia coli enzyme is encoded by four subunits located at three different positions on the E. coli chromosome. The accBC genes lie in a small operon at min 72, whereas accA and accD are located at min 4.3 and 50, respectively. We examined the expression of the genes that encode the E. coli acetyl-CoA carboxylase subunits (accA, accBC, and accD) under a variety of growth conditions by quantitative Northern (RNA) blot analysis. We found a direct correlation between the levels of transcription of the acc genes and the rate of cellular growth. Consistent results were also obtained upon nutritional upshift and downshift experiments and upon dilution of stationary-phase cultures into fresh media. We also determined the 5' end of the accA and accD mRNAs by primer extension and did transcriptional fusion analysis of the previously reported accBC promoter. Several interesting features were found in the promoter regions of these genes, including a bent DNA sequence and an open reading frame within the unusually long leader mRNA of the accBC operon, potential stem-loop structures in the accA and accD mRNA leader regions, and a stretch of GC-rich sequences followed by AT-rich sequences common to all three promoters. In addition, both accA and accD are located in complex gene clusters. For example, the accA promoter was localized within the upstream polC gene (which encodes the DNA polymerase III catalytic subunit), suggesting that additional regulatory mechanisms exist. Images PMID:7678242

Complete genome sequence of Fer-de-Lance Virus reveals a novel gene in reptilian Paramyxoviruses

USGS Publications Warehouse

Kurath, G.; Batts, W.N.; Ahne, W.; Winton, J.R.

2004-01-01

The complete RNA genome sequence of the archetype reptilian paramyxovirus, Fer-de-Lance virus (FDLV), has been determined. The genome is 15,378 nucleotides in length and consists of seven nonoverlapping genes in the order 3??? N-U-P-M-F-HN-L 5???, coding for the nucleocapsid, unknown, phospho-, matrix, fusion, hemagglutinin-neuraminidase, and large polymerase proteins, respectively. The gene junctions contain highly conserved transcription start and stop signal sequences and tri-nucleotide intergenic regions similar to those of other Paramyxoviridae. The FDLV P gene expression strategy is like that of rubulaviruses, which express the accessory V protein from the primary transcript and edit a portion of the mRNA to encode P and I proteins. There is also an overlapping open reading frame potentially encoding a small basic protein in the P gene. The gene designated U (unknown), encodes a deduced protein of 19.4 kDa that has no counterpart in other paramyxoviruses and has no similarity with sequences in the National Center for Biotechnology Information database. Active transcription of the U gene in infected cells was demonstrated by Northern blot analysis, and bicistronic N-U mRNA was also evident. The genomes of two other snake paramyxovirus genotypes were also found to have U genes, with 11 to 16% nucleotide divergence from the FDLV U gene. Pairwise comparisons of amino acid identities and phylogenetic analyses of all deduced FDLV protein sequences with homologous sequences from other Paramyxoviridae indicate that FDLV represents a new genus within the subfamily Paramyxovirinae. We suggest the name Ferlavirus for the new genus, with FDLV as the type species.

Dextransucrase Expression Is Concomitant with that of Replication and Maintenance Functions of the pMN1 Plasmid in Lactobacillus sakei MN1

PubMed Central

Nácher-Vázquez, Montserrat; Ruiz-Masó, José A.; Mohedano, María L.; del Solar, Gloria; Aznar, Rosa; López, Paloma

2017-01-01

The exopolysaccharide synthesized by Lactobacillus sakei MN1 is a dextran with antiviral and immunomodulatory properties of potential utility in aquaculture. In this work we have investigated the genetic basis of dextran production by this bacterium. Southern blot hybridization experiments demonstrated the plasmidic location of the dsrLS gene, which encodes the dextransucrase involved in dextran synthesis. DNA sequencing of the 11,126 kbp plasmid (pMN1) revealed that it belongs to a family which replicates by the theta mechanism, whose prototype is pUCL287. The plasmid comprises the origin of replication, repA, repB, and dsrLS genes, as well as seven open reading frames of uncharacterized function. Lb. sakei MN1 produces dextran when sucrose, but not glucose, is present in the growth medium. Therefore, plasmid copy number and stability, as well as dsrLS expression, were investigated in cultures grown in the presence of either sucrose or glucose. The results revealed that pMN1 is a stable low-copy-number plasmid in both conditions. Gene expression studies showed that dsrLS is constitutively expressed, irrespective of the carbon source present in the medium. Moreover, dsrLS is expressed from a monocistronic transcript as well as from a polycistronic repA-repB-orf1-dsrLS mRNA. To our knowledge, this is the first report of a plasmid-borne dextransucrase-encoding gene, as well as the first time that co-transcription of genes involved in plasmid maintenance and replication with a gene encoding an enzyme has been established. PMID:29209293

The microprotein Minion controls cell fusion and muscle formation

PubMed Central

Zhang, Qiao; Vashisht, Ajay A.; O'Rourke, Jason; Corbel, Stéphane Y; Moran, Rita; Romero, Angelica; Miraglia, Loren; Zhang, Jia; Durrant, Eric; Schmedt, Christian; Sampath, Srinath C.; Sampath, Srihari C.

2017-01-01

Although recent evidence has pointed to the existence of small open reading frame (smORF)-encoded microproteins in mammals, their function remains to be determined. Skeletal muscle development requires fusion of mononuclear progenitors to form multinucleated myotubes, a critical but poorly understood process. Here we report the identification of Minion (microprotein inducer of fusion), a smORF encoding an essential skeletal muscle specific microprotein. Myogenic progenitors lacking Minion differentiate normally but fail to form syncytial myotubes, and Minion-deficient mice die perinatally and demonstrate a marked reduction in fused muscle fibres. The fusogenic activity of Minion is conserved in the human orthologue, and co-expression of Minion and the transmembrane protein Myomaker is sufficient to induce cellular fusion accompanied by rapid cytoskeletal rearrangement, even in non-muscle cells. These findings establish Minion as a novel microprotein required for muscle development, and define a two-component programme for the induction of mammalian cell fusion. Moreover, these data also significantly expand the known functions of smORF-encoded microproteins. PMID:28569745

Molecular Mechanisms of Innate Immune Inhibition by Non-Segmented Negative-Sense RNA Viruses

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

Chatterjee, Srirupa; Basler, Christopher F.; Amarasinghe, Gaya K.

The host innate immune system serves as the first line of defense against viral infections. Germline-encoded pattern recognition receptors detect molecular patterns associated with pathogens and activate innate immune responses. Of particular relevance to viral infections are those pattern recognition receptors that activate type I interferon responses, which establish an antiviral state. The order Mononegavirales is composed of viruses that possess single-stranded, non-segmented negative-sense (NNS) RNA genomes and are important human pathogens that consistently antagonize signaling related to type I interferon responses. NNS viruses have limited encoding capacity compared to many DNA viruses, and as a likely consequence, most openmore » reading frames encode multifunctional viral proteins that interact with host factors in order to evade host cell defenses while promoting viral replication. In this review, we will discuss the molecular mechanisms of innate immune evasion by select NNS viruses. A greater understanding of these interactions will be critical in facilitating the development of effective therapeutics and viral countermeasures.« less

Depth, Spread, and Congruence of Encoding in Memory

DTIC Science & Technology

1980-08-01

Alternatively, Craik and Lockhart proposed a more parsimonious frame- work for research based on a levels -of- processing approach. They assumed that the...44. Craik , F. I. M., & Lockhart , R. S. Levels of processing : A framework for memory research. Journal of Verbal Learning and Verbal Behavior, 1972, 11...the basic concepts of the depth-of- processing or domains-of- processing ( Lockhart , Craik , & Jacoby, 1976) framework, suggesting that qualitative

Compressive Information Extraction: A Dynamical Systems Approach

DTIC Science & Technology

2016-01-24

sparsely encoded in very large data streams. (a) Target tracking in an urban canyon; (b) and (c) sample frames showing contextually abnormal events: onset...extraction to identify contextually abnormal se- quences (see section 2.2.3). Formally, the problem of interest can be stated as establishing whether a noisy...relaxations with optimality guarantees can be obtained using tools from semi-algebraic geometry. 2.2 Application: Detecting Contextually Abnormal Events

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

PubMed Central

Atkins, John F.; Loughran, Gary; Bhatt, Pramod R.; Firth, Andrew E.; Baranov, Pavel V.

2016-01-01

Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression. PMID:27436286

PCR amplification and sequence analysis of the major capsid protein gene of megalocytiviruses isolated in Taiwan.

PubMed

Wang, C S; Chao, S Y; Ku, C C; Wen, C M; Shih, H H

2009-06-01

Viruses belonging to the genus Megalocytivirus in the family Iridoviridae are one of the major agents causing mass mortalities in marine and freshwater fish in Asian countries. Outbreaks of iridovirus disease have been reported among various fish species in Taiwan. However, the genotypes of these iridoviruses have not yet been determined. In this study, seven megalocytivirus isolates from four fish species: king grouper, Epinephelus lanceolatus (Bloch), barramundi perch, Lates calcarifer (Bloch), silver sea bream, Rhabdosargus sarba (Forsskal), and common ponyfish, Leiognathus equulus (Forsskal), cultured in three different regions of Taiwan were collected. The full open reading frame encoding the viral major capsid protein gene was amplified using PCR. The PCR products of approximately 1581 bp were cloned and the nucleotide sequences were phylogenetically analysed. Results showed that all seven PCR products contained a unique open reading frame with 1362 nucleotides and encoded a structural protein with 453 amino acids. Even though the nucleotide sequences were not identical, these seven megalocytiviruses were classified into one cluster and showed very high homology with red sea bream iridovirus (RSIV) with more than 97% identity. Thus, the seven iridovirus strains isolated from cultured marine fish in Taiwan were closer to the RSIV genotype than the infectious spleen and kidney necrosis virus genotype.

Novel Genes Encoding Hexadecanoic Acid Δ6-Desaturase Activity in a Rhodococcus sp.

PubMed

Araki, Hiroyuki; Hagihara, Hiroshi; Takigawa, Hirofumi; Tsujino, Yukiharu; Ozaki, Katsuya

2016-11-01

cis-6-Hexadecenoic acid, a major component of human sebaceous lipids, is involved in the defense mechanism against Staphylococcus aureus infection in healthy skin and closely related to atopic dermatitis. Previously, Koike et al. (Biosci Biotechnol Biochem 64:1064-1066, 2000) reported that a mutant strain of Rhodococcus sp. produced cis-6-hexadecenoate derivatives from palmitate alkyl esters. From the mutant Rhodococcus strain, we identified and sequenced two open reading frames present in an amplified 5.7-kb region; these open reading frames encoded tandemly repeated Δ6-desaturase-like genes, Rdes1 and Rdes2. A phylogenetic tree indicated that Rdes1 and Rdes2 were different from previously known Δ6-desaturase genes, and that they formed a new cluster. Rdes1 and Rdes2 were each introduced into vectors and then expressed separately in Escherichia coli, and the fatty acid composition of the transformed cells was analyzed by gas chromatography and mass spectrometry. The amount of cis-6-hexadecenoic acid was significantly higher in Rdes1- or Rdes2-transformed E. coli cells (twofold and threefold, respectively) than in vector-only control cells. These results showed that cis-6-hexadecenoic acid was produced in E. coli cells by the rhodococcal Δ6-desaturase-like proteins.

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

NASA Technical Reports Server (NTRS)

Cho, G.; Keefe, A. D.; Liu, R.; Wilson, D. S.; Szostak, J. W.

2000-01-01

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

Perceptual video quality comparison of 3DTV broadcasting using multimode service systems

NASA Astrophysics Data System (ADS)

Ok, Jiheon; Lee, Chulhee

2015-05-01

Multimode service (MMS) systems allow broadcasters to provide multichannel services using a single HD channel. Using these systems, it is possible to provide 3DTV programs that can be watched either in three-dimensional (3-D) or two-dimensional (2-D) modes with backward compatibility. In the MMS system for 3DTV broadcasting using the Advanced Television Systems Committee standards, the left and the right views are encoded using MPEG-2 and H.264, respectively, and then transmitted using a dual HD streaming format. The left view, encoded using MPEG-2, assures 2-D backward compatibility while the right view, encoded using H.264, can be optionally combined with the left view to generate stereoscopic 3-D views. We analyze 2-D and 3-D perceptual quality when using the MMS system by comparing items in the frame-compatible format (top-bottom), which is a conventional transmission scheme for 3-D broadcasting. We performed perceptual 2-D and 3-D video quality evaluation assuming 3DTV programs are encoded using the MMS system and top-bottom format. The results show that MMS systems can be preferable with regard to perceptual 2-D and 3-D quality and backward compatibility.

Up by upwest: Is slope like north?

PubMed

Weisberg, Steven M; Nardi, Daniele; Newcombe, Nora S; Shipley, Thomas F

2014-10-01

Terrain slope can be used to encode the location of a goal. However, this directional information may be encoded using a conceptual north (i.e., invariantly with respect to the environment), or in an observer-relative fashion (i.e., varying depending on the direction one faces when learning the goal). This study examines which representation is used, whether the sensory modality in which slope is encoded (visual, kinaesthetic, or both) influences representations, and whether use of slope varies for men and women. In a square room, with a sloped floor explicitly pointed out as the only useful cue, participants encoded the corner in which a goal was hidden. Without direct sensory access to slope cues, participants used a dial to point to the goal. For each trial, the goal was hidden uphill or downhill, and the participants were informed whether they faced uphill or downhill when pointing. In support of observer-relative representations, participants pointed more accurately and quickly when facing concordantly with the hiding position. There was no effect of sensory modality, providing support for functional equivalence. Sex did not interact with the findings on modality or reference frame, but spatial measures correlated with success on the slope task differently for each sex.

The ribosome as a missing link in the evolution of life.

PubMed

Root-Bernstein, Meredith; Root-Bernstein, Robert

2015-02-21

Many steps in the evolution of cellular life are still mysterious. We suggest that the ribosome may represent one important missing link between compositional (or metabolism-first), RNA-world (or genes-first) and cellular (last universal common ancestor) approaches to the evolution of cells. We present evidence that the entire set of transfer RNAs for all twenty amino acids are encoded in both the 16S and 23S rRNAs of Escherichia coli K12; that nucleotide sequences that could encode key fragments of ribosomal proteins, polymerases, ligases, synthetases, and phosphatases are to be found in each of the six possible reading frames of the 16S and 23S rRNAs; and that every sequence of bases in rRNA has information encoding more than one of these functions in addition to acting as a structural component of the ribosome. Ribosomal RNA, in short, is not just a structural scaffold for proteins, but the vestigial remnant of a primordial genome that may have encoded a self-organizing, self-replicating, auto-catalytic intermediary between macromolecules and cellular life. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Development of B cells expressing surface immunoglobulin molecules that lack V(D)J-encoded determinants in the avian embryo bursa of Fabricius

PubMed Central

Sayegh, Camil E.; Demaries, Sandra L.; Iacampo, Sandra; Ratcliffe, Michael J. H.

1999-01-01

Immunoglobulin gene rearrangement in avian B cell precursors generates surface Ig receptors of limited diversity. It has been proposed that specificities encoded by these receptors play a critical role in B lineage development by recognizing endogenous ligands within the bursa of Fabricius. To address this issue directly we have introduced a truncated surface IgM, lacking variable region domains, into developing B precursors by retroviral gene transfer in vivo. Cells expressing this truncated receptor lack endogenous surface IgM, and the low level of endogenous Ig rearrangements that have occurred within this population of cells has not been selected for having a productive reading frame. Such cells proliferate rapidly within bursal epithelial buds of normal morphology. In addition, despite reduced levels of endogenous light chain rearrangement, those light chain rearrangements that have occurred have undergone variable region diversification by gene conversion. Therefore, although surface expression of an Ig receptor is required for bursal colonization and the induction of gene conversion, the specificity encoded by the prediversified receptor is irrelevant and, consequently, there is no obligate ligand for V(D)J-encoded determinants of prediversified avian cell surface IgM receptor. PMID:10485907

Isolation and functional expression of human COQ2, a gene encoding a polyprenyl transferase involved in the synthesis of CoQ.

PubMed

Forsgren, Margareta; Attersand, Anneli; Lake, Staffan; Grünler, Jacob; Swiezewska, Ewa; Dallner, Gustav; Climent, Isabel

2004-09-01

The COQ2 gene in Saccharomyces cerevisiae encodes a Coq2 (p-hydroxybenzoate:polyprenyl transferase), which is required in the biosynthetic pathway of CoQ (ubiquinone). This enzyme catalyses the prenylation of p-hydroxybenzoate with an all-trans polyprenyl group. We have isolated cDNA which we believe encodes the human homologue of COQ2 from a human muscle and liver cDNA library. The clone contained an open reading frame of length 1263 bp, which encodes a polypeptide that has sequence homology with the Coq2 homologues in yeast, bacteria and mammals. The human COQ2 gene, when expressed in yeast Coq2 null mutant cells, rescued the growth of this yeast strain in the absence of a non-fermentable carbon source and restored CoQ biosynthesis. However, the rate of CoQ biosynthesis in the rescued cells was lower when compared with that in cells rescued with the yeast COQ2 gene. CoQ formed when cells were incubated with labelled decaprenyl pyrophosphate and nonaprenyl pyrophosphate, showing that the human enzyme is active and that it participates in the biosynthesis of CoQ.

Cloning of an avilamycin biosynthetic gene cluster from Streptomyces viridochromogenes Tü57.

PubMed Central

Gaisser, S; Trefzer, A; Stockert, S; Kirschning, A; Bechthold, A

1997-01-01

A 65-kb region of DNA from Streptomyces viridochromogenes Tü57, containing genes encoding proteins involved in the biosynthesis of avilamycins, was isolated. The DNA sequence of a 6.4-kb fragment from this region revealed four open reading frames (ORF1 to ORF4), three of which are fully contained within the sequenced fragment. The deduced amino acid sequence of AviM, encoded by ORF2, shows 37% identity to a 6-methylsalicylic acid synthase from Penicillium patulum. Cultures of S. lividans TK24 and S. coelicolor CH999 containing plasmids with ORF2 on a 5.5-kb PstI fragment were able to produce orsellinic acid, an unreduced version of 6-methylsalicylic acid. The amino acid sequence encoded by ORF3 (AviD) is 62% identical to that of StrD, a dTDP-glucose synthase from S. griseus. The deduced amino acid sequence of AviE, encoded by ORF4, shows 55% identity to a dTDP-glucose dehydratase (StrE) from S. griseus. Gene insertional inactivation experiments of aviE abolished avilamycin production, indicating the involvement of aviE in the biosynthesis of avilamycins. PMID:9335272

Ribosomal scanning past the primary initiation codon as a mechanism for expression of CTL epitopes encoded in alternative reading frames

PubMed Central

1996-01-01

An increasing amount of evidence has shown that epitopes restricted to MHC class I molecules and recognized by CTL need not be encoded in a primary open reading frame (ORF). Such epitopes have been demonstrated after stop codons, in alternative reading frames (RF) and within introns. We have used a series of frameshifts (FS) introduced into the Influenza A/PR/8 /34 nucleoprotein (NP) gene to confirm the previous in vitro observations of cryptic epitope expression, and show that they are sufficiently expressed to prime immune responses in vivo. This presentation is not due to sub-dominant epitopes, transcription from cryptic promoters beyond the point of the FS, or internal initiation of translation. By introducing additional mutations to the construct exhibiting the most potent presentation, we have identified initiation codon readthrough (termed scanthrough here, where the scanning ribosome bypasses the conventional initiation codon, initiating translation further downstream) as the likely mechanism of epitope production. Further mutational analysis demonstrated that, while it should operate during the expression of wild-type (WT) protein, scanthrough does not provide a major source of processing substrate in our system. These findings suggest (i) that the full array of self- and pathogen-derived epitopes available during thymic selection and infection has not been fully appreciated and (ii) that cryptic epitope expression should be considered when the specificity of a CTL response cannot be identified or in therapeutic situations when conventional CTL targets are limited, as may be the case with latent viral infections and transformed cells. Finally, initiation codon readthrough provides a plausible explanation for the presentation of exocytic proteins by MHC class I molecules. PMID:8879204

A thermolabile aspartic proteinase from Mucor mucedo DSM 809: gene identification, cloning, and functional expression in Pichia pastoris.

PubMed

Yegin, Sirma; Fernandez-Lahore, Marcelo

2013-06-01

In this study, the cDNA encoding the aspartic proteinase of Mucor mucedo DSM 809 has been identified by RNA ligased-mediated and oligo-capping rapid amplification of cDNA ends (RACE) technique. The gene contained an open reading frame of 1,200 bp and encoded for a signal peptide of 21 amino acid residues. Two N-glycosylation sites were observed within the identified sequence. The proteinase gene was cloned into the vector pGAPZαA and expressed in Pichia pastoris X-33 for the first time. The protein has been secreted in functionally active form into the culture medium. The expression system does not require any acid activation process. The factors affecting the expression level were optimized in shaking flask cultures. Maximum enzyme production was observed with an initial medium pH of 3.5 at 20 °C and 220 rpm shaking speed utilizing 4 % glucose as a carbon and energy source. The enzyme was purified with cation exchange chromatography and further studies revealed that the enzyme was secreted in glycosylated form. The purified enzyme exhibited remarkable sensitivity to thermal treatment and became completely inactivated after incubation at 55 °C for 10 min. These results indicated that the recombinant proteinase could be considered as a potential rennet candidate for the cheese-making industry.

Molecular cloning of a gene encoding translation initiation factor (TIF) from Candida albicans.

PubMed

Mirbod, F; Nakashima, S; Kitajima, Y; Ghannoum, M A; Cannon, R D; Nozawa, Y

1996-01-01

The differential display technique was applied to compare mRNAs from two clinical isolates of Candida albicans with different virulence; high (potent strain, 16240) and low (weak strain, 18084) extracellular phospholipase activities. Complementary DNA fragments corresponding to several apparently differentially expressed mRNAs were recovered and sequenced. A complementary DNA fragment seen distinctly in the potent phospholipase producing strain was highly homologous to the yeast translation initiation factor (TIF). The selected DNA fragment was then used as a probe to isolate its corresponding complementary DNA clone from a library of C. albicans genomic DNA. The sequence of isolated gene revealed an open reading frame of 1194 nucleotides with the potential to encode a protein of 397 amino acids with a predicted molecular weight of 43 kDa. Over its entire length, the amino acid sequence showed strong homology (78-89%) to Saccharomyces cerevisiae TIF and (63-80%) to mouse eIF-4A proteins. Therefore, our C. albicans gene was identified to be TIF (Ca TIF). Northern blot analysis in the two strains of C. albicans revealed that Ca TIF expression is 1.5-fold higher in the potent phospholipase producing strain. The restriction endonuclease digestion of genomic DNA from this potent strain revealed at least two hybridized bands in Southern blot analysis, suggesting two or more closely related sequences in the C. albicans genome.

MOXD2, a Gene Possibly Associated with Olfaction, Is Frequently Inactivated in Birds

PubMed Central

Goh, Chul Jun; Choi, Dongjin; Park, Dong-Bin; Kim, Hyein; Hahn, Yoonsoo

2016-01-01

Vertebrate MOXD2 encodes a monooxygenase DBH-like 2 protein that could be involved in neurotransmitter metabolism, potentially during olfactory transduction. Loss of MOXD2 in apes and whales has been proposed to be associated with evolution of olfaction in these clades. We analyzed 57 bird genomes to identify MOXD2 sequences and found frequent loss of MOXD2 in 38 birds. Among the 57 birds, 19 species appeared to have an intact MOXD2 that encoded a full-length protein; 32 birds had a gene with open reading frame-disrupting point mutations and/or exon deletions; and the remaining 6 species did not show any MOXD2 sequence, suggesting a whole-gene deletion. Notably, among 10 passerine birds examined, 9 species shared a common genomic deletion that spanned several exons, implying the gene loss occurred in a common ancestor of these birds. However, 2 closely related penguin species, each of which had an inactive MOXD2, did not share any mutation, suggesting an independent loss after their divergence. Distribution of the 38 birds without an intact MOXD2 in the bird phylogenetic tree clearly indicates that MOXD2 loss is widespread and independent in bird lineages. We propose that widespread MOXD2 loss in some bird lineages may be implicated in the evolution of olfactory perception in these birds. PMID:27074048

MOXD2, a Gene Possibly Associated with Olfaction, Is Frequently Inactivated in Birds.

