Sample records for accurate trna recognition

  1. Saturation of recognition elements blocks evolution of new tRNA identities

    PubMed Central

    Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D.; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A.; Ribas de Pouplana, Lluís

    2016-01-01

    Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. PMID:27386510

  2. The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis.

    PubMed

    Tuorto, Francesca; Herbst, Friederike; Alerasool, Nader; Bender, Sebastian; Popp, Oliver; Federico, Giuseppina; Reitter, Sonja; Liebers, Reinhard; Stoecklin, Georg; Gröne, Hermann-Josef; Dittmar, Gunnar; Glimm, Hanno; Lyko, Frank

    2015-09-14

    The Dnmt2 enzyme utilizes the catalytic mechanism of eukaryotic DNA methyltransferases to methylate several tRNAs at cytosine 38. Dnmt2 mutant mice, flies, and plants were reported to be viable and fertile, and the biological function of Dnmt2 has remained elusive. Here, we show that endochondral ossification is delayed in newborn Dnmt2-deficient mice, which is accompanied by a reduction of the haematopoietic stem and progenitor cell population and a cell-autonomous defect in their differentiation. RNA bisulfite sequencing revealed that Dnmt2 methylates C38 of tRNA Asp(GTC), Gly(GCC), and Val(AAC), thus preventing tRNA fragmentation. Proteomic analyses from primary bone marrow cells uncovered systematic differences in protein expression that are due to specific codon mistranslation by tRNAs lacking Dnmt2-dependent methylation. Our observations demonstrate that Dnmt2 plays an important role in haematopoiesis and define a novel function of C38 tRNA methylation in the discrimination of near-cognate codons, thereby ensuring accurate polypeptide synthesis. © 2015 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

  3. The Catalytic Domain of Topological Knot tRNA Methyltransferase (TrmH) Discriminates between Substrate tRNA and Nonsubstrate tRNA via an Induced-fit Process*

    PubMed Central

    Ochi, Anna; Makabe, Koki; Yamagami, Ryota; Hirata, Akira; Sakaguchi, Reiko; Hou, Ya-Ming; Watanabe, Kazunori; Nureki, Osamu; Kuwajima, Kunihiro; Hori, Hiroyuki

    2013-01-01

    A conserved guanosine at position 18 (G18) in the D-loop of tRNAs is often modified to 2′-O-methylguanosine (Gm). Formation of Gm18 in eubacterial tRNA is catalyzed by tRNA (Gm18) methyltransferase (TrmH). TrmH enzymes can be divided into two types based on their substrate tRNA specificity. Type I TrmH, including Thermus thermophilus TrmH, can modify all tRNA species, whereas type II TrmH, for example Escherichia coli TrmH, modifies only a subset of tRNA species. Our previous crystal study showed that T. thermophilus TrmH is a class IV S-adenosyl-l-methionine-dependent methyltransferase, which maintains a topological knot structure in the catalytic domain. Because TrmH enzymes have short stretches at the N and C termini instead of a clear RNA binding domain, these stretches are believed to be involved in tRNA recognition. In this study, we demonstrate by site-directed mutagenesis that both N- and C-terminal regions function in tRNA binding. However, in vitro and in vivo chimera protein studies, in which four chimeric proteins of type I and II TrmHs were used, demonstrated that the catalytic domain discriminates substrate tRNAs from nonsubstrate tRNAs. Thus, the N- and C-terminal regions do not function in the substrate tRNA discrimination process. Pre-steady state analysis of complex formation between mutant TrmH proteins and tRNA by stopped-flow fluorescence measurement revealed that the C-terminal region works in the initial binding process, in which nonsubstrate tRNA is not excluded, and that structural movement of the motif 2 region of the catalytic domain in an induced-fit process is involved in substrate tRNA discrimination. PMID:23867454

  4. YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase.

    PubMed

    Harris, Kimberly A; Jones, Victoria; Bilbille, Yann; Swairjo, Manal A; Agris, Paul F

    2011-09-01

    The post-transcriptional nucleoside modifications of tRNA's anticodon domain form the loop structure and dynamics required for effective and accurate recognition of synonymous codons. The N(6)-threonylcarbamoyladenosine modification at position 37 (t(6)A(37)), 3'-adjacent to the anticodon, of many tRNA species in all organisms ensures the accurate recognition of ANN codons by increasing codon affinity, enhancing ribosome binding, and maintaining the reading frame. However, biosynthesis of this complex modification is only partially understood. The synthesis requires ATP, free threonine, a single carbon source for the carbamoyl, and an enzyme yet to be identified. Recently, the universal protein family Sua5/YciO/YrdC was associated with t(6)A(37) biosynthesis. To further investigate the role of YrdC in t(6)A(37) biosynthesis, the interaction of the Escherichia coli YrdC with a heptadecamer anticodon stem and loop of lysine tRNA (ASL(Lys)(UUU)) was examined. YrdC bound the unmodified ASL(Lys)(UUU) with high affinity compared with the t(6)A(37)-modified ASL(Lys)(UUU) (K(d) = 0.27 ± 0.20 μM and 1.36 ± 0.39 μM, respectively). YrdC also demonstrated specificity toward the unmodified versus modified anticodon pentamer UUUUA and toward threonine and ATP. The protein did not significantly alter the ASL architecture, nor was it able to base flip A(37), as determined by NMR, circular dichroism, and fluorescence of 2-aminopuine at position 37. Thus, current data support the hypothesis that YrdC, with many of the properties of a putative threonylcarbamoyl transferase, most likely functions as a component of a heteromultimeric protein complex for t(6)A(37) biosynthesis.

  5. Methylated nucleosides in tRNA and tRNA methyltransferases

    PubMed Central

    Hori, Hiroyuki

    2014-01-01

    To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed. PMID:24904644

  6. Examining ERP correlates of recognition memory: Evidence of accurate source recognition without recollection

    PubMed Central

    Addante, Richard, J.; Ranganath, Charan; Yonelinas, Andrew, P.

    2012-01-01

    Recollection is typically associated with high recognition confidence and accurate source memory. However, subjects sometimes make accurate source memory judgments even for items that are not confidently recognized, and it is not known whether these responses are based on recollection or some other memory process. In the current study, we measured event related potentials (ERPs) while subjects made item and source memory confidence judgments in order to determine whether recollection supported accurate source recognition responses for items that were not confidently recognized. In line with previous studies, we found that recognition memory was associated with two ERP effects: an early on-setting FN400 effect, and a later parietal old-new effect [Late Positive Component (LPC)], which have been associated with familiarity and recollection, respectively. The FN400 increased gradually with item recognition confidence, whereas the LPC was only observed for highly confident recognition responses. The LPC was also related to source accuracy, but only for items that had received a high confidence item recognition response; accurate source judgments to items that were less confidently recognized did not exhibit the typical ERP correlate of recollection or familiarity, but rather showed a late, broadly distributed negative ERP difference. The results indicate that accurate source judgments of episodic context can occur even when recollection fails. PMID:22548808

  7. Accurate forced-choice recognition without awareness of memory retrieval.

    PubMed

    Voss, Joel L; Baym, Carol L; Paller, Ken A

    2008-06-01

    Recognition confidence and the explicit awareness of memory retrieval commonly accompany accurate responding in recognition tests. Memory performance in recognition tests is widely assumed to measure explicit memory, but the generality of this assumption is questionable. Indeed, whether recognition in nonhumans is always supported by explicit memory is highly controversial. Here we identified circumstances wherein highly accurate recognition was unaccompanied by hallmark features of explicit memory. When memory for kaleidoscopes was tested using a two-alternative forced-choice recognition test with similar foils, recognition was enhanced by an attentional manipulation at encoding known to degrade explicit memory. Moreover, explicit recognition was most accurate when the awareness of retrieval was absent. These dissociations between accuracy and phenomenological features of explicit memory are consistent with the notion that correct responding resulted from experience-dependent enhancements of perceptual fluency with specific stimuli--the putative mechanism for perceptual priming effects in implicit memory tests. This mechanism may contribute to recognition performance in a variety of frequently-employed testing circumstances. Our results thus argue for a novel view of recognition, in that analyses of its neurocognitive foundations must take into account the potential for both (1) recognition mechanisms allied with implicit memory and (2) recognition mechanisms allied with explicit memory.

  8. Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10.

    PubMed

    Swinehart, William E; Henderson, Jeremy C; Jackman, Jane E

    2013-08-01

    N-1 Methylation of the nearly invariant purine residue found at position 9 of tRNA is a nucleotide modification found in multiple tRNA species throughout Eukarya and Archaea. First discovered in Saccharomyces cerevisiae, the tRNA methyltransferase Trm10 is a highly conserved protein both necessary and sufficient to catalyze all known instances of m1G9 modification in yeast. Although there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The elements that allow Trm10 to distinguish between structurally similar tRNA species are not known, and sequences that are shared between all substrate or all nonsubstrate tRNAs have not been identified. Here, we demonstrate that the in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity. Similarly, overexpression of Trm10 in yeast yields m1G9 containing tRNA species that are ordinarily unmodified in vivo. Thus, yeast Trm10 has a significantly broader tRNA substrate specificity than is suggested by the observed pattern of modification in wild-type yeast. These results may shed light onto the suggested involvement of Trm10 in other pathways in other organisms, particularly in higher eukaryotes that contain up to three different genes with sequence similarity to the single TRM10 gene in yeast, and where these other enzymes have been implicated in pathways beyond tRNA processing.

  9. RNA versatility governs tRNA function: Why tRNA flexibility is essential beyond the translation cycle.

    PubMed

    Kuhn, Claus-D

    2016-05-01

    tRNAs undergo multiple conformational changes during the translation cycle that are required for tRNA translocation and proper communication between the ribosome and translation factors. Recent structural data on how destabilized tRNAs utilize the CCA-adding enzyme to proofread themselves put a spotlight on tRNA flexibility beyond the translation cycle. In analogy to tRNA surveillance, this review finds that other processes also exploit versatile tRNA folding to achieve, amongst others, specific aminoacylation, translational regulation by riboswitches or a block of bacterial translation. tRNA flexibility is thereby not restricted to the hinges utilized during translation. In contrast, the flexibility of tRNA is distributed all over its L-shape and is actively exploited by the tRNA-interacting partners to discriminate one tRNA from another. Since the majority of tRNA modifications also modulate tRNA flexibility it seems that cells devote enormous resources to tightly sense and regulate tRNA structure. This is likely required for error-free protein synthesis. © 2016 WILEY Periodicals, Inc.

  10. Precursor-product discrimination by La protein during tRNA metabolism.

    PubMed

    Bayfield, Mark A; Maraia, Richard J

    2009-04-01

    La proteins bind pre-tRNAs at their UUU-3'OH ends, facilitating their maturation. Although the mechanism by which La binds pre-tRNA 3' trailers is known, the function of the RNA binding beta-sheet surface of the RNA-recognition motif (RRM1) is unknown. How La dissociates from UUU-3'OH-containing trailers after 3' processing is also unknown. Here we show that La preferentially binds pre-tRNAs over processed tRNAs or 3' trailer products through coupled use of two sites: one on the La motif and another on the RRM1 beta-surface that binds elsewhere on tRNA. Two sites provide stable pre-tRNA binding, whereas the processed tRNA and 3' trailer are released from their single sites relatively fast. RRM1 loop-3 mutations decrease affinity for pre-tRNA and tRNA, but not for the UUU-3'OH trailer, and impair tRNA maturation in vivo. We propose that RRM1 functions in activities that are more complex than UUU-3'OH binding. Accordingly, the RRM1 mutations also impair an RNA chaperone activity of La. The results suggest how La distinguishes precursor from product RNAs, allowing it to recycle onto a new pre-tRNA.

  11. New tRNA contacts facilitate ligand binding in a Mycobacterium smegmatis T box riboswitch.

    PubMed

    Sherwood, Anna V; Frandsen, Jane K; Grundy, Frank J; Henkin, Tina M

    2018-04-10

    T box riboswitches are RNA regulatory elements widely used by organisms in the phyla Firmicutes and Actinobacteria to regulate expression of amino acid-related genes. Expression of T box family genes is down-regulated by transcription attenuation or inhibition of translation initiation in response to increased charging of the cognate tRNA. Three direct contacts with tRNA have been described; however, one of these contacts is absent in a subclass of T box RNAs and the roles of several structural domains conserved in most T box RNAs are unknown. In this study, structural elements of a Mycobacterium smegmatis ileS T box riboswitch variant with an Ultrashort (US) Stem I were sequentially deleted, which resulted in a progressive decrease in binding affinity for the tRNA Ile ligand. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) revealed structural changes in conserved riboswitch domains upon interaction with the tRNA ligand. Cross-linking and mutational analyses identified two interaction sites, one between the S-turn element in Stem II and the T arm of tRNA Ile and the other between the Stem IIA/B pseudoknot and the D loop of tRNA Ile These newly identified RNA contacts add information about tRNA recognition by the T box riboswitch and demonstrate a role for the S-turn and pseudoknot elements, which resemble structural elements that are common in many cellular RNAs.

  12. Rp-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding.

    PubMed Central

    Hardt, W D; Warnecke, J M; Erdmann, V A; Hartmann, R K

    1995-01-01

    We have used Rp-phosphorothioate modifications and a binding interference assay to analyse the role of phosphate oxygens in tRNA recognition by Escherichia coli ribonuclease P (RNase P) RNA. Total (100%) Rp-phosphorothioate modification at A, C or G positions of RNase P RNA strongly impaired tRNA binding and pre-tRNA processing, while effects were less pronounced at U positions. Partially modified E. coli RNase P RNAs were separated into tRNA binding and non-binding fractions by gel retardation. Rp-phosphorothioate modifications that interfered with tRNA binding were found 5' of nucleotides A67, G68, U69, C70, C71, G72, A130, A132, A248, A249, G300, A317, A330, A352, C353 and C354. Manganese rescue at positions U69, C70, A130 and A132 identified, for the first time, sites of direct metal ion coordination in RNase P RNA. Most sites of interference are at strongly conserved nucleotides and nine reside within a long-range base-pairing interaction present in all known RNase P RNAs. In contrast to RNase P RNA, 100% Rp-phosphorothioate substitutions in tRNA showed only moderate effects on binding to RNase P RNAs from E. coli, Bacillus subtilis and Chromatium vinosum, suggesting that pro-Rp phosphate oxygens of mature tRNA contribute relatively little to the formation of the tRNA-RNase P RNA complex. Images PMID:7540978

  13. tRNA biology charges to the front

    PubMed Central

    Phizicky, Eric M.; Hopper, Anita K.

    2010-01-01

    tRNA biology has come of age, revealing an unprecedented level of understanding and many unexpected discoveries along the way. This review highlights new findings on the diverse pathways of tRNA maturation, and on the formation and function of a number of modifications. Topics of special focus include the regulation of tRNA biosynthesis, quality control tRNA turnover mechanisms, widespread tRNA cleavage pathways activated in response to stress and other growth conditions, emerging evidence of signaling pathways involving tRNA and cleavage fragments, and the sophisticated intracellular tRNA trafficking that occurs during and after biosynthesis. PMID:20810645

  14. Structural insights into translational recoding by frameshift suppressor tRNA SufJ

    DOE PAGES

    Fagan, Crystal E.; Maehigashi, Tatsuya; Dunkle, Jack A.; ...

    2014-10-28

    The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant protein production can result from the uncoupled movement of the tRNA in either the 5' or 3' direction on mRNA. Here, we report the biochemical and structural characterization of +1 frameshift suppressor tRNA SufJ, a tRNA known to decode four, instead of three, nucleotides. Frameshift suppressor tRNA SufJ contains an insertion 5' to its anticodon, expanding the anticodon loop from seven to eight nucleotides. Our results indicate that the expansion of the anticodon loop of either ASL SufJ ormore » tRNA SufJ does not affect its affinity for the A site of the ribosome. Structural analyses of both ASL SufJ and ASL Thr bound to the Thermus thermophilus 70S ribosome demonstrate both ASLs decode in the zero frame. Although the anticodon loop residues 34–37 are superimposable with canonical seven-nucleotide ASLs, the single C31.5 insertion between nucleotides 31 and 32 in ASL SufJ imposes a conformational change of the anticodon stem, that repositions and tilts the ASL toward the back of the A site. Further modeling analyses reveal that this tilting would cause a distortion in full-length A-site tRNA SufJ during tRNA selection and possibly impede gripping of the anticodon stem by 16S rRNA nucleotides in the P site. Together, these data implicate tRNA distortion as a major driver of noncanonical translation events such as frameshifting.« less

  15. Monitoring mis-acylated tRNA suppression efficiency in mammalian cells via EGFP fluorescence recovery

    PubMed Central

    Ilegems, Erwin; Pick, Horst M.; Vogel, Horst

    2002-01-01

    A reporter assay was developed to detect and quantify nonsense codon suppression by chemically aminoacylated tRNAs in mammalian cells. It is based on the cellular expression of the enhanced green fluorescent protein (EGFP) as a reporter for the site-specific amino acid incorporation in its sequence using an orthogonal suppressor tRNA derived from Escherichia coli. Suppression of an engineered amber codon at position 64 in the EGFP run-off transcript could be achieved by the incorporation of a leucine via an in vitro aminoacylated suppressor tRNA. Microinjection of defined amounts of mutagenized EGFP mRNA and suppressor tRNA into individual cells allowed us to accurately determine suppression efficiencies by measuring the EGFP fluorescence intensity in individual cells using laser-scanning confocal microscopy. Control experiments showed the absence of natural suppression or aminoacylation of the synthetic tRNA by endogenous aminoacyl-tRNA synthetases. This reporter assay opens the way for the optimization of essential experimental parameters for expanding the scope of the suppressor tRNA technology to different cell types. PMID:12466560

  16. New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria.

    PubMed

    Freyhult, Eva; Cui, Yuanyuan; Nilsson, Olle; Ardell, David H

    2007-10-01

    There are at least 21 subfunctional classes of tRNAs in most cells that, despite a very highly conserved and compact common structure, must interact specifically with different cliques of proteins or cause grave organismal consequences. Protein recognition of specific tRNA substrates is achieved in part through class-restricted tRNA features called tRNA identity determinants. In earlier work we used TFAM, a statistical classifier of tRNA function, to show evidence of unexpectedly large diversity among bacteria in tRNA identity determinants. We also created a data reduction technique called function logos to visualize identity determinants for a given taxon. Here we show evidence that determinants for lysylated isoleucine tRNAs are not the same in Proteobacteria as in other bacterial groups including the Cyanobacteria. Consistent with this, the lysylating biosynthetic enzyme TilS lacks a C-terminal domain in Cyanobacteria that is present in Proteobacteria. We present here, using function logos, a map estimating all potential identity determinants generally operational in Cyanobacteria and Proteobacteria. To further isolate the differences in potential tRNA identity determinants between Proteobacteria and Cyanobacteria, we created two new data reduction visualizations to contrast sequence and function logos between two taxa. One, called Information Difference logos (ID logos), shows the evolutionary gain or retention of functional information associated to features in one lineage. The other, Kullback-Leibler divergence Difference logos (KLD logos), shows recruitments or shifts in the functional associations of features, especially those informative in both lineages. We used these new logos to specifically isolate and visualize the differences in potential tRNA identity determinants between Proteobacteria and Cyanobacteria. Our graphical results point to numerous differences in potential tRNA identity determinants between these groups. Although more differences in

  17. tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

    PubMed Central

    Carter, Charles W.; Wolfenden, Richard

    2016-01-01

    abstract The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyl-tRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology. PMID:26595350

  18. Amino acid signature enables proteins to recognize modified tRNA.

    PubMed

    Spears, Jessica L; Xiao, Xingqing; Hall, Carol K; Agris, Paul F

    2014-02-25

    Human tRNA(Lys3)UUU is the primer for HIV replication. The HIV-1 nucleocapsid protein, NCp7, facilitates htRNA(Lys3)UUU recruitment from the host cell by binding to and remodeling the tRNA structure. Human tRNA(Lys3)UUU is post-transcriptionally modified, but until recently, the importance of those modifications in tRNA recognition by NCp7 was unknown. Modifications such as the 5-methoxycarbonylmethyl-2-thiouridine at anticodon wobble position-34 and 2-methylthio-N(6)-threonylcarbamoyladenosine, adjacent to the anticodon at position-37, are important to the recognition of htRNA(Lys3)UUU by NCp7. Several short peptides selected from phage display libraries were found to also preferentially recognize these modifications. Evolutionary algorithms (Monte Carlo and self-consistent mean field) and assisted model building with energy refinement were used to optimize the peptide sequence in silico, while fluorescence assays were developed and conducted to verify the in silico results and elucidate a 15-amino acid signature sequence (R-W-Q/N-H-X2-F-Pho-X-G/A-W-R-X2-G, where X can be most amino acids, and Pho is hydrophobic) that recognized the tRNA's fully modified anticodon stem and loop domain, hASL(Lys3)UUU. Peptides of this sequence specifically recognized and bound modified htRNA(Lys3)UUU with an affinity 10-fold higher than that of the starting sequence. Thus, this approach provides an effective means of predicting sequences of RNA binding peptides that have better binding properties. Such peptides can be used in cell and molecular biology as well as biochemistry to explore RNA binding proteins and to inhibit those protein functions.