PubMed

Goh, Chul Jun; Choi, Dongjin; Park, Dong-Bin; Kim, Hyein; Hahn, Yoonsoo

2016-01-01

Vertebrate MOXD2 encodes a monooxygenase DBH-like 2 protein that could be involved in neurotransmitter metabolism, potentially during olfactory transduction. Loss of MOXD2 in apes and whales has been proposed to be associated with evolution of olfaction in these clades. We analyzed 57 bird genomes to identify MOXD2 sequences and found frequent loss of MOXD2 in 38 birds. Among the 57 birds, 19 species appeared to have an intact MOXD2 that encoded a full-length protein; 32 birds had a gene with open reading frame-disrupting point mutations and/or exon deletions; and the remaining 6 species did not show any MOXD2 sequence, suggesting a whole-gene deletion. Notably, among 10 passerine birds examined, 9 species shared a common genomic deletion that spanned several exons, implying the gene loss occurred in a common ancestor of these birds. However, 2 closely related penguin species, each of which had an inactive MOXD2, did not share any mutation, suggesting an independent loss after their divergence. Distribution of the 38 birds without an intact MOXD2 in the bird phylogenetic tree clearly indicates that MOXD2 loss is widespread and independent in bird lineages. We propose that widespread MOXD2 loss in some bird lineages may be implicated in the evolution of olfactory perception in these birds.

Carbon source-dependent expansion of the genetic code in bacteria

PubMed Central

Prat, Laure; Heinemann, Ilka U.; Aerni, Hans R.; Rinehart, Jesse; O’Donoghue, Patrick; Söll, Dieter

2012-01-01

Despite the fact that the genetic code is known to vary between organisms in rare cases, it is believed that in the lifetime of a single cell the code is stable. We found Acetohalobium arabaticum cells grown on pyruvate genetically encode 20 amino acids, but in the presence of trimethylamine (TMA), A. arabaticum dynamically expands its genetic code to 21 amino acids including pyrrolysine (Pyl). A. arabaticum is the only known organism that modulates the size of its genetic code in response to its environment and energy source. The gene cassette pylTSBCD, required to biosynthesize and genetically encode UAG codons as Pyl, is present in the genomes of 24 anaerobic archaea and bacteria. Unlike archaeal Pyl-decoding organisms that constitutively encode Pyl, we observed that A. arabaticum controls Pyl encoding by down-regulating transcription of the entire Pyl operon under growth conditions lacking TMA, to the point where no detectable Pyl-tRNAPyl is made in vivo. Pyl-decoding archaea adapted to an expanded genetic code by minimizing TAG codon frequency to typically ∼5% of ORFs, whereas Pyl-decoding bacteria (∼20% of ORFs contain in-frame TAGs) regulate Pyl-tRNAPyl formation and translation of UAG by transcriptional deactivation of genes in the Pyl operon. We further demonstrate that Pyl encoding occurs in a bacterium that naturally encodes the Pyl operon, and identified Pyl residues by mass spectrometry in A. arabaticum proteins including two methylamine methyltransferases. PMID:23185002

Multiple Functional Domains of Enterococcus faecalis Aggregation Substance Asc10 Contribute to Endocarditis Virulence ▿ †

PubMed Central

Chuang, Olivia N.; Schlievert, Patrick M.; Wells, Carol L.; Manias, Dawn A.; Tripp, Timothy J.; Dunny, Gary M.

2009-01-01

Aggregation substance proteins encoded by sex pheromone plasmids increase the virulence of Enterococcus faecalis in experimental pathogenesis models, including infectious endocarditis models. These large surface proteins may contain multiple functional domains involved in various interactions with other bacterial cells and with the mammalian host. Aggregation substance Asc10, encoded by plasmid pCF10, is induced during growth in the mammalian bloodstream, and pCF10 carriage gives E. faecalis a significant selective advantage in this environment. We employed a rabbit model to investigate the role of various functional domains of Asc10 in endocarditis. The data suggested that the bacterial load of the infected tissue was the best indicator of virulence. Isogenic strains carrying either no plasmid, wild-type pCF10, a pCF10 derivative with an in-frame deletion of the prgB gene encoding Asc10, or pCF10 derivatives expressing other alleles of prgB were examined in this model. Previously identified aggregation domains contributed to the virulence associated with the wild-type protein, and a strain expressing an Asc10 derivative in which glycine residues in two RGD motifs were changed to alanine residues showed the greatest reduction in virulence. Remarkably, this strain and the strain carrying the pCF10 derivative with the in-frame deletion of prgB were both significantly less virulent than an isogenic plasmid-free strain. The data demonstrate that multiple functional domains are important in Asc10-mediated interactions with the host during the course of experimental endocarditis and that in the absence of a functional prgB gene, pCF10 carriage is actually disadvantageous in vivo. PMID:18955479

ESSG-based global spatial reference frame for datasets interrelation

NASA Astrophysics Data System (ADS)

Yu, J. Q.; Wu, L. X.; Jia, Y. J.

2013-10-01

To know well about the highly complex earth system, a large volume of, as well as a large variety of, datasets on the planet Earth are being obtained, distributed, and shared worldwide everyday. However, seldom of existing systems concentrates on the distribution and interrelation of different datasets in a common Global Spatial Reference Frame (GSRF), which holds an invisble obstacle to the data sharing and scientific collaboration. Group on Earth Obeservation (GEO) has recently established a new GSRF, named Earth System Spatial Grid (ESSG), for global datasets distribution, sharing and interrelation in its 2012-2015 WORKING PLAN.The ESSG may bridge the gap among different spatial datasets and hence overcome the obstacles. This paper is to present the implementation of the ESSG-based GSRF. A reference spheroid, a grid subdvision scheme, and a suitable encoding system are required to implement it. The radius of ESSG reference spheroid was set to the double of approximated Earth radius to make datasets from different areas of earth system science being covered. The same paramerters of positioning and orienting as Earth Centred Earth Fixed (ECEF) was adopted for the ESSG reference spheroid to make any other GSRFs being freely transformed into the ESSG-based GSRF. Spheroid degenerated octree grid with radius refiment (SDOG-R) and its encoding method were taken as the grid subdvision and encoding scheme for its good performance in many aspects. A triple (C, T, A) model is introduced to represent and link different datasets based on the ESSG-based GSRF. Finally, the methods of coordinate transformation between the ESSGbased GSRF and other GSRFs were presented to make ESSG-based GSRF operable and propagable.

Characterization of two distinct dual specificity phosphatases encoded in alternative open reading frames of a single gene located on human chromosome 10q22.2.

PubMed

Chen, Hsu-Hsin; Luche, Ralf; Wei, Bo; Tonks, Nicholas K

2004-10-01

Dual specificity phosphatases (DSPs) are members of the protein-tyrosine phosphatase superfamily that dephosphorylate both phosphotyrosine and phosphoserine/threonine residues in vitro. Many DSPs have been found to play important roles in various aspects of cellular function and to be involved in human disease. We have identified a gene located on human chromosome 10q22.2, which utilizes alternative open reading frames (ORFs) to encode the following two distinct DSPs: the previously described testis and skeletal muscle-specific dual specificity phosphatase (TMDP) and a novel DSP, muscle-restricted dual specificity phosphatase (MDSP). Use of alternative ORFs encoding distinct proteins from a single gene is extremely rare in eukaryotes, and in all previously reported cases the two proteins produced from one gene are unrelated. To our knowledge this is the first example of a gene from which two distinct proteins of the same family are expressed using alternative ORFs. Here we provide evidence that both MDSP and TMDP proteins are expressed in vivo and are restricted to specific tissues, skeletal muscle and testis, respectively. Most interestingly, the protein expression profiles of both MDSP and TMDP during mouse postnatal development are strikingly similar. MDSP is expressed at very low levels in myotubes and early postnatal muscle. TMDP is not detectable in testis lysate in the first 3 weeks of life. The expression of both MDSP and TMDP proteins was markedly increased at approximately the 3rd week after birth and continued to increase gradually into adulthood, implying that the physiological functions of both DSPs are specific to the mature/late-developing organs. The conserved gene structure and the similarity in postnatal expression profile of these two proteins suggest biological significance of the unusual gene arrangement.

Characterization of the Thermal Stress Response of Campylobacter jejuni

PubMed Central

Konkel, Michael E.; Kim, Bong J.; Klena, John D.; Young, Colin R.; Ziprin, Richard

1998-01-01

Campylobacter jejuni, a microaerophilic, gram-negative bacterium, is a common cause of gastrointestinal disease in humans. Heat shock proteins are a group of highly conserved, coregulated proteins that play important roles in enabling organisms to cope with physiological stresses. The primary aim of this study was to characterize the heat shock response of C. jejuni. Twenty-four proteins were preferentially synthesized by C. jejuni immediately following heat shock. Upon immunoscreening of Escherichia coli transformants harboring a Campylobacter genomic DNA library, one recombinant plasmid that encoded a heat shock protein was isolated. The recombinant plasmid, designated pMEK20, contained an open reading frame of 1,119 bp that was capable of encoding a protein of 372 amino acids with a calculated molecular mass of 41,436 Da. The deduced amino acid sequence of the open reading frame shared similarity with that of DnaJ, which belongs to the Hsp-40 family of molecular chaperones, from a number of bacteria. An E. coli dnaJ mutant was successfully complemented with the pMEK20 recombinant plasmid, as judged by the ability of bacteriophage λ to form plaques, indicating that the C. jejuni gene encoding the 41-kDa protein is a functional homolog of the dnaJ gene from E. coli. The ability of each of two C. jejuni dnaJ mutants to form colonies at 46°C was severely retarded, indicating that DnaJ plays an important role in C. jejuni thermotolerance. Experiments revealed that a C. jejuni DnaJ mutant was unable to colonize newly hatched Leghorn chickens, suggesting that heat shock proteins play a role in vivo. PMID:9673247

Adaptive quantization-parameter clip scheme for smooth quality in H.264/AVC.

PubMed

Hu, Sudeng; Wang, Hanli; Kwong, Sam

2012-04-01

In this paper, we investigate the issues over the smooth quality and the smooth bit rate during rate control (RC) in H.264/AVC. An adaptive quantization-parameter (Q(p)) clip scheme is proposed to optimize the quality smoothness while keeping the bit-rate fluctuation at an acceptable level. First, the frame complexity variation is studied by defining a complexity ratio between two nearby frames. Second, the range of the generated bits is analyzed to prevent the encoder buffer from overflow and underflow. Third, based on the safe range of the generated bits, an optimal Q(p) clip range is developed to reduce the quality fluctuation. Experimental results demonstrate that the proposed Q(p) clip scheme can achieve excellent performance in quality smoothness and buffer regulation.

Pulse Code Modulation (PCM) data storage and analysis using a microcomputer

NASA Technical Reports Server (NTRS)

Massey, D. E.

1986-01-01

The current widespread use of microcomputers has led to the creation of some very low-cost instrumentation. A Pulse Code Modulation (PCM) storage device/data analyzer -- a peripheral plug-in board especially constructed to enable a personal computer to store and analyze data from a PCM source -- was designed and built for use on the NASA Sounding Rocket Program for PMC encoder configuration and testing. This board and custom-written software turns a computer into a snapshot PCM decommutator which will accept and store many hundreds or thousands of PCM telemetry data frames, then sift through them repeatedly. These data can be converted to any number base and displayed, examined for any bit dropouts or changes (in particular, words or frames), graphically plotted, or statistically analyzed.

Promoting the Avoidance of High-Calorie Snacks: Priming Autonomy Moderates Message Framing Effects

PubMed Central

Pavey, Louisa; Churchill, Sue

2014-01-01

The beneficial effects of gain-framed vs. loss-framed messages promoting health protective behaviors have been found to be inconsistent, and consideration of potential moderating variables is essential if framed health promotion messages are to be effective. This research aimed to determine the influence of highlighting autonomy (choice and freedom) and heteronomy (coercion) on the avoidance of high-calorie snacks following reading gain-framed or loss-framed health messages. In Study 1 (N = 152) participants completed an autonomy, neutral, or heteronomy priming task, and read a gain-framed or loss-framed health message. In Study 2 (N = 242) participants read a gain-framed or loss-framed health message with embedded autonomy or heteronomy primes. In both studies, snacking intentions and behavior were recorded after seven days. In both studies, when autonomy was highlighted, the gain-framed message (compared to the loss-framed message) resulted in stronger intentions to avoid high-calorie snacks, and lower self-reported snack consumption after seven days. Study 2 demonstrated this effect occurred only for participants to whom the information was most relevant (BMI>25). The results suggest that messages promoting healthy dietary behavior may be more persuasive if the autonomy-supportive vs. coercive nature of the health information is matched to the message frame. Further research is needed to examine potential mediating processes. PMID:25078965

Promoting the avoidance of high-calorie snacks: priming autonomy moderates message framing effects.

PubMed

Pavey, Louisa; Churchill, Sue

2014-01-01

The beneficial effects of gain-framed vs. loss-framed messages promoting health protective behaviors have been found to be inconsistent, and consideration of potential moderating variables is essential if framed health promotion messages are to be effective. This research aimed to determine the influence of highlighting autonomy (choice and freedom) and heteronomy (coercion) on the avoidance of high-calorie snacks following reading gain-framed or loss-framed health messages. In Study 1 (N = 152) participants completed an autonomy, neutral, or heteronomy priming task, and read a gain-framed or loss-framed health message. In Study 2 (N = 242) participants read a gain-framed or loss-framed health message with embedded autonomy or heteronomy primes. In both studies, snacking intentions and behavior were recorded after seven days. In both studies, when autonomy was highlighted, the gain-framed message (compared to the loss-framed message) resulted in stronger intentions to avoid high-calorie snacks, and lower self-reported snack consumption after seven days. Study 2 demonstrated this effect occurred only for participants to whom the information was most relevant (BMI>25). The results suggest that messages promoting healthy dietary behavior may be more persuasive if the autonomy-supportive vs. coercive nature of the health information is matched to the message frame. Further research is needed to examine potential mediating processes.

Framing of information on the use of public finances, regulatory fit of recipients and tax compliance

PubMed Central

Holler, Marianne; Hoelzl, Erik; Kirchler, Erich; Leder, Susanne; Mannetti, Lucia

2010-01-01

Information campaigns to increase tax compliance could be framed in different ways. They can either highlight the potential gains when tax compliance is high, or the potential losses when compliance is low. According to regulatory focus theory, such framing should be most effective when it is congruent with the promotion or prevention focus of its recipients. Two studies confirmed the hypothesized interaction effects between recipients' regulatory focus and framing of information campaigns, with tax compliance being highest under conditions of regulatory fit. To address taxpayers effectively, information campaigns by tax authorities should consider the positive and negative framing of information, and the moderating effect of recipients' regulatory focus. PMID:20495689

Framing of information on the use of public finances, regulatory fit of recipients and tax compliance.

PubMed

Holler, Marianne; Hoelzl, Erik; Kirchler, Erich; Leder, Susanne; Mannetti, Lucia

2008-08-01

Information campaigns to increase tax compliance could be framed in different ways. They can either highlight the potential gains when tax compliance is high, or the potential losses when compliance is low. According to regulatory focus theory, such framing should be most effective when it is congruent with the promotion or prevention focus of its recipients. Two studies confirmed the hypothesized interaction effects between recipients' regulatory focus and framing of information campaigns, with tax compliance being highest under conditions of regulatory fit. To address taxpayers effectively, information campaigns by tax authorities should consider the positive and negative framing of information, and the moderating effect of recipients' regulatory focus.

Frames for exact inversion of the rank order coder.

PubMed

Masmoudi, Khaled; Antonini, Marc; Kornprobst, Pierre

2012-02-01

Our goal is to revisit rank order coding by proposing an original exact decoding procedure for it. Rank order coding was proposed by Thorpe et al. who stated that the order in which the retina cells are activated encodes for the visual stimulus. Based on this idea, the authors proposed in [1] a rank order coder/decoder associated to a retinal model. Though, it appeared that the decoding procedure employed yields reconstruction errors that limit the model bit-cost/quality performances when used as an image codec. The attempts made in the literature to overcome this issue are time consuming and alter the coding procedure, or are lacking mathematical support and feasibility for standard size images. Here we solve this problem in an original fashion by using the frames theory, where a frame of a vector space designates an extension for the notion of basis. Our contribution is twofold. First, we prove that the analyzing filter bank considered is a frame, and then we define the corresponding dual frame that is necessary for the exact image reconstruction. Second, to deal with the problem of memory overhead, we design a recursive out-of-core blockwise algorithm for the computation of this dual frame. Our work provides a mathematical formalism for the retinal model under study and defines a simple and exact reverse transform for it with over than 265 dB of increase in the peak signal-to-noise ratio quality compared to [1]. Furthermore, the framework presented here can be extended to several models of the visual cortical areas using redundant representations.

A highly divergent gene cluster in honey bees encodes a novel silk family.

PubMed

Sutherland, Tara D; Campbell, Peter M; Weisman, Sarah; Trueman, Holly E; Sriskantha, Alagacone; Wanjura, Wolfgang J; Haritos, Victoria S

2006-11-01

The pupal cocoon of the domesticated silk moth Bombyx mori is the best known and most extensively studied insect silk. It is not widely known that Apis mellifera larvae also produce silk. We have used a combination of genomic and proteomic techniques to identify four honey bee fiber genes (AmelFibroin1-4) and two silk-associated genes (AmelSA1 and 2). The four fiber genes are small, comprise a single exon each, and are clustered on a short genomic region where the open reading frames are GC-rich amid low GC intergenic regions. The genes encode similar proteins that are highly helical and predicted to form unusually tight coiled coils. Despite the similarity in size, structure, and composition of the encoded proteins, the genes have low primary sequence identity. We propose that the four fiber genes have arisen from gene duplication events but have subsequently diverged significantly. The silk-associated genes encode proteins likely to act as a glue (AmelSA1) and involved in silk processing (AmelSA2). Although the silks of honey bees and silkmoths both originate in larval labial glands, the silk proteins are completely different in their primary, secondary, and tertiary structures as well as the genomic arrangement of the genes encoding them. This implies independent evolutionary origins for these functionally related proteins.

Two T7-like Bacteriophages, K5-2 and K5-4, Each Encodes Two Capsule Depolymerases: Isolation and Functional Characterization.

PubMed

Hsieh, Pei-Fang; Lin, Hsiao-Hsuan; Lin, Tzu-Lung; Chen, Yi-Yin; Wang, Jin-Town

2017-07-04

Two Klebsiella bacteriophages K5-2 and K5-4, which are able to infect and grow on either capsular types K30/K69 and K5 or K8 and K5 of Klebsiella strains, were isolated and characterized. Each phage contained two open reading frames (ORFs), which encoded two putative capsule depolymerases, respectively. The first ORF encoded tail fiber proteins, which have K30/K69 depolymerase and K8 depolymerase activities. The second ORF encoded hypothetical proteins, which are almost identical in amino acid sequences, and have K5 depolymerase activity. Alcian blue staining of enzyme-treated capsular polysaccharides (CPS) showed that purified depolymerases can cleave purified Klebsiella CPS in vitro and liberate monosaccharaides. Capsule K5 deletion mutants were not lysed by either phage, suggesting that the capsule was essential for phage infection. Bacterial killing was observed when incubated Klebsiella strains with phages but not with purified depolymerases. Treatment with the K5-4 phage significantly increased the survival of mice infected with a K. pneumoniae K5 strain. In conclusion, two dual host-specific Klebsiella phages and their tailspikes exhibit capsule depolymerase activity were characterized. Each phage and phage-encoded depolymerase has specificity for capsular type K30/K69, K8 or K5, and could be used for the typing and treatment of K. pneumoniae infection.

Functional expression of a Bombyx mori cocoonase: potential application for silk degumming.

PubMed

Rodbumrer, Prangprapai; Arthan, Dumrongkiet; Uyen, Utai; Yuvaniyama, Jirundon; Svasti, Jisnuson; Wongsaengchantra, Pramvadee Y

2012-12-01

Cocoon, a shelter for larva development to silk moth, contains the fibrous protein fibroin, which is coated by the globular protein sericin. Emergence of the silk moth requires the action of cocoonase, a protease secreted by the pupa. The full-length prococoonase cDNA, with 780 bp open reading frame encoding 260 amino acids, was cloned by reverse transcription from total RNA of the head of 6-day-old Thai-silk Bombyx mori pupa. Only the gene fragment lacking the propeptide encoding sequence was successfully expressed in Pichia pastoris, yielding an extracellularly active cocoonase. The recombinant cocoonase was purified to homogeneity by 80% ammonium-sulfate fractionation and CM-Sepharose chromatography, and its internal peptide sequences were analyzed by nano liquid chromatography-mass spectrometry/mass spectrometry. This monomeric protein has native molecular weight of 26 kDa by gel exclusion analysis and 25 kDa subunit size by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The enzyme hydrolyses sericin but does not hydrolyse fibroin, as shown by radial diffusion on thin-layer enzyme assay (RD-TEA). Scanning electron microscopy showed that purified recombinant cocoonase could remove sericin from natural silk completely in 24 h, without damaging fibroin, using only 1 immobilized sericin unit (ISU) of enzyme as determined by RD-TEA. Natural cocoonase isolated from B. mori pupa could also digest sericin effectively, but required more enzymes (2 ISU) and longer time (48 h). In comparison, a commercial enzyme, alcalase, with the same activity not only showed less complete digestion of sericin but also caused damage of fibroin. These results suggest that recombinant B. mori cocoonase is potentially useful for silk degumming.

Cloning and characterization of microsomal triglyceride transfer protein gene and its potential connection with peroxisome proliferator-activated receptor (PPAR) in blunt snout bream (Megalobrama amblycephala).

PubMed

Li, Jun-Yi; Zhang, Ding-Dong; Jiang, Guang-Zhen; Li, Xiang-Fei; Zhang, Chun-Nuan; Zhou, Man; Liu, Wen-Bin; Xu, Wei-Na

2015-11-01

Microsomal triglyceride transfer protein (MTTP), a major intracellular protein capable of transferring neutral lipids, plays a pivotal role in the assembly and secretion of apolipoprotein B-containing lipoproteins. In this study, MTTP cDNA was firstly cloned from the liver of blunt snout bream (Megalobrama amblycephala), the full-length cDNA covered 3457-bp with an open reading frame of 2661-bp, which encodes 886 amino acids, including a putative signal peptide of 24 amino acids long. After the feeding trial, a graded tissue-specific expression pattern of MTTP was observed and high expression abundance in the liver and intestine indicated its major function in lipid transport in this fish species. In addition, expression of genes encoding MTTP as well as peroxisome proliferator-activated receptor (PPAR), which are transcription factors and serve as key regulators in lipid homoeostasis, was all affected by dietary lipid and choline supplementations. Elevated dietary lipid levels significantly increased the liver, intestinal and muscle MTTP mRNA abundance. Additionally, the down-regulation of MTTP expression in the liver and muscle was observed when fish were fed with inadequate choline supplementation in high-fat diet, yet up-regulated as supplementing extra choline in diet. Expressions of PPARα and PPARβ in the liver and muscle showed similar trend of MTTP expression. The results suggested the potential connection of MTTP and PPAR in response to different dietary nutritional factors. Furthermore, extra choline supplementations could promote lipid transfer and enhance fatty acid oxidation, which indicated a molecular mechanism of choline on diminishing fat accumulation in blunt snout bream. Copyright © 2015 Elsevier Inc. All rights reserved.

Identification of novel substrates of Shigella T3SA through analysis of its virulence plasmid-encoded secretome

PubMed Central

Pinaud, Laurie; Ferrari, Mariana L.; Friedman, Robin; Jehmlich, Nico; von Bergen, Martin; Phalipon, Armelle; Sansonetti, Philippe J.

2017-01-01

Many human Gram-negative bacterial pathogens express a Type Three Secretion Apparatus (T3SA), including among the most notorious Shigella spp., Salmonella enterica, Yersinia enterocolitica and enteropathogenic Escherichia coli (EPEC). These bacteria express on their surface multiple copies of the T3SA that mediate the delivery into host cells of specific protein substrates critical to pathogenesis. Shigella spp. are Gram-negative bacterial pathogens responsible for human bacillary dysentery. The effector function of several Shigella T3SA substrates has largely been studied but their potential cellular targets are far from having been comprehensively delineated. In addition, it is likely that some T3SA substrates have escaped scrutiny as yet. Indeed, sequencing of the virulence plasmid of Shigella flexneri has revealed numerous open reading frames with unknown functions that could encode additional T3SA substrates. Taking advantage of label-free mass spectrometry detection of proteins secreted by a constitutively secreting strain of S. flexneri, we identified five novel substrates of the T3SA. We further confirmed their secretion through the T3SA and translocation into host cells using β-lactamase assays. The coding sequences of two of these novel T3SA substrates (Orf13 and Orf131a) have a guanine-cytosine content comparable to those of T3SA components and effectors. The three other T3SA substrates identified (Orf48, Orf86 and Orf176) have significant homology with antitoxin moieties of type II Toxin-Antitoxin systems usually implicated in the maintenance of low copy plasmids. While Orf13 and Orf131a might constitute new virulence effectors contributing to S. flexneri pathogenicity, potential roles for the translocation into host cells of antitoxins or antitoxin-like proteins during Shigella infection are discussed. PMID:29073283

Up to Four Distinct Polypeptides Are Produced from the γ34.5 Open Reading Frame of Herpes Simplex Virus 2

PubMed Central

Korom, Maria; Davis, Katie L.

2014-01-01

ABSTRACT The herpes simplex virus 1 (HSV-1) ICP34.5 protein strongly influences neurovirulence and regulates several cellular antiviral responses. Despite the clinical importance of HSV-2, relatively little is known about its ICP34.5 ortholog. We found that HSV-2 produces up to four distinct forms of ICP34.5 in infected cells: a full-length protein, one shorter form sharing the N terminus, and two shorter forms sharing the C terminus. These forms appeared with similar kinetics and accumulated in cells over much of the replication cycle. We confirmed that the N-terminal form is translated from the primary unspliced transcript to a stop codon within the intron unique to HSV-2 γ34.5. We found that the N-terminal form was produced in a variety of cell types and by 9 of 10 clinical isolates. ICP27 influenced but was not required for expression of the N-terminal form. Western blotting and reverse transcription-PCR indicated the C-terminal forms did not contain the N terminus and were not products of alternative splicing or internal transcript initiation. Expression plasmids encoding methionine at amino acids 56 and 70 generated products that comigrated in SDS-PAGE with the C1 and C2 forms, respectively, and mutation of these sites abolished C1 and C2. Using a recombinant HSV-2 encoding hemagglutinin (HA)-tagged ICP34.5, we demonstrated that the C-terminal forms were also produced during infection of many human and mouse cell types but were not detectable in mouse primary neurons. The protein diversity generated from the HSV-2 γ34.5 open reading frame implies additional layers of cellular regulation through potential independent activities associated with the various forms of ICP34.5. IMPORTANCE The herpes simplex virus 1 (HSV-1) protein ICP34.5, encoded by the γ34.5 gene, interferes with several host defense mechanisms by binding cellular proteins that would otherwise stimulate the cell's autophagic, translational-arrest, and type I interferon responses to virus infection. ICP34.5 also plays a crucial role in determining the severity of nervous system infections with HSV-1 and HSV-2. The HSV-2 γ34.5 gene contains an intron not present in HSV-1 γ34.5. A shorter N-terminal form of HSV-2 ICP34.5 can be translated from the unspliced γ34.5 mRNA. Here, we show that two additional forms consisting of the C-terminal portion of ICP34.5 are generated in infected cells. Production of these N- and C-terminal forms is highly conserved among HSV-2 strains, including many clinical isolates, and they are broadly expressed in several cell types, but not mouse primary neurons. Multiple ICP34.5 polypeptides add additional complexity to potential functional interactions influencing HSV-2 neurovirulence. PMID:25031346

Study of the Met Tyrosine Kinase in the Pathogenesis of Breast Cancer.

DTIC Science & Technology

1998-10-01

cDNA clones appeared to encode for open reading frames, however, and neither clone showed any homology to the protein Gab1 , which is a signal...domain, and tissue characterization using specific antibodies , will hopefully determine whether these clones represent important c-met targets. In...Behrens J, Birchmeier W. Interaction between Gab1 and the c-met receptor tyrosine kinase is responsible for epithelial morphogenesis. Nature 1996;384:173

Driving along the Road or Heading for the Village? Conceptual Differences Underlying Motion Event Encoding in French, German, and French-German L2 Users

ERIC Educational Resources Information Center

Flecken, Monique; Carroll, Mary; Weimar, Katja; Von Stutterheim, Christiane

2015-01-01

The typological contrast between verb- and satellite-framed languages (Talmy, 1985) has set the basis for many empirical studies on L2 acquisition. The current analysis goes beyond this typology by looking in detail at the conceptualization of the path of motion in a motion event. We take as a starting point the cognitive salience of specific…

Can older adults resist the positivity effect in neural responding? The impact of verbal framing on event-related brain potentials elicited by emotional images.

PubMed

Rehmert, Andrea E; Kisley, Michael A

2013-10-01

Older adults have demonstrated an avoidance of negative information, presumably with a goal of greater emotional satisfaction. Understanding whether avoidance of negative information is a voluntary, motivated choice or an involuntary, automatic response will be important to differentiate, as decision making often involves emotional factors. With the use of an emotional framing event-related potential (ERP) paradigm, the present study investigated whether older adults could alter neural responses to negative stimuli through verbal reframing of evaluative response options. The late positive potential (LPP) response of 50 older adults and 50 younger adults was recorded while participants categorized emotional images in one of two framing conditions: positive ("more or less positive") or negative ("more or less negative"). It was hypothesized that older adults would be able to overcome a presumed tendency to down-regulate neural responding to negative stimuli in the negative framing condition, thus leading to larger LPP wave amplitudes to negative images. A similar effect was predicted for younger adults, but for positively valenced images, such that LPP responses would be increased in the positive framing condition compared with the negative framing condition. Overall, younger adults' LPP wave amplitudes were modulated by framing condition, including a reduction in the negativity bias in the positive frame. Older adults' neural responses were not significantly modulated, even though task-related behavior supported the notion that older adults were able to successfully adopt the negative framing condition.

Can Older Adults Resist the Positivity Effect in Neural Responding: The Impact of Verbal Framing on Event-Related Brain Potentials Elicited by Emotional Images

PubMed Central

Rehmert, Andrea E.; Kisley, Michael A.

2014-01-01

Older adults have demonstrated an avoidance of negative information presumably with a goal of greater emotional satisfaction. Understanding whether avoidance of negative information is a voluntary, motivated choice, or an involuntary, automatic response will be important to differentiate, as decision-making often involves emotional factors. With the use of an emotional framing event-related potential (ERP) paradigm, the present study investigated whether older adults could alter neural responses to negative stimuli through verbal reframing of evaluative response options. The late-positive potential (LPP) response of 50 older adults and 50 younger adults was recorded while participants categorized emotional images in one of two framing conditions: positive (“more or less positive”) or negative (“more or less negative”). It was hypothesized that older adults would be able to overcome a presumed tendency to down-regulate neural responding to negative stimuli in the negative framing condition thus leading to larger LPP wave amplitudes to negative images. A similar effect was predicted for younger adults but for positively valenced images such that LPP responses would be increased in the positive framing condition compared to the negative framing condition. Overall, younger adults' LPP wave amplitudes were modulated by framing condition, including a reduction in the negativity bias in the positive frame. Older adults' neural responses were not significantly modulated even though task-related behavior supported the notion that older adults were able to successfully adopt the negative framing condition. PMID:23731435

Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium.

PubMed

Yan, Hong-Bin; Lou, Zhong-Zi; Li, Li; Brindley, Paul J; Zheng, Yadong; Luo, Xuenong; Hou, Junling; Guo, Aijiang; Jia, Wan-Zhong; Cai, Xuepeng

2014-06-04

Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of current drugs to prevent re-infection, identification of novel vaccines and chemotherapeutic agents against Taenia solium and related helminth pathogens is a public health priority. The T. solium genome and the predicted proteome were reported recently, providing a wealth of information from which new interventional targets might be identified. In order to characterize and classify the entire repertoire of protease-encoding genes of T. solium, which act fundamental biological roles in all life processes, we analyzed the predicted proteins of this cestode through a combination of bioinformatics tools. Functional annotation was performed to yield insights into the signaling processes relevant to the complex developmental cycle of this tapeworm and to highlight a suite of the proteases as potential intervention targets. Within the genome of this helminth parasite, we identified 200 open reading frames encoding proteases from five clans, which correspond to 1.68% of the 11,902 protein-encoding genes predicted to be present in its genome. These proteases include calpains, cytosolic, mitochondrial signal peptidases, ubiquitylation related proteins, and others. Many not only show significant similarity to proteases in the Conserved Domain Database but have conserved active sites and catalytic domains. KEGG Automatic Annotation Server (KAAS) analysis indicated that ~60% of these proteases share strong sequence identities with proteins of the KEGG database, which are involved in human disease, metabolic pathways, genetic information processes, cellular processes, environmental information processes and organismal systems. Also, we identified signal peptides and transmembrane helices through comparative analysis with classes of important regulatory proteases. Phylogenetic analysis using Bayes approach provided support for inferring functional divergence among regulatory cysteine and serine proteases. Numerous putative proteases were identified for the first time in T. solium, and important regulatory proteases have been predicted. This comprehensive analysis not only complements the growing knowledge base of proteolytic enzymes, but also provides a platform from which to expand knowledge of cestode proteases and to explore their biochemistry and potential as intervention targets.

Efficient exon skipping of SGCG mutations mediated by phosphorodiamidate morpholino oligomers.

PubMed

Wyatt, Eugene J; Demonbreun, Alexis R; Kim, Ellis Y; Puckelwartz, Megan J; Vo, Andy H; Dellefave-Castillo, Lisa M; Gao, Quan Q; Vainzof, Mariz; Pavanello, Rita C M; Zatz, Mayana; McNally, Elizabeth M

2018-05-03

Exon skipping uses chemically modified antisense oligonucleotides to modulate RNA splicing. Therapeutically, exon skipping can bypass mutations and restore reading frame disruption by generating internally truncated, functional proteins to rescue the loss of native gene expression. Limb-girdle muscular dystrophy type 2C is caused by autosomal recessive mutations in the SGCG gene, which encodes the dystrophin-associated protein γ-sarcoglycan. The most common SGCG mutations disrupt the transcript reading frame abrogating γ-sarcoglycan protein expression. In order to treat most SGCG gene mutations, it is necessary to skip 4 exons in order to restore the SGCG transcript reading frame, creating an internally truncated protein referred to as Mini-Gamma. Using direct reprogramming of human cells with MyoD, myogenic cells were tested with 2 antisense oligonucleotide chemistries, 2'-O-methyl phosphorothioate oligonucleotides and vivo-phosphorodiamidate morpholino oligomers, to induce exon skipping. Treatment with vivo-phosphorodiamidate morpholino oligomers demonstrated efficient skipping of the targeted exons and corrected the mutant reading frame, resulting in the expression of a functional Mini-Gamma protein. Antisense-induced exon skipping of SGCG occurred in normal cells and those with multiple distinct SGCG mutations, including the most common 521ΔT mutation. These findings demonstrate a multiexon-skipping strategy applicable to the majority of limb-girdle muscular dystrophy 2C patients.

Motor memory is encoded as a gain-field combination of intrinsic and extrinsic action representations.

PubMed

Brayanov, Jordan B; Press, Daniel Z; Smith, Maurice A

2012-10-24

Actions can be planned in either an intrinsic (body-based) reference frame or an extrinsic (world-based) frame, and understanding how the internal representations associated with these frames contribute to the learning of motor actions is a key issue in motor control. We studied the internal representation of this learning in human subjects by analyzing generalization patterns across an array of different movement directions and workspaces after training a visuomotor rotation in a single movement direction in one workspace. This provided a dense sampling of the generalization function across intrinsic and extrinsic reference frames, which allowed us to dissociate intrinsic and extrinsic representations and determine the manner in which they contributed to the motor memory for a trained action. A first experiment showed that the generalization pattern reflected a memory that was intermediate between intrinsic and extrinsic representations. A second experiment showed that this intermediate representation could not arise from separate intrinsic and extrinsic learning. Instead, we find that the representation of learning is based on a gain-field combination of local representations in intrinsic and extrinsic coordinates. This gain-field representation generalizes between actions by effectively computing similarity based on the (Mahalanobis) distance across intrinsic and extrinsic coordinates and is in line with neural recordings showing mixed intrinsic-extrinsic representations in motor and parietal cortices.

Variation in spatial language and cognition: exploring visuo-spatial thinking and speaking cross-linguistically.

PubMed

Soroli, Efstathia

2012-08-01

Languages differ strikingly in how they encode spatial information. This variability is realized with spatial semantic elements mapped across languages in very different ways onto lexical/syntactic structures. For example, satellite-framed languages (e.g., English) express MANNER: in the verb and PATH: in satellites, while verb-framed languages (e.g., French) lexicalize PATH: in the verb, leaving MANNER: implicit or peripheral. Some languages are harder to classify into these categories, rather presenting equipollently framed systems, such as Chinese (serial-verb constructions) or Greek (parallel verb- and satellite-framed structures in equally frequent contexts). Such properties seem to have implications not only on the formulation/articulation levels, but also on the conceptualization level, thereby reviving questions concerning the language-thought interface. The present study investigates the relative impact of language-independent and language-specific factors on spatial representations across three typologically different languages (English-French-Greek) combining a variety of complementary tasks (production, non-verbal, and verbal categorization). The findings show that typological properties of languages can have an impact on both linguistic and non-linguistic organization of spatial information, open new perspectives for the investigation of conceptualization, and contribute more generally to the debate concerning the universal and language-specific dimensions of cognition.

Testing general relativity with compact-body orbits: a modified Einstein–Infeld–Hoffmann framework

NASA Astrophysics Data System (ADS)

Will, Clifford M.

2018-04-01

We describe a general framework for analyzing orbits of systems containing compact objects (neutron stars or black holes) in a class of Lagrangian-based alternative theories of gravity that also admit a global preferred reference frame. The framework is based on a modified Einstein–Infeld–Hoffmann (EIH) formalism developed by Eardley and by Will, generalized to include the possibility of Lorentz-violating, preferred-frame effects. It uses a post-Newtonian N-body Lagrangian with arbitrary parameters that depend on the theory of gravity and on ‘sensitivities’ that encode the effects of the bodies’ internal structure on their motion. We determine the modified EIH parameters for the Einstein-Æther and Khronometric vector-tensor theories of gravity. We find the effects of motion relative to a preferred universal frame on the orbital parameters of binary systems containing neutron stars, such as a class of ultra-circular pulsar-white dwarf binaries; the amplitudes of the effects depend upon ‘strong-field’ preferred-frame parameters \\hatα1 and \\hatα2 , which we relate to the fundamental modified EIH parameters. We also determine the amplitude of the ‘Nordtvedt effect’ in a triple system containing the pulsar J0337+1715 in terms of the modified EIH parameters.

The role of porcine reproductive and respiratory syndrome (PRRS) virus structural and non-structural proteins in virus pathogenesis.

PubMed

Music, Nedzad; Gagnon, Carl A

2010-12-01

Porcine reproductive and respiratory syndrome (PRRS) is an economically devastating viral disease affecting the swine industry worldwide. The etiological agent, PRRS virus (PRRSV), possesses a RNA viral genome with nine open reading frames (ORFs). The ORF1a and ORF1b replicase-associated genes encode the polyproteins pp1a and pp1ab, respectively. The pp1a is processed in nine non-structural proteins (nsps): nsp1α, nsp1β, and nsp2 to nsp8. Proteolytic cleavage of pp1ab generates products nsp9 to nsp12. The proteolytic pp1a cleavage products process and cleave pp1a and pp1ab into nsp products. The nsp9 to nsp12 are involved in virus genome transcription and replication. The 3' end of the viral genome encodes four minor and three major structural proteins. The GP(2a), GP₃ and GP₄ (encoded by ORF2a, 3 and 4), are glycosylated membrane associated minor structural proteins. The fourth minor structural protein, the E protein (encoded by ORF2b), is an unglycosylated membrane associated protein. The viral envelope contains two major structural proteins: a glycosylated major envelope protein GP₅ (encoded by ORF5) and an unglycosylated membrane M protein (encoded by ORF6). The third major structural protein is the nucleocapsid N protein (encoded by ORF7). All PRRSV non-structural and structural proteins are essential for virus replication, and PRRSV infectivity is relatively intolerant to subtle changes within the structural proteins. PRRSV virulence is multigenic and resides in both the non-structural and structural viral proteins. This review discusses the molecular characteristics, biological and immunological functions of the PRRSV structural and nsps and their involvement in the virus pathogenesis.

Solenopsis invicta virus 3: mapping of structural proteins, ribosomal frameshifting, and similarities to Acyrthosiphon pisum virus and Kelp fly virus.

PubMed

Valles, Steven M; Bell, Susanne; Firth, Andrew E

2014-01-01

Solenopsis invicta virus 3 (SINV-3) is a positive-sense single-stranded RNA virus that infects the red imported fire ant, Solenopsis invicta. We show that the second open reading frame (ORF) of the dicistronic genome is expressed via a frameshifting mechanism and that the sequences encoding the structural proteins map to both ORF2 and the 3' end of ORF1, downstream of the sequence that encodes the RNA-dependent RNA polymerase. The genome organization and structural protein expression strategy resemble those of Acyrthosiphon pisum virus (APV), an aphid virus. The capsid protein that is encoded by the 3' end of ORF1 in SINV-3 and APV is predicted to have a jelly-roll fold similar to the capsid proteins of picornaviruses and caliciviruses. The capsid-extension protein that is produced by frameshifting, includes the jelly-roll fold domain encoded by ORF1 as its N-terminus, while the C-terminus encoded by the 5' half of ORF2 has no clear homology with other viral structural proteins. A third protein, encoded by the 3' half of ORF2, is associated with purified virions at sub-stoichiometric ratios. Although the structural proteins can be translated from the genomic RNA, we show that SINV-3 also produces a subgenomic RNA encoding the structural proteins. Circumstantial evidence suggests that APV may also produce such a subgenomic RNA. Both SINV-3 and APV are unclassified picorna-like viruses distantly related to members of the order Picornavirales and the family Caliciviridae. Within this grouping, features of the genome organization and capsid domain structure of SINV-3 and APV appear more similar to caliciviruses, perhaps suggesting the basis for a "Calicivirales" order.

Gaining perspective: the effects of message frame on viewer attention to and recall of osteoporosis prevention print advertisements.

PubMed

O'Malley, Deborah A; Latimer-Cheung, Amy E

2013-11-01

This study examined how framed messages affect viewer attention to and cognitive processing of osteoporosis prevention print ads. Attention was measured with eye tracking technology. Cognitive processing was assessed through masked recall. A total of 60 college-aged women viewed 12 gain-framed, 12 loss-framed, and 12 neutral-framed ads. Number of fixations, dwell time, and recall of gain-framed osteoporosis prevention ads were higher than loss-framed or neutral-framed ads, p < .01. Message recall was positively correlated with the number of fixations and dwell time for the gain-framed and neutral-framed messages, p < .01. These findings provide preliminary insight into potential mechanisms underlying message framing effects.

VLSI design of lossless frame recompression using multi-orientation prediction

NASA Astrophysics Data System (ADS)

Lee, Yu-Hsuan; You, Yi-Lun; Chen, Yi-Guo

2016-01-01

Pursuing an experience of high-end visual quality drives human to demand a higher display resolution and a higher frame rate. Hence, a lot of powerful coding tools are aggregated together in emerging video coding standards to improve coding efficiency. This also makes video coding standards suffer from two design challenges: heavy computation and tremendous memory bandwidth. The first issue can be properly solved by a careful hardware architecture design with advanced semiconductor processes. Nevertheless, the second one becomes a critical design bottleneck for a modern video coding system. In this article, a lossless frame recompression using multi-orientation prediction technique is proposed to overcome this bottleneck. This work is realised into a silicon chip with the technology of TSMC 0.18 µm CMOS process. Its encoding capability can reach full-HD (1920 × 1080)@48 fps. The chip power consumption is 17.31 mW@100 MHz. Core area and chip area are 0.83 × 0.83 mm2 and 1.20 × 1.20 mm2, respectively. Experiment results demonstrate that this work exhibits an outstanding performance on lossless compression ratio with a competitive hardware performance.

An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators

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

Damiani, R.D. Jr.; Wessler, S.R.

1993-09-01

The R/B genes of maize encode a family of basic helix-loop-helix proteins that determine where and when the anthocyanin-pigment pathway will be expressed in the plant. Previous studies showed that allelic diversity among family members reflects differences in gene expression, specifically in transcription initiation. The authors present evidence that the R gene Lc is under translational control. They demonstrate that the 235-nt transcript leader of Lc represses expression 25- to 30-fold in an in vivo assay. Repression is mediated by the presence in cis of a 38-codon upstream open reading frame. Furthermore, the coding capacity of the upstream open readingmore » frame influences the magnitude of repression. It is proposed that translational control does not contribute to tissue specificity but prevents overexpression of the Lc protein. The diversity of promoter and 5' untranslated leader sequences among the R/B genes provides an opportunity to study the coevolution of transcriptional and translational mechanisms of gene regulation. 36 refs., 5 figs.« less

Insight into others' minds: spatio-temporal representations by intrinsic frame of reference.

PubMed

Sun, Yanlong; Wang, Hongbin

2014-01-01

Recent research has seen a growing interest in connections between domains of spatial and social cognition. Much evidence indicates that processes of representing space in distinct frames of reference (FOR) contribute to basic spatial abilities as well as sophisticated social abilities such as tracking other's intention and belief. Argument remains, however, that belief reasoning in social domain requires an innately dedicated system and cannot be reduced to low-level encoding of spatial relationships. Here we offer an integrated account advocating the critical roles of spatial representations in intrinsic frame of reference. By re-examining the results from a spatial task (Tamborello etal., 2012) and a false-belief task (Onishi and Baillargeon, 2005), we argue that spatial and social abilities share a common origin at the level of spatio-temporal association and predictive learning, where multiple FOR-based representations provide the basic building blocks for efficient and flexible partitioning of the environmental statistics. We also discuss neuroscience evidence supporting these mechanisms. We conclude that FOR-based representations may bridge the conceptual as well as the implementation gaps between the burgeoning fields of social and spatial cognition.

Gain versus loss-framed messaging and colorectal cancer screening among African Americans: A preliminary examination of perceived racism and culturally targeted dual messaging.