  19. The m1A(58) modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI.

    PubMed

    Dégut, Clément; Ponchon, Luc; Folly-Klan, Marcia; Barraud, Pierre; Tisné, Carine

    2016-03-01

    The enzymes of the TrmI family catalyze the formation of the m(1)A58 modification in tRNA. We previously solved the crystal structure of the Thermus thermophilus enzyme and conducted a biophysical study to characterize the interaction between TrmI and tRNA. TrmI enzymes are active as a tetramer and up to two tRNAs can bind to TrmI simultaneously. In this paper, we present the structures of two TrmI mutants (D170A and Y78A). These residues are conserved in the active site of TrmIs and their mutations result in a dramatic alteration of TrmI activity. Both structures of TrmI mutants revealed the flexibility of the N-terminal domain that is probably important to bind tRNA. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine. This structure reinforces the previously proposed role of Y78, i.e. stabilize the conformation of the A58 ribose needed to hold the adenosine in the active site. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site. This structure and recent data confirms the central role of D170 residue binding the amino moiety of SAM and the exocyclic amino group of adenine. Possible mechanisms for methyl transfer are then discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. A Highly Accurate Face Recognition System Using Filtering Correlation

    NASA Astrophysics Data System (ADS)

    Watanabe, Eriko; Ishikawa, Sayuri; Kodate, Kashiko

    2007-09-01

    The authors previously constructed a highly accurate fast face recognition optical correlator (FARCO) [E. Watanabe and K. Kodate: Opt. Rev. 12 (2005) 460], and subsequently developed an improved, super high-speed FARCO (S-FARCO), which is able to process several hundred thousand frames per second. The principal advantage of our new system is its wide applicability to any correlation scheme. Three different configurations were proposed, each depending on correlation speed. This paper describes and evaluates a software correlation filter. The face recognition function proved highly accurate, seeing that a low-resolution facial image size (64 × 64 pixels) has been successfully implemented. An operation speed of less than 10 ms was achieved using a personal computer with a central processing unit (CPU) of 3 GHz and 2 GB memory. When we applied the software correlation filter to a high-security cellular phone face recognition system, experiments on 30 female students over a period of three months yielded low error rates: 0% false acceptance rate and 2% false rejection rate. Therefore, the filtering correlation works effectively when applied to low resolution images such as web-based images or faces captured by a monitoring camera.

  1. Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes

    PubMed Central

    2016-01-01

    Cells respond to stress by controlling gene expression at several levels, with little known about the role of translation. Here, we demonstrate a coordinated translational stress response system involving stress-specific reprogramming of tRNA wobble modifications that leads to selective translation of codon-biased mRNAs representing different classes of critical response proteins. In budding yeast exposed to four oxidants and five alkylating agents, tRNA modification patterns accurately distinguished among chemically similar stressors, with 14 modified ribonucleosides forming the basis for a data-driven model that predicts toxicant chemistry with >80% sensitivity and specificity. tRNA modification subpatterns also distinguish SN1 from SN2 alkylating agents, with SN2-induced increases in m3C in tRNA mechanistically linked to selective translation of threonine-rich membrane proteins from genes enriched with ACC and ACT degenerate codons for threonine. These results establish tRNA modifications as predictive biomarkers of exposure and illustrate a novel regulatory mechanism for translational control of cell stress response. PMID:25772370

  2. Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks.

    PubMed

    Caetano-Anollés, Derek; Caetano-Anollés, Gustavo

    2016-12-02

    The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates.

  3. Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks

    PubMed Central

    Caetano-Anollés, Derek; Caetano-Anollés, Gustavo

    2016-01-01

    The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates. PMID:27918435

  4. The ribosome as an optimal decoder: a lesson in molecular recognition.

    PubMed

    Savir, Yonatan; Tlusty, Tsvi

    2013-04-11

    The ribosome is a complex molecular machine that, in order to synthesize proteins, has to decode mRNAs by pairing their codons with matching tRNAs. Decoding is a major determinant of fitness and requires accurate and fast selection of correct tRNAs among many similar competitors. However, it is unclear whether the modern ribosome, and in particular its large conformational changes during decoding, are the outcome of adaptation to its task as a decoder or the result of other constraints. Here, we derive the energy landscape that provides optimal discrimination between competing substrates and thereby optimal tRNA decoding. We show that the measured landscape of the prokaryotic ribosome is sculpted in this way. This model suggests that conformational changes of the ribosome and tRNA during decoding are means to obtain an optimal decoder. Our analysis puts forward a generic mechanism that may be utilized broadly by molecular recognition systems. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. tRNA acceptor stem and anticodon bases form independent codes related to protein folding

    PubMed Central

    Carter, Charles W.; Wolfenden, Richard

    2015-01-01

    Aminoacyl-tRNA synthetases recognize tRNA anticodon and 3′ acceptor stem bases. Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition. Representing tRNA identity elements with two bits per base, we show that the anticodon encodes the hydrophobicity of each amino acid side-chain as represented by its water-to-cyclohexane distribution coefficient, and this relationship holds true over the entire temperature range of liquid water. The acceptor stem codes preferentially for the surface area or size of each side-chain, as represented by its vapor-to-cyclohexane distribution coefficient. These orthogonal experimental properties are both necessary to account satisfactorily for the exposed surface area of amino acids in folded proteins. Moreover, the acceptor stem codes correctly for β-branched and carboxylic acid side-chains, whereas the anticodon codes for a wider range of such properties, but not for size or β-branching. These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water. PMID:26034281

  6. Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch

    PubMed Central

    Caserta, Enrico; Liu, Liang-Chun; Grundy, Frank J.; Henkin, Tina M.

    2015-01-01

    Many amino acid-related genes in Gram-positive bacteria are regulated by the T box riboswitch. The leader RNA of genes in the T box family controls the expression of downstream genes by monitoring the aminoacylation status of the cognate tRNA. Previous studies identified a three-nucleotide codon, termed the “Specifier Sequence,” in the riboswitch that corresponds to the amino acid identity of the downstream genes. Pairing of the Specifier Sequence with the anticodon of the cognate tRNA is the primary determinant of specific tRNA recognition. This interaction mimics codon-anticodon pairing in translation but occurs in the absence of the ribosome. The goal of the current study was to determine the effect of a full range of mismatches for comparison with codon recognition in translation. Mutations were individually introduced into the Specifier Sequence of the glyQS leader RNA and tRNAGly anticodon to test the effect of all possible pairing combinations on tRNA binding affinity and antitermination efficiency. The functional role of the conserved purine 3′ of the Specifier Sequence was also verifiedin this study. We found that substitutions at the Specifier Sequence resulted in reduced binding, the magnitude of which correlates well with the predicted stability of the RNA-RNA pairing. However, the tolerance for specific mismatches in antitermination was generally different from that during decoding, which reveals a unique tRNA recognition pattern in the T box antitermination system. PMID:26229106

  7. tRNA travels from the cytoplasm to organelles

    PubMed Central

    Rubio, Mary Anne T.; Hopper, Anita K.

    2011-01-01

    Transfer RNAs (tRNAs) encoded by the nuclear genome are surprisingly dynamic. Although tRNAs function in protein synthesis occurring on cytoplasmic ribosomes, tRNAs can transit from the cytoplasm to the nucleus and then again return to the cytoplasm by a process known as the tRNA retrograde process. Subsets of the cytoplasmic tRNAs are also imported into mitochondria and function in mitochondrial protein synthesis. The numbers of tRNA species that are imported into mitchondria differ among organisms, ranging from just a few to the entire set needed to decode mitochondrially encoded mRNAs. For some tRNAs, import is dependent on the mitochondrial protein import machinery, whereas the majority of tRNA mitochondrial import is independent of this machinery. Although cytoplasmic proteins and proteins located on the mitochondrial surface participating in the tRNA import process have been described for several organisms, the identity of these proteins differ among organisms. Likewise, the tRNA determinants required for mitochondrial import differ among tRNA species and organisms. Here, we present an overview and discuss the current state of knowledge regarding the mechanisms involved in the tRNA retrograde process and continue with an overview of tRNA import into mitochondria. Finally, we highlight areas of future research to understand the function and regulation of movement of tRNAs between the cytoplasm and organelles. PMID:21976284

  8. A new accurate pill recognition system using imprint information

    NASA Astrophysics Data System (ADS)

    Chen, Zhiyuan; Kamata, Sei-ichiro

    2013-12-01

    Great achievements in modern medicine benefit human beings. Also, it has brought about an explosive growth of pharmaceuticals that current in the market. In daily life, pharmaceuticals sometimes confuse people when they are found unlabeled. In this paper, we propose an automatic pill recognition technique to solve this problem. It functions mainly based on the imprint feature of the pills, which is extracted by proposed MSWT (modified stroke width transform) and described by WSC (weighted shape context). Experiments show that our proposed pill recognition method can reach an accurate rate up to 92.03% within top 5 ranks when trying to classify more than 10 thousand query pill images into around 2000 categories.

  9. An aminoacylation-dependent nuclear tRNA export pathway in yeast.

    PubMed

    Grosshans, H; Hurt, E; Simos, G

    2000-04-01

    Yeast Los1p, the homolog of human exportin-t, mediates nuclear export of tRNA. Using fluorescence in situ hybridization, we could show that the export of some intronless tRNA species is not detectably affected by the disruption of LOS1. To find other factors that facilitate tRNA export, we performed a suppressor screen of a synthetically lethal los1 mutant and identified the essential translation elongation factor eEF-1A. Mutations in eEF-1A impaired nuclear export of all tRNAs tested, which included both spliced and intronless species. An even stronger defect in nuclear exit of tRNA was observed under conditions that inhibited tRNA aminoacylation. In all cases, inhibition of tRNA export led to nucleolar accumulation of mature tRNAs. Our data show that tRNA aminoacylation and eEF-1A are required for efficient nuclear tRNA export in yeast and suggest coordination between the protein translation and the nuclear tRNA processing and transport machineries.

  10. An aminoacylation-dependent nuclear tRNA export pathway in yeast

    PubMed Central

    Grosshans, Helge; Hurt, Ed; Simos, George

    2000-01-01

    Yeast Los1p, the homolog of human exportin-t, mediates nuclear export of tRNA. Using fluorescence in situ hybridization, we could show that the export of some intronless tRNA species is not detectably affected by the disruption of LOS1. To find other factors that facilitate tRNA export, we performed a suppressor screen of a synthetically lethal los1 mutant and identified the essential translation elongation factor eEF-1A. Mutations in eEF-1A impaired nuclear export of all tRNAs tested, which included both spliced and intronless species. An even stronger defect in nuclear exit of tRNA was observed under conditions that inhibited tRNA aminoacylation. In all cases, inhibition of tRNA export led to nucleolar accumulation of mature tRNAs. Our data show that tRNA aminoacylation and eEF-1A are required for efficient nuclear tRNA export in yeast and suggest coordination between the protein translation and the nuclear tRNA processing and transport machineries. PMID:10766739

  11. Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria).

    PubMed Central

    Edmonds, C G; Crain, P F; Gupta, R; Hashizume, T; Hocart, C H; Kowalak, J A; Pomerantz, S C; Stetter, K O; McCloskey, J A

    1991-01-01

    Nucleoside modification has been studied in unfractionated tRNA from 11 thermophilic archaea (archaebacteria), including phylogenetically diverse representatives of thermophilic methanogens and sulfur-metabolizing hyperthermophiles which grow optimally in the temperature range of 56 (Thermoplasma acidophilum) to 105 degrees C (Pyrodictium occultum), and for comparison from the most thermophilic bacterium (eubacterium) known, Thermotoga maritima (80 degrees C). Nine nucleosides are found to be unique to the archaea, six of which are structurally novel in being modified both in the base and by methylation in ribose and occur primarily in tRNA from the extreme thermophiles in the Crenarchaeota of the archaeal phylogenetic tree. 2-Thiothymine occurs in tRNA from Thermococcus sp., and constitutes the only known occurrence of the thymine moiety in archaeal RNA, in contrast to its near-ubiquitous presence in tRNA from bacteria and eukarya. A total of 33 modified nucleosides are rigorously characterized in archaeal tRNA in the present study, demonstrating that the structural range of posttranscriptional modifications in archaeal tRNA is more extensive than previously known. From a phylogenetic standpoint, certain tRNA modifications occur in the archaea which are otherwise unique to either the bacterial or eukaryal domain, although the overall patterns of modification are more typical of eukaryotes than bacteria. PMID:1708763

  12. Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity

    PubMed Central

    López, Ana; Castelló, María José; Gil, María José; Zheng, Bo; Chen, Peng; Vera, Pablo

    2015-01-01

    tRNA is the most highly modified class of RNA species, and modifications are found in tRNAs from all organisms that have been examined. Despite their vastly different chemical structures and their presence in different tRNAs, occurring in different locations in tRNA, the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent discoveries have revealed unprecedented complexity in the modification patterns of tRNA, their regulation and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge on the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance and activation of defenses in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal SCS9 encodes a tRNA methyltransferase that mediates the 2´-O-ribose methylation of selected tRNA species in the anticodon loop. These SCS9-mediated tRNA modifications enhance during the course of infection with the bacterial pathogen Pseudomonas syringae DC3000, and lack of such tRNA modification, as observed in scs9 mutants, severely compromise plant immunity against the same pathogen without affecting the salicylic acid (SA) signaling pathway which regulates plant immune responses. Our results support a model that gives importance to the control of certain tRNA modifications for mounting an effective immune response in Arabidopsis, and therefore expands the repertoire of molecular components essential for an efficient disease resistance response. PMID:26492405

  13. A robust recognition and accurate locating method for circular coded diagonal target

    NASA Astrophysics Data System (ADS)

    Bao, Yunna; Shang, Yang; Sun, Xiaoliang; Zhou, Jiexin

    2017-10-01

    As a category of special control points which can be automatically identified, artificial coded targets have been widely developed in the field of computer vision, photogrammetry, augmented reality, etc. In this paper, a new circular coded target designed by RockeTech technology Corp. Ltd is analyzed and studied, which is called circular coded diagonal target (CCDT). A novel detection and recognition method with good robustness is proposed in the paper, and implemented on Visual Studio. In this algorithm, firstly, the ellipse features of the center circle are used for rough positioning. Then, according to the characteristics of the center diagonal target, a circular frequency filter is designed to choose the correct center circle and eliminates non-target noise. The precise positioning of the coded target is done by the correlation coefficient fitting extreme value method. Finally, the coded target recognition is achieved by decoding the binary sequence in the outer ring of the extracted target. To test the proposed algorithm, this paper has carried out simulation experiments and real experiments. The results show that the CCDT recognition and accurate locating method proposed in this paper can robustly recognize and accurately locate the targets in complex and noisy background.

  14. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function.

    PubMed

    Väre, Ville Y P; Eruysal, Emily R; Narendran, Amithi; Sarachan, Kathryn L; Agris, Paul F

    2017-03-16

    RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

  15. tRNA wobble modifications and protein homeostasis

    PubMed Central

    Ranjan, Namit; Rodnina, Marina V.

    2016-01-01

    Abstract tRNA is a central component of the protein synthesis machinery in the cell. In living cells, tRNAs undergo numerous post-transcriptional modifications. In particular, modifications at the anticodon loop play an important role in ensuring efficient protein synthesis, maintaining protein homeostasis, and helping cell adaptation and survival. Hypo-modification of the wobble position of the tRNA anticodon loop is of particular relevance for translation regulation and is implicated in various human diseases. In this review we summarize recent evidence of how methyl and thiol modifications in eukaryotic tRNA at position 34 affect cellular fitness and modulate regulatory circuits at normal conditions and under stress. PMID:27335723

  16. Cytosolic Hsp70 and co-chaperones constitute a novel system for tRNA import into the nucleus

    PubMed Central

    Takano, Akira; Kajita, Takuya; Mochizuki, Makoto; Endo, Toshiya; Yoshihisa, Tohru

    2015-01-01

    tRNAs are unique among various RNAs in that they shuttle between the nucleus and the cytoplasm, and their localization is regulated by nutrient conditions. Although nuclear export of tRNAs has been well documented, the import machinery is poorly understood. Here, we identified Ssa2p, a major cytoplasmic Hsp70 in Saccharomyces cerevisiae, as a tRNA-binding protein whose deletion compromises nuclear accumulation of tRNAs upon nutrient starvation. Ssa2p recognizes several structural features of tRNAs through its nucleotide-binding domain, but prefers loosely-folded tRNAs, suggesting that Ssa2p has a chaperone-like activity for RNAs. Ssa2p also binds Nup116, one of the yeast nucleoporins. Sis1p and Ydj1p, cytoplasmic co-chaperones for Ssa proteins, were also found to contribute to the tRNA import. These results unveil a novel function of the Ssa2p system as a tRNA carrier for nuclear import by a novel mode of substrate recognition. Such Ssa2p-mediated tRNA import likely contributes to quality control of cytosolic tRNAs. DOI: http://dx.doi.org/10.7554/eLife.04659.001 PMID:25853343

  17. Processing of Archaebacterial Intron-Containing tRNA Gene Transcripts.

    DTIC Science & Technology

    1987-07-31

    1{ 1. Project Goals: A. To determine the mechanism of tRNA intron processing in the halophilic archaebacteria. B. Characterize and compare the...enzyme(s) responsible for the removal of 5’-flanking sequences from halophilic and sulfur-dependent tRNA gene transcripts. C. Examine the structure and...distribution of tRNA introns in the halophilic archaebacteria. 2. Accomplishments: A. Intron processing mechanism We have succeeded in our primary

  18. Structural insights into the polyphyletic origins of glycyl tRNA synthetases

    DOE PAGES

    Valencia-Sánchez, Marco Igor; Rodríguez-Hernández, Annia; Ferreira, Ruben; ...

    2016-05-23

    Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α 2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α 2β 2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanism of amino acid recognition is also dissimilar. Here, we show that the α-subunit of the α 2β 2more » GlyRS from the bacterium Aquifex aeolicus is able to perform the first step of the aminoacylation reaction, which involves the activation of the amino acid with ATP. The crystal structure of the α-subunit in the complex with an analog of glycyl adenylate at 2.8 Å resolution presents a conformational arrangement that properly positions the cognate amino acid. This work shows that glycine is recognized by a subset of different residues in the two types of GlyRS. Furthermore, a structural and sequence analysis of class II catalytic domains shows that bacterial GlyRS is closely related to alanyl tRNA synthetase, which led us to define a new subclassification of these ancient enzymes and to propose an evolutionary path of α 2β 2 GlyRS, convergent with α 2 GlyRS and divergent from AlaRS, thus providing a possible explanation for the puzzling existence of two proteins sharing the same fold and function but not a common ancestor.« less

  19. Internal control regions for transcription of eukaryotic tRNA genes.

    PubMed Central

    Sharp, S; DeFranco, D; Dingermann, T; Farrell, P; Söll, D

    1981-01-01

    We have identified the region within a eukaryotic tRNA gene required for initiation of transcription. These results were obtained by systematically constructing deletions extending from the 5' or the 3' flanking regions into a cloned Drosophila tRNAArg gene by using nuclease BAL 31. The ability of the newly generated deletion clones to direct the in vitro synthesis of tRNA precursors was measured in transcription systems from Xenopus laevis oocytes, Drosophila Kc cells, and HeLa cells. Two control regions within the coding sequence were identified. The first was essential for transcription and was contained between nucleotides 8 and 25 of the mature tRNA sequence. Genes devoid of the second control region, which was contained between nucleotides 50 and 58 of the mature tRNA sequence, could be transcribed but with reduced efficiency. Thus, the promoter regions within a tRNA gene encode the tRNA sequences of the D stem and D loop, the invariant uridine at position 8, and the semi-invariant G-T-psi-C sequence. Images PMID:6947245

  20. Sleep deprivation impairs the accurate recognition of human emotions.

    PubMed

    van der Helm, Els; Gujar, Ninad; Walker, Matthew P

    2010-03-01

    Investigate the impact of sleep deprivation on the ability to recognize the intensity of human facial emotions. Randomized total sleep-deprivation or sleep-rested conditions, involving between-group and within-group repeated measures analysis. Experimental laboratory study. Thirty-seven healthy participants, (21 females) aged 18-25 y, were randomly assigned to the sleep control (SC: n = 17) or total sleep deprivation group (TSD: n = 20). Participants performed an emotional face recognition task, in which they evaluated 3 different affective face categories: Sad, Happy, and Angry, each ranging in a gradient from neutral to increasingly emotional. In the TSD group, the task was performed once under conditions of sleep deprivation, and twice under sleep-rested conditions following different durations of sleep recovery. In the SC group, the task was performed twice under sleep-rested conditions, controlling for repeatability. In the TSD group, when sleep-deprived, there was a marked and significant blunting in the recognition of Angry and Happy affective expressions in the moderate (but not extreme) emotional intensity range; differences that were most reliable and significant in female participants. No change in the recognition of Sad expressions was observed. These recognition deficits were, however, ameliorated following one night of recovery sleep. No changes in task performance were observed in the SC group. Sleep deprivation selectively impairs the accurate judgment of human facial emotions, especially threat relevant (Anger) and reward relevant (Happy) categories, an effect observed most significantly in females. Such findings suggest that sleep loss impairs discrete affective neural systems, disrupting the identification of salient affective social cues.

  1. Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes

    PubMed Central

    Leimkühler, Silke; Bühning, Martin; Beilschmidt, Lena

    2017-01-01

    Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm5s2U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT). Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco) and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes. PMID:28098827

  2. Regulation of tRNA Bidirectional Nuclear-Cytoplasmic Trafficking in Saccharomyces cerevisiae

    PubMed Central

    Murthi, Athulaprabha; Shaheen, Hussam H.; Huang, Hsiao-Yun; Preston, Melanie A.; Lai, Tsung-Po; Phizicky, Eric M.

    2010-01-01

    tRNAs in yeast and vertebrate cells move bidirectionally and reversibly between the nucleus and the cytoplasm. We investigated roles of members of the β-importin family in tRNA subcellular dynamics. Retrograde import of tRNA into the nucleus is dependent, directly or indirectly, upon Mtr10. tRNA nuclear export utilizes at least two members of the β-importin family. The β-importins involved in nuclear export have shared and exclusive functions. Los1 functions in both the tRNA primary export and the tRNA reexport processes. Msn5 is unable to export tRNAs in the primary round of export if the tRNAs are encoded by intron-containing genes, and for these tRNAs Msn5 functions primarily in their reexport to the cytoplasm. The data support a model in which tRNA retrograde import to the nucleus is a constitutive process; in contrast, reexport of the imported tRNAs back to the cytoplasm is regulated by the availability of nutrients to cells and by tRNA aminoacylation in the nucleus. Finally, we implicate Tef1, the yeast orthologue of translation elongation factor eEF1A, in the tRNA reexport process and show that its subcellular distribution between the nucleus and cytoplasm is dependent upon Mtr10 and Msn5. PMID:20032305

  3. Regulation of tRNA bidirectional nuclear-cytoplasmic trafficking in Saccharomyces cerevisiae.

    PubMed

    Murthi, Athulaprabha; Shaheen, Hussam H; Huang, Hsiao-Yun; Preston, Melanie A; Lai, Tsung-Po; Phizicky, Eric M; Hopper, Anita K

    2010-02-15

    tRNAs in yeast and vertebrate cells move bidirectionally and reversibly between the nucleus and the cytoplasm. We investigated roles of members of the beta-importin family in tRNA subcellular dynamics. Retrograde import of tRNA into the nucleus is dependent, directly or indirectly, upon Mtr10. tRNA nuclear export utilizes at least two members of the beta-importin family. The beta-importins involved in nuclear export have shared and exclusive functions. Los1 functions in both the tRNA primary export and the tRNA reexport processes. Msn5 is unable to export tRNAs in the primary round of export if the tRNAs are encoded by intron-containing genes, and for these tRNAs Msn5 functions primarily in their reexport to the cytoplasm. The data support a model in which tRNA retrograde import to the nucleus is a constitutive process; in contrast, reexport of the imported tRNAs back to the cytoplasm is regulated by the availability of nutrients to cells and by tRNA aminoacylation in the nucleus. Finally, we implicate Tef1, the yeast orthologue of translation elongation factor eEF1A, in the tRNA reexport process and show that its subcellular distribution between the nucleus and cytoplasm is dependent upon Mtr10 and Msn5.

  4. tRNA gene copy number variation in humans

    PubMed Central

    Iben, James R.; Maraia, Richard J.

    2014-01-01

    The human tRNAome consists of more than 500 interspersed tRNA genes comprising 51 anticodon families of largely unequal copy number. We examined tRNA gene copy number variation (tgCNV) in six individuals; two kindreds of two parents and a child, using high coverage whole genome sequence data. Such differences may be important because translation of some mRNAs is sensitive to the relative amounts of tRNAs and because tRNA competition determines translational efficiency vs. fidelity and production of native vs. misfolded proteins. We identified several tRNA gene clusters with CNV, which in some cases were part of larger iterations. In addition there was an isolated tRNALysCUU gene that was absent as a homozygous deletion in one of the parents. When assessed by semiquantitative PCR in 98 DNA samples representing a wide variety of ethnicities, this allele was found deleted in hetero- or homozygosity in all groups at ~50% frequency. This is the first report of copy number variation of human tRNA genes. We conclude that tgCNV exists at significant levels among individual humans and discuss the results in terms of genetic diversity and prior genome wide association studies (GWAS) that suggest the importance of the ratio of tRNALys isoacceptors in Type-2 diabetes. PMID:24342656

  5. Shaping tRNA

    ERIC Educational Resources Information Center

    Priano, Christine

    2013-01-01

    This model-building activity provides a quick, visual, hands-on tool that allows students to examine more carefully the cloverleaf structure of a typical tRNA molecule. When used as a supplement to lessons that involve gene expression, this exercise reinforces several concepts in molecular genetics, including nucleotide base-pairing rules, the…

  6. Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device

    PubMed Central

    Smith, Andrew M.; Abu-Shumays, Robin; Akeson, Mark; Bernick, David L.

    2015-01-01

    Transfer RNAs (tRNA) are the most common RNA molecules in cells and have critical roles as both translators of the genetic code and regulators of protein synthesis. As such, numerous methods have focused on studying tRNA abundance and regulation, with the most widely used methods being RNA-seq and microarrays. Though revolutionary to transcriptomics, these assays are limited by an inability to encode tRNA modifications in the requisite cDNA. These modifications are abundant in tRNA and critical to their function. Here, we describe proof-of-concept experiments where individual tRNA molecules are examined as linear strands using a biological nanopore. This method utilizes an enzymatically ligated synthetic DNA adapter to concentrate tRNA at the lipid bilayer of the nanopore device and efficiently denature individual tRNA molecules, as they are pulled through the α-hemolysin (α-HL) nanopore. Additionally, the DNA adapter provides a loading site for ϕ29 DNA polymerase (ϕ29 DNAP), which acts as a brake on the translocating tRNA. This increases the dwell time of adapted tRNA in the nanopore, allowing us to identify the region of the nanopore signal that is produced by the translocating tRNA itself. Using adapter-modified Escherichia coli tRNAfMet and tRNALys, we show that the nanopore signal during controlled translocation is dependent on the identity of the tRNA. This confirms that adapter-modified tRNA can translocate end-to-end through nanopores and provide the foundation for future work in direct sequencing of individual transfer RNA with a nanopore-based device. PMID:26157798

  7. Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases*♦

    PubMed Central

    Valencia-Sánchez, Marco Igor; Rodríguez-Hernández, Annia; Ferreira, Ruben; Santamaría-Suárez, Hugo Aníbal; Arciniega, Marcelino; Dock-Bregeon, Anne-Catherine; Moras, Dino; Beinsteiner, Brice; Brieba, Luis G.; Grøtli, Morten

    2016-01-01

    Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α2β2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanism of amino acid recognition is also dissimilar. Here, we show that the α-subunit of the α2β2 GlyRS from the bacterium Aquifex aeolicus is able to perform the first step of the aminoacylation reaction, which involves the activation of the amino acid with ATP. The crystal structure of the α-subunit in the complex with an analog of glycyl adenylate at 2.8 Å resolution presents a conformational arrangement that properly positions the cognate amino acid. This work shows that glycine is recognized by a subset of different residues in the two types of GlyRS. A structural and sequence analysis of class II catalytic domains shows that bacterial GlyRS is closely related to alanyl tRNA synthetase, which led us to define a new subclassification of these ancient enzymes and to propose an evolutionary path of α2β2 GlyRS, convergent with α2 GlyRS and divergent from AlaRS, thus providing a possible explanation for the puzzling existence of two proteins sharing the same fold and function but not a common ancestor. PMID:27226617

  8. Molecular mimicry between protein and tRNA.

    PubMed

    Nakamura, Y

    2001-01-01

    Mimicry is a sophisticated development in animals, fish, and plants that allows them to fool others by imitating a shape or color for diverse purposes, such as to prey, evade, lure, pollinate, or threaten. This is not restricted to the macro-world, but extends to the micro-world as molecular mimicry. Recent advances in structural and molecular biology uncovered a set of translation factors that resembles a tRNA shape and, in one case, even mimics a tRNA function for deciphering the genetic code. Nature must have evolved this art of molecular mimicry between protein and ribonucleic acid by using different protein structures until the translation factors sat in the cockpit of a ribosome machine, on behalf of tRNA, and achieved diverse actions. Structural, functional, and evolutionary aspects of molecular mimicry will be discussed.

  9. Genome-wide screen uncovers novel pathways for tRNA processing and nuclear-cytoplasmic dynamics.

    PubMed

    Wu, Jingyan; Bao, Alicia; Chatterjee, Kunal; Wan, Yao; Hopper, Anita K

    2015-12-15

    Transfer ribonucleic acids (tRNAs) are essential for protein synthesis. However, key gene products involved in tRNA biogenesis and subcellular movement remain to be discovered. We conducted the first comprehensive unbiased analysis of the role of nearly an entire proteome in tRNA biology and describe 162 novel and 12 previously known Saccharomyces cerevisiae gene products that function in tRNA processing, turnover, and subcellular movement. tRNA nuclear export is of particular interest because it is essential, but the known tRNA exporters (Los1 [exportin-t] and Msn5 [exportin-5]) are unessential. We report that mutations of CRM1 (Exportin-1), MEX67/MTR2 (TAP/p15), and five nucleoporins cause accumulation of unspliced tRNA, a hallmark of defective tRNA nuclear export. CRM1 mutation genetically interacts with los1Δ and causes altered tRNA nuclear-cytoplasmic distribution. The data implicate roles for the protein and mRNA nuclear export machineries in tRNA nuclear export. Mutations of genes encoding actin cytoskeleton components and mitochondrial outer membrane proteins also cause accumulation of unspliced tRNA, likely due to defective splicing on mitochondria. Additional gene products, such as chromatin modification enzymes, have unanticipated effects on pre-tRNA end processing. Thus, this genome-wide screen uncovered putative novel pathways for tRNA nuclear export and extensive links between tRNA biology and other aspects of cell physiology. © 2015 Wu et al.; Published by Cold Spring Harbor Laboratory Press.

  10. Genome-wide screen uncovers novel pathways for tRNA processing and nuclear–cytoplasmic dynamics

    PubMed Central

    Wu, Jingyan; Bao, Alicia; Chatterjee, Kunal; Wan, Yao; Hopper, Anita K.

    2015-01-01

    Transfer ribonucleic acids (tRNAs) are essential for protein synthesis. However, key gene products involved in tRNA biogenesis and subcellular movement remain to be discovered. We conducted the first comprehensive unbiased analysis of the role of nearly an entire proteome in tRNA biology and describe 162 novel and 12 previously known Saccharomyces cerevisiae gene products that function in tRNA processing, turnover, and subcellular movement. tRNA nuclear export is of particular interest because it is essential, but the known tRNA exporters (Los1 [exportin-t] and Msn5 [exportin-5]) are unessential. We report that mutations of CRM1 (Exportin-1), MEX67/MTR2 (TAP/p15), and five nucleoporins cause accumulation of unspliced tRNA, a hallmark of defective tRNA nuclear export. CRM1 mutation genetically interacts with los1Δ and causes altered tRNA nuclear–cytoplasmic distribution. The data implicate roles for the protein and mRNA nuclear export machineries in tRNA nuclear export. Mutations of genes encoding actin cytoskeleton components and mitochondrial outer membrane proteins also cause accumulation of unspliced tRNA, likely due to defective splicing on mitochondria. Additional gene products, such as chromatin modification enzymes, have unanticipated effects on pre-tRNA end processing. Thus, this genome-wide screen uncovered putative novel pathways for tRNA nuclear export and extensive links between tRNA biology and other aspects of cell physiology. PMID:26680305

  11. Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition.

    PubMed

    McCrate, Nina E; Varner, Mychel E; Kim, Kenneth I; Nagan, Maria C

    2006-01-01

    Accuracy in translation of the genetic code into proteins depends upon correct tRNA-mRNA recognition in the context of the ribosome. In human tRNA(Lys,3)UUU three modified bases are present in the anticodon stem-loop--2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms2t6A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm5s2U34) and pseudouridine (psi) at position 39--two of which, ms2t6A37 and mcm5s2U34, are required to achieve wild-type binding activity of wild-type human tRNA(Lys,3)UUU [C. Yarian, M. Marszalek, E. Sochacka, A. Malkiewicz, R. Guenther, A. Miskiewicz and P. F. Agris (2000) Biochemistry, 39, 13390-13395]. Molecular dynamics simulations of nine tRNA anticodon stem-loops with different combinations of nonstandard bases were performed. The wild-type simulation exhibited a canonical anticodon stair-stepped conformation. The ms2t6 modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms2t6A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to psi39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps.

  12. tRNA nuclear export in saccharomyces cerevisiae: in situ hybridization analysis.

    PubMed

    Sarkar, S; Hopper, A K

    1998-11-01

    To understand the factors specifically affecting tRNA nuclear export, we adapted in situ hybridization procedures to locate endogenous levels of individual tRNA families in wild-type and mutant yeast cells. Our studies of tRNAs encoded by genes lacking introns show that nucleoporin Nup116p affects both poly(A) RNA and tRNA export, whereas Nup159p affects only poly(A) RNA export. Los1p is similar to exportin-t, which facilitates vertebrate tRNA export. A los1 deletion mutation affects tRNA but not poly(A) RNA export. The data support the notion that Los1p and exportin-t are functional homologues. Because LOS1 is nonessential, tRNA export in vertebrate and yeast cells likely involves factors in addition to exportin-t. Mutation of RNA1, which encodes RanGAP, causes nuclear accumulation of tRNAs and poly(A) RNA. Many yeast mutants, including those with the rna1-1 mutation, affect both pre-tRNA splicing and RNA export. Our studies of the location of intron-containing pre-tRNAs in the rna1-1 mutant rule out the possibility that this results from tRNA export occurring before splicing. Our results also argue against inappropriate subnuclear compartmentalization causing defects in pre-tRNA splicing. Rather, the data support "feedback" of nucleus/cytosol exchange to the pre-tRNA splicing machinery.

  13. Distribution of Cytokinin-active Ribonucleosides in Wheat Germ tRNA Species 1

    PubMed Central

    Struxness, Leslie A.; Armstrong, Donald J.; Gillam, Ian; Tener, Gordon M.; Burrows, William J.; Skoog, Folke

    1979-01-01

    The distribution of cytokinin activity in wheat (Triticum aestivum) germ tRNA fractionated by BD-cellulose and RPC-5 chromatography has been examined. As in other organisms, the cytokinin moieties in wheat germ tRNA appear to be restricted to tRNA species that would be expected to respond to codons beginning with U. Only a few of the wheat germ tRNA species in this coding group actually contain cytokinin modifications. Cytokinin activity was associated with isoaccepting tRNASer species and with a minor tRNALeu species from wheat germ. All other wheat germ tRNA species corresponding to codons beginning with U were devoid of cytokinin activity in the tobacco callus bioassay. PMID:16660688

  14. Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint.

    PubMed

    Ghavidel, Ata; Kislinger, Thomas; Pogoutse, Oxana; Sopko, Richelle; Jurisica, Igor; Emili, Andrew

    2007-11-30

    In response to genotoxic stress, cells evoke a plethora of physiological responses collectively aimed at enhancing viability and maintaining the integrity of the genome. Here, we report that unspliced tRNA rapidly accumulates in the nuclei of yeast Saccharomyces cerevisiae after DNA damage. This response requires an intact MEC1- and RAD53-dependent signaling pathway that impedes the nuclear export of intron-containing tRNA via differential relocalization of the karyopherin Los1 to the cytoplasm. The accumulation of unspliced tRNA in the nucleus signals the activation of Gcn4 transcription factor, which, in turn, contributes to cell-cycle arrest in G1 in part by delaying accumulation of the cyclin Cln2. The regulated nucleocytoplasmic tRNA trafficking thus constitutes an integral physiological adaptation to DNA damage. These data further illustrate how signal-mediated crosstalk between distinct functional modules, namely, tRNA nucleocytoplasmic trafficking, protein synthesis, and checkpoint execution, allows for functional coupling of tRNA biogenesis and cell-cycle progression.

  15. Functional expansion of human tRNA synthetases achieved by structural inventions

    PubMed Central

    Guo, Min; Schimmel, Paul; Yang, Xiang-Lei

    2010-01-01

    Known as an essential component of the translational apparatus, the aminoacyl-tRNA synthetase family catalyzes the first step reaction in protein synthesis, that is, to specifically attach each amino acid to its cognate tRNA. While preserving this essential role, tRNA synthetases developed other roles during evolution. Human tRNA synthetases, in particular, have diverse functions in different pathways involving angiogenesis, inflammation and apoptosis. The functional diversity is further illustrated in the association with various diseases through genetic mutations that do not affect aminoacylation or protein synthesis. Here we review the accumulated knowledge on how human tRNA synthetases used structural inventions to achieve functional expansions. PMID:19932696

  16. tRNA Nuclear Export in Saccharomyces cerevisiae: In Situ Hybridization Analysis

    PubMed Central

    Sarkar, Srimonti; Hopper, Anita K.

    1998-01-01

    To understand the factors specifically affecting tRNA nuclear export, we adapted in situ hybridization procedures to locate endogenous levels of individual tRNA families in wild-type and mutant yeast cells. Our studies of tRNAs encoded by genes lacking introns show that nucleoporin Nup116p affects both poly(A) RNA and tRNA export, whereas Nup159p affects only poly(A) RNA export. Los1p is similar to exportin-t, which facilitates vertebrate tRNA export. A los1 deletion mutation affects tRNA but not poly(A) RNA export. The data support the notion that Los1p and exportin-t are functional homologues. Because LOS1 is nonessential, tRNA export in vertebrate and yeast cells likely involves factors in addition to exportin-t. Mutation of RNA1, which encodes RanGAP, causes nuclear accumulation of tRNAs and poly(A) RNA. Many yeast mutants, including those with the rna1-1 mutation, affect both pre-tRNA splicing and RNA export. Our studies of the location of intron-containing pre-tRNAs in the rna1-1 mutant rule out the possibility that this results from tRNA export occurring before splicing. Our results also argue against inappropriate subnuclear compartmentalization causing defects in pre-tRNA splicing. Rather, the data support “feedback” of nucleus/cytosol exchange to the pre-tRNA splicing machinery. PMID:9802895

  17. Snapshots of Dynamics in Synthesizing N6-isopentenyladenosine at tRNA Anticodon†,‡

    PubMed Central

    Chimnaronk, Sarin; Forouhar, Farhad; Sakai, Junichi; Yao, Min; Tron, Cecile M.; Atta, Mohamed; Fontecave, Marc; Hunt, John F.; Tanaka, Isao

    2009-01-01

    Bacterial and eukaryotic transfer RNAs that decode codons starting with uridine have a hydrophobically-hypermodified adenosine at the position 37 (A37) adjacent to the 3′-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of the crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during modification of RNA. A compact evolutionary inserted domain (herein ‘swinging domain’) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A36 and A38 together to squeeze out A37 into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate-binding of MiaA. PMID:19435325

  18. Inorganic phosphate deprivation causes tRNA nuclear accumulation via retrograde transport in Saccharomyces cerevisiae.

    PubMed

    Hurto, Rebecca L; Tong, Amy Hin Yan; Boone, Charles; Hopper, Anita K

    2007-06-01

    Nuclear export of tRNA is an essential eukaryotic function, yet the one known yeast tRNA nuclear exporter, Los1, is nonessential. Moreover recent studies have shown that tRNAs can move retrograde from the cytosol to the nucleus by an undefined process. Therefore, additional gene products involved in tRNA nucleus-cytosol dynamics have yet to be identified. Synthetic genetic array (SGA) analysis was employed to identify proteins involved in Los1-independent tRNA transport and in regulating tRNA nucleus-cytosol distribution. These studies uncovered synthetic interactions between los1Delta and pho88Delta involved in inorganic phopsphate uptake. Further analysis revealed that inorganic phosphate deprivation causes transient, temperature-dependent nuclear accumulation of mature cytoplasmic tRNA within nuclei via a Mtr10- and retrograde-dependent pathway, providing a novel connection between tRNA subcellular dynamics and phosphate availability.

  19. Inorganic Phosphate Deprivation Causes tRNA Nuclear Accumulation via Retrograde Transport in Saccharomyces cerevisiae

    PubMed Central

    Hurto, Rebecca L.; Tong, Amy Hin Yan; Boone, Charles; Hopper, Anita K.