PubMed

Lucas, Todd; Hayman, Lenwood W; Blessman, James E; Asabigi, Kanzoni; Novak, Julie M

2016-05-01

This preliminary study examined the effect of gain versus loss-framed messaging as well as culturally targeted personal prevention messaging on African Americans' receptivity to colorectal cancer (CRC) screening. This research also examined mechanistic functions of perceived racism in response to message framing. Community samples of African Americans (N = 132) and White Americans (N = 50) who were non-compliant with recommended CRC screening completed an online education module about CRC, and were either exposed to a gain-framed or loss-framed message about CRC screening. Half of African Americans were exposed to an additional and culturally targeted self-control message about personal prevention of CRC. Theory of planned behavior measures of attitudes, normative beliefs, perceived behavioural control, and intentions to obtain a CRC screen served as primary outcomes. The effect of messaging on perceived racism was also measured as an outcome. Consistent with prior research, White Americans were more receptive to CRC screening when exposed to a loss-framed message. However, African Americans were more receptive when exposed to a gain-framed message. The contrary effect of loss-framed messaging on receptivity to screening among African Americans was mediated by an increase in perceived racism. However, including an additional and culturally targeted prevention message mitigated the adverse effect of a loss-framed message. This study identifies an important potential cultural difference in the effect of message framing on illness screening among African Americans, while also suggesting a culturally relevant linking mechanism. This study also suggests the potential for simultaneously presented and culturally targeted messaging to alter the effects of gain and loss-framed messaging on African Americans. What is already known on this subject? African Americans are at an increased risk of both developing and dying from colorectal cancer (CRC). These disparities can be attributed in large part to deficits in the use of CRC screening among African Americans. Guided by prospect theory, available literature suggests that selectively pairing gain and loss-framed messaging with illness prevention and detection can better promote adaptive health behaviour. Specifically, loss-framed messages that emphasize the potential costs of failing to act may promote better use of illness detection behaviours, such as CRC screening. Emerging literature highlights the potential for cultural differences in the effects of gain and loss messaging on health behaviour, especially among collectivist or interdependent cultures. What does this study add? This study is the first to identify a potential and important cultural difference in the effect of message framing on cancer screening among African Americans, whereby gain-framed messaging better compelled receptivity to CRC screening. This study is also the first to show that the use of loss-framed messaging may reduce receptivity to CRC screening among African Americans by increasing perceived racism. This study demonstrates that simultaneously including a culturally targeted personal prevention message may attenuate the negative effects of loss-framed messaging on CRC screening among African Americans. © 2015 The British Psychological Society.

Not all memories are the same: Situational context influences spatial recall within one's city of residency.

PubMed

Meilinger, Tobias; Frankenstein, Julia; Simon, Nadine; Bülthoff, Heinrich H; Bresciani, Jean-Pierre

2016-02-01

Reference frames in spatial memory encoding have been examined intensively in recent years. However, their importance for recall has received considerably less attention. In the present study, passersby used tags to arrange a configuration map of prominent city center landmarks. It has been shown that such configurational knowledge is memorized within a north-up reference frame. However, participants adjusted their maps according to their body orientations. For example, when participants faced south, the maps were likely to face south-up. Participants also constructed maps along their location perspective-that is, the self-target direction. If, for instance, they were east of the represented area, their maps were oriented west-up. If the location perspective and body orientation were in opposite directions (i.e., if participants faced away from the city center), participants relied on location perspective. The results indicate that reference frames in spatial recall depend on the current situation rather than on the organization in long-term memory. These results cannot be explained by activation spread within a view graph, which had been used to explain similar results in the recall of city plazas. However, the results are consistent with forming and transforming a spatial image of nonvisible city locations from the current location. Furthermore, prior research has almost exclusively focused on body- and environment-based reference frames. The strong influence of location perspective in an everyday navigational context indicates that such a reference frame should be considered more often when examining human spatial cognition.

Simulations of VLBI observations of a geodetic satellite providing co-location in space

NASA Astrophysics Data System (ADS)

Anderson, James M.; Beyerle, Georg; Glaser, Susanne; Liu, Li; Männel, Benjamin; Nilsson, Tobias; Heinkelmann, Robert; Schuh, Harald

2018-02-01

We performed Monte Carlo simulations of very-long-baseline interferometry (VLBI) observations of Earth-orbiting satellites incorporating co-located space-geodetic instruments in order to study how well the VLBI frame and the spacecraft frame can be tied using such measurements. We simulated observations of spacecraft by VLBI observations, time-of-flight (TOF) measurements using a time-encoded signal in the spacecraft transmission, similar in concept to precise point positioning, and differential VLBI (D-VLBI) observations using angularly nearby quasar calibrators to compare their relative performance. We used the proposed European Geodetic Reference Antenna in Space (E-GRASP) mission as an initial test case for our software. We found that the standard VLBI technique is limited, in part, by the present lack of knowledge of the absolute offset of VLBI time to Coordinated Universal Time at the level of microseconds. TOF measurements are better able to overcome this problem and provide frame ties with uncertainties in translation and scale nearly a factor of three smaller than those yielded from VLBI measurements. If the absolute time offset issue can be resolved by external means, the VLBI results can be significantly improved and can come close to providing 1 mm accuracy in the frame tie parameters. D-VLBI observations with optimum performance assumptions provide roughly a factor of two higher uncertainties for the E-GRASP orbit. We additionally simulated how station and spacecraft position offsets affect the frame tie performance.

An atomistic fingerprint algorithm for learning ab initio molecular force fields

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

A potential germ cell-specific marker in Japanese flounder, Paralichthys olivaceus: identification and characterization of lymphocyte antigen 75 (Ly75/CD205)

NASA Astrophysics Data System (ADS)

Yang, Yang; Liu, Qinghua; Ma, Daoyuan; Song, Zongchen; Li, Jun

2018-04-01

Some germ cell marker genes, such as vasa, nanos, and dead end (dnd), have been identified in fish. Recently, lymphocyte antigen 75 (Ly75/CD205) has been identified as a mitotic germ cell-specific cell-surface marker in several fish species. In this study, the Japanese flounder ly75 homolog (ly75) was cloned and its expression pattern in gonads was analyzed. The full-length cDNA of ly75 was 7 346 bp, with an open reading frame (ORF) of 5 229 bp. The ORF encoded a protein containing 1 742 amino acids with a predicted molecular mass of 196.89 kDa. In adult tissues, ly75 transcripts were detected in all analyzed tissues but abundantly in the testis. In in-situ hybridization analyses, ly75 mRNA was predominantly localized in oocytes in the ovary and spermatogonia in the testis, but ly75 mRNA was not detected in oogonia, spermatocytes, spermatids, or spermatozoa. These results indicated that ly75 could be a potential germ cell-specific marker in P. olivaceus, as in other fishes.

The kinematic dipole in galaxy redshift surveys

NASA Astrophysics Data System (ADS)

Maartens, Roy; Clarkson, Chris; Chen, Song

2018-01-01

In the concordance model of the Universe, the matter distribution—as observed in galaxy number counts or the intensity of line emission (such as the 21cm line of neutral hydrogen) —should have a kinematic dipole due to the Sun's motion relative to the CMB rest-frame. This dipole should be aligned with the kinematic dipole in the CMB temperature. Accurate measurement of the direction of the matter dipole will become possible with future galaxy surveys, and this will be a critical test of the foundations of the concordance model. The amplitude of the matter dipole is also a potential cosmological probe. We derive formulas for the amplitude of the kinematic dipole in galaxy redshift and intensity mapping surveys, taking into account the Doppler, aberration and other relativistic effects. The amplitude of the matter dipole can be significantly larger than that of the CMB dipole. Its redshift dependence encodes information on the evolution of the Universe and on the tracers, and we discuss possible ways to determine the amplitude.

Real-time WebRTC-based design for a telepresence wheelchair.

PubMed

Van Kha Ly Ha; Rifai Chai; Nguyen, Hung T

2017-07-01

This paper presents a novel approach to the telepresence wheelchair system which is capable of real-time video communication and remote interaction. The investigation of this emerging technology aims at providing a low-cost and efficient way for assisted-living of people with disabilities. The proposed system has been designed and developed by deploying the JavaScript with Hyper Text Markup Language 5 (HTML5) and Web Real-time Communication (WebRTC) in which the adaptive rate control algorithm for video transmission is invoked. We conducted experiments in real-world environments, and the wheelchair was controlled from a distance using the Internet browser to compare with existing methods. The results show that the adaptively encoded video streaming rate matches the available bandwidth. The video streaming is high-quality with approximately 30 frames per second (fps) and round trip time less than 20 milliseconds (ms). These performance results confirm that the WebRTC approach is a potential method for developing a telepresence wheelchair system.

Characterization of a chitinolytic enzyme from Serratia sp. KCK isolated from kimchi juice.

PubMed

Kim, Hyun-Soo; Timmis, Kenneth N; Golyshin, Peter N

2007-07-01

The novel chitinolytic bacterium Serratia sp. KCK, which was isolated from kimchi juice, produced chitinase A. The gene coding for the chitinolytic enzyme was cloned on the basis of sequencing of internal peptides, homology search, and design of degenerated primers. The cloned open reading frame of chiA encodes for deduced polypeptide of 563 amino acid residues with a calculated molecular mass of 61 kDa and appears to correspond to a molecular mass of about 57 kDa, which excluded the signal sequence. The deduced amino acid sequence showed high similarity to those of bacterial chitinases classified as family 18 of glycosyl hydrolases. The chitinase A is an exochitinase and exhibits a greater pH range (5.0-10.0), thermostability with a temperature optimum of 40 degrees C, and substrate range other than Serratia chitinases thus far described. These results suggested that Serratia sp. KCK chitinase A can be used for biotechnological applications with good potential.

Composition-dependent Membrane Disruption by the Proapoptotic Protein PB1F2 from HK97 Influenza A Virus.

PubMed

Wang, Yujuan; Yang, Jing; Wang, Jiarong; Zhu, Lei; Wang, Junfeng

2018-06-22

PB1F2 is a proapoptotic protein encoded by an alternative reading frame in the influenza A virus. Its accumulation accelerates mitochondrial fragmentation by decreasing the mitochondrial membrane potential following translocation into the mitochondrial inner membrane space, but the mechanistic underpinnings remain unclear. Herein, the PB1F2 from HK97 was expressed and purified in soluble form. The interaction between PB1F2 and the mitochondrial membrane were investigated using three membrane mimics, liposomes, bicelles and nanodiscs. We show that the interactions between PB1F2 and membrane mimics depend on lipid type and are time- and dose-dependent. The primary membrane target of PB1F2 is phosphatidylcholine, the lipid that forms the major component of mitochondrial inner membranes. PB1F2 disrupts the integrity of lipid membranes by forming micelle-like PB1F2-lipid assemblies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Multimodal ophthalmic imaging using swept source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography

NASA Astrophysics Data System (ADS)

Malone, Joseph D.; El-Haddad, Mohamed T.; Tye, Logan A.; Majeau, Lucas; Godbout, Nicolas; Rollins, Andrew M.; Boudoux, Caroline; Tao, Yuankai K.

2016-03-01

Scanning laser ophthalmoscopy (SLO) and optical coherence tomography (OCT) benefit clinical diagnostic imaging in ophthalmology by enabling in vivo noninvasive en face and volumetric visualization of retinal structures, respectively. Spectrally encoding methods enable confocal imaging through fiber optics and reduces system complexity. Previous applications in ophthalmic imaging include spectrally encoded confocal scanning laser ophthalmoscopy (SECSLO) and a combined SECSLO-OCT system for image guidance, tracking, and registration. However, spectrally encoded imaging suffers from speckle noise because each spectrally encoded channel is effectively monochromatic. Here, we demonstrate in vivo human retinal imaging using a swept source spectrally encoded scanning laser ophthalmoscope and OCT (SSSESLO- OCT) at 1060 nm. SS-SESLO-OCT uses a shared 100 kHz Axsun swept source, shared scanner and imaging optics, and are detected simultaneously on a shared, dual channel high-speed digitizer. SESLO illumination and detection was performed using the single mode core and multimode inner cladding of a double clad fiber coupler, respectively, to preserve lateral resolution while improving collection efficiency and reducing speckle contrast at the expense of confocality. Concurrent en face SESLO and cross-sectional OCT images were acquired with 1376 x 500 pixels at 200 frames-per-second. Our system design is compact and uses a shared light source, imaging optics, and digitizer, which reduces overall system complexity and ensures inherent co-registration between SESLO and OCT FOVs. En face SESLO images acquired concurrent with OCT cross-sections enables lateral motion tracking and three-dimensional volume registration with broad applications in multivolume OCT averaging, image mosaicking, and intraoperative instrument tracking.

Effects of context on risk taking and decision times in obsessive-compulsive disorder.

PubMed

Sip, Kamila E; Muratore, Alexandra F; Stern, Emily R

2016-04-01

Despite the fact that OCD patients show altered decision making in everyday life, few studies have investigated how patients make risky decisions and what contextual factors impact choices. We investigated cognitive context with the use of the "framing effect" task, which investigates decision making based on whether monetarily equivalent choice options are framed in terms of a potential to either lose (lose $20 out of $50) or gain (gain $30 out of $50) money. In addition, we manipulated social context by providing positive or neutral feedback on subjects' choices. Overall, participants were risk taking for options framed in terms of potential loss and risk averse for options framed in terms of potential gain (the classic framing effect). Although OCD patients were generally more risk averse, the effect of the frame on choices did not differ significantly from healthy participants and choices were not impacted by social context. Within OCD patients, greater self-reported indecisiveness was associated with a larger effect of the frame on choices. OCD patients were also significantly slower to make choices in the loss compared to gain frame, an effect that was not observed among healthy participants. Overall, our results suggest that the framing of choice options has a differential effect on decision times but not the actual choices made by OCD patients, and that patients are not sensitive to social feedback when making choices. The correlation between indecisiveness and the framing effect in OCD suggests that further work interrogating the relationship between specific symptoms and decision making among patients may yield new insights into the disorder. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of the Lomofungin Biosynthesis Gene Cluster and Associated Flavin-Dependent Monooxygenase Gene in Streptomyces lomondensis S015

PubMed Central

Zhang, Chunxiao; Sheng, Chaolan; Wang, Wei; Hu, Hongbo; Peng, Huasong; Zhang, Xuehong

2015-01-01

Streptomyces lomondensis S015 synthesizes the broad-spectrum phenazine antibiotic lomofungin. Whole genome sequencing of this strain revealed a genomic locus consisting of 23 open reading frames that includes the core phenazine biosynthesis gene cluster lphzGFEDCB. lomo10, encoding a putative flavin-dependent monooxygenase, was also identified in this locus. Inactivation of lomo10 by in-frame partial deletion resulted in the biosynthesis of a new phenazine metabolite, 1-carbomethoxy-6-formyl-4,9-dihydroxy-phenazine, along with the absence of lomofungin. This result suggests that lomo10 is responsible for the hydroxylation of lomofungin at its C-7 position. This is the first description of a phenazine hydroxylation gene in Streptomyces, and the results of this study lay the foundation for further investigation of phenazine metabolite biosynthesis in Streptomyces. PMID:26305803

GPS Enabled Semi-Autonomous Robot

DTIC Science & Technology

2017-09-01

equal and the goal has not yet been reached (i.e., any time the robot has reached a local minimum), and direct the robot to travel in a specific...whether the robot was turning or not. The challenge is overcome by ensuring the robot travels at its maximum speed at all times . Further research into...robot’s fixed reference frame was recalculated each time through the control loop. If the encoder data allows for the robot to appear to have travelled

A Research Program in Computer Technology

DTIC Science & Technology

1976-07-01

K PROGRAM VERIFICATION 12 [Shaw76b] Shaw, M., W. A. Wulf, and R. L. London, Abstraction and Verification ain Aiphard: Iteration and Generators...millisecond trame of speech: pitch, gain, and 10 k -parameters (often called reflection coefficients). The 12 parameters from each frame are encoded into...del rey, CA 90291 Program Code 3D30 & 3P1O I,%’POLLING OFFICE NAME AND ADDRESS 12 REPORT DATE Defense Advanced Research Projects Agency July 1976 1400

The VP35 and VP40 proteins of filoviruses. Homology between Marburg and Ebola viruses.

PubMed

Bukreyev, A A; Volchkov, V E; Blinov, V M; Netesov, S V

1993-05-03

The fragments of genomic RNA sequences of Marburg (MBG) and Ebola (EBO) viruses are reported. These fragments were found to encode the VP35 and VP40 proteins. The canonic sequences were revealed before and after each open reading frame. It is suggested that these sequences are mRNA extremities and at the same time the regulatory elements for mRNA transcription. Homology between the MBG and EBO proteins was discovered.

Structure, sequence and expression of the hepatitis delta (δ) viral genome

NASA Astrophysics Data System (ADS)

Wang, Kang-Sheng; Choo, Qui-Lim; Weiner, Amy J.; Ou, Jing-Hsiung; Najarian, Richard C.; Thayer, Richard M.; Mullenbach, Guy T.; Denniston, Katherine J.; Gerin, John L.; Houghton, Michael

1986-10-01

Biochemical and electron microscopic data indicate that the human hepatitis δ viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants. The sequence of the viral genome (1,678 nucleotides) has been determined and an open reading frame within the complementary strand has been shown to encode an antigen that binds specifically to antisera from patients with chronic hepatitis δ viral infections.

Ventromedial prefrontal and anterior cingulate cortex adopt choice and default reference frames during sequential multialternative choice

PubMed Central

Boorman, Erie D; Rushworth, Matthew F; Behrens, Tim E

2013-01-01

Although damage to medial frontal cortex causes profound decision-making impairments, it has been difficult to pinpoint the relative contributions of key anatomical subdivisions. Here we use fMRI to examine the contributions of human ventromedial prefrontal cortex (vmPFC) and dorsal anterior cingulate cortex (dACC) during sequential choices between multiple alternatives – two key features of choices made in ecological settings. By carefully constructing options whose current value at any given decision was dissociable from their longer-term value, we were able to examine choices in current and long-term frames of reference. We present evidence showing that activity at choice and feedback in vmPFC and dACC was tied to the current choice and the best long-term option, respectively. vmPFC, mid-cingulate, and PCC encoded the relative value between the chosen and next-best option at each sequential decision, whereas dACC encoded the relative value of adapting choices from the option with the highest value in the longer-term. Furthermore, at feedback we identify temporally dissociable effects that predict repetition of the current choice and adaptation away from the long-term best option in vmPFC and dACC, respectively. These functional dissociations at choice and feedback suggest that sequential choices are subject to competing cortical mechanisms. PMID:23392656

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.

PubMed

Atkins, John F; Loughran, Gary; Bhatt, Pramod R; Firth, Andrew E; Baranov, Pavel V

2016-09-06

Genetic decoding is not 'frozen' as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational 'correction' of problem or 'savior' indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5' or 3' of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3' from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The pro1(+) gene from Sordaria macrospora encodes a C6 zinc finger transcription factor required for fruiting body development.

PubMed Central

Masloff, S; Pöggeler, S; Kück, U

1999-01-01

During sexual morphogenesis, the filamentous ascomycete Sordaria macrospora differentiates into multicellular fruiting bodies called perithecia. Previously it has been shown that this developmental process is under polygenic control. To further understand the molecular mechanisms involved in fruiting body formation, we generated the protoperithecia forming mutant pro1, in which the normal development of protoperithecia into perithecia has been disrupted. We succeeded in isolating a cosmid clone from an indexed cosmid library, which was able to complement the pro1(-) mutation. Deletion analysis, followed by DNA sequencing, subsequently demonstrated that fertility was restored to the pro1 mutant by an open reading frame encoding a 689-amino-acid polypeptide, which we named PRO1. A region from this polypeptide shares significant homology with the DNA-binding domains found in fungal C6 zinc finger transcription factors, such as the GAL4 protein from yeast. However, other typical regions of C6 zinc finger proteins, such as dimerization elements, are absent in PRO1. The involvement of the pro1(+) gene in fruiting body development was further confirmed by trying to complement the mutant phenotype with in vitro mutagenized and truncated versions of the pro1 open reading frame. Southern hybridization experiments also indicated that pro1(+) homologues are present in other sexually propagating filamentous ascomycetes. PMID:10224253

The pro1(+) gene from Sordaria macrospora encodes a C6 zinc finger transcription factor required for fruiting body development.

PubMed

Masloff, S; Pöggeler, S; Kück, U

1999-05-01

During sexual morphogenesis, the filamentous ascomycete Sordaria macrospora differentiates into multicellular fruiting bodies called perithecia. Previously it has been shown that this developmental process is under polygenic control. To further understand the molecular mechanisms involved in fruiting body formation, we generated the protoperithecia forming mutant pro1, in which the normal development of protoperithecia into perithecia has been disrupted. We succeeded in isolating a cosmid clone from an indexed cosmid library, which was able to complement the pro1(-) mutation. Deletion analysis, followed by DNA sequencing, subsequently demonstrated that fertility was restored to the pro1 mutant by an open reading frame encoding a 689-amino-acid polypeptide, which we named PRO1. A region from this polypeptide shares significant homology with the DNA-binding domains found in fungal C6 zinc finger transcription factors, such as the GAL4 protein from yeast. However, other typical regions of C6 zinc finger proteins, such as dimerization elements, are absent in PRO1. The involvement of the pro1(+) gene in fruiting body development was further confirmed by trying to complement the mutant phenotype with in vitro mutagenized and truncated versions of the pro1 open reading frame. Southern hybridization experiments also indicated that pro1(+) homologues are present in other sexually propagating filamentous ascomycetes.

Codon Optimization of the Human Papillomavirus E7 Oncogene Induces a CD8+ T Cell Response to a Cryptic Epitope Not Harbored by Wild-Type E7

PubMed Central

Lorenz, Felix K. M.; Wilde, Susanne; Voigt, Katrin; Kieback, Elisa; Mosetter, Barbara; Schendel, Dolores J.; Uckert, Wolfgang

2015-01-01

Codon optimization of nucleotide sequences is a widely used method to achieve high levels of transgene expression for basic and clinical research. Until now, immunological side effects have not been described. To trigger T cell responses against human papillomavirus, we incubated T cells with dendritic cells that were pulsed with RNA encoding the codon-optimized E7 oncogene. All T cell receptors isolated from responding T cell clones recognized target cells expressing the codon-optimized E7 gene but not the wild type E7 sequence. Epitope mapping revealed recognition of a cryptic epitope from the +3 alternative reading frame of codon-optimized E7, which is not encoded by the wild type E7 sequence. The introduction of a stop codon into the +3 alternative reading frame protected the transgene product from recognition by T cell receptor gene-modified T cells. This is the first experimental study demonstrating that codon optimization can render a transgene artificially immunogenic through generation of a dominant cryptic epitope. This finding may be of great importance for the clinical field of gene therapy to avoid rejection of gene-corrected cells and for the design of DNA- and RNA-based vaccines, where codon optimization may artificially add a strong immunogenic component to the vaccine. PMID:25799237

Molecular cloning and expression of rat liver bile acid CoA ligase.

PubMed

Falany, Charles N; Xie, Xiaowei; Wheeler, James B; Wang, Jin; Smith, Michelle; He, Dongning; Barnes, Stephen

2002-12-01

Bile acid CoA ligase (BAL) is responsible for catalyzing the first step in the conjugation of bile acids with amino acids. Sequencing of putative rat liver BAL cDNAs identified a cDNA (rBAL-1) possessing a 51 nucleotide 5'-untranslated region, an open reading frame of 2,070 bases encoding a 690 aa protein with a molecular mass of 75,960 Da, and a 138 nucleotide 3'-nontranslated region followed by a poly(A) tail. Identity of the cDNA was established by: 1) the rBAL-1 open reading frame encoded peptides obtained by chemical sequencing of the purified rBAL protein; 2) expressed rBAL-1 protein comigrated with purified rBAL during SDS-polyacrylamide gel electrophoresis; and 3) rBAL-1 expressed in insect Sf9 cells had enzymatic properties that were comparable to the enzyme isolated from rat liver. Evidence for a relationship between fatty acid and bile acid metabolism is suggested by specific inhibition of rBAL-1 by cis-unsaturated fatty acids and its high homology to a human very long chain fatty acid CoA ligase. In summary, these results indicate that the cDNA for rat liver BAL has been isolated and expression of the rBAL cDNA in insect Sf9 cells results in a catalytically active enzyme capable of utilizing several different bile acids as substrates.