    2007-01-01

    Nuclear export of tRNA is an essential eukaryotic function, yet the one known yeast tRNA nuclear exporter, Los1, is nonessential. Moreover recent studies have shown that tRNAs can move retrograde from the cytosol to the nucleus by an undefined process. Therefore, additional gene products involved in tRNA nucleus–cytosol dynamics have yet to be identified. Synthetic genetic array (SGA) analysis was employed to identify proteins involved in Los1-independent tRNA transport and in regulating tRNA nucleus–cytosol distribution. These studies uncovered synthetic interactions between los1Δ and pho88Δ involved in inorganic phopshate uptake. Further analysis revealed that inorganic phosphate deprivation causes transient, temperature-dependent nuclear accumulation of mature cytoplasmic tRNA within nuclei via a Mtr10- and retrograde-dependent pathway, providing a novel connection between tRNA subcellular dynamics and phosphate availability. PMID:17409072

  20. The Selenocysteine tRNA STAF-Binding Region is Essential for Adequate Selenocysteine tRNA Status, Selenoprotein Expression and Early Age Survival of Mice

    USDA-ARS?s Scientific Manuscript database

    STAF is a transcription activating factor for a number of RNA Pol III-and RNA Pol II-dependent genes including the selenocysteine (Sec) tRNA gene. Here, the role of STAF in regulating expression of Sec tRNA and selenoproteins was examined in an invivo model. Heterozygous inactivation of the Staf gen...

  1. Beyond tRNA cleavage: novel essential function for yeast tRNA splicing endonuclease unrelated to tRNA processing

    PubMed Central

    Dhungel, Nripesh; Hopper, Anita K.

    2012-01-01

    Pre-tRNA splicing is an essential process in all eukaryotes. In yeast and vertebrates, the enzyme catalyzing intron removal from pre-tRNA is a heterotetrameric complex (splicing endonuclease [SEN] complex). Although the SEN complex is conserved, the subcellular location where pre-tRNA splicing occurs is not. In yeast, the SEN complex is located at the cytoplasmic surface of mitochondria, whereas in vertebrates, pre-tRNA splicing is nuclear. We engineered yeast to mimic the vertebrate cell biology and demonstrate that all three steps of pre-tRNA splicing, as well as tRNA nuclear export and aminoacylation, occur efficiently when the SEN complex is nuclear. However, nuclear pre-tRNA splicing fails to complement growth defects of cells with defective mitochondrial-located splicing, suggesting that the yeast SEN complex surprisingly serves a novel and essential function in the cytoplasm that is unrelated to tRNA splicing. The novel function requires all four SEN complex subunits and the catalytic core. A subset of pre-rRNAs accumulates when the SEN complex is restricted to the nucleus, indicating that the SEN complex moonlights in rRNA processing. Thus, findings suggest that selection for the subcellular distribution of the SEN complex may reside not in its canonical, but rather in a novel, activity. PMID:22391451

  2. Role of Nuclear Pools of Aminoacyl-tRNA Synthetases in tRNA Nuclear Export

    PubMed Central

    Azad, Abul K.; Stanford, David R.; Sarkar, Srimonti; Hopper, Anita K.

    2001-01-01

    Reports of nuclear tRNA aminoacylation and its role in tRNA nuclear export (Lund and Dahlberg, 1998; Sarkar et al., 1999; Grosshans et al., 2000a) have led to the prediction that there should be nuclear pools of aminoacyl-tRNA synthetases. We report that in budding yeast there are nuclear pools of tyrosyl-tRNA synthetase, Tys1p. By sequence alignments we predicted a Tys1p nuclear localization sequence and showed it to be sufficient for nuclear location of a passenger protein. Mutations of this nuclear localization sequence in endogenous Tys1p reduce nuclear Tys1p pools, indicating that the motif is also important for nucleus location. The mutations do not significantly affect catalytic activity, but they do cause defects in export of tRNAs to the cytosol. Despite export defects, the cells are viable, indicating that nuclear tRNA aminoacylation is not required for all tRNA nuclear export paths. Because the tRNA nuclear exportin, Los1p, is also unessential, we tested whether tRNA aminoacylation and Los1p operate in alternative tRNA nuclear export paths. No genetic interactions between aminoacyl-tRNA synthetases and Los1p were detected, indicating that tRNA nuclear aminoacylation and Los1p operate in the same export pathway or there are more than two pathways for tRNA nuclear export. PMID:11359929

  3. Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear export.

    PubMed

    Azad, A K; Stanford, D R; Sarkar, S; Hopper, A K

    2001-05-01

    Reports of nuclear tRNA aminoacylation and its role in tRNA nuclear export (Lund and Dahlberg, 1998; Sarkar et al., 1999; Grosshans et al., 20001) have led to the prediction that there should be nuclear pools of aminoacyl-tRNA synthetases. We report that in budding yeast there are nuclear pools of tyrosyl-tRNA synthetase, Tys1p. By sequence alignments we predicted a Tys1p nuclear localization sequence and showed it to be sufficient for nuclear location of a passenger protein. Mutations of this nuclear localization sequence in endogenous Tys1p reduce nuclear Tys1p pools, indicating that the motif is also important for nucleus location. The mutations do not significantly affect catalytic activity, but they do cause defects in export of tRNAs to the cytosol. Despite export defects, the cells are viable, indicating that nuclear tRNA aminoacylation is not required for all tRNA nuclear export paths. Because the tRNA nuclear exportin, Los1p, is also unessential, we tested whether tRNA aminoacylation and Los1p operate in alternative tRNA nuclear export paths. No genetic interactions between aminoacyl-tRNA synthetases and Los1p were detected, indicating that tRNA nuclear aminoacylation and Los1p operate in the same export pathway or there are more than two pathways for tRNA nuclear export.

  4. Nuclear pore proteins are involved in the biogenesis of functional tRNA.

    PubMed

    Simos, G; Tekotte, H; Grosjean, H; Segref, A; Sharma, K; Tollervey, D; Hurt, E C

    1996-05-01

    Los1p and Pus1p, which are involved in tRNA biogenesis, were found in a genetic screen for components interacting with the nuclear pore protein Nsp1p. LOS1, PUS1 and NSP1 interact functionally, since the combination of mutations in the three genes causes synthetic lethality. Pus1p is an intranuclear protein which exhibits a nucleotide-specific and intron-dependent tRNA pseudouridine synthase activity. Los1p was shown previously to be required for efficient pre-tRNA splicing; we report here that Los1p localizes to the nuclear pores and is linked functionally to several components of the tRNA biogenesis machinery including Pus1p and Tfc4p. When the formation of functional tRNA was analyzed by an in vivo assay, the los1(-) pus1(-) double mutant, as well as several thermosensitive nucleoporin mutants including nsp1, nup116, nup133 and nup85, exhibited loss of suppressor tRNA activity even at permissive temperatures. These data suggest that nuclear pore proteins are required for the biogenesis of functional tRNA.

  5. Nuclear pore proteins are involved in the biogenesis of functional tRNA.

    PubMed Central

    Simos, G; Tekotte, H; Grosjean, H; Segref, A; Sharma, K; Tollervey, D; Hurt, E C

    1996-01-01

    Los1p and Pus1p, which are involved in tRNA biogenesis, were found in a genetic screen for components interacting with the nuclear pore protein Nsp1p. LOS1, PUS1 and NSP1 interact functionally, since the combination of mutations in the three genes causes synthetic lethality. Pus1p is an intranuclear protein which exhibits a nucleotide-specific and intron-dependent tRNA pseudouridine synthase activity. Los1p was shown previously to be required for efficient pre-tRNA splicing; we report here that Los1p localizes to the nuclear pores and is linked functionally to several components of the tRNA biogenesis machinery including Pus1p and Tfc4p. When the formation of functional tRNA was analyzed by an in vivo assay, the los1(-) pus1(-) double mutant, as well as several thermosensitive nucleoporin mutants including nsp1, nup116, nup133 and nup85, exhibited loss of suppressor tRNA activity even at permissive temperatures. These data suggest that nuclear pore proteins are required for the biogenesis of functional tRNA. Images PMID:8641292

  6. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

    PubMed Central

    Jühling, Frank; Pütz, Joern; Bernt, Matthias; Donath, Alexander; Middendorf, Martin; Florentz, Catherine; Stadler, Peter F.

    2012-01-01

    Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading ‘pseudogenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders. PMID:22139921

  7. P-body components, Dhh1 and Pat1, are involved in tRNA nuclear-cytoplasmic dynamics

    PubMed Central

    Hurto, Rebecca L.; Hopper, Anita K.

    2011-01-01

    The nuclear-cytoplasmic distribution of tRNA depends on the balance between tRNA nuclear export/re-export and retrograde tRNA nuclear import in Saccharomyces cerevisiae. The distribution of tRNA is sensitive to nutrient availability as cells deprived of various nutrients exhibit tRNA nuclear accumulation. Starvation induces numerous events that result in translational repression and P-body formation. This study investigated the possible coordination of these responses with tRNA nuclear-cytoplasmic distribution. Dhh1 and Pat1 function in parallel to promote translation repression and P-body formation in response to starvation. Loss of both, Dhh1 and Pat1, results in a failure to repress translation and to induce P-body formation in response to glucose starvation. This study reports that nutrient deprived dhh1 pat1 cells also fail to accumulate tRNA within nuclei. Conversely, inhibition of translation initiation and induction of P-body formation by overproduction of Dhh1 or Pat1 cause tRNA nuclear accumulation in nutrient-replete conditions. Also, loss of the mRNA decapping activator, Lsm1, causes tRNA nuclear accumulation. However, the coordination between P-body formation, translation repression, and tRNA distribution is limited to the early part of the P-body formation/translation repression pathway as loss of mRNA decapping or 5′ to 3′ degradation does not influence tRNA nuclear-cytoplasmic dynamics. The data provide the first link between P-body formation/translation initiation and tRNA nuclear-cytoplasmic dynamics. The current model is that Dhh1 and Pat1 function in parallel to promote starvation-induced tRNA nuclear accumulation. PMID:21398402

  8. Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage.

    PubMed

    Brok-Volchanskaya, Vera S; Kadyrov, Farid A; Sivogrivov, Dmitry E; Kolosov, Peter M; Sokolov, Andrey S; Shlyapnikov, Michael G; Kryukov, Valentine M; Granovsky, Igor E

    2008-04-01

    Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3' 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA TpsiC stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages.

  9. Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage

    PubMed Central

    Brok-Volchanskaya, Vera S.; Kadyrov, Farid A.; Sivogrivov, Dmitry E.; Kolosov, Peter M.; Sokolov, Andrey S.; Shlyapnikov, Michael G.; Kryukov, Valentine M.; Granovsky, Igor E.

    2008-01-01

    Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3′ 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA TψC stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages. PMID:18281701

  10. tRNA modification profiles of the fast-proliferating cancer cells

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

    Dong, Chao; Niu, Leilei; Song, Wei

    Despite the recent progress in RNA modification study, a comprehensive modification profile is still lacking for mammalian cells. Using a quantitative HPLC/MS/MS assay, we present here a study where RNA modifications are examined in term of the major RNA species. With paired slow- and fast-proliferating cell lines, distinct RNA modification profiles are first revealed for diverse RNA species. Compared to mRNAs, increased ribose and nucleobase modifications are shown for the highly-structured tRNAs and rRNAs, lending support to their contribution to the formation of high-order structures. This study also reveals a dynamic tRNA modification profile in the fast-proliferating cells. In additionmore » to cultured cells, this unique tRNA profile has been further confirmed with endometrial cancers and their adjacent normal tissues. Taken together, the results indicate that tRNA is a actively regulated RNA species in the fast-proliferating cancer cells, and suggest that they may play a more active role in biological process than expected. -- Highlights: •RNA modifications were first examined in term of the major RNA species. •A dynamic tRNA modifications was characterized for the fast-proliferating cells. •The unique tRNA profile was confirmed with endometrial cancers and their adjacent normal tissues. •tRNA was predicted as an actively regulated RNA species in the fast-proliferating cancer cells.« less

  11. Review: transport of tRNA out of the nucleus-direct channeling to the ribosome?

    PubMed

    Grosshans, H; Simos, G; Hurt, E

    2000-04-01

    Although tRNA was the first substrate whose export from the nuclei of eukaryotic cells had been shown to be carrier-mediated and active, it has only been in the last 2 years that the first mechanistic details of this nucleocytoplasmic transport pathway have begun to emerge. A member of the importin/karyopherin beta superfamily, Los1p in yeast and Xpo-t in vertebrates, has been shown to export tRNA in cooperation with the small GTPase Ran (Gsp1p) from the nucleus into the cytoplasm, where tRNA becomes available for translation. However, Los1p is not essential for viability in yeast cells, suggesting that alternative tRNA export pathways exist. Recent results show that aminoacylation and a translation factor are also required for efficient nuclear tRNA export. Thus, protein translation and nuclear export of tRNA appear to be coupled processes. Copyright 2000 Academic Press.

  12. Preferences of AAA/AAG codon recognition by modified nucleosides, τm5s2U34 and t6A37 present in tRNALys.

    PubMed

    Sonawane, Kailas D; Kamble, Asmita S; Fandilolu, Prayagraj M

    2017-12-27

    Deficiency of 5-taurinomethyl-2-thiouridine, τm 5 s 2 U at the 34th 'wobble' position in tRNA Lys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNA Lys , recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level. Hence, multiple MD simulations of various molecular models of anticodon stem loop (ASL) of mt tRNA Lys in presence and absence of τm 5 s 2 U 34 and N 6 -threonylcarbamoyl adenosine (t 6 A 37 ) along with AAA and AAG codons have been accomplished. Additional four MD simulations of multiple ASL mt tRNA Lys models in the context of ribosomal A-site residues have also been performed to investigate the role of A-site in recognition of AAA/AAG codons. MD simulation results show that, ASL models in presence of τm 5 s 2 U 34 and t 6 A 37 with codons AAA/AAG are more stable than the ASL lacking these modified bases. MD trajectories suggest that τm 5 s 2 U recognizes the codons initially by 'wobble' hydrogen bonding interactions, and then tRNA Lys might leave the explicit codon by a novel 'single' hydrogen bonding interaction in order to run the protein biosynthesis process smoothly. We propose this model as the 'Foot-Step Model' for codon recognition, in which the single hydrogen bond plays a crucial role. MD simulation results suggest that, tRNA Lys with τm 5 s 2 U and t 6 A recognizes AAA codon more preferably than AAG. Thus, these results reveal the consequences of τm 5 s 2 U and t 6 A in recognition of AAA/AAG codons in mitochondrial disease, MERRF.

  13. Processing of Archaebacterial Intron-Containing tRNA Gene Transcripts

    DTIC Science & Technology

    1988-07-27

    number) The overall goal of this project is to develop an understanding of tRNA gene structure and transcript processing in the halophilic Archaebacteria...containing precursor tRNAs in the halophilic Archaebecteria suggest that tRNATr p may be the only interrupted tR?4A gene in these organisms...1 August 1986 RESEARCH OBJECTIVE: To determine the mechanism of tRNA intron processing in the halophilic archaebacteria; characterize the enzyme

  14. Quality Control Pathways for Nucleus-Encoded Eukaryotic tRNA Biosynthesis and Subcellular Trafficking

    PubMed Central

    Huang, Hsiao-Yun

    2015-01-01

    tRNAs perform an essential role in translating the genetic code. They are long-lived RNAs that are generated via numerous posttranscriptional steps. Eukaryotic cells have evolved numerous layers of quality control mechanisms to ensure that the tRNAs are appropriately structured, processed, and modified. We describe the known tRNA quality control processes that check tRNAs and correct or destroy aberrant tRNAs. These mechanisms employ two types of exonucleases, CCA end addition, tRNA nuclear aminoacylation, and tRNA subcellular traffic. We arrange these processes in order of the steps that occur from generation of precursor tRNAs by RNA polymerase (Pol) III transcription to end maturation and modification in the nucleus to splicing and additional modifications in the cytoplasm. Finally, we discuss the tRNA retrograde pathway, which allows tRNA reimport into the nucleus for degradation or repair. PMID:25848089

  15. Mod5 protein binds to tRNA gene complexes and affects local transcriptional silencing

    PubMed Central

    Pratt-Hyatt, Matthew; Pai, Dave A.; Haeusler, Rebecca A.; Wozniak, Glenn G.; Good, Paul D.; Miller, Erin L.; McLeod, Ian X.; Yates, John R.; Hopper, Anita K.; Engelke, David R.

    2013-01-01

    The tRNA gene-mediated (tgm) silencing of RNA polymerase II promoters is dependent on subnuclear clustering of the tRNA genes, but genetic analysis shows that the silencing requires additional mechanisms. We have identified proteins that bind tRNA gene transcription complexes and are required for tgm silencing but not required for gene clustering. One of the proteins, Mod5, is a tRNA modifying enzyme that adds an N6-isopentenyl adenosine modification at position 37 on a small number of tRNAs in the cytoplasm, although a subpopulation of Mod5 is also found in the nucleus. Recent publications have also shown that Mod5 has tumor suppressor characteristics in humans as well as confers drug resistance through prion-like misfolding in yeast. Here, we show that a subpopulation of Mod5 associates with tRNA gene complexes in the nucleolus. This association occurs and is required for tgm silencing regardless of whether the pre-tRNA transcripts are substrates for Mod5 modification. In addition, Mod5 is bound to nuclear pre-tRNA transcripts, although they are not substrates for the A37 modification. Lastly, we show that truncation of the tRNA transcript to remove the normal tRNA structure also alleviates silencing, suggesting that synthesis of intact pre-tRNAs is required for the silencing mechanism. These results are discussed in light of recent results showing that silencing near tRNA genes also requires chromatin modification. PMID:23898186

  16. Effect of PEG and mPEG-anthracene on tRNA aggregation and particle formation.

    PubMed

    Froehlich, E; Mandeville, J S; Arnold, D; Kreplak, L; Tajmir-Riahi, H A

    2012-01-09

    Poly(ethylene glycol) (PEG) and its derivatives are synthetic polymers with major applications in gene and drug delivery systems. Synthetic polymers are also used to transport miRNA and siRNA in vitro. We studied the interaction of tRNA with several PEGs of different compositions, such as PEG 3350, PEG 6000, and mPEG-anthracene under physiological conditions. FTIR, UV-visible, CD, and fluorescence spectroscopic methods as well as atomic force microscopy (AFM) were used to analyze the PEG binding mode, the binding constant, and the effects of polymer complexation on tRNA stability, aggregation, and particle formation. Structural analysis showed that PEG-tRNA interaction occurs via RNA bases and the backbone phosphate group with both hydrophilic and hydrophobic contacts. The overall binding constants of K(PEG 3350-tRNA)= 1.9 (±0.5) × 10(4) M(-1), K(PEG 6000-tRNA) = 8.9 (±1) × 10(4) M(-1), and K(mPEG-anthracene)= 1.2 (±0.40) × 10(3) M(-1) show stronger polymer-RNA complexation by PEG 6000 and by PEG 3350 than the mPEG-anthracene. AFM imaging showed that PEG complexes contain on average one tRNA with PEG 3350, five tRNA with PEG 6000, and ten tRNA molecules with mPEG-anthracene. tRNA aggregation and particle formation occurred at high polymer concentrations, whereas it remains in A-family structure.

  17. The nuclear tRNA aminoacylation-dependent pathway may be the principal route used to export tRNA from the nucleus in Saccharomyces cerevisiae.

    PubMed

    Steiner-Mosonyi, Marta; Mangroo, Dev

    2004-03-15

    Nuclear tRNA export in Saccharomyces cerevisiae has been proposed to involve three pathways, designated Los1p-dependent, Los1p-independent nuclear aminoacylation-dependent, and Los1p- and nuclear aminoacylation-independent. Here, a comprehensive biochemical analysis was performed to identify tRNAs exported by the aminoacylation-dependent and -independent pathways of S. cerevisiae. Interestingly, the major tRNA species of at least 19 families were found in the aminoacylated form in the nucleus. tRNAs known to be exported by the export receptor Los1p were also aminoacylated in the nucleus of both wild-type and mutant Los1p strains. FISH (fluorescence in situ hybridization) analyses showed that tRNA(Tyr) co-localizes with the U18 small nucleolar RNA in the nucleolus of a tyrosyl-tRNA synthetase mutant strain defective in nuclear tRNA(Tyr) export because of a block in nuclear tRNA(Tyr) aminoacylation. tRNA(Tyr) was also found in the nucleolus of a utp8 mutant strain defective in nuclear tRNA export but not nuclear tRNA aminoacylation. These results strongly suggest that the nuclear aminoacylation-dependent pathway is principally responsible for tRNA export in S. cerevisiae and that Los1p is an export receptor of this pathway. It is also likely that in mammalian cells tRNAs are mainly exported from the nucleus by the nuclear aminoacylation-dependent pathway. In addition, the data are consistent with the idea that nuclear aminoacylation is used as a quality control mechanism for ensuring nuclear export of only mature and functional tRNAs, and that this quality assurance step occurs in the nucleolus.

  18. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection.

    PubMed

    Johansson, Magnus; Zhang, Jingji; Ehrenberg, Måns

    2012-01-03

    Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg(2+) concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon-anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell.

  19. Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes

    PubMed Central

    Adir, Idan; Dahan, Orna; Broday, Limor; Pilpel, Yitzhak; Rechavi, Oded

    2016-01-01

    Codon usage bias affects protein translation because tRNAs that recognize synonymous codons differ in their abundance. Although the current dogma states that tRNA expression is exclusively regulated by intrinsic control elements (A- and B-box sequences), we revealed, using a reporter that monitors the levels of individual tRNA genes in Caenorhabditis elegans, that eight tryptophan tRNA genes, 100% identical in sequence, are expressed in different tissues and change their expression dynamically. Furthermore, the expression levels of the sup-7 tRNA gene at day 6 were found to predict the animal’s lifespan. We discovered that the expression of tRNAs that reside within introns of protein-coding genes is affected by the host gene’s promoter. Pairing between specific Pol II genes and the tRNAs that are contained in their introns is most likely adaptive, since a genome-wide analysis revealed that the presence of specific intronic tRNAs within specific orthologous genes is conserved across Caenorhabditis species. PMID:27560950

  20. Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.