Translational and structural requirements of the early nodulin gene enod40, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex.

PubMed

Sousa, C; Johansson, C; Charon, C; Manyani, H; Sautter, C; Kondorosi, A; Crespi, M

2001-01-01

A diversity of mRNAs containing only short open reading frames (sORF-RNAs; encoding less than 30 amino acids) have been shown to be induced in growth and differentiation processes. The early nodulin gene enod40, coding for a 0.7-kb sORF-RNA, is expressed in the nodule primordium developing in the root cortex of leguminous plants after infection by symbiotic bacteria. Ballistic microtargeting of this gene into Medicago roots induced division of cortical cells. Translation of two sORFs (I and II, 13 and 27 amino acids, respectively) present in the conserved 5' and 3' regions of enod40 was required for this biological activity. These sORFs may be translated in roots via a reinitiation mechanism. In vitro translation products starting from the ATG of sORF I were detectable by mutating enod40 to yield peptides larger than 38 amino acids. Deletion of a Medicago truncatula enod40 region between the sORFs, spanning a predicted RNA structure, did not affect their translation but resulted in significantly decreased biological activity. Our data reveal a complex regulation of enod40 action, pointing to a role of sORF-encoded peptides and structured RNA signals in developmental processes involving sORF-RNAs.

Modality dependence and intermodal transfer in the Corsi Spatial Sequence Task: Screen vs. Floor.

PubMed

Röser, Andrea; Hardiess, Gregor; Mallot, Hanspeter A

2016-07-01

Four versions of the Corsi Spatial Sequence Task (CSST) were tested in a complete within-subject design, investigating whether participants' performance depends on the modality of task presentation and reproduction that put different demands on spatial processing. Presentation of the sequence (encoding phase) and the reproduction (recall phase) were each carried out either on a computer screen or on the floor of a room, involving actual walking in the recall phase. Combinations of the two different encoding and recall procedures result in the modality conditions Screen-Screen, Screen-Floor, Floor-Screen, and Floor-Floor. Results show the expected decrease in performance with increasing sequence length, which is likely due to processing limitations of working memory. We also found differences in performance between the modality conditions indicating different involvements of spatial working memory processes. Participants performed best in the Screen-Screen modality condition. Floor-Screen and Floor-Floor modality conditions require additional working memory resources for reference frame transformation and spatial updating, respectively; the resulting impairment of the performance was about the same in these two conditions. Finally, the Screen-Floor modality condition requires both types of additional spatial demands and led to the poorest performance. Therefore, we suggest that besides the well-known spatial requirements of CSST, additional working memory resources are demanded in walking CSST supporting processes such as spatial updating, mental rotation, reference frame transformation, and the control of walking itself.

Translational control of Nrf2 within the open reading frame

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

Perez-Leal, Oscar, E-mail: operez@temple.edu; Barrero, Carlos A.; Merali, Salim, E-mail: smerali@temple.edu

2013-07-19

Highlights: •Identification of a novel Nrf2 translational repression mechanism. •The repressor is within the 3′ portion of the Nrf2 ORF. •The translation of Nrf2 or eGFP is reduced by the regulatory element. •The translational repression can be reversed with synonymous codon substitutions. •The molecular mechanism requires the mRNA sequence, but not the encoded amino acids. -- Abstract: Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2) is a transcription factor that is essential for the regulation of an effective antioxidant and detoxifying response. The regulation of its activity can occur at transcription, translation and post-translational levels. Evidence suggests that under environmental stressmore » conditions, new synthesis of Nrf2 is required – a process that is regulated by translational control and is not fully understood. Here we described the identification of a novel molecular process that under basal conditions strongly represses the translation of Nrf2 within the open reading frame (ORF). This mechanism is dependent on the mRNA sequence within the 3′ portion of the ORF of Nrf2 but not in the encoded amino acid sequence. The Nrf2 translational repression can be reversed with the use of synonymous codon substitutions. This discovery suggests an additional layer of control to explain the reason for the low Nrf2 concentration under quiescent state.« less

The IRC7 gene encodes cysteine desulphydrase activity and confers on yeast the ability to grow on cysteine as a nitrogen source.

PubMed

Santiago, Margarita; Gardner, Richard C

2015-07-01

Although cysteine desulphydrase activity has been purified and characterized from Saccharomyces cerevisiae, the gene encoding this activity in vivo has never been defined. We show that the full-length IRC7 gene, encoded by the YFR055W open reading frame, encodes a protein with cysteine desulphydrase activity. Irc7p purified to homogeneity is able to utilize l-cysteine as a substrate, producing pyruvate and hydrogen sulphide as products of the reaction. Purified Irc7p also utilized l-cystine and some other cysteine conjugates, but not l-cystathionine or l-methionine, as substrates. We further show that, in vivo, the IRC7 gene is both necessary and sufficient for yeast to grow on l-cysteine as a nitrogen source, and that overexpression of the gene results in increased H2 S production. Strains overexpressing IRC7 are also hypersensitive to a toxic analogue, S-ethyl-l-cysteine. While IRC7 has been identified as playing a critical role in converting cysteine conjugates to volatile thiols that are important in wine aroma, its biological role in yeast cells is likely to involve regulation of cysteine and redox homeostasis. Copyright © 2015 John Wiley & Sons, Ltd.

Nonlethal sec71-1 and sec72-1 mutations eliminate proteins associated with the Sec63p-BiP complex from S. cerevisiae.

PubMed Central

Fang, H; Green, N

1994-01-01

The sec71-1 and sec72-1 mutations were identified by a genetic assay that monitored membrane protein integration into the endoplasmic reticulum (ER) membrane of the yeast Saccharomyces cerevisiae. The mutations inhibited integration of various chimeric membrane proteins and translocation of a subset of water soluble proteins. In this paper we show that SEC71 encodes the 31.5-kDa transmembrane glycoprotein (p31.5) and SEC72 encodes the 23-kDa protein (p23) of the Sec63p-BiP complex. SEC71 is therefore identical to SEC66 (HSS1), which was previously shown to encode p31.5. DNA sequence analyses reveal that sec71-1 cells contain a nonsense mutation that removes approximately two-thirds of the cytoplasmic C-terminal domain of p31.5. The sec72-1 mutation shifts the reading frame of the gene encoding p23. Unexpectedly, the sec71-1 mutant lacks p31.5 and p23. Neither mutation is lethal, although sec71-1 cells exhibit a growth defect at 37 degrees C. These results show that p31.5 and p23 are important for the trafficking of a subset of proteins to the ER membrane. Images PMID:7841522

30 CFR 77.701-2 - Approved methods of grounding metallic frames, casings, and other enclosures of electric...

Code of Federal Regulations, 2014 CFR

2014-07-01

... representative of the Secretary, which insures that there is no difference in potential between such metal... there is no difference in potential between such frames, casings, and other enclosures, and the earth. ...

30 CFR 77.701-2 - Approved methods of grounding metallic frames, casings, and other enclosures of electric...

Code of Federal Regulations, 2013 CFR

2013-07-01

... representative of the Secretary, which insures that there is no difference in potential between such metal... there is no difference in potential between such frames, casings, and other enclosures, and the earth. ...

The cloning, characterization, and functional analysis of a gene encoding an isopentenyl diphosphate isomerase involved in triterpene biosynthesis in the Lingzhi or reishi medicinal mushroom Ganoderma lucidum (higher Basidiomycetes).

PubMed

Wu, Feng-Li; Shi, Liang; Yao, Jian; Ren, Ang; Zhou, Chao; Mu, Da-Shuai; Zhao, Ming-Wen

2013-01-01

An isopentenyl diphosphate isomerase (IDI) gene, GlIDI, was isolated from Ganoderma lucidum, which produces triterpenes through the mevalonate pathway. The open reading frame of GlIDI encodes a 252 amino acid polypeptide with a theoretical molecular mass of 28.71 kDa and a theoretical isoelectric point of 5.36. GlIDI is highly homologous to other fungal IDIs and contains conserved active residues and nudix motifs shared by the IDI protein family. The color complementation assay indicated that GlIDI can accelerate the accumulation of β-carotene and confirmed that the cloned complementary DNA encoded a functional GlIDI protein. Gene expression analysis showed that the GlIDI transcription level was relatively low in the mycelia and reached a relatively high level in the mushroom primordia. In addition, its expression level could be up-regulated by 254 µM methyl jasmonate. Our results suggest that this enzyme may play an important role in triterpene biosynthesis.

A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast.

PubMed

Jaschke, Paul R; Lieberman, Erica K; Rodriguez, Jon; Sierra, Adrian; Endy, Drew

2012-12-20

The 5386 nucleotide bacteriophage øX174 genome has a complicated architecture that encodes 11 gene products via overlapping protein coding sequences spanning multiple reading frames. We designed a 6302 nucleotide synthetic surrogate, øX174.1, that fully separates all primary phage protein coding sequences along with cognate translation control elements. To specify øX174.1f, a decompressed genome the same length as wild type, we truncated the gene F coding sequence. We synthesized DNA encoding fragments of øX174.1f and used a combination of in vitro- and yeast-based assembly to produce yeast vectors encoding natural or designer bacteriophage genomes. We isolated clonal preparations of yeast plasmid DNA and transfected E. coli C strains. We recovered viable øX174 particles containing the øX174.1f genome from E. coli C strains that independently express full-length gene F. We expect that yeast can serve as a genomic 'drydock' within which to maintain and manipulate clonal lineages of other obligate lytic phage. Copyright © 2012 Elsevier Inc. All rights reserved.

Heterozygous variants in ACTL6A, encoding a component of the BAF complex, are associated with intellectual disability.

PubMed

Marom, Ronit; Jain, Mahim; Burrage, Lindsay C; Song, I-Wen; Graham, Brett H; Brown, Chester W; Stevens, Servi J C; Stegmann, Alexander P A; Gunter, Andrew T; Kaplan, Julie D; Gavrilova, Ralitza H; Shinawi, Marwan; Rosenfeld, Jill A; Bae, Yangjin; Tran, Alyssa A; Chen, Yuqing; Lu, James T; Gibbs, Richard A; Eng, Christine; Yang, Yaping; Rousseau, Justine; de Vries, Bert B A; Campeau, Philippe M; Lee, Brendan

2017-10-01

Pathogenic variants in genes encoding components of the BRG1-associated factor (BAF) chromatin remodeling complex have been associated with intellectual disability syndromes. We identified heterozygous, novel variants in ACTL6A, a gene encoding a component of the BAF complex, in three subjects with varying degrees of intellectual disability. Two subjects have missense variants affecting highly conserved amino acid residues within the actin-like domain. Missense mutations in the homologous region in yeast actin were previously reported to be dominant lethal and were associated with impaired binding of the human ACTL6A to β-actin and BRG1. A third subject has a splicing variant that creates an in-frame deletion. Our findings suggest that the variants identified in our subjects may have a deleterious effect on the function of the protein by disturbing the integrity of the BAF complex. Thus, ACTL6A gene mutation analysis should be considered in patients with intellectual disability, learning disabilities, or developmental language disorder. © 2017 Wiley Periodicals, Inc.

A Cryptosporidium parvum genomic region encoding hemolytic activity.

PubMed Central

Steele, M I; Kuhls, T L; Nida, K; Meka, C S; Halabi, I M; Mosier, D A; Elliott, W; Crawford, D L; Greenfield, R A

1995-01-01

Successful parasitization by Cryptosporidium parvum requires multiple disruptions in both host and protozoan cell membranes as cryptosporidial sporozoites invade intestinal epithelial cells and subsequently develop into asexual and sexual life stages. To identify cryptosporidial proteins which may play a role in these membrane alterations, hemolytic activity was used as a marker to screen a C. parvum genomic expression library. A stable hemolytic clone (H4) containing a 5.5-kb cryptosporidial genomic fragment was identified. The hemolytic activity encoded on H4 was mapped to a 1-kb region that contained a complete 690-bp open reading frame (hemA) ending in a common stop codon. A 21-kDa plasmid-encoded recombinant protein was expressed in maxicells containing H4. Subclones of H4 which contained only a portion of hemA did not induce hemolysis on blood agar or promote expression of the recombinant protein in maxicells. Reverse transcriptase-mediated PCR analysis of total RNA isolated from excysted sporozoites and the intestines of infected adult mice with severe combined immunodeficiency demonstrated that hemA is actively transcribed during the cryptosporidial life cycle. PMID:7558289

African swine fever virus encodes two genes which share significant homology with the two largest subunits of DNA-dependent RNA polymerases.

PubMed Central

Yáñez, R J; Boursnell, M; Nogal, M L; Yuste, L; Viñuela, E

1993-01-01

A random sequencing strategy applied to two large SalI restriction fragments (SB and SD) of the African swine fever virus (ASFV) genome revealed that they might encode proteins similar to the two largest RNA polymerase subunits of eukaryotes, poxviruses and Escherichia coli. After further mapping by dot-blot hybridization, two large open reading frames (ORFs) were completely sequenced. The first ORF (NP1450L) encodes a protein of 1450 amino acids with extensive similarity to the largest subunit of RNA polymerases. The second one (EP1242L) codes for a protein of 1242 amino acids similar to the second largest RNA polymerase subunit. Proteins NP1450L and EP1242L are more similar to the corresponding subunits of eukaryotic RNA polymerase II than to those of vaccinia virus, the prototype poxvirus, which shares many functional characteristics with ASFV. ORFs NP1450L and EP1242L are mainly expressed late in ASFV infection, after the onset of DNA replication. Images PMID:8506138

Identification of a novel fusion gene HMGA2-EGFR in glioblastoma.

PubMed

Komuro, Akiyoshi; Raja, Erna; Iwata, Caname; Soda, Manabu; Isogaya, Kazunobu; Yuki, Keiko; Ino, Yasushi; Morikawa, Masato; Todo, Tomoki; Aburatani, Hiroyuki; Suzuki, Hiromichi; Ranjit, Melissa; Natsume, Atsushi; Mukasa, Akitake; Saito, Nobuhito; Okada, Hitoshi; Mano, Hiroyuki; Miyazono, Kohei; Koinuma, Daizo

2018-04-15

Glioblastoma is one of the most malignant forms of cancer, for which no effective targeted therapy has been found. Although The Cancer Genome Atlas has provided a list of fusion genes in glioblastoma, their role in progression of glioblastoma remains largely unknown. To search for novel fusion genes, we obtained RNA-seq data from TGS-01 human glioma-initiating cells, and identified a novel fusion gene (HMGA2-EGFR), encoding a protein comprising the N-terminal region of the high-mobility group AT-hook protein 2 (HMGA2) fused to the C-terminal region of epidermal growth factor receptor (EGFR), which retained the transmembrane and kinase domains of the EGFR. This fusion gene product showed transforming potential and a high tumor-forming capacity in cell culture and in vivo. Mechanistically, HMGA2-EGFR constitutively induced a higher level of phosphorylated STAT5B than EGFRvIII, an in-frame exon deletion product of the EGFR gene that is commonly found in primary glioblastoma. Forced expression of HMGA2-EGFR enhanced orthotopic tumor formation of the U87MG human glioma cell line. Furthermore, the EGFR kinase inhibitor erlotinib blocked sphere formation of TGS-01 cells in culture and inhibited tumor formation in vivo. These findings suggest that, in addition to gene amplification and in-frame exon deletion, EGFR signaling can also be activated by gene fusion, suggesting a possible avenue for treatment of glioblastoma. © 2017 UICC.

Countermeasures for unintentional and intentional video watermarking attacks

NASA Astrophysics Data System (ADS)

Deguillaume, Frederic; Csurka, Gabriela; Pun, Thierry

2000-05-01

These last years, the rapidly growing digital multimedia market has revealed an urgent need for effective copyright protection mechanisms. Therefore, digital audio, image and video watermarking has recently become a very active area of research, as a solution to this problem. Many important issues have been pointed out, one of them being the robustness to non-intentional and intentional attacks. This paper studies some attacks and proposes countermeasures applied to videos. General attacks are lossy copying/transcoding such as MPEG compression and digital/analog (D/A) conversion, changes of frame-rate, changes of display format, and geometrical distortions. More specific attacks are sequence edition, and statistical attacks such as averaging or collusion. Averaging attack consists of averaging locally consecutive frames to cancel the watermark. This attack works well for schemes which embed random independent marks into frames. In the collusion attack the watermark is estimated from single frames (based on image denoising), and averaged over different scenes for better accuracy. The estimated watermark is then subtracted from each frame. Collusion requires that the same mark is embedded into all frames. The proposed countermeasures first ensures robustness to general attacks by spread spectrum encoding in the frequency domain and by the use of an additional template. Secondly, a Bayesian criterion, evaluating the probability of a correctly decoded watermark, is used for rejection of outliers, and to implement an algorithm against statistical attacks. The idea is to embed randomly chosen marks among a finite set of marks, into subsequences of videos which are long enough to resist averaging attacks, but short enough to avoid collusion attacks. The Bayesian criterion is needed to select the correct mark at the decoding step. Finally, the paper presents experimental results showing the robustness of the proposed method.

Event-Based Tone Mapping for Asynchronous Time-Based Image Sensor

PubMed Central

Simon Chane, Camille; Ieng, Sio-Hoi; Posch, Christoph; Benosman, Ryad B.

2016-01-01

The asynchronous time-based neuromorphic image sensor ATIS is an array of autonomously operating pixels able to encode luminance information with an exceptionally high dynamic range (>143 dB). This paper introduces an event-based methodology to display data from this type of event-based imagers, taking into account the large dynamic range and high temporal accuracy that go beyond available mainstream display technologies. We introduce an event-based tone mapping methodology for asynchronously acquired time encoded gray-level data. A global and a local tone mapping operator are proposed. Both are designed to operate on a stream of incoming events rather than on time frame windows. Experimental results on real outdoor scenes are presented to evaluate the performance of the tone mapping operators in terms of quality, temporal stability, adaptation capability, and computational time. PMID:27642275

Deep and shallow encoding effects on face recognition: an ERP study.

PubMed

Marzi, Tessa; Viggiano, Maria Pia

2010-12-01

Event related potentials (ERPs) were employed to investigate whether and when brain activity related to face recognition varies according to the processing level undertaken at encoding. Recognition was assessed when preceded by a "shallow" (orientation judgement) or by a "deep" study task (occupation judgement). Moreover, we included a further manipulation by presenting at encoding faces either in the upright or inverted orientation. As expected, deeply encoded faces were recognized more accurately and more quickly with respect to shallowly encoded faces. The ERP showed three main findings: i) as witnessed by more positive-going potentials for deeply encoded faces, at early and later processing stage, face recognition was influenced by the processing strategy adopted during encoding; ii) structural encoding, indexed by the N170, turned out to be "cognitively penetrable" showing repetition priming effects for deeply encoded faces; iii) face inversion, by disrupting configural processing during encoding, influenced memory related processes for deeply encoded faces and impaired the recognition of faces shallowly processed. The present study adds weight to the concept that the depth of processing during memory encoding affects retrieval. We found that successful retrieval following deep encoding involved both familiarity- and recollection-related processes showing from 500 ms a fronto-parietal distribution, whereas shallow encoding affected only earlier processing stages reflecting perceptual priming. Copyright © 2010 Elsevier B.V. All rights reserved.

Spatially encoded phase-contrast MRI-3D MRI movies of 1D and 2D structures at millisecond resolution.

PubMed

Merboldt, Klaus-Dietmar; Uecker, Martin; Voit, Dirk; Frahm, Jens

2011-10-01

This work demonstrates that the principles underlying phase-contrast MRI may be used to encode spatial rather than flow information along a perpendicular dimension, if this dimension contains an MRI-visible object at only one spatial location. In particular, the situation applies to 3D mapping of curved 2D structures which requires only two projection images with different spatial phase-encoding gradients. These phase-contrast gradients define the field of view and mean spin-density positions of the object in the perpendicular dimension by respective phase differences. When combined with highly undersampled radial fast low angle shot (FLASH) and image reconstruction by regularized nonlinear inversion, spatial phase-contrast MRI allows for dynamic 3D mapping of 2D structures in real time. First examples include 3D MRI movies of the acting human hand at a temporal resolution of 50 ms. With an even simpler technique, 3D maps of curved 1D structures may be obtained from only three acquisitions of a frequency-encoded MRI signal with two perpendicular phase encodings. Here, 3D MRI movies of a rapidly rotating banana were obtained at 5 ms resolution or 200 frames per second. In conclusion, spatial phase-contrast 3D MRI of 2D or 1D structures is respective two or four orders of magnitude faster than conventional 3D MRI. Copyright © 2011 Wiley-Liss, Inc.

The Genome of S-PM2, a “Photosynthetic” T4-Type Bacteriophage That Infects Marine Synechococcus Strains

PubMed Central

Mann, Nicholas H.; Clokie, Martha R. J.; Millard, Andrew; Cook, Annabel; Wilson, William H.; Wheatley, Peter J.; Letarov, Andrey; Krisch, H. M.

2005-01-01

Bacteriophage S-PM2 infects several strains of the abundant and ecologically important marine cyanobacterium Synechococcus. A large lytic phage with an isometric icosahedral head, S-PM2 has a contractile tail and by this criterion is classified as a myovirus (1). The linear, circularly permuted, 196,280-bp double-stranded DNA genome of S-PM2 contains 37.8% G+C residues. It encodes 239 open reading frames (ORFs) and 25 tRNAs. Of these ORFs, 19 appear to encode proteins associated with the cell envelope, including a putative S-layer-associated protein. Twenty additional S-PM2 ORFs have homologues in the genomes of their cyanobacterial hosts. There is a group I self-splicing intron within the gene encoding the D1 protein. A total of 40 ORFs, organized into discrete clusters, encode homologues of T4 proteins involved in virion morphogenesis, nucleotide metabolism, gene regulation, and DNA replication and repair. The S-PM2 genome encodes a few surprisingly large (e.g., 3,779 amino acids) ORFs of unknown function. Our analysis of the S-PM2 genome suggests that many of the unknown S-PM2 functions may be involved in the adaptation of the metabolism of the host cell to the requirements of phage infection. This hypothesis originates from the identification of multiple phage-mediated modifications of the host's photosynthetic apparatus that appear to be essential for maintaining energy production during the lytic cycle. PMID:15838046

Aerobic Exercise During Encoding Impairs Hippocampus-Dependent Memory.

PubMed

Soga, Keishi; Kamijo, Keita; Masaki, Hiroaki

2017-08-01

We investigated how aerobic exercise during encoding affects hippocampus-dependent memory through a source memory task that assessed hippocampus-independent familiarity and hippocampus-dependent recollection processes. Using a within-participants design, young adult participants performed a memory-encoding task while performing a cycling exercise or being seated. The subsequent retrieval phase was conducted while sitting on a chair. We assessed behavioral and event-related brain potential measures of familiarity and recollection processes during the retrieval phase. Results indicated that source accuracy was lower for encoding with exercise than for encoding in the resting condition. Event-related brain potential measures indicated that the parietal old/new effect, which has been linked to recollection processing, was observed in the exercise condition, whereas it was absent in the rest condition, which is indicative of exercise-induced hippocampal activation. These findings suggest that aerobic exercise during encoding impairs hippocampus-dependent memory, which may be attributed to inefficient source encoding during aerobic exercise.

Characterization of Durham virus, a novel rhabdovirus that encodes both a C and SH protein.