    PubMed

    Fischer, Niels; Konevega, Andrey L; Wintermeyer, Wolfgang; Rodnina, Marina V; Stark, Holger

    2010-07-15

    The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.

  1. tRNA and Its Activation Targets as Biomarkers and Regulators of Breast Cancer

    DTIC Science & Technology

    2013-09-01

    linked tRNA misregulation to cancer. We have previously reported that tRNA levels are significantly elevated in breast cancer and multiple myeloma ...significantly elevated in breast cancer and multiple myeloma cells. To further investigate the cellular and physiological effects of tRNA overexpression, we...tRNA levels are elevated in breast cancer and multiple myeloma cell lines (Pavon-Eternod et al. 2009; Zhou et al. 2009). Though abnormal RNA polymerase

  2. tRNA thiolation links translation to stress responses in Saccharomyces cerevisiae.

    PubMed

    Damon, Jadyn R; Pincus, David; Ploegh, Hidde L

    2015-01-15

    Although tRNA modifications have been well catalogued, the precise functions of many modifications and their roles in mediating gene expression are still being elucidated. Whereas tRNA modifications were long assumed to be constitutive, it is now apparent that the modification status of tRNAs changes in response to different environmental conditions. The URM1 pathway is required for thiolation of the cytoplasmic tRNAs tGlu(UUC), tGln(UUG), and tLys(UUU) in Saccharomyces cerevisiae. We demonstrate that URM1 pathway mutants have impaired translation, which results in increased basal activation of the Hsf1-mediated heat shock response; we also find that tRNA thiolation levels in wild-type cells decrease when cells are grown at elevated temperature. We show that defects in tRNA thiolation can be conditionally advantageous, conferring resistance to endoplasmic reticulum stress. URM1 pathway proteins are unstable and hence are more sensitive to changes in the translational capacity of cells, which is decreased in cells experiencing stresses. We propose a model in which a stress-induced decrease in translation results in decreased levels of URM1 pathway components, which results in decreased tRNA thiolation levels, which further serves to decrease translation. This mechanism ensures that tRNA thiolation and translation are tightly coupled and coregulated according to need. © 2015 Damon et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  3. Incorporation of excess wild-type and mutant tRNA(3Lys) into human immunodeficiency virus type 1.

    PubMed Central

    Huang, Y; Mak, J; Cao, Q; Li, Z; Wainberg, M A; Kleiman, L

    1994-01-01

    Human immunodeficiency virus (HIV) particles produced in COS-7 cells transfected with HIV type 1 (HIV-1) proviral DNA contain 8 molecules of tRNA(3Lys) per 2 molecules of genomic RNA and 12 molecules of tRNA1,2Lys per 2 molecules of genomic RNA. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a human tRNA3Lys gene, there is a large increase in the amount of cytoplasmic tRNA3Lys per microgram of total cellular RNA, and the tRNA3Lys content in the virus increases from 8 to 17 molecules per 2 molecules of genomic RNA. However, the total number of tRNALys molecules per 2 molecules of genomic RNA remains constant at 20; i.e., the viral tRNA1,2Lys content decreases from 12 to 3 molecules per 2 molecules of genomic RNA. All detectable tRNA3Lys is aminoacylated in the cytoplasm of infected cells and deacylated in the virus. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a mutant amber suppressor tRNA3Lys gene (in which the anticodon is changed from TTT to CTA), there is also a large increase in the relative concentration of cytoplasmic tRNA3Lys, and the tRNA3Lys content in the virus increases from 8 to 15 molecules per 2 molecules of genomic RNA, with a decrease in viral tRNA1,2Lys from 12 to 5 molecules per 2 molecules of genomic RNA. Thus, the total number of molecules of tRNALys in the virion remains at 20. The alteration of the anticodon has little effect on the viral packaging of this mutant tRNA in spite of the fact that it no longer contains the modified base mcm 5s2U at position 34, and its ability to be aminoacylated is significantly impaired compared with that of wild-type tRNA3Lys. Viral particles which have incorporated either excess wild-type tRNA3Lys or mutant suppressor tRNA3Lys show no differences in viral infectivity compared with wild-type HIV-1. Images PMID:7966556

  4. Evidence that tRNA modifying enzymes are important in vivo targets for 5-fluorouracil in yeast

    PubMed Central

    Gustavsson, Marie; Ronne, Hans

    2008-01-01

    We have screened a collection of haploid yeast knockout strains for increased sensitivity to 5-fluorouracil (5-FU). A total of 138 5-FU sensitive strains were found. Mutants affecting rRNA and tRNA maturation were particularly sensitive to 5-FU, with the tRNA methylation mutant trm10 being the most sensitive mutant. This is intriguing since trm10, like many other tRNA modification mutants, lacks a phenotype under normal conditions. However, double mutants for nonessential tRNA modification enzymes are frequently temperature sensitive, due to destabilization of hypomodified tRNAs. We therefore tested if the sensitivity of our mutants to 5-FU is affected by the temperature. We found that the cytotoxic effect of 5-FU is strongly enhanced at 38°C for tRNA modification mutants. Furthermore, tRNA modification mutants show similar synthetic interactions for temperature sensitivity and sensitivity to 5-FU. A model is proposed for how 5-FU kills these mutants by reducing the number of tRNA modifications, thus destabilizing tRNA. Finally, we found that also wild-type cells are temperature sensitive at higher concentrations of 5-FU. This suggests that tRNA destabilization contributes to 5-FU cytotoxicity in wild-type cells and provides a possible explanation why hyperthermia can enhance the effect of 5-FU in cancer therapy. PMID:18314501

  5. Strategies for investigating nuclear-cytoplasmic tRNA dynamics in yeast and mammalian cells.

    PubMed

    Pierce, Jacqueline B; Chafe, Shawn C; Eswara, Manoja B K; van der Merwe, George; Mangroo, Dev

    2014-01-01

    Nuclear-cytoplasmic tRNA transport involves multiple pathways that are segregated by the involvement of distinct proteins. The tRNA export process begins in the nucleolus, where the functionality of newly produced tRNAs are tested by aminoacylation, and ends with the delivery of the exported aminoacyl tRNAs to the eukaryotic elongation factor eEF-1A for utilization in protein synthesis in the cytoplasm. Recent studies have identified a number of proteins that participate in nuclear tRNA export in both yeast and mammals. However, genetic and biochemical evidence suggest that additional components, which have yet to be identified, also participate in nuclear-cytoplasmic tRNA trafficking. Here we review key strategies that have led to the identification and characterization of proteins that are involved in the nuclear tRNA export process in yeasts and mammals. The approaches described will greatly facilitate the identification and delineation of the roles of new proteins involved in nuclear export of tRNAs to the cytoplasm. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Regulated capture by exosomes of mRNAs for cytoplasmic tRNA synthetases.

    PubMed

    Wang, Feng; Xu, Zhiwen; Zhou, Jie; Lo, Wing-Sze; Lau, Ching-Fun; Nangle, Leslie A; Yang, Xiang-Lei; Zhang, Mingjie; Schimmel, Paul

    2013-10-11

    Although tRNA synthetases are enzymes that catalyze the first step of translation in the cytoplasm, surprising functions unrelated to translation have been reported. These studies, and the demonstration of novel activities of splice variants, suggest a far broader reach of tRNA synthetases into cell biology than previously recognized. Here we show that mRNAs for most tRNA synthetases can be detected in exosomes. Also detected in exosomes was an mRNA encoding a unique splice variant that others had associated with prostate cancer. The exosomal mRNAs encoding the native synthetase and its cancer-associated splice variant could be translated in vitro and in mammalian cells into stable proteins. Other results showed that selection by exosomes of the splice variant mRNA could be regulated by an external stimulus. Thus, a broad and diverse regulated pool of tRNA synthetase-derived mRNAs is packaged for genetic exchange.

  7. A genetically encoded fluorescent tRNA is active in live-cell protein synthesis

    PubMed Central

    Masuda, Isao; Igarashi, Takao; Sakaguchi, Reiko; Nitharwal, Ram G.; Takase, Ryuichi; Han, Kyu Young; Leslie, Benjamin J.; Liu, Cuiping; Gamper, Howard; Ha, Taekjip; Sanyal, Suparna

    2017-01-01

    Abstract Transfer RNAs (tRNAs) perform essential tasks for all living cells. They are major components of the ribosomal machinery for protein synthesis and they also serve in non-ribosomal pathways for regulation and signaling metabolism. We describe the development of a genetically encoded fluorescent tRNA fusion with the potential for imaging in live Escherichia coli cells. This tRNA fusion carries a Spinach aptamer that becomes fluorescent upon binding of a cell-permeable and non-toxic fluorophore. We show that, despite having a structural framework significantly larger than any natural tRNA species, this fusion is a viable probe for monitoring tRNA stability in a cellular quality control mechanism that degrades structurally damaged tRNA. Importantly, this fusion is active in E. coli live-cell protein synthesis allowing peptidyl transfer at a rate sufficient to support cell growth, indicating that it is accommodated by translating ribosomes. Imaging analysis shows that this fusion and ribosomes are both excluded from the nucleoid, indicating that the fusion and ribosomes are in the cytosol together possibly engaged in protein synthesis. This fusion methodology has the potential for developing new tools for live-cell imaging of tRNA with the unique advantage of both stoichiometric labeling and broader application to all cells amenable to genetic engineering. PMID:27956502

  8. The origin and evolution of tRNA inferred from phylogenetic analysis of structure.

    PubMed

    Sun, Feng-Jie; Caetano-Anollés, Gustavo

    2008-01-01

    The evolutionary history of the two structural and functional domains of tRNA is controversial but harbors the secrets of early translation and the genetic code. To explore the origin and evolution of tRNA, we reconstructed phylogenetic trees directly from molecular structure. Forty-two structural characters describing the geometry of 571 tRNAs and three statistical parameters describing thermodynamic and mechanical features of molecules quantitatively were used to derive phylogenetic trees of molecules and molecular substructures. Trees of molecules failed to group tRNA according to amino acid specificity and did not reveal the tripartite nature of life, probably due to loss of phylogenetic signal or because tRNA diversification predated organismal diversification. Trees of substructures derived from both structural and statistical characters support the origin of tRNA in the acceptor arm and the hypothesis that the top half domain composed of acceptor and pseudouridine (TPsiC) arms is more ancient than the bottom half domain composed of dihydrouridine (DHU) and anticodon arms. This constitutes the cornerstone of the genomic tag hypothesis that postulates tRNAs were ancient telomeres in the RNA world. The trees of substructures suggest a model for the evolution of the major functional and structural components of tRNA. In this model, short RNA hairpins with stems homologous to the acceptor arm of present day tRNAs were extended with regions homologous to TPsiC and anticodon arms. The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures.

  9. Precursor-product discrimination by La protein during tRNA metabolism

    PubMed Central

    Bayfield, Mark A.; Maraia, Richard J.

    2009-01-01

    SUMMARY La proteins bind pre-tRNAs at their UUU-3'OH ends, facilitating their maturation. While the mechanism by which La binds pre-tRNA 3' trailers is known, the function of the RNA-binding β-sheet surface of RRM1 is unknown. How La dissociates from UUU-3'OH-containing trailers after 3' processing is also unknown. La preferentially binds pre-tRNAs over processed tRNAs or 3' trailer products through coupled use of two sites: one on the La motif and another on the RRM1 β surface that binds elsewhere on tRNA. Two sites provide stable pre-tRNA binding while processed tRNA and 3' trailer are released from their single sites relatively fast. RRM1 loop-3 mutations decrease affinity for pre-tRNA and tRNA but not UUU-3'OH trailer, and impair tRNA maturation in vivo. We propose that RRM1 functions in activities that are more complex than UUU-3'OH binding. Accordingly, the RRM1 mutations also impair a RNA chaperone activity of La. The results suggest how La distinguishes precursor from product RNAs, allowing it to recycle onto a new pre-tRNA. PMID:19287396

  10. Metazoan tRNA introns generate stable circular RNAs in vivo

    PubMed Central

    Lu, Zhipeng; Filonov, Grigory S.; Noto, John J.; Schmidt, Casey A.; Hatkevich, Talia L.; Wen, Ying; Jaffrey, Samie R.; Matera, A. Gregory

    2015-01-01

    We report the discovery of a class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric)RNAs, are conserved features of animal transcriptomes. Biogenesis of tricRNAs requires anciently conserved tRNA sequence motifs and processing enzymes, and their expression is regulated in an age-dependent and tissue-specific manner. Furthermore, we exploited this biogenesis pathway to develop an in vivo expression system for generating “designer” circular RNAs in human cells. Reporter constructs expressing RNA aptamers such as Spinach and Broccoli can be used to follow the transcription and subcellular localization of tricRNAs in living cells. Owing to the superior stability of circular vs. linear RNA isoforms, this expression system has a wide range of potential applications, from basic research to pharmaceutical science. PMID:26194134

  11. Nucleotide composition analysis of tRNA from leukemia patient cell samples and human cell lines.

    PubMed Central

    Agris, P F

    1975-01-01

    A technique developed for analysis of less than microgram quantities of tRNA has been applied to the study of human leukemia. Leucocytes from peripheal blood and bone marrow samples of six, untreated leukemia patients and cells of five different established human cell lines were maintained for 18 hours in media containing (32P)-phosphate. Incorporation of radioactive phosphate into the cells from the patient samples was slightly less than that of the cell lines. Likewise, incorporation of (32P)-phosphate into the tRNA of the patient samples (approximately 5 x 106 DPM/mug tRNA) was also less then that incorporated into the tRNA of the cell lines. The major and minor nucleotide compositions of the unfractionated tRNA preparations from each patient sample and each cell line were determined and compared. Similarities and differences in the major and minor nucleotide compositions of the tRNA preparations are discussed with reference to types of leukemia and the importance of patient sample analysis versus analysis of cultured human cells. PMID:1057159

  12. Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation.

    PubMed

    Huang, Ying; Bayfield, Mark A; Intine, Robert V; Maraia, Richard J

    2006-07-01

    By sequence-specific binding to 3' UUU-OH, the La protein shields precursor (pre)-RNAs from 3' end digestion and is required to protect defective pre-transfer RNAs from decay. Although La is comprised of a La motif and an RNA-recognition motif (RRM), a recent structure indicates that the RRM beta-sheet surface is not involved in UUU-OH recognition, raising questions as to its function. Progressively defective suppressor tRNAs in Schizosaccharomyces pombe reveal differential sensitivities to La and Rrp6p, a 3' exonuclease component of pre-tRNA decay. 3' end protection is compromised by mutations to the La motif but not the RRM surface. The most defective pre-tRNAs require a second activity of La, in addition to 3' protection, that requires an intact RRM surface. The two activities of La in tRNA maturation map to its two conserved RNA-binding surfaces and suggest a modular model that has implications for its other ligands.

  13. N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network.

    PubMed

    Tomikawa, Chie; Yokogawa, Takashi; Kanai, Tamotsu; Hori, Hiroyuki

    2010-01-01

    N(7)-methylguanine at position 46 (m(7)G46) in tRNA is produced by tRNA (m(7)G46) methyltransferase (TrmB). To clarify the role of this modification, we made a trmB gene disruptant (DeltatrmB) of Thermus thermophilus, an extreme thermophilic eubacterium. The absence of TrmB activity in cell extract from the DeltatrmB strain and the lack of the m(7)G46 modification in tRNA(Phe) were confirmed by enzyme assay, nucleoside analysis and RNA sequencing. When the DeltatrmB strain was cultured at high temperatures, several modified nucleotides in tRNA were hypo-modified in addition to the lack of the m(7)G46 modification. Assays with tRNA modification enzymes revealed hypo-modifications of Gm18 and m(1)G37, suggesting that the m(7)G46 positively affects their formations. Although the lack of the m(7)G46 modification and the hypo-modifications do not affect the Phe charging activity of tRNA(Phe), they cause a decrease in melting temperature of class I tRNA and degradation of tRNA(Phe) and tRNA(Ile). (35)S-Met incorporation into proteins revealed that protein synthesis in DeltatrmB cells is depressed above 70 degrees C. At 80 degrees C, the DeltatrmB strain exhibits a severe growth defect. Thus, the m(7)G46 modification is required for cell viability at high temperatures via a tRNA modification network, in which the m(7)G46 modification supports introduction of other modifications.

  14. Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae.

    PubMed

    Kramer, Emily B; Hopper, Anita K

    2013-12-24

    In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional--from the nucleus to the cytoplasm. It is now known that mature tRNAs also move in a retrograde direction from the cytoplasm to the nucleus via retrograde tRNA nuclear import, a process that is conserved from yeast to vertebrates. The biological significance of this tRNA nuclear import is not entirely clear. We hypothesized that retrograde tRNA nuclear import might function in proofreading tRNAs to ensure that only proper tRNAs reside in the cytoplasm and interact with the translational machinery. Here we identify two major types of aberrant tRNAs in yeast: a 5', 3' end-extended, spliced tRNA and hypomodified tRNAs. We show that both types of aberrant tRNAs accumulate in mutant cells that are defective in tRNA nuclear traffic, suggesting that they are normally imported into the nucleus and are repaired or degraded. The retrograde pathway functions in parallel with the cytoplasmic rapid tRNA decay pathway previously demonstrated to monitor tRNA quality, and cells are not viable if they lack both pathways. Our data support the hypothesis that the retrograde process provides a newly discovered level of tRNA quality control as a pathway that monitors both end processing of pre-tRNAs and the modification state of mature tRNAs.

  15. Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae

    PubMed Central

    Kramer, Emily B.; Hopper, Anita K.

    2013-01-01

    In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional—from the nucleus to the cytoplasm. It is now known that mature tRNAs also move in a retrograde direction from the cytoplasm to the nucleus via retrograde tRNA nuclear import, a process that is conserved from yeast to vertebrates. The biological significance of this tRNA nuclear import is not entirely clear. We hypothesized that retrograde tRNA nuclear import might function in proofreading tRNAs to ensure that only proper tRNAs reside in the cytoplasm and interact with the translational machinery. Here we identify two major types of aberrant tRNAs in yeast: a 5′, 3′ end-extended, spliced tRNA and hypomodified tRNAs. We show that both types of aberrant tRNAs accumulate in mutant cells that are defective in tRNA nuclear traffic, suggesting that they are normally imported into the nucleus and are repaired or degraded. The retrograde pathway functions in parallel with the cytoplasmic rapid tRNA decay pathway previously demonstrated to monitor tRNA quality, and cells are not viable if they lack both pathways. Our data support the hypothesis that the retrograde process provides a newly discovered level of tRNA quality control as a pathway that monitors both end processing of pre-tRNAs and the modification state of mature tRNAs. PMID:24297920

  16. Mitochondrial tRNA cleavage by tRNA-targeting ribonuclease causes mitochondrial dysfunction observed in mitochondrial disease

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

    Ogawa, Tetsuhiro, E-mail: atetsu@mail.ecc.u-tokyo.ac.jp; Shimizu, Ayano; Takahashi, Kazutoshi

    2014-08-15

    Highlights: • MTS-tagged ribonuclease was translocated successfully to the mitochondrial matrix. • MTS-tagged ribonuclease cleaved mt tRNA and reduced COX activity. • Easy and reproducible method of inducing mt tRNA dysfunction. - Abstract: Mitochondrial DNA (mtDNA) is a genome possessed by mitochondria. Since reactive oxygen species (ROS) are generated during aerobic respiration in mitochondria, mtDNA is commonly exposed to the risk of DNA damage. Mitochondrial disease is caused by mitochondrial dysfunction, and mutations or deletions on mitochondrial tRNA (mt tRNA) genes are often observed in mtDNA of patients with the disease. Hence, the correlation between mt tRNA activity and mitochondrialmore » dysfunction has been assessed. Then, cybrid cells, which are constructed by the fusion of an enucleated cell harboring altered mtDNA with a ρ{sup 0} cell, have long been used for the analysis due to difficulty in mtDNA manipulation. Here, we propose a new method that involves mt tRNA cleavage by a bacterial tRNA-specific ribonuclease. The ribonuclease tagged with a mitochondrial-targeting sequence (MTS) was successfully translocated to the mitochondrial matrix. Additionally, mt tRNA cleavage, which resulted in the decrease of cytochrome c oxidase (COX) activity, was observed.« less

  17. Maf1 Protein, Repressor of RNA Polymerase III, Indirectly Affects tRNA Processing*

    PubMed Central

    Karkusiewicz, Iwona; Turowski, Tomasz W.; Graczyk, Damian; Towpik, Joanna; Dhungel, Nripesh; Hopper, Anita K.; Boguta, Magdalena

    2011-01-01

    Maf1 is negative regulator of RNA polymerase III in yeast. We observed high levels of both primary transcript and end-matured, intron-containing pre-tRNAs in the maf1Δ strain. This pre-tRNA accumulation could be overcome by transcription inhibition, arguing against a direct role of Maf1 in tRNA maturation and suggesting saturation of processing machinery by the increased amounts of primary transcripts. Saturation of the tRNA exportin, Los1, is one reason why end-matured intron-containing pre-tRNAs accumulate in maf1Δ cells. However, it is likely possible that other components of the processing pathway are also limiting when tRNA transcription is increased. According to our model, Maf1-mediated transcription control and nuclear export by Los1 are two major stages of tRNA biosynthesis that are regulated by environmental conditions in a coordinated manner. PMID:21940626

  18. Maf1 protein, repressor of RNA polymerase III, indirectly affects tRNA processing.

    PubMed

    Karkusiewicz, Iwona; Turowski, Tomasz W; Graczyk, Damian; Towpik, Joanna; Dhungel, Nripesh; Hopper, Anita K; Boguta, Magdalena

    2011-11-11

    Maf1 is negative regulator of RNA polymerase III in yeast. We observed high levels of both primary transcript and end-matured, intron-containing pre-tRNAs in the maf1Δ strain. This pre-tRNA accumulation could be overcome by transcription inhibition, arguing against a direct role of Maf1 in tRNA maturation and suggesting saturation of processing machinery by the increased amounts of primary transcripts. Saturation of the tRNA exportin, Los1, is one reason why end-matured intron-containing pre-tRNAs accumulate in maf1Δ cells. However, it is likely possible that other components of the processing pathway are also limiting when tRNA transcription is increased. According to our model, Maf1-mediated transcription control and nuclear export by Los1 are two major stages of tRNA biosynthesis that are regulated by environmental conditions in a coordinated manner.