PubMed

Allison, A B; Palacios, G; Travassos da Rosa, A; Popov, V L; Lu, L; Xiao, S Y; DeToy, K; Briese, T; Lipkin, W I; Keel, M K; Stallknecht, D E; Bishop, G R; Tesh, R B

2011-01-01

The family Rhabdoviridae is a diverse group of non-segmented, negative-sense RNA viruses that are distributed worldwide and infect a wide range of hosts including vertebrates, invertebrates, and plants. Of the 114 currently recognized vertebrate rhabdoviruses, relatively few have been well characterized at both the antigenic and genetic level; hence, the phylogenetic relationships between many of the vertebrate rhabdoviruses remain unknown. The present report describes a novel rhabdovirus isolated from the brain of a moribund American coot (Fulica americana) that exhibited neurological signs when found in Durham County, North Carolina, in 2005. Antigenic characterization of the virus revealed that it was serologically unrelated to 68 other known vertebrate rhabdoviruses. Genomic sequencing of the virus indicated that it shared the highest identity to Tupaia rhabdovirus (TUPV), and as only previously observed in TUPV, the genome encoded a putative C protein in an overlapping open reading frame (ORF) of the phosphoprotein gene and a small hydrophobic (SH) protein located in a novel ORF between the matrix and glycoprotein genes. Phylogenetic analysis of partial amino acid sequences of the nucleoprotein and polymerase protein indicated that, in addition to TUPV, the virus was most closely related to avian and small mammal rhabdoviruses from Africa and North America. In this report, we present the morphological, pathological, antigenic, and genetic characterization of the new virus, tentatively named Durham virus (DURV), and discuss its potential evolutionary relationship to other vertebrate rhabdoviruses. Copyright © 2010 Elsevier B.V. All rights reserved.

Learning Relative Motion Concepts in Immersive and Non-immersive Virtual Environments

NASA Astrophysics Data System (ADS)

Kozhevnikov, Michael; Gurlitt, Johannes; Kozhevnikov, Maria

2013-12-01

The focus of the current study is to understand which unique features of an immersive virtual reality environment have the potential to improve learning relative motion concepts. Thirty-seven undergraduate students learned relative motion concepts using computer simulation either in immersive virtual environment (IVE) or non-immersive desktop virtual environment (DVE) conditions. Our results show that after the simulation activities, both IVE and DVE groups exhibited a significant shift toward a scientific understanding in their conceptual models and epistemological beliefs about the nature of relative motion, and also a significant improvement on relative motion problem-solving tests. In addition, we analyzed students' performance on one-dimensional and two-dimensional questions in the relative motion problem-solving test separately and found that after training in the simulation, the IVE group performed significantly better than the DVE group on solving two-dimensional relative motion problems. We suggest that egocentric encoding of the scene in IVE (where the learner constitutes a part of a scene they are immersed in), as compared to allocentric encoding on a computer screen in DVE (where the learner is looking at the scene from "outside"), is more beneficial than DVE for studying more complex (two-dimensional) relative motion problems. Overall, our findings suggest that such aspects of virtual realities as immersivity, first-hand experience, and the possibility of changing different frames of reference can facilitate understanding abstract scientific phenomena and help in displacing intuitive misconceptions with more accurate mental models.

Characterization of Durham virus, a novel rhabdovirus that encodes both a C and SH protein

PubMed Central

Allison, A. B.; Palacios, G.; Rosa, A. Travassos da; Popov, V. L.; Lu, L.; Xiao, S. Y.; DeToy, K.; Briese, T.; Lipkin, W. Ian; Keel, M. K.; Stallknecht, D. E.; Bishop, G. R.; Tesh, R. B.

2010-01-01

The family Rhabdoviridae is a diverse group of non-segmented, negative-sense RNA viruses that are distributed worldwide and infect a wide range of hosts including vertebrates, invertebrates, and plants. Of the 114 currently recognized vertebrate rhabdoviruses, relatively few have been well characterized at both the antigenic and genetic level; hence, the phylogenetic relationships between many of the vertebrate rhabdoviruses remain unknown. The present report describes a novel rhabdovirus isolated from the brain of a moribund American coot (Fulica americana) that exhibited neurological signs when found in Durham County, North Carolina, in 2005. Antigenic characterization of the virus revealed that it was serologically unrelated to 68 other known vertebrate rhabdoviruses. Genomic sequencing of the virus indicated that it shared the highest identity to Tupaia rhabdovirus (TUPV), and as only previously observed in TUPV, the genome encoded a putative C protein in an overlapping open reading frame (ORF) of the phosphoprotein gene and a small hydrophobic protein located in a novel ORF between the matrix and glycoprotein genes. Phylogenetic analysis of partial amino acid sequences of the nucleoprotein and polymerase proteins indicated that, in addition to TUPV, the virus was most closely related to avian and small mammal rhabdoviruses from Africa and North America. In this report, we present the morphological, pathological, antigenic, and genetic characterization of the new virus, tentatively named Durham virus (DURV), and discuss its potential evolutionary relationship to other vertebrate rhabdoviruses. PMID:20863863

Complete genome sequence of Vibrio parahaemolyticus strain FORC_008, a foodborne pathogen from a flounder fish in South Korea.

PubMed

Kim, Suyeon; Chung, Han Young; Lee, Dong-Hoon; Lim, Jong Gyu; Kim, Se Keun; Ku, Hye-Jin; Kim, You-Tae; Kim, Heebal; Ryu, Sangryeol; Lee, Ju-Hoon; Choi, Sang Ho

2016-07-01

Vibrio parahaemolyticus is a Gram-negative, motile, nonspore-forming pathogen that causes foodborne illness associated with the consumption of contaminated seafoods. Although many cases of foodborne outbreaks caused by V. parahaemolyticus have been reported, the genomes of only five strains have been completely sequenced and analyzed using bioinformatics. In order to characterize overall virulence factors and pathogenesis of V. parahaemolyticus associated with foodborne outbreak in South Korea, a new strain FORC_008 was isolated from flounder fish and its genome was completely sequenced. The genomic analysis revealed that the genome of FORC_008 consists of two circular DNA chromosomes of 3266 132 bp (chromosome I) and 1772 036 bp (chromosome II) with a GC content of 45.36% and 45.53%, respectively. The entire genome contains 4494 predicted open reading frames, 129 tRNAs and 31 rRNA genes. While the strain FORC_008 does not have genes encoding thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), its genome encodes many other virulence factors including hemolysins, pathogenesis-associated secretion systems and iron acquisition systems, suggesting that it may be a potential pathogen. This report provides an extended understanding on V. parahaemolyticus in genomic level and would be helpful for rapid detection, epidemiological investigation and prevention of foodborne outbreak in South Korea. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular and functional characterization of CaLEA6, the gene for a hydrophobic LEA protein from Capsicum annuum.

PubMed

Kim, Hyung-Sae; Lee, Jee Hyun; Kim, Jae Joon; Kim, Chang-Hoon; Jun, Sung-Soo; Hong, Young-Nam

2005-01-03

We used differential screening to isolate a full-length dehydration-responsive cDNA clone encoding a hydrophobic late embryogenesis abundant (LEA)-like protein from PEG-treated hot pepper leaves. Named CaLEA6 (for Capsicum annuum LEA), this gene belongs to the atypical hydrophobic LEA Group 6. The full-length CaLEA6 is 709 bp long with an open reading frame encoding 164 amino acids. It is predicted to produce a highly hydrophobic, but cytoplasmic, protein. The putative M(r) of CaLEA6 protein is 18 kDa, with a theoretical pI of 4.63. Based on our Southern blot analysis, CaLEA6 appears to exist as a small gene family. CaLEA6 was not expressed prior to any treatment, but its transcript was rapidly and greatly increased following trials with PEG, ABA, and NaCl. Chilling also induced its rapid induction, but to a much lesser extent. Accumulation of CaLEA6 protein occurred soon after NaCl applications, but considerably delayed after treatment with PEG. Tobacco plants that overexpressed CaLEA6 showed enhanced tolerance to dehydration and NaCl but not to chilling, as defined by their leaf fresh weights, Chl contents, and the general health status of the leaves. Therefore, we suggest that CaLEA6 protein plays a potentially protective role when water deficit is induced by dehydration and high salinity, but not low temperature.

Identification of a novel transcript disrupted by a balanced translocation associated with DiGeorge syndrome

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

Sutherland, H.F.; Wadey, R.; McKie, J.M.

1996-07-01

Most cases of DiGeorge syndrome (DGS) and related abnormalities are associated with deletions within 22q11. Shortest region on deletion overlap (SRO) mapping previously identified a critical region (the DGCR) of 500 kb, which was presumed to contain a gene or genes of major effect in the haploinsufficiency syndromes. The DGCR also contains sequences disrupted by a balanced translocation that is associated with DGS - the ADU breakpoint. We have cloned sequences at the breakpoint and screened for novel genes in its vicinity. A series of alternatively spliced transcripts expressed during human and murine embryogenesis, but with no obvious protein encodingmore » potential, were identified. The gene encoding these RNAs has been named DGCR5 and it is disrupted by the patient ADU breakpoint. DGCR5 is distinct from the DGCR3 open reading frame (ORF) previously shown to be interrupted by the ADU translocation, although DGCR3 is embedded within a DGCR5 intron and in the same (predicted) transcriptional orientation. No mutations of DGCR5 have yet been detected. By analogy to other loci encoding conserved, nontranslated RNAs, it is possible that DGCR5 originates from a cis-acting transcriptional control element in the vicinity of the ADU/VDU breakpoint. Disruption of such an element would result in altered transcription of neighboring genes secondary to a position effect, a hypothesis in keeping with recent refinement of the SRO placing the ADU breakpoint outside the DGCR. 38 refs., 3 figs., 1 tab.« less

Cathepsin O is involved in the innate immune response and metamorphosis of Antheraea pernyi.

PubMed

Sun, Yu-Xuan; Zhu, Bao-Jian; Tang, Lin; Sun, Yu; Chen, Chen; Nadeem Abbas, Muhammad; Wang, Lei; Qian, Cen; Wei, Guo-Qing; Liu, Chao-Liang

2017-11-01

Cathepsins are key members of mammalian papain-like cysteine proteases that play an important role in the immune response. In this study, a fragment of cDNA encoding cathepsin O proteinase (ApCathepsin O) was cloned from Antheraea pernyi. It contains an open reading frame of 1170bp and encodes a protein with 390 amino acid residues, including a conserved I29 inhibitor domain and a peptidase C1A (clan CA of cysteine proteases, papain family C1 subfamily) domain. Comparison with other previously reported cathepsin O proteins showed identity ranging from 45% to 79%. Quantitative real-time PCR (qRT-PCR) and Western blot analysis revealed that ApCathepsin O was highly expressed in the fat body; furthermore, the high expression during the pupal stage indicated that it might be involved during metamorphosis. After exposure to four different heat-killed pathogens (Escherichia coli, Beauveria bassiana, Micrococcus luteus, and A. pernyi nucleopolyhedrovirus), the expression levels of ApCathepsin O mRNA significantly increased and showed variable expression patterns. This indicates that ApCathepsin O is potentially involved in the innate immune system of A. pernyi. Interestingly, ApCathepsin O expression was upregulated after 20-hydroxyecdysone (20E) injection, which suggested that it might be regulated by 20E. In conclusion, ApCathepsin O is a protease that may play an important role in the innate immune response and metamorphosis of A. pernyi. Copyright © 2017. Published by Elsevier Inc.

Sphingomonas paucimobilis beta-glucosidase Bgl1: a member of a new bacterial subfamily in glycoside hydrolase family 1.

PubMed Central

Marques, Ana Rita; Coutinho, Pedro M; Videira, Paula; Fialho, Arsénio M; Sá-Correia, Isabel

2003-01-01

The Sphingomonas paucimobilis beta-glucosidase Bgl1 is encoded by the bgl1 gene, associated with an 1308 bp open reading frame. The deduced protein has a potential signal peptide of 24 amino acids in the N-terminal region, and experimental evidence is consistent with the processing and export of the Bgl1 protein through the inner membrane to the periplasmic space. A His(6)-tagged 44.3 kDa protein was over-produced in the cytosol of Escherichia coli from a recombinant plasmid, which contained the S. paucimobilis bgl1 gene lacking the region encoding the putative signal peptide. Mature beta-glucosidase Bgl1 is specific for aryl-beta-glucosides and has no apparent activity with oligosaccharides derived from cellulose hydrolysis and other saccharides. A structure-based alignment established structural relations between S. paucimobilis Bgl1 and other members of the glycoside hydrolase (GH) family 1 enzymes. At subsite -1, the conserved residues required for catalysis by GH1 enzymes are present in Bgl1 with only minor differences. Major differences are found at subsite +1, the aglycone binding site. This alignment seeded a sequence-based phylogenetic analysis of GH1 enzymes, revealing an absence of horizontal transfer between phyla. Bootstrap analysis supported the definition of subfamilies and revealed that Bgl1, the first characterized beta-glucosidase from the genus Sphingomonas, represents a very divergent bacterial subfamily, closer to archaeal subfamilies than to others of bacterial origin. PMID:12444924

iso-Migrastatin, migrastatin, and dorrigocin production in Streptomyces platensis NRRL 18993 is governed by a single biosynthetic machinery featuring an acyltransferase-less type I polyketide synthase.

PubMed

Lim, Si-Kyu; Ju, Jianhua; Zazopoulos, Emmanuel; Jiang, Hui; Seo, Jeong-Woo; Chen, Yihua; Feng, Zhiyang; Rajski, Scott R; Farnet, Chris M; Shen, Ben

2009-10-23

iso-Migrastatin and related glutarimide-containing polyketides are potent inhibitors of tumor cell migration and their implied potential as antimetastatic agents for human cancers has garnered significant attention. Genome scanning of Streptomyces platensis NRRL 18993 unveiled two candidate gene clusters (088D and mgs); each encodes acyltransferase-less type I polyketide synthases commensurate with iso-migrastatin biosynthesis. Both clusters were inactivated by lambda-RED-mediated PCR-targeting mutagenesis in S. platensis; iso-migrastatin production was completely abolished in the DeltamgsF mutant SB11012 strain, whereas inactivation of 088D-orf7 yielded the SB11006 strain that exhibited no discernible change in iso-migrastatin biosynthesis. These data indicate that iso-migrastatin production is governed by the mgs cluster. Systematic gene inactivation allowed determination of the precise boundaries of the mgs cluster and the essentiality of the genes within the mgs cluster in iso-migrastatin production. The mgs cluster consists of 11 open reading frames that encode three acyltransferase-less type I polyketide synthases (MgsEFG), one discrete acyltransferase (MgsH), a type II thioesterase (MgsB), three post-PKS tailoring enzymes (MgsIJK), two glutarimide biosynthesis enzymes (MgsCD), and one regulatory protein (MgsA). A model for iso-migrastatin biosynthesis is proposed based on functional assignments derived from bioinformatics and is further supported by the results of in vivo gene inactivation experiments.

iso-Migrastatin, Migrastatin, and Dorrigocin Production in Streptomyces platensis NRRL 18993 Is Governed by a Single Biosynthetic Machinery Featuring an Acyltransferase-less Type I Polyketide Synthase*

PubMed Central

Lim, Si-Kyu; Ju, Jianhua; Zazopoulos, Emmanuel; Jiang, Hui; Seo, Jeong-Woo; Chen, Yihua; Feng, Zhiyang; Rajski, Scott R.; Farnet, Chris M.; Shen, Ben

2009-01-01

iso-Migrastatin and related glutarimide-containing polyketides are potent inhibitors of tumor cell migration and their implied potential as antimetastatic agents for human cancers has garnered significant attention. Genome scanning of Streptomyces platensis NRRL 18993 unveiled two candidate gene clusters (088D and mgs); each encodes acyltransferase-less type I polyketide synthases commensurate with iso-migrastatin biosynthesis. Both clusters were inactivated by λ-RED-mediated PCR-targeting mutagenesis in S. platensis; iso-migrastatin production was completely abolished in the ΔmgsF mutant SB11012 strain, whereas inactivation of 088D-orf7 yielded the SB11006 strain that exhibited no discernible change in iso-migrastatin biosynthesis. These data indicate that iso-migrastatin production is governed by the mgs cluster. Systematic gene inactivation allowed determination of the precise boundaries of the mgs cluster and the essentiality of the genes within the mgs cluster in iso-migrastatin production. The mgs cluster consists of 11 open reading frames that encode three acyltransferase-less type I polyketide synthases (MgsEFG), one discrete acyltransferase (MgsH), a type II thioesterase (MgsB), three post-PKS tailoring enzymes (MgsIJK), two glutarimide biosynthesis enzymes (MgsCD), and one regulatory protein (MgsA). A model for iso-migrastatin biosynthesis is proposed based on functional assignments derived from bioinformatics and is further supported by the results of in vivo gene inactivation experiments. PMID:19726666

Genome-Wide Protein Interaction Screens Reveal Functional Networks Involving Sm-Like Proteins

PubMed Central

Fromont-Racine, Micheline; Mayes, Andrew E.; Brunet-Simon, Adeline; Rain, Jean-Christophe; Colley, Alan; Dix, Ian; Decourty, Laurence; Joly, Nicolas; Ricard, Florence; Beggs, Jean D.

2000-01-01

A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence of Saccharomyces cerevisiae has identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (Like Sm) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein–protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale. PMID:10900456

A cilevirus infects ornamental hibiscus in Hawaii

PubMed Central

Melzer, Michael J.; Simbajon, Nelson; Carillo, James; Borth, Wayne B.; Freitas-Astúa, Juliana; Kitajima, Elliot W.; Neupane, Kabi R.; Hu, John S.

2013-01-01

The complete nucleotide sequence of a virus infecting ornamental hibiscus (Hibiscus sp.) in Hawaii with symptoms of green ringspots on senescing leaves was determined from double-stranded RNA isolated from symptomatic tissue. Excluding polyadenylated regions at the 3′ termini, the bipartite RNA genome was 8748 and 5019 nt in length for RNA1 and RNA2, respectively. The genome organization was typical of a cilevirus: RNA1 encoded a large replication-associated protein with methyltransferase, protease, helicase and RNA-dependent RNA polymerase domains as well as a 29-kDa protein of unknown function. RNA2 possessed five open reading frames that potentially encoded proteins with molecular masses of 15, 7, 62, 32, and 24 kDa. The 32-kDa protein is homologous to 3A movement proteins of RNA viruses; the other proteins are of unknown function. A proteome comparison revealed that this virus was 92% identical to citrus leprosis virus cytoplasmic type 2 (CiLV-C2), a recently characterized cilevirus infecting citrus with leprosis-like symptoms in Colombia. The high sequence similarity suggests that the virus described in this study could be a strain of CiLV-C2, but since the new genus Cilevirus does not have species demarcation criteria established at present, the classification of this virus infecting hibiscus is open to interpretation. This study represents the first documented case of a cilevirus established in the United States and provides insight into the diversity within the genus Cilevirus. PMID:23732930

Heterogeneous RNA-binding protein M4 is a receptor for carcinoembryonic antigen in Kupffer cells.

PubMed

Bajenova, O V; Zimmer, R; Stolper, E; Salisbury-Rowswell, J; Nanji, A; Thomas, P

2001-08-17

Here we report the isolation of the recombinant cDNA clone from rat macrophages, Kupffer cells (KC) that encodes a protein interacting with carcinoembryonic antigen (CEA). To isolate and identify the CEA receptor gene we used two approaches: screening of a KC cDNA library with a specific antibody and the yeast two-hybrid system for protein interaction using as a bait the N-terminal part of the CEA encoding the binding site. Both techniques resulted in the identification of the rat heterogeneous RNA-binding protein (hnRNP) M4 gene. The rat ortholog cDNA sequence has not been previously described. The open reading frame for this gene contains a 2351-base pair sequence with the polyadenylation signal AATAAA and a termination poly(A) tail. The mRNA shows ubiquitous tissue expression as a 2.4-kilobase transcript. The deduced amino acid sequence comprised a 78-kDa membrane protein with 3 putative RNA-binding domains, arginine/methionine/glutamine-rich C terminus and 3 potential membrane spanning regions. When hnRNP M4 protein is expressed in pGEX4T-3 vector system in Escherichia coli it binds (125)I-labeled CEA in a Ca(2+)-dependent fashion. Transfection of rat hnRNP M4 cDNA into a non-CEA binding mouse macrophage cell line p388D1 resulted in CEA binding. These data provide evidence for a new function of hnRNP M4 protein as a CEA-binding protein in Kupffer cells.

30 CFR 77.701-2 - Approved methods of grounding metallic frames, casings, and other enclosures of electric...

Code of Federal Regulations, 2012 CFR

2012-07-01

... enclosures and the earth. (b) A method of grounding of metallic frames, casings, and other enclosures of... there is no difference in potential between such frames, casings, and other enclosures, and the earth. ...

Achievement and Retention of Spanish Presented Via Videodisc in Linear, Segmented and Interactive Modes.

DTIC Science & Technology

1987-01-01

with non-emotional mate- rial . . . . P5. Students who are able to choose from a ’ menu ’ of topics to provide the general con- text of the exercise...smaller version of the videodisc encoded digitally and capable of storing vast numbers of still frames and text files, presents yet another opportunity for...37. En el restaurante , Ramiro pide . a. chorizo y tinto. b. sardinas y vino. c. tortilla y vino. 38. Cuando es t comiendo en el restaurante , Ramiro

A two-component response regulator, gltR, is required for glucose transport activity in Pseudomonas aeruginosa PAO1.

PubMed Central

Sage, A E; Proctor, W D; Phibbs, P V

1996-01-01

A 729-bp open reading frame (gltR) was identified in Pseudomonas aeruginosa PAO1 that encodes a product homologous to the two-component response regulator family of proteins. Disruption of gltR caused loss of glucose transport activity. Restoration of gltR resulted in wild-type levels of glucose transport. These findings indicate that gltR is required for expression of the glucose transport system in P. aeruginosa. PMID:8830708

When good is stickier than bad: Understanding gain/loss asymmetries in sequential framing effects.

PubMed

Sparks, Jehan; Ledgerwood, Alison

2017-08-01

Considerable research has demonstrated the power of the current positive or negative frame to shape people's current judgments. But humans must often learn about positive and negative information as they encounter that information sequentially over time. It is therefore crucial to consider the potential importance of sequencing when developing an understanding of how humans think about valenced information. Indeed, recent work looking at sequentially encountered frames suggests that some frames can linger outside the context in which they are first encountered, sticking in the mind so that subsequent frames have a muted effect. The present research builds a comprehensive account of sequential framing effects in both the loss and the gain domains. After seeing information about a potential gain or loss framed in positive terms or negative terms, participants saw the same issue reframed in the opposing way. Across 5 studies and 1566 participants, we find accumulating evidence for the notion that in the gain domain, positive frames are stickier than negative frames for novel but not familiar scenarios, whereas in the loss domain, negative frames are always stickier than positive frames. Integrating regulatory focus theory with the literatures on negativity dominance and positivity offset, we develop a new and comprehensive account of sequential framing effects that emphasizes the adaptive value of positivity and negativity biases in specific contexts. Our findings highlight the fact that research conducted solely in the loss domain risks painting an incomplete and oversimplified picture of human bias and suggest new directions for future research. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Motor Memory Is Encoded as a Gain-Field Combination of Intrinsic and Extrinsic Action Representations

PubMed Central

Brayanov, Jordan B.; Press, Daniel Z.; Smith, Maurice A.