  19. tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast.

    PubMed

    Klassen, Roland; Ciftci, Akif; Funk, Johanna; Bruch, Alexander; Butter, Falk; Schaffrath, Raffael

    2016-12-15

    Using budding yeast, we investigated a negative interaction network among genes for tRNA modifications previously implicated in anticodon-codon interaction: 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm 5 s 2 U34: ELP3, URM1), pseudouridine (Ψ38/39: DEG1) and cyclic N6-threonyl-carbamoyl-adenosine (ct 6 A37: TCD1). In line with functional cross talk between these modifications, we find that combined removal of either ct 6 A37 or Ψ38/39 and mcm 5 U34 or s 2 U34 results in morphologically altered cells with synthetic growth defects. Phenotypic suppression by tRNA overexpression suggests that these defects are caused by malfunction of tRNA Lys UUU or tRNA Gln UUG , respectively. Indeed, mRNA translation and synthesis of the Gln-rich prion Rnq1 are severely impaired in the absence of Ψ38/39 and mcm 5 U34 or s 2 U34, and this defect can be rescued by overexpression of tRNA Gln UUG Surprisingly, we find that combined modification defects in the anticodon loops of different tRNAs induce similar cell polarity- and nuclear segregation defects that are accompanied by increased aggregation of cellular proteins. Since conditional expression of an artificial aggregation-prone protein triggered similar cytological aberrancies, protein aggregation is likely responsible for loss of morphogenesis and cytokinesis control in mutants with inappropriate tRNA anticodon loop modifications. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. The fractionation of t-RNA on N,N′-bis(3-aminopropyl)-piperazine substituted-Sepharose

    PubMed Central

    Leberman, Reuben; Giovanelli, Ruth; Acosta, Zenobio

    1974-01-01

    An anion exchange agarose has been prepared by modifying sepharose 6B with N,N′-bis (-3-aminopropyl) piperazine. This material (BAPP-Sepharose) has been used for the fractionation of t-RNA from E.coli by column chromatography. The results obtained with gram quantities of crude t-RNA at pH 4.6 and pH 8.0 as measured by the elution patterns of alanyl, arginyl, aspartyl, leucyl, lysyl, methionyl, phenylalanyl, prolyl, seryl, tyrosyl, and valyl t-RNA are described. PMID:10793731

  1. Metazoan tRNA introns generate stable circular RNAs in vivo.

    PubMed

    Lu, Zhipeng; Filonov, Grigory S; Noto, John J; Schmidt, Casey A; Hatkevich, Talia L; Wen, Ying; Jaffrey, Samie R; Matera, A Gregory

    2015-09-01

    We report the discovery of a class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric)RNAs, are conserved features of animal transcriptomes. Biogenesis of tricRNAs requires anciently conserved tRNA sequence motifs and processing enzymes, and their expression is regulated in an age-dependent and tissue-specific manner. Furthermore, we exploited this biogenesis pathway to develop an in vivo expression system for generating "designer" circular RNAs in human cells. Reporter constructs expressing RNA aptamers such as Spinach and Broccoli can be used to follow the transcription and subcellular localization of tricRNAs in living cells. Owing to the superior stability of circular vs. linear RNA isoforms, this expression system has a wide range of potential applications, from basic research to pharmaceutical science. © 2015 Lu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  2. Cex1p is a novel cytoplasmic component of the Saccharomyces cerevisiae nuclear tRNA export machinery.

    PubMed

    McGuire, Andrew T; Mangroo, Dev

    2007-01-24

    The Saccharomyces cerevisiae Yor112wp, which we named Cex1p, was identified using a yeast tRNA three-hybrid interaction approach and an in vivo nuclear tRNA export assay as a cytoplasmic component of the nuclear tRNA export machinery. Cex1p binds tRNA saturably, and associates with the nuclear pore complex by interacting directly with Nup116p. Cex1p co-purifies with the nuclear tRNA export receptors Los1p and Msn5p, the eukaryotic elongation factor eEF-1A, which delivers aminoacylated tRNAs to the ribosome, and the RanGTPase Gsp1p, but not with Cca1p, a tRNA maturation enzyme that facilitates translocation of non-aminoacylated tRNAs across the nuclear pore complex. Depletion of Cex1p and eEF-1A or Los1p significantly reduced the efficiency of nuclear tRNA export. Cex1p interacts with Los1p but not with eEF-1A in vitro. These findings suggest that Cex1p is a component of the nuclear aminoacylation-dependent tRNA export pathway in S. cerevisiae. They also suggest that Cex1p collects aminoacyl-tRNAs from the nuclear export receptors at the cytoplasmic side of the nuclear pore complex, and transfers them to eEF-1A using a channelling mechanism.

  3. Cex1p is a novel cytoplasmic component of the Saccharomyces cerevisiae nuclear tRNA export machinery

    PubMed Central

    McGuire, Andrew T; Mangroo, Dev

    2007-01-01

    The Saccharomyces cerevisiae Yor112wp, which we named Cex1p, was identified using a yeast tRNA three-hybrid interaction approach and an in vivo nuclear tRNA export assay as a cytoplasmic component of the nuclear tRNA export machinery. Cex1p binds tRNA saturably, and associates with the nuclear pore complex by interacting directly with Nup116p. Cex1p co-purifies with the nuclear tRNA export receptors Los1p and Msn5p, the eukaryotic elongation factor eEF-1A, which delivers aminoacylated tRNAs to the ribosome, and the RanGTPase Gsp1p, but not with Cca1p, a tRNA maturation enzyme that facilitates translocation of non-aminoacylated tRNAs across the nuclear pore complex. Depletion of Cex1p and eEF-1A or Los1p significantly reduced the efficiency of nuclear tRNA export. Cex1p interacts with Los1p but not with eEF-1A in vitro. These findings suggest that Cex1p is a component of the nuclear aminoacylation-dependent tRNA export pathway in S. cerevisiae. They also suggest that Cex1p collects aminoacyl-tRNAs from the nuclear export receptors at the cytoplasmic side of the nuclear pore complex, and transfers them to eEF-1A using a channelling mechanism. PMID:17203074

  4. Selective Packaging of Host tRNA's by Murine Leukemia Virus Particles Does Not Require Genomic RNA

    PubMed Central

    Levin, Judith G.; Seidman, J. G.

    1979-01-01

    The 4S RNA contained in RNA tumor virus particles consists of a selected population of host tRNA's. However, the mechanism by which virions select host tRNA's has not been elucidated. We have considered a model which specifies that 35S genomic RNA determines which tRNA's are to be encapsidated as well as the relative amounts of these tRNA's within the virion. The model was tested by comparing the free 4S RNA composition of normal murine leukemia virus (MuLV) particles and noninfectious virions from actinomycin D (ActD)-treated cells, which are deficient in genomic RNA (ActD virions). Viral 4S RNA was analyzed by two-dimensional polyacrylamide gel electrophoresis. Surprisingly, the patterns obtained for control and ActD 4S RNA were identical to each other and were clearly distinct from the cell 4S RNA pattern. The viral patterns had three prominent areas of radioactivity. One of the spots was identified on the basis of its oligonucleotide fingerprint as tRNA Pro, the primer for MuLV RNA-directed DNA synthesis. These results were obtained with two different MuLV strains, AKR and Moloney, each grown in SC-1 cells. The demonstration that ActD virions contain primer tRNA and in general exhibit the characteristic MuLV tRNA pattern rather than the complete representation of cell 4S RNA leads to the conclusion that genomic RNA is not the major determinant in selective packaging of host tRNA's. A possible role for one or more viral proteins, including reverse transcriptase, is suggested. Images PMID:219227

  5. The effect of tRNA levels on decoding times of mRNA codons.

    PubMed

    Dana, Alexandra; Tuller, Tamir

    2014-08-01

    The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (-0.38 to -0.66, all P values <0.006); in addition, we show that when considering tRNA concentrations, codons decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast.

    PubMed

    Saini, Natalie; Roberts, Steven A; Sterling, Joan F; Malc, Ewa P; Mieczkowski, Piotr A; Gordenin, Dmitry A

    2017-05-01

    Variations in mutation rates across the genome have been demonstrated both in model organisms and in cancers. This phenomenon is largely driven by the damage specificity of diverse mutagens and the differences in DNA repair efficiency in given genomic contexts. Here, we demonstrate that the single-strand DNA-specific cytidine deaminase APOBEC3B (A3B) damages tRNA genes at a 1000-fold higher efficiency than other non-tRNA genomic regions in budding yeast. We found that A3B-induced lesions in tRNA genes were predominantly located on the non-transcribed strand, while no transcriptional strand bias was observed in protein coding genes. Furthermore, tRNA gene mutations were exacerbated in cells where RNaseH expression was completely abolished (Δrnh1Δrnh35). These data suggest a transcription-dependent mechanism for A3B-induced tRNA gene hypermutation. Interestingly, in strains proficient in DNA repair, only 1% of the abasic sites formed upon excision of A3B-deaminated cytosines were not repaired leading to mutations in tRNA genes, while 18% of these lesions failed to be repaired in the remainder of the genome. A3B-induced mutagenesis in tRNA genes was found to be efficiently suppressed by the redundant activities of both base excision repair (BER) and the error-free DNA damage bypass pathway. On the other hand, deficiencies in BER did not have a profound effect on A3B-induced mutations in CAN1, the reporter for protein coding genes. We hypothesize that differences in the mechanisms underlying ssDNA formation at tRNA genes and other genomic loci are the key determinants of the choice of the repair pathways and consequently the efficiency of DNA damage repair in these regions. Overall, our results indicate that tRNA genes are highly susceptible to ssDNA-specific DNA damaging agents. However, increased DNA repair efficacy in tRNA genes can prevent their hypermutation and maintain both genome and proteome homeostasis. Published by Elsevier B.V.

  7. Fast and accurate face recognition based on image compression

    NASA Astrophysics Data System (ADS)

    Zheng, Yufeng; Blasch, Erik

    2017-05-01

    Image compression is desired for many image-related applications especially for network-based applications with bandwidth and storage constraints. The face recognition community typical reports concentrate on the maximal compression rate that would not decrease the recognition accuracy. In general, the wavelet-based face recognition methods such as EBGM (elastic bunch graph matching) and FPB (face pattern byte) are of high performance but run slowly due to their high computation demands. The PCA (Principal Component Analysis) and LDA (Linear Discriminant Analysis) algorithms run fast but perform poorly in face recognition. In this paper, we propose a novel face recognition method based on standard image compression algorithm, which is termed as compression-based (CPB) face recognition. First, all gallery images are compressed by the selected compression algorithm. Second, a mixed image is formed with the probe and gallery images and then compressed. Third, a composite compression ratio (CCR) is computed with three compression ratios calculated from: probe, gallery and mixed images. Finally, the CCR values are compared and the largest CCR corresponds to the matched face. The time cost of each face matching is about the time of compressing the mixed face image. We tested the proposed CPB method on the "ASUMSS face database" (visible and thermal images) from 105 subjects. The face recognition accuracy with visible images is 94.76% when using JPEG compression. On the same face dataset, the accuracy of FPB algorithm was reported as 91.43%. The JPEG-compressionbased (JPEG-CPB) face recognition is standard and fast, which may be integrated into a real-time imaging device.

  8. Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies

    NASA Astrophysics Data System (ADS)

    Islam, Md. Maidul; Pandya, Prateek; Chowdhury, Sebanti Roy; Kumar, Surat; Kumar, Gopinatha Suresh

    2008-11-01

    The interaction of two natural protoberberine plant alkaloids berberine and palmatine with tRNA phe was studied using various biophysical techniques and molecular modeling and the data were compared with the binding of the classical DNA intercalator, ethidium. Circular dichroic studies revealed that the tRNA conformation was moderately perturbed on binding of the alkaloids. The cooperative binding of both the alkaloids and ethidium to tRNA was revealed from absorbance and fluorescence studies. Fluorescence quenching studies advanced a conclusion that while berberine and palmatine are partially intercalated, ethidium is fully intercalated on the tRNA molecule. The binding of the alkaloids as well as ethidium stabilized the tRNA melting, and the binding constant evaluated from the averaged optical melting temperature data was in agreement with fluorescence spectral-binding data. Differential scanning calorimetry revealed that the tRNA melting showed three close transitions that were affected on binding of these small molecules. Molecular docking calculations performed showed the preferred regions of binding of these small molecules on the tRNA. Taken together, the results suggest that the binding of the alkaloids berberine and palmatine on the tRNA structure appears to be mostly by partial intercalation while ethidium intercalates fully on the tRNA. These results further advance our knowledge on the molecular aspects on the interaction of these alkaloids to tRNA.

  9. Sharing the load: Mex67-Mtr2 cofunctions with Los1 in primary tRNA nuclear export.

    PubMed

    Chatterjee, Kunal; Majumder, Shubhra; Wan, Yao; Shah, Vijay; Wu, Jingyan; Huang, Hsiao-Yun; Hopper, Anita K

    2017-11-01

    Eukaryotic transfer RNAs (tRNAs) are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function for protein synthesis. The evolutionarily conserved β-importin family member Los1 (Exportin-t) has been the only exporter known to execute nuclear export of newly transcribed intron-containing pre-tRNAs. Interestingly, LOS1 is unessential in all tested organisms. As tRNA nuclear export is essential, we previously interrogated the budding yeast proteome to identify candidates that function in tRNA nuclear export. Here, we provide molecular, genetic, cytological, and biochemical evidence that the Mex67-Mtr2 (TAP-p15) heterodimer, best characterized for its essential role in mRNA nuclear export, cofunctions with Los1 in tRNA nuclear export. Inactivation of Mex67 or Mtr2 leads to rapid accumulation of end-matured unspliced tRNAs in the nucleus. Remarkably, merely fivefold overexpression of Mex67-Mtr2 can substitute for Los1 in los1 Δ cells. Moreover, in vivo coimmunoprecipitation assays with tagged Mex67 document that the Mex67 binds tRNAs. Our data also show that tRNA exporters surprisingly exhibit differential tRNA substrate preferences. The existence of multiple tRNA exporters, each with different tRNA preferences, may indicate that the proteome can be regulated by tRNA nuclear export. Thus, our data show that Mex67-Mtr2 functions in primary nuclear export for a subset of yeast tRNAs. © 2017 Chatterjee et al.; Published by Cold Spring Harbor Laboratory Press.

  10. Structures of the tRNA export factor in the nuclear and cytosolic states.

    PubMed

    Cook, Atlanta G; Fukuhara, Noemi; Jinek, Martin; Conti, Elena

    2009-09-03

    Transfer RNAs are among the most ubiquitous molecules in cells, central to decoding information from messenger RNAs on translating ribosomes. In eukaryotic cells, tRNAs are actively transported from their site of synthesis in the nucleus to their site of function in the cytosol. This is mediated by a dedicated nucleo-cytoplasmic transport factor of the karyopherin-beta family (Xpot, also known as Los1 in Saccharomyces cerevisiae). Here we report the 3.2 A resolution structure of Schizosaccharomyces pombe Xpot in complex with tRNA and RanGTP, and the 3.1 A structure of unbound Xpot, revealing both nuclear and cytosolic snapshots of this transport factor. Xpot undergoes a large conformational change on binding cargo, wrapping around the tRNA and, in particular, binding to the tRNA 5' and 3' ends. The binding mode explains how Xpot can recognize all mature tRNAs in the cell and yet distinguish them from those that have not been properly processed, thus coupling tRNA export to quality control.

  11. Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase.

    PubMed

    Muruganandam, Gopinath; Raasakka, Arne; Myllykoski, Matti; Kursula, Inari; Kursula, Petri

    2017-05-16

    Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5'-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase). We employed different biophysical and biochemical methods to elucidate the overall structural and functional features of the tRNA healing enzymes yeast Trl1 PNK/CPDase and lancelet PNK/CPDase and compared them with vertebrate CNPase. The yeast and the lancelet enzymes have cyclic phosphodiesterase and polynucleotide kinase activity, while vertebrate CNPase lacks PNK activity. In addition, we also show that the healing enzymes are structurally similar to the vertebrate CNPase by applying synchrotron radiation circular dichroism spectroscopy and small-angle X-ray scattering. We provide a structural analysis of the tRNA healing enzyme PNK and CPDase domains together. Our results support evolution of vertebrate CNPase from tRNA healing enzymes with a loss of function at its N-terminal PNK-like domain.

  12. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    NASA Astrophysics Data System (ADS)

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

  13. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.

    PubMed

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-21

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

  14. Structural-conformational aspects of tRNA complexation with chloroethyl nitrosourea derivatives: A molecular modeling and spectroscopic investigation.

    PubMed

    Agarwal, Shweta; Tyagi, Gunjan; Chadha, Deepti; Mehrotra, Ranjana

    2017-01-01

    Chloroethyl nitrosourea derivatives (CENUs) represent an important family of anticancer chemotherapeutic agents, which are used in the treatment of different types of cancer such as brain tumors, resistant or relapsed Hodgkin's disease, small cell lung cancer and malignant melanoma. This work focuses towards understanding the interaction of chloroethyl nitrosourea derivatives; lomustine, nimustine and semustine with tRNA using spectroscopic approach in order to elucidate their auxiliary anticancer action mechanism inside the cell. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), Fourier transform infrared difference spectroscopy, circular dichroism spectroscopy and UV-visible spectroscopy were employed to investigate the binding parameters of tRNA-CENUs complexation. Results of present study demonstrate that all CENUs, studied here, interact with tRNA through guanine nitrogenous base residues and possibly further crosslink cytosine residues in paired region of tRNA. Moreover, spectral data collected for nimustine-tRNA and semustine-tRNA complex formation indicates towards the groove-directed-alkylation as their anti-malignant action, which involves the participation of uracil moiety located in major groove of tRNA. Besides this, tRNA-CENUs adduct formation did not alter the native conformation of biopolymer and tRNA remains in A-form after its interaction with all three nitrosourea derivatives studied. The binding constants (K a ) estimated for tRNA complexation with lomustine, nimustine and semustine are 2.55×10 2 M -1 , 4.923×10 2 M -1 and 4.223×10 2 M -1 respectively, which specify weak type of CENU's binding with tRNA. Moreover, molecular modeling simulations were also performed to predict preferential binding orientation of CENUs with tRNA that corroborates well with spectral outcomes. The findings, presented here, recognize tRNA binding properties of CENUs that can further help in rational designing of more specific and

  15. tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.

    PubMed

    Abe, Takashi; Inokuchi, Hachiro; Yamada, Yuko; Muto, Akira; Iwasaki, Yuki; Ikemura, Toshimichi

    2014-01-01

    The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

  16. Sharing the load: Mex67–Mtr2 cofunctions with Los1 in primary tRNA nuclear export

    PubMed Central

    Chatterjee, Kunal; Majumder, Shubhra; Wan, Yao; Shah, Vijay; Wu, Jingyan; Huang, Hsiao-Yun

    2017-01-01

    Eukaryotic transfer RNAs (tRNAs) are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function for protein synthesis. The evolutionarily conserved β-importin family member Los1 (Exportin-t) has been the only exporter known to execute nuclear export of newly transcribed intron-containing pre-tRNAs. Interestingly, LOS1 is unessential in all tested organisms. As tRNA nuclear export is essential, we previously interrogated the budding yeast proteome to identify candidates that function in tRNA nuclear export. Here, we provide molecular, genetic, cytological, and biochemical evidence that the Mex67–Mtr2 (TAP–p15) heterodimer, best characterized for its essential role in mRNA nuclear export, cofunctions with Los1 in tRNA nuclear export. Inactivation of Mex67 or Mtr2 leads to rapid accumulation of end-matured unspliced tRNAs in the nucleus. Remarkably, merely fivefold overexpression of Mex67–Mtr2 can substitute for Los1 in los1Δ cells. Moreover, in vivo coimmunoprecipitation assays with tagged Mex67 document that the Mex67 binds tRNAs. Our data also show that tRNA exporters surprisingly exhibit differential tRNA substrate preferences. The existence of multiple tRNA exporters, each with different tRNA preferences, may indicate that the proteome can be regulated by tRNA nuclear export. Thus, our data show that Mex67–Mtr2 functions in primary nuclear export for a subset of yeast tRNAs. PMID:29212662

  17. Viral tRNA Mimicry from a Biocommunicative Perspective

    PubMed Central

    Ariza-Mateos, Ascensión; Gómez, Jordi

    2017-01-01

    RNA viruses have very small genomes which limits the functions they can encode. One of the strategies employed by these viruses is to mimic key factors of the host cell so they can take advantage of the interactions and activities these factors typically participate in. The viral RNA genome itself was first observed to mimic cellular tRNA over 40 years ago. Since then researchers have confirmed that distinct families of RNA viruses are accessible to a battery of cellular factors involved in tRNA-related activities. Recently, potential tRNA-like structures have been detected within the sequences of a 100 mRNAs taken from human cells, one of these being the host defense interferon-alpha mRNA; these are then additional to the examples found in bacterial and yeast mRNAs. The mimetic relationship between tRNA, cellular mRNA, and viral RNA is the central focus of two considerations described below. These are subsequently used as a preface for a final hypothesis drawing on concepts relating to mimicry from the social sciences and humanities, such as power relations and creativity. Firstly, the presence of tRNA-like structures in mRNAs indicates that the viral tRNA-like signal could be mimicking tRNA-like elements that are contextualized by the specific carrier mRNAs, rather than, or in addition to, the tRNA itself, which would significantly increase the number of potential semiotic relations mediated by the viral signals. Secondly, and in particular, mimicking a host defense mRNA could be considered a potential new viral strategy for survival. Finally, we propose that mRNA’s mimicry of tRNA could be indicative of an ancestral intracellular conflict in which species of mRNAs invaded the cell, but from within. As the meaning of the mimetic signal depends on the context, in this case, the conflict that arises when the viral signal enters the cell can change the meaning of the mRNAs’ internal tRNA-like signals, from their current significance to that they had in the

  18. Unique pathway of expression of an opal suppressor phosphoserine tRNA.

    PubMed Central

    Lee, B J; de la Peña, P; Tobian, J A; Zasloff, M; Hatfield, D

    1987-01-01

    An opal suppressor phosphoserine tRNA gene is present in single copy in the genomes of higher vertebrates. We have shown that the product of this gene functions as a suppressor in an in vitro assay, and we have proposed that it may donate a modified amino acid directly to protein in response to specific UGA codons. In this report, we show through in vitro and in vivo studies that the human and Xenopus opal suppressor phosphoserine tRNAs are synthesized by a pathway that is, to the best of our knowledge, unlike that of any known eukaryotic tRNA. The primary transcript of this gene does not contain a 5'-leader sequence; and, therefore, transcription of this suppressor is initiated at the first nucleotide within the coding sequence. The 5'-terminal triphosphate, present on the primary transcript, remains intact through 3'-terminal maturation and through subsequent transport of the tRNA to the cytoplasm. The unique biosynthetic pathway of this opal suppressor may underlie its distinctive role in eukaryotic cells. Images PMID:3114749

  19. How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA

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

    B Pan; Y Xiong; T Steitz

    2011-12-31

    CCA-adding enzymes [ATP(CTP):tRNA nucleotidyltransferases] add CCA onto the 3' end of transfer RNA (tRNA) precursors without using a nucleic acid template. Although the mechanism by which cytosine (C) is selected at position 75 of tRNA has been established, the mechanism by which adenine (A) is selected at position 76 remains elusive. Here, we report five cocrystal structures of the enzyme complexed with both a tRNA mimic and nucleoside triphosphates under catalytically active conditions. These structures suggest that adenosine 5'-monophosphate is incorporated onto the A76 position of the tRNA via a carboxylate-assisted, one-metal-ion mechanism with aspartate 110 functioning as a generalmore » base. The discrimination against incorporation of cytidine 5'-triphosphate (CTP) at position 76 arises from improper placement of the {alpha} phosphate of the incoming CTP, which results from the interaction of C with arginine 224 and prevents the nucleophilic attack by the 3' hydroxyl group of cytidine75.« less

  20. Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.

    PubMed

    Konevega, Andrey L; Fischer, Niels; Semenkov, Yuri P; Stark, Holger; Wintermeyer, Wolfgang; Rodnina, Marina V

    2007-04-01

    During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement.

  1. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    PubMed Central

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine–pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

  2. CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration.

    PubMed

    Schaffer, Ashleigh E; Eggens, Veerle R C; Caglayan, Ahmet Okay; Reuter, Miriam S; Scott, Eric; Coufal, Nicole G; Silhavy, Jennifer L; Xue, Yuanchao; Kayserili, Hulya; Yasuno, Katsuhito; Rosti, Rasim Ozgur; Abdellateef, Mostafa; Caglar, Caner; Kasher, Paul R; Cazemier, J Leonie; Weterman, Marian A; Cantagrel, Vincent; Cai, Na; Zweier, Christiane; Altunoglu, Umut; Satkin, N Bilge; Aktar, Fesih; Tuysuz, Beyhan; Yalcinkaya, Cengiz; Caksen, Huseyin; Bilguvar, Kaya; Fu, Xiang-Dong; Trotta, Christopher R; Gabriel, Stacey; Reis, André; Gunel, Murat; Baas, Frank; Gleeson, Joseph G

    2014-04-24

    Neurodegenerative diseases can occur so early as to affect neurodevelopment. From a cohort of more than 2,000 consanguineous families with childhood neurological disease, we identified a founder mutation in four independent pedigrees in cleavage and polyadenylation factor I subunit 1 (CLP1). CLP1 is a multifunctional kinase implicated in tRNA, mRNA, and siRNA maturation. Kinase activity of the CLP1 mutant protein was defective, and the tRNA endonuclease complex (TSEN) was destabilized, resulting in impaired pre-tRNA cleavage. Germline clp1 null zebrafish showed cerebellar neurodegeneration that was rescued by wild-type, but not mutant, human CLP1 expression. Patient-derived induced neurons displayed both depletion of mature tRNAs and accumulation of unspliced pre-tRNAs. Transfection of partially processed tRNA fragments into patient cells exacerbated an oxidative stress-induced reduction in cell survival. Our data link tRNA maturation to neuronal development and neurodegeneration through defective CLP1 function in humans. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA

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

    Pan, Baocheng; Xiong, Yong; Steitz, Thomas A.

    2010-11-22

    CCA-adding enzymes [ATP(CTP):tRNA nucleotidyltransferases] add CCA onto the 3{prime} end of transfer RNA (tRNA) precursors without using a nucleic acid template. Although the mechanism by which cytosine (C) is selected at position 75 of tRNA has been established, the mechanism by which adenine (A) is selected at position 76 remains elusive. Here, we report five cocrystal structures of the enzyme complexed with both a tRNA mimic and nucleoside triphosphates under catalytically active conditions. These structures suggest that adenosine 5{prime}-monophosphate is incorporated onto the A76 position of the tRNA via a carboxylate-assisted, one-metal-ion mechanism with aspartate 110 functioning as a generalmore » base. The discrimination against incorporation of cytidine 5{prime}-triphosphate (CTP) at position 76 arises from improper placement of the {alpha} phosphate of the incoming CTP, which results from the interaction of C with arginine 224 and prevents the nucleophilic attack by the 3{prime} hydroxyl group of cytidine75.« less

  4. A cross-race effect in metamemory: Predictions of face recognition are more accurate for members of our own race

    PubMed Central

    Hourihan, Kathleen L.; Benjamin, Aaron S.; Liu, Xiping

    2012-01-01

    The Cross-Race Effect (CRE) in face recognition is the well-replicated finding that people are better at recognizing faces from their own race, relative to other races. The CRE reveals systematic limitations on eyewitness identification accuracy and suggests that some caution is warranted in evaluating cross-race identification. The CRE is a problem because jurors value eyewitness identification highly in verdict decisions. In the present paper, we explore how accurate people are in predicting their ability to recognize own-race and other-race faces. Caucasian and Asian participants viewed photographs of Caucasian and Asian faces, and made immediate judgments of learning during study. An old/new recognition test replicated the CRE: both groups displayed superior discriminability of own-race faces, relative to other-race faces. Importantly, relative metamnemonic accuracy was also greater for own-race faces, indicating that the accuracy of predictions about face recognition is influenced by race. This result indicates another source of concern when eliciting or evaluating eyewitness identification: people are less accurate in judging whether they will or will not recognize a face when that face is of a different race than they are. This new result suggests that a witness’s claim of being likely to recognize a suspect from a lineup should be interpreted with caution when the suspect is of a different race than the witness. PMID:23162788

  5. Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

    PubMed Central

    Gupta, Asmita; Kailasam, Senthilkumar; Bansal, Manju

    2016-01-01

    Exportin-t (Xpot) transports mature 5′- and 3′-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes. PMID:27028637

  6. Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast.

    PubMed

    Chen, Miao; Gartenberg, Marc R

    2014-05-01

    tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC-tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs.

  7. Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast

    PubMed Central

    Chen, Miao; Gartenberg, Marc R.

    2014-01-01

    tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC–tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs. PMID:24788517

  8. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.

    PubMed

    Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang

    2016-09-14

    Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.

  9. Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

    PubMed

    Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

    2011-01-01

    We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

  10. A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus

    PubMed Central

    Zaborske, John M.; Bauer DuMont, Vanessa L.; Wallace, Edward W. J.; Pan, Tao; Aquadro, Charles F.; Drummond, D. Allan

    2014-01-01

    Natural selection favors efficient expression of encoded proteins, but the causes, mechanisms, and fitness consequences of evolved coding changes remain an area of aggressive inquiry. We report a large-scale reversal in the relative translational accuracy of codons across 12 fly species in the Drosophila/Sophophora genus. Because the reversal involves pairs of codons that are read by the same genomically encoded tRNAs, we hypothesize, and show by direct measurement, that a tRNA anticodon modification from guanosine to queuosine has coevolved with these genomic changes. Queuosine modification is present in most organisms but its function remains unclear. Modification levels vary across developmental stages in D. melanogaster, and, consistent with a causal effect, genes maximally expressed at each stage display selection for codons that are most accurate given stage-specific queuosine modification levels. In a kinetic model, the known increased affinity of queuosine-modified tRNA for ribosomes increases the accuracy of cognate codons while reducing the accuracy of near-cognate codons. Levels of queuosine modification in D. melanogaster reflect bioavailability of the precursor queuine, which eukaryotes scavenge from the tRNAs of bacteria and absorb in the gut. These results reveal a strikingly direct mechanism by which recoding of entire genomes results from changes in utilization of a nutrient. PMID:25489848

  11. Enhanced dynamics of hydrated tRNA on nanodiamond surfaces: A combined neutron scattering and MD simulation study

    DOE PAGES

    Dhindsa, Gurpreet K.; Bhowmik, Debsindhu; Goswami, Monojoy; ...

    2016-09-01

    Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on NDmore » surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. As a result, our new findings may provide new design principles for safer, improved drug delivery platforms.« less

  12. Macromolecular recognition: Structural aspects of the origin of the genetic system

    NASA Technical Reports Server (NTRS)

    Rein, Robert; Barak, Dov; Luo, Ning; Zielinski, Theresa Julia; Shibata, Masayuki

    1991-01-01

    Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and

  13. Toward More Accurate Iris Recognition Using Cross-Spectral Matching.

    PubMed

    Nalla, Pattabhi Ramaiah; Kumar, Ajay

    2017-01-01

    Iris recognition systems are increasingly deployed for large-scale applications such as national ID programs, which continue to acquire millions of iris images to establish identity among billions. However, with the availability of variety of iris sensors that are deployed for the iris imaging under different illumination/environment, significant performance degradation is expected while matching such iris images acquired under two different domains (either sensor-specific or wavelength-specific). This paper develops a domain adaptation framework to address this problem and introduces a new algorithm using Markov random fields model to significantly improve cross-domain iris recognition. The proposed domain adaptation framework based on the naive Bayes nearest neighbor classification uses a real-valued feature representation, which is capable of learning domain knowledge. Our approach to estimate corresponding visible iris patterns from the synthesis of iris patches in the near infrared iris images achieves outperforming results for the cross-spectral iris recognition. In this paper, a new class of bi-spectral iris recognition system that can simultaneously acquire visible and near infra-red images with pixel-to-pixel correspondences is proposed and evaluated. This paper presents experimental results from three publicly available databases; PolyU cross-spectral iris image database, IIITD CLI and UND database, and achieve outperforming results for the cross-sensor and cross-spectral iris matching.

  14. Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

    PubMed Central

    Caulfield, Thomas R.; Devkota, Batsal; Rollins, Geoffrey C.

    2011-01-01

    We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16. PMID:21716650

  15. Protein kinase A is part of a mechanism that regulates nuclear reimport of the nuclear tRNA export receptors Los1p and Msn5p.

    PubMed

    Pierce, Jacqueline B; van der Merwe, George; Mangroo, Dev

    2014-02-01

    The two main signal transduction mechanisms that allow eukaryotes to sense and respond to changes in glucose availability in the environment are the cyclic AMP (cAMP)/protein kinase A (PKA) and AMP-activated protein kinase (AMPK)/Snf1 kinase-dependent pathways. Previous studies have shown that the nuclear tRNA export process is inhibited in Saccharomyces cerevisiae deprived of glucose. However, the signal transduction pathway involved and the mechanism by which glucose availability regulates nuclear-cytoplasmic tRNA trafficking are not understood. Here, we show that inhibition of nuclear tRNA export is caused by a block in nuclear reimport of the tRNA export receptors during glucose deprivation. Cytoplasmic accumulation of the tRNA export receptors during glucose deprivation is not caused by activation of Snf1p. Evidence obtained suggests that PKA is part of the mechanism that regulates nuclear reimport of the tRNA export receptors in response to glucose availability. This mechanism does not appear to involve phosphorylation of the nuclear tRNA export receptors by PKA. The block in nuclear reimport of the tRNA export receptors appears to be caused by activation of an unidentified mechanism when PKA is turned off during glucose deprivation. Taken together, the data suggest that PKA facilitates return of the tRNA export receptors to the nucleus by inhibiting an unidentified activity that facilitates cytoplasmic accumulation of the tRNA export receptors when glucose in the environment is limiting. A PKA-independent mechanism was also found to regulate nuclear tRNA export in response to glucose availability. This mechanism, however, does not regulate nuclear reimport of the tRNA export receptors.

  16. Protein Kinase A Is Part of a Mechanism That Regulates Nuclear Reimport of the Nuclear tRNA Export Receptors Los1p and Msn5p

    PubMed Central

    Pierce, Jacqueline B.; van der Merwe, George

    2014-01-01

    The two main signal transduction mechanisms that allow eukaryotes to sense and respond to changes in glucose availability in the environment are the cyclic AMP (cAMP)/protein kinase A (PKA) and AMP-activated protein kinase (AMPK)/Snf1 kinase-dependent pathways. Previous studies have shown that the nuclear tRNA export process is inhibited in Saccharomyces cerevisiae deprived of glucose. However, the signal transduction pathway involved and the mechanism by which glucose availability regulates nuclear-cytoplasmic tRNA trafficking are not understood. Here, we show that inhibition of nuclear tRNA export is caused by a block in nuclear reimport of the tRNA export receptors during glucose deprivation. Cytoplasmic accumulation of the tRNA export receptors during glucose deprivation is not caused by activation of Snf1p. Evidence obtained suggests that PKA is part of the mechanism that regulates nuclear reimport of the tRNA export receptors in response to glucose availability. This mechanism does not appear to involve phosphorylation of the nuclear tRNA export receptors by PKA. The block in nuclear reimport of the tRNA export receptors appears to be caused by activation of an unidentified mechanism when PKA is turned off during glucose deprivation. Taken together, the data suggest that PKA facilitates return of the tRNA export receptors to the nucleus by inhibiting an unidentified activity that facilitates cytoplasmic accumulation of the tRNA export receptors when glucose in the environment is limiting. A PKA-independent mechanism was also found to regulate nuclear tRNA export in response to glucose availability. This mechanism, however, does not regulate nuclear reimport of the tRNA export receptors. PMID:24297441

  17. Binding of the 3' terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation.

    PubMed Central

    Lill, R; Robertson, J M; Wintermeyer, W

    1989-01-01

    A key event in ribosomal protein synthesis is the translocation of deacylated tRNA, peptidyl tRNA and mRNA, which is catalyzed by elongation factor G (EF-G) and requires GTP. To address the molecular mechanism of the reaction we have studied the functional role of a tRNA exit site (E site) for tRNA release during translocation. We show that modifications of the 3' end of tRNAPhe, which considerably decrease the affinity of E-site binding, lower the translocation rate up to 40-fold. Furthermore, 3'-end modifications lower or abolish the stimulation by P site-bound tRNA of the GTPase activity of EF-G on the ribosome. The results suggest that a hydrogen-bonding interaction of the 3'-terminal adenine of the leaving tRNA in the E site, most likely base-pairing with 23S rRNA, is essential for the translocation reaction. Furthermore, this interaction stimulates the GTP hydrolyzing activity of EF-G on the ribosome. We propose the following molecular model of translocation: after the binding of EF-G.GTP, the P site-bound tRNA, by a movement of the 3'-terminal single-stranded ACCA tail, establishes an interaction with 23S rRNA in the adjacent E site, thereby initiating the tRNA transfer from the P site to the E site and promoting GTP hydrolysis. The co-operative interaction between the E site and the EF-G binding site, which are distantly located on the 50S ribosomal subunit, is probably mediated by a conformational change of 23S rRNA. PMID:2583120

  18. tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote

    PubMed Central

    Iben, James R.; Maraia, Richard J.

    2012-01-01

    tRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of whole-genome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced relative to the other yeasts, while genes for synonymous wobble iso-acceptors are amplified, indicating wobble use not apparent in any other eukaryote. We identified a subset of japonicus-specific wobbles that improves correlation of codon use and tRNA gene content in japonicus. We conclude that tgCNV is high among Schizo species and occurs in related laboratory strains of S. pombe (and expectedly other species), and tRNAome-codon analyses can provide insight into species-specific wobble decoding. PMID:22586155

  19. Rearrangement of mitochondrial tRNA genes in flat bugs (Hemiptera: Aradidae).

    PubMed

    Song, Fan; Li, Hu; Shao, Renfu; Shi, Aimin; Bai, Xiaoshuan; Zheng, Xiaorong; Heiss, Ernst; Cai, Wanzhi

    2016-05-16

    The typical insect mitochondrial (mt) genome organization, which contains a single chromosome with 37 genes, was found in the infraorder Pentatomomorpha (suborder Heteroptera). The arrangement of mt genes in these true bugs is usually the same as the ancestral mt gene arrangement of insects. Rearrangement of transfer RNA (tRNA) genes, however, has been found in two subfamilies of flat bugs (Mezirinae and Calisiinae, family Aradidae). In this study, we sequenced the complete mt genomes of four species from three other subfamilies (Aradinae, Carventinae and Aneurinae). We found tRNA gene rearrangement in all of these four species. All of the rearranged tRNA genes are located between the mitochondrial control region and cox1, indicating this region as a hotspot for gene rearrangement in flat bugs; the rearrangement is likely caused by events of tandem duplication and random deletion of genes. Furthermore, our phylogenetic and dating analyses indicated that the swap of positions between trnQ and trnI occurred ~162 million years ago (MYA) in the most recent common ancestor of the five subfamilies of flat bugs investigated to date, whereas the swap of positions between trnC and trnW occurred later in the lineage leading to Calisiinae, and the translocation of trnC and trnY occurred later than 134 MYA in the lineage leading to Aradinae.

  20. Rearrangement of mitochondrial tRNA genes in flat bugs (Hemiptera: Aradidae)

    PubMed Central

    Song, Fan; Li, Hu; Shao, Renfu; Shi, Aimin; Bai, Xiaoshuan; Zheng, Xiaorong; Heiss, Ernst; Cai, Wanzhi

    2016-01-01

    The typical insect mitochondrial (mt) genome organization, which contains a single chromosome with 37 genes, was found in the infraorder Pentatomomorpha (suborder Heteroptera). The arrangement of mt genes in these true bugs is usually the same as the ancestral mt gene arrangement of insects. Rearrangement of transfer RNA (tRNA) genes, however, has been found in two subfamilies of flat bugs (Mezirinae and Calisiinae, family Aradidae). In this study, we sequenced the complete mt genomes of four species from three other subfamilies (Aradinae, Carventinae and Aneurinae). We found tRNA gene rearrangement in all of these four species. All of the rearranged tRNA genes are located between the mitochondrial control region and cox1, indicating this region as a hotspot for gene rearrangement in flat bugs; the rearrangement is likely caused by events of tandem duplication and random deletion of genes. Furthermore, our phylogenetic and dating analyses indicated that the swap of positions between trnQ and trnI occurred ~162 million years ago (MYA) in the most recent common ancestor of the five subfamilies of flat bugs investigated to date, whereas the swap of positions between trnC and trnW occurred later in the lineage leading to Calisiinae, and the translocation of trnC and trnY occurred later than 134 MYA in the lineage leading to Aradinae. PMID:27180804

  1. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance

    PubMed Central

    Hong, Ha; Solomon, Ethan A.; DiCarlo, James J.