2013-01-01

Actions can be planned in either an intrinsic (body-based) reference frame or an extrinsic (world-based) frame, and understanding how the internal representations associated with these frames contribute to the learning of motor actions is a key issue in motor control. We studied the internal representation of this learning in human subjects by analyzing generalization patterns across an array of different movement directions and workspaces after training a visuomotor rotation in a single movement direction in one workspace. This provided a dense sampling of the generalization function across intrinsic and extrinsic reference frames, which allowed us to dissociate intrinsic and extrinsic representations and determine the manner in which they contributed to the motor memory for a trained action. A first experiment showed that the generalization pattern reflected a memory that was intermediate between intrinsic and extrinsic representations. A second experiment showed that this intermediate representation could not arise from separate intrinsic and extrinsic learning. Instead, we find that the representation of learning is based on a gain-field combination of local representations in intrinsic and extrinsic coordinates. This gain-field representation generalizes between actions by effectively computing similarity based on the (Mahalanobis) distance across intrinsic and extrinsic coordinates and is in line with neural recordings showing mixed intrinsic-extrinsic representations in motor and parietal cortices. PMID:23100418

Indexing and retrieval of MPEG compressed video

NASA Astrophysics Data System (ADS)

Kobla, Vikrant; Doermann, David S.

1998-04-01

To keep pace with the increased popularity of digital video as an archival medium, the development of techniques for fast and efficient analysis of ideo streams is essential. In particular, solutions to the problems of storing, indexing, browsing, and retrieving video data from large multimedia databases are necessary to a low access to these collections. Given that video is often stored efficiently in a compressed format, the costly overhead of decompression can be reduced by analyzing the compressed representation directly. In earlier work, we presented compressed domain parsing techniques which identified shots, subshots, and scenes. In this article, we present efficient key frame selection, feature extraction, indexing, and retrieval techniques that are directly applicable to MPEG compressed video. We develop a frame type independent representation which normalizes spatial and temporal features including frame type, frame size, macroblock encoding, and motion compensation vectors. Features for indexing are derived directly from this representation and mapped to a low- dimensional space where they can be accessed using standard database techniques. Spatial information is used as primary index into the database and temporal information is used to rank retrieved clips and enhance the robustness of the system. The techniques presented enable efficient indexing, querying, and retrieval of compressed video as demonstrated by our system which typically takes a fraction of a second to retrieve similar video scenes from a database, with over 95 percent recall.

Intricacies of cosmological bounce in polynomial metric f(R) gravity for flat FLRW spacetime

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

Bhattacharya, Kaushik; Chakrabarty, Saikat, E-mail: kaushikb@iitk.ac.in, E-mail: snilch@iitk.ac.in

2016-02-01

In this paper we present the techniques for computing cosmological bounces in polynomial f(R) theories, whose order is more than two, for spatially flat FLRW spacetime. In these cases the conformally connected Einstein frame shows up multiple scalar potentials predicting various possibilities of cosmological evolution in the Jordan frame where the f(R) theory lives. We present a reasonable way in which one can associate the various possible potentials in the Einstein frame, for cubic f(R) gravity, to the cosmological development in the Jordan frame. The issue concerning the energy conditions in f(R) theories is presented. We also point out themore » very important relationships between the conformal transformations connecting the Jordan frame and the Einstein frame and the various instabilities of f(R) theory. All the calculations are done for cubic f(R) gravity but we hope the results are sufficiently general for higher order polynomial gravity.« less

Intermediate accelerated solutions as generic late-time attractors in a modified Jordan-Brans-Dicke theory

NASA Astrophysics Data System (ADS)

Cid, Antonella; Leon, Genly; Leyva, Yoelsy

2016-02-01

In this paper we investigate the evolution of a Jordan-Brans-Dicke scalar field, Φ, with a power-law potential in the presence of a second scalar field, phi, with an exponential potential, in both the Jordan and the Einstein frames. We present the relation of our model with the induced gravity model with power-law potential and the integrability of this kind of models is discussed when the quintessence field phi is massless, and has a small velocity. The fact that for some fine-tuned values of the parameters we may get some integrable cosmological models, makes our choice of potentials very interesting. We prove that in Jordan-Brans-Dicke theory, the de Sitter solution is not a natural attractor. Instead, we show that the attractor in the Jordan frame corresponds to an ``intermediate accelerated'' solution of the form a(t) simeq eα1 tp1, as t → ∞ where α1 > 0 and 0 < p1 < 1, for a wide range of parameters. Furthermore, when we work in the Einstein frame we get that the attractor is also an ``intermediate accelerated'' solution of the form fraktur a(fraktur t) simeq eα2 fraktur tp2 as fraktur t → ∞ where α2 > 0 and 0

Does message framing predict willingness to participate in a hypothetical HIV vaccine trial: an application of Prospect Theory.

PubMed

Evangeli, Michael; Kafaar, Zuhayr; Kagee, Ashraf; Swartz, Leslie; Bullemor-Day, Philippa

2013-01-01

It is vital that enough participants are willing to participate in clinical trials to test HIV vaccines adequately. It is, therefore, necessary to explore what affects peoples' willingness to participate (WTP) in such trials. Studies have only examined individual factors associated with WTP and not the effect of messages about trial participation on potential participants (e.g., whether losses or gains are emphasized, or whether the outcome is certain or uncertain). This study explores whether the effects of message framing on WTP in a hypothetical HIV vaccine trial are consistent with Prospect Theory. This theory suggests that people are fundamentally risk averse and that (1) under conditions of low risk and high certainty, gain-framed messages will be influential (2) under conditions of high risk and low certainty, loss-framed messages will be influential. This cross-sectional study recruited 283 HIV-negative students from a South African university who were given a questionnaire that contained matched certain gain-framed, certain loss-framed, uncertain gain-framed, and uncertain loss-framed statements based on common barriers and facilitators of WTP. Participants were asked to rate how likely each statement was to result in their participation in a hypothetical preventative HIV vaccine trial. Consistent with Prospect Theory predictions, for certain outcomes, gain-framed messages were more likely to result in WTP than loss-framed messages. Inconsistent with predictions, loss-framed message were not more likely to be related to WTP for uncertain outcomes than gain-framed messages. Older students were less likely to express their WTP across the different message frames. Recruitment for HIV vaccine trials should pay attention to how messages about the trial are presented to potential participants.

Supergravity contributions to inflation in models with non-minimal coupling to gravity

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

Das, Kumar; Dutta, Koushik; Domcke, Valerie, E-mail: kumar.das@saha.ac.in, E-mail: valerie.domcke@apc.univ-paris7.fr, E-mail: koushik.dutta@saha.ac.in

2017-03-01

This paper provides a systematic study of supergravity contributions relevant for inflationary model building in Jordan frame supergravity. In this framework, canonical kinetic terms in the Jordan frame result in the separation of the Jordan frame scalar potential into a tree-level term and a supergravity contribution which is potentially dangerous for sustaining inflation. We show that if the vacuum energy necessary for driving inflation originates dominantly from the F-term of an auxiliary field (i.e. not the inflaton), the supergravity corrections to the Jordan frame scalar potential are generically suppressed. Moreover, these supergravity contributions identically vanish if the superpotential vanishes alongmore » the inflationary trajectory. On the other hand, if the F-term associated with the inflaton dominates the vacuum energy, the supergravity contributions are generically comparable to the globally supersymmetric contributions. In addition, the non-minimal coupling to gravity inherent to Jordan frame supergravity significantly impacts the inflationary model depending on the size and sign of this coupling. We discuss the phenomenology of some representative inflationary models, and point out the relation to the recently much discussed cosmological 'attractor' models.« less

Compression Algorithm Analysis of In-Situ (S)TEM Video: Towards Automatic Event Detection and Characterization

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

Teuton, Jeremy R.; Griswold, Richard L.; Mehdi, Beata L.

Precise analysis of both (S)TEM images and video are time and labor intensive processes. As an example, determining when crystal growth and shrinkage occurs during the dynamic process of Li dendrite deposition and stripping involves manually scanning through each frame in the video to extract a specific set of frames/images. For large numbers of images, this process can be very time consuming, so a fast and accurate automated method is desirable. Given this need, we developed software that uses analysis of video compression statistics for detecting and characterizing events in large data sets. This software works by converting the datamore » into a series of images which it compresses into an MPEG-2 video using the open source “avconv” utility [1]. The software does not use the video itself, but rather analyzes the video statistics from the first pass of the video encoding that avconv records in the log file. This file contains statistics for each frame of the video including the frame quality, intra-texture and predicted texture bits, forward and backward motion vector resolution, among others. In all, avconv records 15 statistics for each frame. By combining different statistics, we have been able to detect events in various types of data. We have developed an interactive tool for exploring the data and the statistics that aids the analyst in selecting useful statistics for each analysis. Going forward, an algorithm for detecting and possibly describing events automatically can be written based on statistic(s) for each data type.« less

The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation and is specifically induced in the presence of aromatic compounds.

PubMed

de Vries, Ronald P; vanKuyk, Patricia A; Kester, Harry C M; Visser, Jaap

2002-04-15

The faeB gene encoding a second feruloyl esterase from Aspergillus niger has been cloned and characterized. It consists of an open reading frame of 1644 bp containing one intron. The gene encodes a protein of 521 amino acids that has sequence similarity to that of an Aspergillus oryzae tannase. However, the encoded enzyme, feruloyl esterase B (FAEB), does not have tannase activity. Comparison of the physical characteristics and substrate specificity of FAEB with those of a cinnamoyl esterase from A. niger [Kroon, Faulds and Williamson (1996) Biotechnol. Appl. Biochem. 23, 255-262] suggests that they are in fact the same enzyme. The expression of faeB is specifically induced in the presence of certain aromatic compounds, but not in the presence of other constituents present in plant-cell-wall polysaccharides such as arabinoxylan or pectin. The expression profile of faeB in the presence of aromatic compounds was compared with the expression of A. niger faeA, encoding feruloyl esterase A (FAEA), and A. niger bphA, the gene encoding a benzoate-p-hydroxylase. All three genes have different subsets of aromatic compounds that induce their expression, indicating the presence of different transcription activating systems in A. niger that respond to aromatic compounds. Comparison of the activity of FAEA and FAEB on sugar-beet pectin and wheat arabinoxylan demonstrated that they are both involved in the degradation of both polysaccharides, but have opposite preferences for these substrates. FAEA is more active than FAEB towards wheat arabinoxylan, whereas FAEB is more active than FAEA towards sugar-beet pectin.

The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation and is specifically induced in the presence of aromatic compounds.

PubMed Central

de Vries, Ronald P; vanKuyk, Patricia A; Kester, Harry C M; Visser, Jaap

2002-01-01

The faeB gene encoding a second feruloyl esterase from Aspergillus niger has been cloned and characterized. It consists of an open reading frame of 1644 bp containing one intron. The gene encodes a protein of 521 amino acids that has sequence similarity to that of an Aspergillus oryzae tannase. However, the encoded enzyme, feruloyl esterase B (FAEB), does not have tannase activity. Comparison of the physical characteristics and substrate specificity of FAEB with those of a cinnamoyl esterase from A. niger [Kroon, Faulds and Williamson (1996) Biotechnol. Appl. Biochem. 23, 255-262] suggests that they are in fact the same enzyme. The expression of faeB is specifically induced in the presence of certain aromatic compounds, but not in the presence of other constituents present in plant-cell-wall polysaccharides such as arabinoxylan or pectin. The expression profile of faeB in the presence of aromatic compounds was compared with the expression of A. niger faeA, encoding feruloyl esterase A (FAEA), and A. niger bphA, the gene encoding a benzoate-p-hydroxylase. All three genes have different subsets of aromatic compounds that induce their expression, indicating the presence of different transcription activating systems in A. niger that respond to aromatic compounds. Comparison of the activity of FAEA and FAEB on sugar-beet pectin and wheat arabinoxylan demonstrated that they are both involved in the degradation of both polysaccharides, but have opposite preferences for these substrates. FAEA is more active than FAEB towards wheat arabinoxylan, whereas FAEB is more active than FAEA towards sugar-beet pectin. PMID:11931668

Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: Homology to Epstein-Barr virus open reading frame BCRFI

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

Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.

1991-02-15

The authors demonstrated the existence of human cytokine synthesis inhibitory factor (DSIF) (interleukin 10 (IL-10)). cDNA clones encoding human IL-10 (hIL-10) were isolated from a tetanus toxin-specific human T-cell clone. Like mouse IL-10, hIL-10 exhibits strong DNA and amino acid sequence homology to an open reading frame in the Epstein-Barr virus, BDRFL. hIL-10 and the BCRFI product inhibit cytokine synthesis by activated human peripheral blood mononuclear cells and by a mouse Th1 clone. Both hIL-10 and mouse IL-10 sustain the viability of a mouse mast cell line in culture, but BCRFI lacks comparable activity in this way, suggesting that BCRFImore » may have conserved only a subset of hIL-10 activities.« less

Hyperchromatic lens for recording time-resolved phenomena

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

Frayer, Daniel K.

A method and apparatus for the capture of a high number of quasi-continuous effective frames of 2-D data from an event at very short time scales (from less than 10.sup.-12 to more than 10.sup.-8 seconds) is disclosed which allows for short recording windows and effective number of frames. Active illumination, from a chirped laser pulse directed to the event creates a reflection where wavelength is dependent upon time and spatial position is utilized to encode temporal phenomena onto wavelength. A hyperchromatic lens system receives the reflection and maps wavelength onto axial position. An image capture device, such as holography ormore » plenoptic imaging device, captures the resultant focal stack from the hyperchromatic lens system in both spatial (imaging) and longitudinal (temporal) axes. The hyperchromatic lens system incorporates a combination of diffractive and refractive components to maximally separate focal position as a function of wavelength.« less

Expression, purification and biochemical characterization of a single-stranded DNA binding protein from Herbaspirillum seropedicae.

PubMed

Vernal, Javier; Serpa, Viviane I; Tavares, Carolina; Souza, Emanuel M; Pedrosa, Fábio O; Terenzi, Hernán

2007-05-01

An open reading frame encoding a protein similar in size and sequence to the Escherichia coli single-stranded DNA binding protein (SSB protein) was identified in the Herbaspirillum seropedicae genome. This open reading frame was cloned into the expression plasmid pET14b. The SSB protein from H. seropedicae, named Hs_SSB, was overexpressed in E. coli strain BL21(DE3) and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein. The apparent molecular mass of the native Hs_SSB was estimated by gel filtration, suggesting that the native protein is a tetramer made up of four similar subunits. The purified protein binds to single-stranded DNA (ssDNA) in a similar manner to other SSB proteins. The production of this recombinant protein in good yield opens up the possibility of obtaining its 3D-structure and will help further investigations into DNA metabolism.

Determination of the complete genomic sequence and analysis of the gene products of the virus of Spring Viremia of Carp, a fish rhabdovirus.

PubMed

Hoffmann, Bernd; Schütze, Heike; Mettenleiter, Thomas C

2002-03-20

The complete genome of spring viremia of carp virus (SVCV) was cloned and the sequence of 11019 nucleotides was determined. It contains five open reading frames (ORF's) encoding for the nucleoprotein N; phosphoprotein P; matrix protein M; glycoprotein G; and the viral RNA dependent RNA polymerase L. Genes are organised in the order typical for rhabdoviruses: 3'-N-P-M-G-L-5'. The short leader and trailer regions of SVCV exhibit inverse complementarity and are similar to the respective 3' and 5' ends of the genome of vesicular stomatitis virus. To verify the predicted open reading frames proteins were expressed in bacteria and analysed with a polyclonal anti-SVCV serum. Furthermore, monospecific antisera against the distinct viral proteins were generated. Comparison of genome and protein confirm the assignment of SVCV to the genus Vesiculovirus.

Translation of the mRNA of the maize transcriptional activator Opaque-2 is inhibited by upstream open reading frames present in the leader sequence.

PubMed Central

Lohmer, S; Maddaloni, M; Motto, M; Salamini, F; Thompson, R D

1993-01-01

The protein encoded by the Opaque-2 (O2) gene is a transcription factor, translated from an mRNA that possesses an unusually long 5' leader sequence containing three upstream open reading frames (uORFs). The efficiency of translation of O2 mRNA has been tested in vivo by a transient assay in which the level of activation of the b32 promoter, a natural target of O2 protein, is measured. We show that uORF-less O2 alleles possess a higher transactivation value than the wild-type allele and that the reduction in transactivation due to the uORFs is a cis-dominant effect. The data presented indicate that both uORF1 and uORF2 are involved in the reducing effect and suggest that both are likely to be translated. PMID:8439744

Frameshifting in the expression of the Escherichia coli trpR gene is modulated by translation initiation.

PubMed Central

Benhar, I; Miller, C; Engelberg-Kulka, H

1993-01-01

The Escherichia coli trpR gene encodes the 108-amino-acid-long Trp repressor. We have shown previously that a +1 frameshifting event occurs during the expression of trpR, resulting in the synthesis of an additional (+1 frame) polypeptide. Using trpR-lac'Z fusions, we have recently found that the transition from the 0 to the +1 frame occurs via the bypassing of a 55-nucleotide-long segment of the trpR+1-lac'Z mRNA (I. Benhar, and H. Engelberg-Kulka, Cell 72:121-130, 1993). Here we show that the frequency of trpR frameshifting (or bypassing) can be regulated both in vivo and in vitro. This frequency is inversely proportional to the rate of initiation of translation of the trpR gene. Hence, modulating the level of translation initiation affects the frequency of frameshifting. Images PMID:8491735

Cross-sensory reference frame transfer in spatial memory: the case of proprioceptive learning.

PubMed

Avraamides, Marios N; Sarrou, Mikaella; Kelly, Jonathan W

2014-04-01

In three experiments, we investigated whether the information available to visual perception prior to encoding the locations of objects in a path through proprioception would influence the reference direction from which the spatial memory was formed. Participants walked a path whose orientation was misaligned to the walls of the enclosing room and to the square sheet that covered the path prior to learning (Exp. 1) and, in addition, to the intrinsic structure of a layout studied visually prior to walking the path and to the orientation of stripes drawn on the floor (Exps. 2 and 3). Despite the availability of prior visual information, participants constructed spatial memories that were aligned with the canonical axes of the path, as opposed to the reference directions primed by visual experience. The results are discussed in the context of previous studies documenting transfer of reference frames within and across perceptual modalities.

Coding for Communication Channels with Dead-Time Constraints

NASA Technical Reports Server (NTRS)

Moision, Bruce; Hamkins, Jon

2004-01-01

Coding schemes have been designed and investigated specifically for optical and electronic data-communication channels in which information is conveyed via pulse-position modulation (PPM) subject to dead-time constraints. These schemes involve the use of error-correcting codes concatenated with codes denoted constrained codes. These codes are decoded using an interactive method. In pulse-position modulation, time is partitioned into frames of Mslots of equal duration. Each frame contains one pulsed slot (all others are non-pulsed). For a given channel, the dead-time constraints are defined as a maximum and a minimum on the allowable time between pulses. For example, if a Q-switched laser is used to transmit the pulses, then the minimum allowable dead time is the time needed to recharge the laser for the next pulse. In the case of bits recorded on a magnetic medium, the minimum allowable time between pulses depends on the recording/playback speed and the minimum distance between pulses needed to prevent interference between adjacent bits during readout. The maximum allowable dead time for a given channel is the maximum time for which it is possible to satisfy the requirement to synchronize slots. In mathematical shorthand, the dead-time constraints for a given channel are represented by the pair of integers (d,k), where d is the minimum allowable number of zeroes between ones and k is the maximum allowable number of zeroes between ones. A system of the type to which the present schemes apply is represented by a binary- input, real-valued-output channel model illustrated in the figure. At the transmitting end, information bits are first encoded by use of an error-correcting code, then further encoded by use of a constrained code. Several constrained codes for channels subject to constraints of (d,infinity) have been investigated theoretically and computationally. The baseline codes chosen for purposes of comparison were simple PPM codes characterized by M-slot PPM frames separated by d-slot dead times.

Glutathione S-transferase-encoding gene as a potential probe for environmental bacterial isolates capable of degrading polycyclic aromatic hydrocarbons.

PubMed Central

Lloyd-Jones, G; Lau, P C

1997-01-01

Homologs of the glutathione S-transferase (GST)-encoding gene were identified in a collection of aromatic hydrocarbon-degrading Sphingomonas spp. isolated from New Zealand, Antarctica, and the United States by using PCR primers designed from the GST-encoding gene of Sphingomonas paucimobilis EPA505. Sequence analysis of PCR fragments generated from these isolates and of the GST gene amplified from DNA extracted from polycyclic aromatic hydrocarbon (PAH)-contaminated soil revealed a high degree of conservation, which may make the GST-encoding gene a potentially useful marker for PAH-degrading bacteria. PMID:9251217

Chemical Space of DNA-Encoded Libraries.

PubMed

Franzini, Raphael M; Randolph, Cassie

2016-07-28

In recent years, DNA-encoded chemical libraries (DECLs) have attracted considerable attention as a potential discovery tool in drug development. Screening encoded libraries may offer advantages over conventional hit discovery approaches and has the potential to complement such methods in pharmaceutical research. As a result of the increased application of encoded libraries in drug discovery, a growing number of hit compounds are emerging in scientific literature. In this review we evaluate reported encoded library-derived structures and identify general trends of these compounds in relation to library design parameters. We in particular emphasize the combinatorial nature of these libraries. Generally, the reported molecules demonstrate the ability of this technology to afford hits suitable for further lead development, and on the basis of them, we derive guidelines for DECL design.

Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1).

PubMed Central

Fukumori, F; Saint, C P

1997-01-01

A 9,233-bp HindIII fragment of the aromatic amine catabolic plasmid pTDN1, isolated from a derivative of Pseudomonas putida mt-2 (UCC22), confers the ability to degrade aniline on P. putida KT2442. The fragment encodes six open reading frames which are arranged in the same direction. Their 5' upstream region is part of the direct-repeat sequence of pTDN1. Nucleotide sequence of 1.8 kb of the repeat sequence revealed only a single base pair change compared to the known sequence of IS1071 which is involved in the transposition of the chlorobenzoate genes (C. Nakatsu, J. Ng, R. Singh, N. Straus, and C. Wyndham, Proc. Natl. Acad. Sci. USA 88:8312-8316, 1991). Four open reading frames encode proteins with considerable homology to proteins found in other aromatic-compound degradation pathways. On the basis of sequence similarity, these genes are proposed to encode the large and small subunits of aniline oxygenase (tdnA1 and tdnA2, respectively), a reductase (tdnB), and a LysR-type regulatory gene (tdnR). The putative large subunit has a conserved [2Fe-2S]R Rieske-type ligand center. Two genes, tdnQ and tdnT, which may be involved in amino group transfer, are localized upstream of the putative oxygenase genes. The tdnQ gene product shares about 30% similarity with glutamine synthetases; however, a pUC-based plasmid carrying tdnQ did not support the growth of an Escherichia coli glnA strain in the absence of glutamine. TdnT possesses domains that are conserved among amidotransferases. The tdnQ, tdnA1, tdnA2, tdnB, and tdnR genes are essential for the conversion of aniline to catechol. PMID:8990291

Mapping of Transcription Termination within the S Segment of SFTS Phlebovirus Facilitated Generation of NSs Deletant Viruses

PubMed Central

Rezelj, Veronica V.; Elliott, Richard M.

2017-01-01

ABSTRACT SFTS phlebovirus (SFTSV) is an emerging tick-borne bunyavirus that was first reported in China in 2009. Here we report the generation of a recombinant SFTSV (rHB29NSsKO) that cannot express the viral nonstructural protein (NSs) upon infection of cells in culture. We show that rHB29NSsKO replication kinetics are greater in interferon (IFN)-incompetent cells and that the virus is unable to suppress IFN induced in response to viral replication. The data confirm for the first time in the context of virus infection that NSs acts as a virally encoded IFN antagonist and that NSs is dispensable for virus replication. Using 3′ rapid amplification of cDNA ends (RACE), we mapped the 3′ end of the N and NSs mRNAs, showing that the mRNAs terminate within the coding region of the opposite open reading frame. We show that the 3′ end of the N mRNA terminates upstream of a 5′-GCCAGCC-3′ motif present in the viral genomic RNA. With this knowledge, and using virus-like particles, we could demonstrate that the last 36 nucleotides of the NSs open reading frame (ORF) were needed to ensure the efficient termination of the N mRNA and were required for recombinant virus rescue. We demonstrate that it is possible to recover viruses lacking NSs (expressing just a 12-amino-acid NSs peptide or encoding enhanced green fluorescent protein [eGFP]) or an NSs-eGFP fusion protein in the NSs locus. This opens the possibility for further studies of NSs and potentially the design of attenuated viruses for vaccination studies. IMPORTANCE SFTS phlebovirus (SFTSV) and related tick-borne viruses have emerged globally since 2009. SFTSV has been shown to cause severe disease in humans. For bunyaviruses, it has been well documented that the nonstructural protein (NSs) enables the virus to counteract the human innate antiviral defenses and that NSs is one of the major determinants of virulence in infection. Therefore, the use of reverse genetics systems to engineer viruses lacking NSs is an attractive strategy to rationally attenuate bunyaviruses. Here we report the generation of several recombinant SFTS viruses that cannot express the NSs protein or have the NSs open reading frame replaced with a reporter gene. These viruses cannot antagonize the mammalian interferon (IFN) response mounted to virus infection. The generation of NSs-lacking viruses was achieved by mapping the transcriptional termination of two S-segment-derived subgenomic mRNAs, which revealed that transcription termination occurs upstream of a 5′-GCCAGCC-3′ motif present in the virus genomic S RNA. PMID:28592543

Mapping of Transcription Termination within the S Segment of SFTS Phlebovirus Facilitated Generation of NSs Deletant Viruses.

PubMed

Brennan, Benjamin; Rezelj, Veronica V; Elliott, Richard M

2017-08-15

SFTS phlebovirus (SFTSV) is an emerging tick-borne bunyavirus that was first reported in China in 2009. Here we report the generation of a recombinant SFTSV (rHB29NSsKO) that cannot express the viral nonstructural protein (NSs) upon infection of cells in culture. We show that rHB29NSsKO replication kinetics are greater in interferon (IFN)-incompetent cells and that the virus is unable to suppress IFN induced in response to viral replication. The data confirm for the first time in the context of virus infection that NSs acts as a virally encoded IFN antagonist and that NSs is dispensable for virus replication. Using 3' rapid amplification of cDNA ends (RACE), we mapped the 3' end of the N and NSs mRNAs, showing that the mRNAs terminate within the coding region of the opposite open reading frame. We show that the 3' end of the N mRNA terminates upstream of a 5'-GCCAGCC-3' motif present in the viral genomic RNA. With this knowledge, and using virus-like particles, we could demonstrate that the last 36 nucleotides of the NSs open reading frame (ORF) were needed to ensure the efficient termination of the N mRNA and were required for recombinant virus rescue. We demonstrate that it is possible to recover viruses lacking NSs (expressing just a 12-amino-acid NSs peptide or encoding enhanced green fluorescent protein [eGFP]) or an NSs-eGFP fusion protein in the NSs locus. This opens the possibility for further studies of NSs and potentially the design of attenuated viruses for vaccination studies. IMPORTANCE SFTS phlebovirus (SFTSV) and related tick-borne viruses have emerged globally since 2009. SFTSV has been shown to cause severe disease in humans. For bunyaviruses, it has been well documented that the nonstructural protein (NSs) enables the virus to counteract the human innate antiviral defenses and that NSs is one of the major determinants of virulence in infection. Therefore, the use of reverse genetics systems to engineer viruses lacking NSs is an attractive strategy to rationally attenuate bunyaviruses. Here we report the generation of several recombinant SFTS viruses that cannot express the NSs protein or have the NSs open reading frame replaced with a reporter gene. These viruses cannot antagonize the mammalian interferon (IFN) response mounted to virus infection. The generation of NSs-lacking viruses was achieved by mapping the transcriptional termination of two S-segment-derived subgenomic mRNAs, which revealed that transcription termination occurs upstream of a 5'-GCCAGCC-3' motif present in the virus genomic S RNA. Copyright © 2017 Brennan et al.

How consumers are affected by product descriptions in online shopping: Event-related potentials evidence of the attribute framing effect.

PubMed

Jin, Jia; Zhang, Wuke; Chen, Mingliang

2017-12-01

Due to the limitations of the human ability to process information, e-consumers' decisions are likely to be influenced by various cognitive biases, such as the attribute framing effect. This effect has been well studied by numerous scholars; however, the associated underlying neural mechanisms with a critical temporal resolution have not been revealed. Thus, this study applies the measurement of event-related potentials (ERPs) to directly examine the role of attribute framing in information processing and decision-making in online shopping. The behavioral results showed that participants demonstrated a higher purchase intention with a shorter reaction time under a positive framing condition compared to participants under a negative framing condition. Compared with positive framing messages, the results of ERPs indicated that negative framing messages attracted more attention resources at the early stage of rapid automatic processing (larger P2 amplitude) and resulted in greater cognitive conflict and decision difficulty (larger P2-N2 complex). Moreover, compared with negative messages, positive framing messages allowed consumers to perceive a better future performance of products and classify these products as a categorization of higher evaluation (larger LPP amplitude) at the late cognitive processing stage of evaluation. Based on these results, we provide evidence for a better understanding of how different attribute framing messages are processed and ultimately lead to the framing effect. Copyright © 2017 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

Rearrangement of Influenza Virus Spliced Segments for the Development of Live-Attenuated Vaccines

PubMed Central

Nogales, Aitor; DeDiego, Marta L.; Topham, David J.

2016-01-01

ABSTRACT Influenza viral infections represent a serious public health problem, with influenza virus causing a contagious respiratory disease which is most effectively prevented through vaccination. Segments 7 (M) and 8 (NS) of the influenza virus genome encode mRNA transcripts that are alternatively spliced to express two different viral proteins. This study describes the generation, using reverse genetics, of three different recombinant influenza A/Puerto Rico/8/1934 (PR8) H1N1 viruses containing M or NS viral segments individually or modified M or NS viral segments combined in which the overlapping open reading frames of matrix 1 (M1)/M2 for the modified M segment and the open reading frames of nonstructural protein 1 (NS1)/nuclear export protein (NEP) for the modified NS segment were split by using the porcine teschovirus 1 (PTV-1) 2A autoproteolytic cleavage site. Viruses with an M split segment were impaired in replication at nonpermissive high temperatures, whereas high viral titers could be obtained at permissive low temperatures (33°C). Furthermore, viruses containing the M split segment were highly attenuated in vivo, while they retained their immunogenicity and provided protection against a lethal challenge with wild-type PR8. These results indicate that influenza viruses can be effectively attenuated by the rearrangement of spliced segments and that such attenuated viruses represent an excellent option as safe, immunogenic, and protective live-attenuated vaccines. Moreover, this is the first time in which an influenza virus containing a restructured M segment has been described. Reorganization of the M segment to encode M1 and M2 from two separate, nonoverlapping, independent open reading frames represents a useful tool to independently study mutations in the M1 and M2 viral proteins without affecting the other viral M product. IMPORTANCE Vaccination represents our best therapeutic option against influenza viral infections. However, the efficacy of current influenza vaccines is suboptimal, and novel approaches are necessary for the prevention of disease caused by this important human respiratory pathogen. In this work, we describe a novel approach to generate safer and more efficient live-attenuated influenza virus vaccines (LAIVs) based on recombinant viruses whose genomes encode nonoverlapping and independent M1/M2 (split M segment [Ms]) or both M1/M2 and NS1/NEP (Ms and split NS segment [NSs]) open reading frames. Viruses containing a modified M segment were highly attenuated in mice but were able to confer, upon a single intranasal immunization, complete protection against a lethal homologous challenge with wild-type virus. Notably, the protection efficacy conferred by our viruses with split M segments was better than that conferred by the current temperature-sensitive LAIV. Altogether, these results open a new avenue for the development of safer and more protective LAIVs on the basis of the reorganization of spliced viral RNA segments in the genome. PMID:27122587

Posture-based processing in visual short-term memory for actions.

PubMed

Vicary, Staci A; Stevens, Catherine J

2014-01-01

Visual perception of human action involves both form and motion processing, which may rely on partially dissociable neural networks. If form and motion are dissociable during visual perception, then they may also be dissociable during their retention in visual short-term memory (VSTM). To elicit form-plus-motion and form-only processing of dance-like actions, individual action frames can be presented in the correct or incorrect order. The former appears coherent and should elicit action perception, engaging both form and motion pathways, whereas the latter appears incoherent and should elicit posture perception, engaging form pathways alone. It was hypothesized that, if form and motion are dissociable in VSTM, then recognition of static body posture should be better after viewing incoherent than after viewing coherent actions. However, as VSTM is capacity limited, posture-based encoding of actions may be ineffective with increased number of items or frames. Using a behavioural change detection task, recognition of a single test posture was significantly more likely after studying incoherent than after studying coherent stimuli. However, this effect only occurred for spans of two (but not three) items and for stimuli with five (but not nine) frames. As in perception, posture and motion are dissociable in VSTM.

Max CAPR: high-resolution 3D contrast-enhanced MR angiography with acquisition times under 5 seconds.

PubMed

Haider, Clifton R; Borisch, Eric A; Glockner, James F; Mostardi, Petrice M; Rossman, Phillip J; Young, Phillip M; Riederer, Stephen J

2010-10-01

High temporal and spatial resolution is desired in imaging of vascular abnormalities having short arterial-to-venous transit times. Methods that exploit temporal correlation to reduce the observed frame time demonstrate temporal blurring, obfuscating bolus dynamics. Previously, a Cartesian acquisition with projection reconstruction-like (CAPR) sampling method has been demonstrated for three-dimensional contrast-enhanced angiographic imaging of the lower legs using two-dimensional sensitivity-encoding acceleration and partial Fourier acceleration, providing 1mm isotropic resolution of the calves, with 4.9-sec frame time and 17.6-sec temporal footprint. In this work, the CAPR acquisition is further undersampled to provide a net acceleration approaching 40 by eliminating all view sharing. The tradeoff of frame time and temporal footprint in view sharing is presented and characterized in phantom experiments. It is shown that the resultant 4.9-sec acquisition time, three-dimensional images sets have sufficient spatial and temporal resolution to clearly portray arterial and venous phases of contrast passage. It is further hypothesized that these short temporal footprint sequences provide diagnostic quality images. This is tested and shown in a series of nine contrast-enhanced MR angiography patient studies performed with the new method.

On scalable lossless video coding based on sub-pixel accurate MCTF

NASA Astrophysics Data System (ADS)

Yea, Sehoon; Pearlman, William A.

2006-01-01

We propose two approaches to scalable lossless coding of motion video. They achieve SNR-scalable bitstream up to lossless reconstruction based upon the subpixel-accurate MCTF-based wavelet video coding. The first approach is based upon a two-stage encoding strategy where a lossy reconstruction layer is augmented by a following residual layer in order to obtain (nearly) lossless reconstruction. The key advantages of our approach include an 'on-the-fly' determination of bit budget distribution between the lossy and the residual layers, freedom to use almost any progressive lossy video coding scheme as the first layer and an added feature of near-lossless compression. The second approach capitalizes on the fact that we can maintain the invertibility of MCTF with an arbitrary sub-pixel accuracy even in the presence of an extra truncation step for lossless reconstruction thanks to the lifting implementation. Experimental results show that the proposed schemes achieve compression ratios not obtainable by intra-frame coders such as Motion JPEG-2000 thanks to their inter-frame coding nature. Also they are shown to outperform the state-of-the-art non-scalable inter-frame coder H.264 (JM) lossless mode, with the added benefit of bitstream embeddedness.

In Vivo Mammalian Brain Imaging Using One- and Two-Photon Fluorescence Microendoscopy

PubMed Central

Jung, Juergen C.; Mehta, Amit D.; Aksay, Emre; Stepnoski, Raymond; Schnitzer, Mark J.

2010-01-01

One of the major limitations in the current set of techniques available to neuroscientists is a dearth of methods for imaging individual cells deep within the brains of live animals. To overcome this limitation, we developed two forms of minimally invasive fluorescence microendoscopy and tested their abilities to image cells in vivo. Both one- and two-photon fluorescence microendoscopy are based on compound gradient refractive index (GRIN) lenses that are 350–1,000 μm in diameter and provide micron-scale resolution. One-photon microendoscopy allows full-frame images to be viewed by eye or with a camera, and is well suited to fast frame-rate imaging. Two-photon microendoscopy is a laser-scanning modality that provides optical sectioning deep within tissue. Using in vivo microendoscopy we acquired video-rate movies of thalamic and CA1 hippocampal red blood cell dynamics and still-frame images of CA1 neurons and dendrites in anesthetized rats and mice. Microendoscopy will help meet the growing demand for in vivo cellular imaging created by the rapid emergence of new synthetic and genetically encoded fluorophores that can be used to label specific brain areas or cell classes. PMID:15128753

Architecture for VLSI design of Reed-Solomon encoders

NASA Technical Reports Server (NTRS)

Liu, K. Y.

1981-01-01

The logic structure of a universal VLSI chip called the symbol-slice Reed-Solomon (RS) encoder chip is discussed. An RS encoder can be constructed by cascading and properly interconnecting a group of such VLSI chips. As a design example, it is shown that a (255,223) RD encoder requiring around 40 discrete CMOS ICs may be replaced by an RS encoder consisting of four identical interconnected VLSI RS encoder chips. Besides the size advantage, the VLSI RS encoder also has the potential advantages of requiring less power and having a higher reliability.

T Cell Epitope Mapping of JC Polyoma Virus-Encoded Proteome Reveals Reduced T Cell Responses in HLA-DRB1*04:01+ Donors

PubMed Central

Jelčić, Ilijas; Aly, Lilian; Binder, Thomas M. C.; Jelčić, Ivan; Bofill-Mas, Sílvia; Planas, Raquel; Demina, Victoria; Eiermann, Thomas H.; Weber, Thomas; Girones, Rosina; Sospedra, Mireia

2013-01-01

JC polyomavirus (JCV) infection is highly prevalent and usually kept in a persistent state without clinical signs and symptoms. It is only during immunocompromise and especially impaired CD4+ T cell function in the brain, as seen in AIDS patients or natalizumab-treated multiple sclerosis patients, that JCV may cause progressive multifocal leukoencephalopathy (PML), an often life-threatening brain disease. Since CD4+ T cells likely play an important role in controlling JCV infection, we here describe the T cell response to JCV in a group of predominantly HLA-DR-heterozygotic healthy donors (HD) by using a series of overlapping 15-mer peptides spanning all JCV-encoded open reading frames. We identified immunodominant epitopes and compared T cell responses with anti-JCV VP1 antibody production and with the presence of urinary viral shedding. We observed positive JCV-specific T cell responses in 28.6% to 77.6%, humoral immune response in 42.6% to 89.4%, and urinary viral shedding in 36.4% to 45.5% of HD depending on the threshold. Four immunodominant peptides were mapped, and at least one immunogenic peptide per HLA-DRB1 allele was detected in DRB1*01+, DRB1*07+, DRB1*11+, DRB1*13+, DRB1*15+, and DRB1*03+ individuals. We show for the first time that JCV-specific T cell responses may be directed not only against JCV VP1 and large T antigen but also against all other JCV-encoded proteins. Heterozygotic DRB1*04:01+ individuals showed very low T cell responses to JCV together with normal anti-VP1 antibody levels and no urinary viral shedding, indicating a dominant-negative effect of this allele on global JCV-directed T cell responses. Our data are potentially relevant for the development of vaccines against JCV. PMID:23302880

Relational Frame Theory and Industrial/Organizational Psychology

ERIC Educational Resources Information Center

Stewart, Ian; Barnes-Holmes, Dermot; Barnes-Holmes, Yvonne; Bond, Frank W.; Hayes, Steven C.

2006-01-01

The current paper argues that a Relational Frame Theory account of complex human behavior including an analysis of relational frames, relational networks, rules and the concept of self can provide a potentially powerful new perspective on phenomena in the applied science of industrial/organizational (I/O) psychology. In this article, we first…

Minimum stiffness criteria for ring frame stiffeners of space launch vehicles

NASA Astrophysics Data System (ADS)

Friedrich, Linus; Schröder, Kai-Uwe

2016-12-01

Frame stringer-stiffened shell structures show high load carrying capacity in conjunction with low structural mass and are for this reason frequently used as primary structures of aerospace applications. Due to the great number of design variables, deriving suitable stiffening configurations is a demanding task and needs to be realized using efficient analysis methods. The structural design of ring frame stringer-stiffened shells can be subdivided into two steps. One, the design of a shell section between two ring frames. Two, the structural design of the ring frames such that a general instability mode is avoided. For sizing stringer-stiffened shell sections, several methods were recently developed, but existing ring frame sizing methods are mainly based on empirical relations or on smeared models. These methods do not mandatorily lead to reliable designs and in some cases the lightweight design potential of stiffened shell structures can thus not be exploited. In this paper, the explicit physical behaviour of ring frame stiffeners of space launch vehicles at the onset of panel instability is described using mechanical substitute models. Ring frame stiffeners of a stiffened shell structure are sized applying existing methods and the method suggested in this paper. To verify the suggested method and to demonstrate its potential, geometrically non-linear finite element analyses are performed using detailed finite element models.

Identification of a two-component signal transduction system involved in fimbriation of Porphyromonas gingivalis.

PubMed

Hayashi, J; Nishikawa, K; Hirano, R; Noguchi, T; Yoshimura, F

2000-01-01

Porphyromonas gingivalis, a periodontopathogen, is an oral anaerobic gram-negative bacterium with numerous fimbriae on the cell surface. Fimbriae have been considered to be an important virulence factor in this organism. We analyzed the genomic DNA of transposon-induced, fimbria-deficient mutants derived from ATCC 33277 and found that seven independent mutants had transposon insertions within the same restriction fragment. Cloning and sequencing of the disrupted region from one of the mutants revealed two adjacent open reading frames (ORFs) which seemed to encode a two-component signal transduction system. We also found that six of the mutants had insertions in a gene, fimS, a homologue of the genes encoding sensor kinase, and that the insertion in the remaining one disrupted the gene immediately downstream, fimR, a homologue of the response regulator genes in other bacteria. These findings suggest that this two-component regulatory system is involved in fimbriation of P. gingivalis.

Molecular cloning of actin genes in Trichomonas vaginalis and phylogeny inferred from actin sequences.

PubMed

Bricheux, G; Brugerolle, G

1997-08-01

The parasitic protozoan Trichomonas vaginalis is known to contain the ubiquitous and highly conserved protein actin. A genomic library and a cDNA library have been screened to identify and clone the actin gene(s) of T. vaginalis. The nucleotide sequence of one gene and its flanking regions have been determined. The open reading frame encodes a protein of 376 amino acids. The sequence is not interrupted by any introns and the promoter could be represented by a 10 bp motif close to a consensus motif also found upstream of most sequenced T. vaginalis genes. The five different clones isolated from the cDNA library have similar sequences and encode three actin proteins differing only by one or two amino acids. A phylogenetic analysis of 31 actin sequences by distance matrix and parsimony methods, using centractin as outgroup, gives congruent trees with Parabasala branching above Diplomonadida.

High-quality animation of 2D steady vector fields.

PubMed

Lefer, Wilfrid; Jobard, Bruno; Leduc, Claire

2004-01-01

Simulators for dynamic systems are now widely used in various application areas and raise the need for effective and accurate flow visualization techniques. Animation allows us to depict direction, orientation, and velocity of a vector field accurately. This paper extends a former proposal for a new approach to produce perfectly cyclic and variable-speed animations for 2D steady vector fields (see [1] and [2]). A complete animation of an arbitrary number of frames is encoded in a single image. The animation can be played using the color table animation technique, which is very effective even on low-end workstations. A cyclic set of textures can be produced as well and then encoded in a common animation format or used for texture mapping on 3D objects. As compared to other approaches, the method presented in this paper produces smoother animations and is more effective, both in memory requirements to store the animation, and in computation time.

Identification of the mpl gene encoding UDP-N-acetylmuramate: L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase in Escherichia coli and its role in recycling of cell wall peptidoglycan.

PubMed Central

Mengin-Lecreulx, D; van Heijenoort, J; Park, J T

1996-01-01

A gene, mpl, encoding UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelat e ligase was recognized by its amino acid sequence homology with murC as the open reading frame yjfG present at 96 min on the Escherichia coli map. The existence of such an enzymatic activity was predicted from studies indicating that reutilization of the intact tripeptide L-alanyl-gamma-D-glutamyl-meso-diaminopimelate occurred and accounted for well over 30% of new cell wall synthesis. Murein tripeptide ligase activity could be demonstrated in crude extracts, and greatly increased activity was produced when the gene was cloned and expressed under control of the trc promoter. A null mutant totally lacked activity but was viable, showing that the enzyme is not essential for growth. PMID:8808921

Cloning and characterization of a novel zinc finger gene in Xp11.2

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

Derry, J.M.J.; Jess, U.; Francke, U.

1995-11-20

During a systematic search for open reading frames in chromosome band Xp11.2, a novel gene (ZNF157) that encodes a putative 506-amino-acid protein with the sequence characteristics of a zinc-finger-containing transcription factor was isolated. ZNF157 is encoded by four exons distributed over >20 kb of genomic DNA. The second and third exons contain sequences similar to those of the previously described KRAB-A and KRAB-B domains, motifs that have been shown to mediate transcriptional repression in other members of the protein family. A fourth exon contains 12 zinc finger DNA binding motifs and finger linking regions characteristic of ZNF proteins of themore » Krueppel family. ZNF157 maps to the telomeric end of a cluster of ZNF genes that includes ZNF21, ZNF41, and ZNF81. 19 refs., 2 figs.« less

The 86-kilodalton antigen from Schistosoma mansoni is a heat-shock protein homologous to yeast HSP-90.

PubMed

Johnson, K S; Wells, K; Bock, J V; Nene, V; Taylor, D W; Cordingley, J S

1989-08-01

We report the sequence of a cDNA clone encoding an 86-kDa polypeptide antigen (p86) from Schistosoma mansoni. Fusion proteins made in Escherichia coli are recognized by human infection sera. The reading frame of this antigen is highly homologous to those of the large heat-shock proteins of Saccharomyces cerevisiae (HSP90) and Drosophila melanogaster (HSP83). mRNA encoding p86 increases in response to heat shock of adult worms, as does HSP70. Comparisons of the sequences of HSP70 and HSP83 homologues show that these two families of heat-shock proteins are not significantly related except for the last four amino acid residues, which are Glu-Glu-Val-Asp in every case. This sequence is not found at the carboxy terminus of any other protein in the current databases.

Influence of encoding focus and stereotypes on source monitoring event-related-potentials.

PubMed

Leynes, P Andrew; Nagovsky, Irina

2016-01-01

Source memory, memory for the origin of a memory, can be influenced by stereotypes and the information of focus during encoding processes. Participants studied words from two different speakers (male or female) using self-focus or other-focus encoding. Source judgments for the speaker׳s voice and Event-Related Potentials (ERPs) were recorded during test. Self-focus encoding increased dependence on stereotype information and the Late Posterior Negativity (LPN). The results link the LPN with an increase in systematic decision processes such as consulting prior knowledge to support an episodic memory judgment. In addition, other-focus encoding increased conditional source judgments and resulted in weaker old/new recognition relative to the self-focus encoding. The putative correlate of recollection (LPC) was absent during this condition and this was taken as evidence that recollection of partial information supported source judgments. Collectively, the results suggest that other-focus encoding changes source monitoring processing by altering the weight of specific memory features. Copyright © 2015 Elsevier B.V. All rights reserved.