    2015-01-01

    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior. PMID:26424887

  2. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance.

    PubMed

    Majaj, Najib J; Hong, Ha; Solomon, Ethan A; DiCarlo, James J

    2015-09-30

    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior. Copyright © 2015 the authors 0270-6474/15/3513402-17$15.00/0.

  3. Celebrating wobble decoding: Half a century and still much is new.

    PubMed

    Agris, Paul F; Eruysal, Emily R; Narendran, Amithi; Väre, Ville Y P; Vangaveti, Sweta; Ranganathan, Srivathsan V

    2017-08-16

    A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.

  4. In vivo biochemical analyses reveal distinct roles of β-importins and eEF1A in tRNA subcellular traffic

    PubMed Central

    Huang, Hsiao-Yun

    2015-01-01

    Bidirectional tRNA movement between the nucleus and the cytoplasm serves multiple biological functions. To gain a biochemical understanding of the mechanisms for tRNA subcellular dynamics, we developed in vivo β-importin complex coimmunoprecipitation (co-IP) assays using budding yeast. Our studies provide the first in vivo biochemical evidence that two β-importin family members, Los1 (exportin-t) and Msn5 (exportin-5), serve overlapping but distinct roles in tRNA nuclear export. Los1 assembles complexes with RanGTP and tRNA. Both intron-containing pre-tRNAs and spliced tRNAs, regardless of whether they are aminoacylated, assemble into Los1–RanGTP complexes, documenting that Los1 participates in both primary nuclear export and re-export of tRNAs to the cytoplasm. In contrast, β-importin Msn5 preferentially assembles with RanGTP and spliced, aminoacylated tRNAs, documenting its role in tRNA nuclear re-export. Tef1/2 (the yeast form of translation elongation factor 1α [eEF1A]) aids the specificity of Msn5 for aminoacylated tRNAs to form a quaternary complex consisting of Msn5, RanGTP, aminoacylated tRNA, and Tef1/2. Assembly and/or stability of this quaternary complex requires Tef1/2, thereby facilitating efficient re-export of aminoacylated tRNAs to the cytoplasm. PMID:25838545

  5. Cloning and characterization of LOS1, a Saccharomyces cerevisiae gene that affects tRNA splicing.

    PubMed

    Hurt, D J; Wang, S S; Lin, Y H; Hopper, A K

    1987-03-01

    Saccharomyces cerevisiae strains carrying los1-1 mutations are defective in tRNA processing; at 37 degrees C, such strains accumulate tRNA precursors which have mature 5' and 3' ends but contain intervening sequences. Strains bearing los1-1 and an intron-containing ochre-suppressing tRNA gene, SUP4(0), also fail to suppress the ochre mutations ade2-1(0) and can1-100(0) at 34 degrees C. To understand the role of the LOS1 product in tRNA splicing, we initiated a molecular study of the LOS1 gene. Two plasmids, YEpLOS1 and YCpLOS1, that complement the los1-1 phenotype were isolated from the YEp24 and YCp50 libraries, respectively. YEpLOS1 and YCpLOS1 had overlapping restriction maps, indicating that the DNA in the overlapping segment could complement los1-1 when present in multiple or single copy. Integration of plasmid DNA at the LOS1 locus confirmed that these clones contained authentic LOS1 sequences. Southern analyses showed that LOS1 is a single copy gene. The locations of the LOS1 gene within YEpLOS1 and YCpLOS1 were determined by deletion and gamma-delta mapping. Two genomic disruptions of the LOS1 gene were constructed, i.e., an insertion of a 1.2-kilobase fragment carrying the yeast URA3 gene, los1::URA3, and a 2.4-kilobase deletion from the LOS1 gene, los1-delta V. Disruption or deletion of most of the LOS1 gene was not lethal; cells carrying the disrupted los1 alleles were viable and had phenotypes similar to those of cells carrying the los1-1 allele. Thus, it appears that the los1 gene product expedites tRNA splicing at elevated temperatures but is not essential for this process.

  6. An Electrophysiological Signature of Unconscious Recognition Memory

    PubMed Central

    Voss, Joel L.; Paller, Ken A.

    2009-01-01

    Contradicting the common assumption that accurate recognition reflects explicit-memory processing, we describe evidence for recognition lacking two hallmark explicit-memory features: awareness of memory retrieval and facilitation by attentive encoding. Kaleidoscope images were encoded in conjunction with an attentional diversion and subsequently recognized more accurately than those encoded without diversion. Confidence in recognition was superior following attentive encoding, though recognition was remarkably accurate when people claimed to be unaware of memory retrieval. This “implicit recognition” was associated with frontal-occipital negative brain potentials at 200-400 ms post-stimulus-onset, which were spatially and temporally distinct from positive brain potentials corresponding to explicit recollection and familiarity. This dissociation between behavioral and electrophysiological characteristics of “implicit recognition” versus explicit recognition indicates that a neurocognitive mechanism with properties similar to those that produce implicit memory can be operative in standard recognition tests. People can accurately discriminate repeat stimuli from new stimuli without necessarily knowing it. PMID:19198606

  7. Hydration of protein–RNA recognition sites

    PubMed Central

    Barik, Amita; Bahadur, Ranjit Prasad

    2014-01-01

    We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less than protein–DNA interfaces, but more than protein–protein interfaces. Majority of the waters at protein–RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein–DNA interfaces, mainly due to the presence of the 2′OH, the ribose in protein–RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein–RNA interfaces is hydrated more than the major groove, while in protein–DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein–RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein–RNA recognition and should be carefully treated while engineering protein–RNA interfaces. PMID:25114050

  8. TRNA mutations that affect decoding fidelity deregulate development and the proteostasis network in zebrafish

    PubMed Central

    Reverendo, Marisa; Soares, Ana R; Pereira, Patrícia M; Carreto, Laura; Ferreira, Violeta; Gatti, Evelina; Pierre, Philippe; Moura, Gabriela R; Santos, Manuel A

    2014-01-01

    Mutations in genes that encode tRNAs, aminoacyl-tRNA syntheases, tRNA modifying enzymes and other tRNA interacting partners are associated with neuropathies, cancer, type-II diabetes and hearing loss, but how these mutations cause disease is unclear. We have hypothesized that levels of tRNA decoding error (mistranslation) that do not fully impair embryonic development can accelerate cell degeneration through proteome instability and saturation of the proteostasis network. To test this hypothesis we have induced mistranslation in zebrafish embryos using mutant tRNAs that misincorporate Serine (Ser) at various non-cognate codon sites. Embryo viability was affected and malformations were observed, but a significant proportion of embryos survived by activating the unfolded protein response (UPR), the ubiquitin proteasome pathway (UPP) and downregulating protein biosynthesis. Accumulation of reactive oxygen species (ROS), mitochondrial and nuclear DNA damage and disruption of the mitochondrial network, were also observed, suggesting that mistranslation had a strong negative impact on protein synthesis rate, ER and mitochondrial homeostasis. We postulate that mistranslation promotes gradual cellular degeneration and disease through protein aggregation, mitochondrial dysfunction and genome instability. PMID:25483040

  9. Yeast Los1p Has Properties of an Exportin-Like Nucleocytoplasmic Transport Factor for tRNA

    PubMed Central

    Hellmuth, Klaus; Lau, Denise M.; Bischoff, F. Ralf; Künzler, Markus; Hurt, Ed; Simos, George

    1998-01-01

    Saccharomyces cerevisiae Los1p, which is genetically linked to the nuclear pore protein Nsp1p and several tRNA biogenesis factors, was recently grouped into the family of importin/karyopherin-β-like proteins on the basis of its sequence similarity. In a two-hybrid screen, we identified Nup2p as a nucleoporin interacting with Los1p. Subsequent purification of Los1p from yeast demonstrates its physical association not only with Nup2p but also with Nsp1p. By the use of the Gsp1p-G21V mutant, Los1p was shown to preferentially bind to the GTP-bound form of yeast Ran. Furthermore, overexpression of full-length or N-terminally truncated Los1p was shown to have dominant-negative effects on cell growth and different nuclear export pathways. Finally, Los1p could interact with Gsp1p-GTP, but only in the presence of tRNA, as revealed in an indirect in vitro binding assay. These data confirm the homology between Los1p and the recently identified human exportin for tRNA and reinforce the possibility of a role for Los1p in nuclear export of tRNA in yeast. PMID:9774653

  10. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

    PubMed Central

    Mustoe, Anthony M.; Brooks, Charles L.; Al-Hashimi, Hashim M.

    2014-01-01

    Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding. PMID:25217593

  11. T box transcription antitermination riboswitch: Influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element

    PubMed Central

    Fauzi, Hamid; Agyeman, Akwasi; Hines, Jennifer V.

    2008-01-01

    Many bacteria utilize riboswitch transcription regulation to monitor and appropriately respond to cellular levels of important metabolites or effector molecules. The T box transcription antitermination riboswitch responds to cognate uncharged tRNA by specifically stabilizing an antiterminator element in the 5′-untranslated mRNA leader region and precluding formation of a thermodynamically more stable terminator element. Stabilization occurs when the tRNA acceptor end base pairs with the first four nucleotides in the seven nucleotide bulge of the highly conserved antiterminator element. The significance of the conservation of the antiterminator bulge nucleotides that do not base pair with the tRNA is unknown, but they are required for optimal function. In vitro selection was used to determine if the isolated antiterminator bulge context alone dictates the mode in which the tRNA acceptor end binds the bulge nucleotides. No sequence conservation beyond complementarity was observed and the location was not constrained to the first four bases of the bulge. The results indicate that formation of a structure that recognizes the tRNA acceptor end in isolation is not the determinant driving force for the high phylogenetic sequence conservation observed within the antiterminator bulge. Additional factors or T box leader features more likely influenced the phylogenetic sequence conservation. PMID:19152843

  12. Small tandemly repeated DNA sequences of higher plants likely originate from a tRNA gene ancestor.

    PubMed Central

    Benslimane, A A; Dron, M; Hartmann, C; Rode, A

    1986-01-01

    Several monomers (177 bp) of a tandemly arranged repetitive nuclear DNA sequence of Brassica oleracea have been cloned and sequenced. They share up to 95% homology between one another and up to 80% with other satellite DNA sequences of Cruciferae, suggesting a common ancestor. Both strands of these monomers show more than 50% homology with many tRNA genes; the best homologies have been obtained with Lys and His yeast mitochondrial tRNA genes (respectively 64% and 60%). These results suggest that small tandemly repeated DNA sequences of plants may have evolved from a tRNA gene ancestor. These tandem repeats have probably arisen via a process involving reverse transcription of polymerase III RNA intermediates, as is the case for interspersed DNA sequences of mammalians. A model is proposed to explain the formation of such small tandemly repeated DNA sequences. Images PMID:3774553

  13. tRNA Shifts the G-quadruplex-Hairpin Conformational Equilibrium in RNA towards the Hairpin Conformer.

    PubMed

    Rode, Ambadas B; Endoh, Tamaki; Sugimoto, Naoki

    2016-11-07

    Non-coding RNAs play important roles in cellular homeostasis and are involved in many human diseases including cancer. Intermolecular RNA-RNA interactions are the basis for the diverse functions of many non-coding RNAs. Herein, we show how the presence of tRNA influences the equilibrium between hairpin and G-quadruplex conformations in the 5' untranslated regions of oncogenes and model sequences. Kinetic and equilibrium analyses of the hairpin to G-quadruplex conformational transition of purified RNA as well as during co-transcriptional folding indicate that tRNA significantly shifts the equilibrium toward the hairpin conformer. The enhancement of relative translation efficiency in a reporter gene assay is shown to be due to the tRNA-mediated shift in hairpin-G-quadruplex equilibrium of oncogenic mRNAs. Our findings suggest that tRNA is a possible therapeutic target in diseases in which RNA conformational equilibria is dysregulated. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Substrate recognition by ribonucleoprotein ribonuclease MRP

    PubMed Central

    Esakova, Olga; Perederina, Anna; Quan, Chao; Berezin, Igor; Krasilnikov, Andrey S.

    2011-01-01

    The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5′ ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed. PMID:21173200

  15. Substrate recognition by ribonucleoprotein ribonuclease MRP.

    PubMed

    Esakova, Olga; Perederina, Anna; Quan, Chao; Berezin, Igor; Krasilnikov, Andrey S

    2011-02-01

    The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5' ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed.

  16. In vivo biochemical analyses reveal distinct roles of β-importins and eEF1A in tRNA subcellular traffic.

    PubMed

    Huang, Hsiao-Yun; Hopper, Anita K

    2015-04-01

    Bidirectional tRNA movement between the nucleus and the cytoplasm serves multiple biological functions. To gain a biochemical understanding of the mechanisms for tRNA subcellular dynamics, we developed in vivo β-importin complex coimmunoprecipitation (co-IP) assays using budding yeast. Our studies provide the first in vivo biochemical evidence that two β-importin family members, Los1 (exportin-t) and Msn5 (exportin-5), serve overlapping but distinct roles in tRNA nuclear export. Los1 assembles complexes with RanGTP and tRNA. Both intron-containing pre-tRNAs and spliced tRNAs, regardless of whether they are aminoacylated, assemble into Los1-RanGTP complexes, documenting that Los1 participates in both primary nuclear export and re-export of tRNAs to the cytoplasm. In contrast, β-importin Msn5 preferentially assembles with RanGTP and spliced, aminoacylated tRNAs, documenting its role in tRNA nuclear re-export. Tef1/2 (the yeast form of translation elongation factor 1α [eEF1A]) aids the specificity of Msn5 for aminoacylated tRNAs to form a quaternary complex consisting of Msn5, RanGTP, aminoacylated tRNA, and Tef1/2. Assembly and/or stability of this quaternary complex requires Tef1/2, thereby facilitating efficient re-export of aminoacylated tRNAs to the cytoplasm. © 2015 Huang and Hopper; Published by Cold Spring Harbor Laboratory Press.

  17. Accurate palm vein recognition based on wavelet scattering and spectral regression kernel discriminant analysis

    NASA Astrophysics Data System (ADS)

    Elnasir, Selma; Shamsuddin, Siti Mariyam; Farokhi, Sajad

    2015-01-01

    Palm vein recognition (PVR) is a promising new biometric that has been applied successfully as a method of access control by many organizations, which has even further potential in the field of forensics. The palm vein pattern has highly discriminative features that are difficult to forge because of its subcutaneous position in the palm. Despite considerable progress and a few practical issues, providing accurate palm vein readings has remained an unsolved issue in biometrics. We propose a robust and more accurate PVR method based on the combination of wavelet scattering (WS) with spectral regression kernel discriminant analysis (SRKDA). As the dimension of WS generated features is quite large, SRKDA is required to reduce the extracted features to enhance the discrimination. The results based on two public databases-PolyU Hyper Spectral Palmprint public database and PolyU Multi Spectral Palmprint-show the high performance of the proposed scheme in comparison with state-of-the-art methods. The proposed approach scored a 99.44% identification rate and a 99.90% verification rate [equal error rate (EER)=0.1%] for the hyperspectral database and a 99.97% identification rate and a 99.98% verification rate (EER=0.019%) for the multispectral database.

  18. The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules.

    PubMed

    Aldinger, Carolin A; Leisinger, Anne-Katrin; Gaston, Kirk W; Limbach, Patrick A; Igloi, Gabor L

    2012-10-01

    It is a prevalent concept that, in line with the Wobble Hypothesis, those tRNAs having an adenosine in the first position of the anticodon become modified to an inosine at this position. Sequencing the cDNA derived from the gene coding for cytoplasmic tRNA (Arg) ACG from several higher plants as well as mass spectrometric analysis of the isoacceptor has revealed that for this kingdom an unmodified A in the wobble position of the anticodon is the rule rather than the exception. In vitro translation shows that in the plant system the absence of inosine in the wobble position of tRNA (Arg) does not prevent decoding. This isoacceptor belongs to the class of tRNA that is imported from the cytoplasm into the mitochondria of higher plants. Previous studies on the mitochondrial tRNA pool have demonstrated the existence of tRNA (Arg) ICG in this organelle. In moss the mitochondrial encoded distinct tRNA (Arg) ACG isoacceptor possesses the I34 modification. The implication is that for mitochondrial protein biosynthesis A-to-I editing is necessary and occurs by a mitochondrion-specific deaminase after import of the unmodified nuclear encoded tRNA (Arg) ACG.

  19. Independent suppression of ribosomal +1 frameshifts by different tRNA anticodon loop modifications.

    PubMed

    Klassen, Roland; Bruch, Alexander; Schaffrath, Raffael

    2017-09-02

    Recently, a role for the anticodon wobble uridine modification 5-methoxycarbonylmethyl-2-thiouridine (mcm 5 s 2 U) has been revealed in the suppression of translational +1 frameshifts in Saccharomyces cerevisiae. Loss of either the mcm 5 U or s 2 U parts of the modification elevated +1 frameshift rates and results obtained with reporters involving a tRNA Lys UUU dependent frameshift site suggested these effects are caused by reduced ribosomal A-site binding of the hypomodified tRNA. Combined loss of mcm 5 U and s 2 U leads to increased ribosome pausing at tRNA Lys UUU dependent codons and synergistic growth defects but effects on +1 frameshift rates remained undefined to this end. We show in here that simultaneous removal of mcm 5 U and s 2 U results in synergistically increased +1 frameshift rates that are suppressible by extra copies of tRNA Lys UUU . Thus, two distinct chemical modifications of the same wobble base independently contribute to reading frame maintenance, loss of which may cause or contribute to observed growth defects. Since the thiolation pathway is sensitive to moderately elevated temperatures in yeast, we observe a heat-induced increase of +1 frameshift rates in wild type cells that depends on the sulfur transfer protein Urm1. Furthermore, we find that temperature-induced frameshifting is kept in check by the dehydration of N6-threonylcarbamoyladenosine (t 6 A) to its cyclic derivative (ct 6 A) at the anticodon adjacent position 37. Since loss of ct 6 A in elp3 or urm1 mutant cells is detrimental for temperature stress resistance we assume that conversion of t 6 A to ct 6 A serves to limit deleterious effects on translational fidelity caused by hypomodified states of wobble uridine bases.

  20. Fluorescence probing of T box antiterminator RNA: Insights into riboswitch discernment of the tRNA discriminator base

    PubMed Central

    Means, John A.; Simson, Crystal M.; Zhou, Shu; Rachford, Aaron A.; Rack, Jeffrey J.; Hines, Jennifer V.

    2009-01-01

    The T box transcription antitermination riboswitch is one of the main regulatory mechanisms utilized by Gram-positive bacteria to regulate genes that are involved in amino acid metabolism. The details of the antitermination event, including the role that Mg2+ plays, in this riboswitch have not been completely elucidated. In these studies, details of the antitermination event were investigated utilizing 2-aminopurine to monitor structural changes of a model antiterminator RNA when it was bound to model tRNA. Based on the results of these fluorescence studies, the model tRNA binds the model antiterminator RNA via an induced fit. This binding is enhanced by the presence of Mg2+, facilitating the complete base pairing of the model tRNA acceptor end with the complementary bases in the model antiterminator bulge. PMID:19755116

  1. Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways

    PubMed Central

    Čavužić, Mirela; Liu, Yuchen

    2017-01-01

    Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s2U) derivatives, 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A). Their biosynthetic pathways have two major types depending on the requirement of iron–sulfur (Fe–S) clusters. In all cases, the first step in bacteria and eukaryotes is to activate the sulfur atom of free l-cysteine by cysteine desulfurases, generating a persulfide (R-S-SH) group. In some archaea, a cysteine desulfurase is missing. The following steps of the bacterial s2U and s4U formation are Fe–S cluster independent, and the activated sulfur is transferred by persulfide-carrier proteins. By contrast, the biosynthesis of bacterial s2C and ms2A require Fe–S cluster dependent enzymes. A recent study shows that the archaeal s4U synthetase (ThiI) and the eukaryotic cytosolic 2-thiouridine synthetase (Ncs6) are Fe–S enzymes; this expands the role of Fe–S enzymes in tRNA thiolation to the Archaea and Eukarya domains. The detailed reaction mechanisms of Fe–S cluster depend s2U and s4U formation await further investigations. PMID:28287455

  2. PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes.

    PubMed

    Damiano, F; Gallerani, R; Liuni, S; Licciulli, F; Ceci, L R

    2001-01-01

    The PLMItRNA database for mitochondrial tRNA molecules and genes in VIRIDIPLANTAE: (green plants) [Volpetti,V., Gallerani,R., DeBenedetto,C., Liuni,S., Licciulli,F. and Ceci,L.R. (2000) Nucleic Acids Res., 28, 159-162] has been enlarged to include algae. The database now contains 436 genes and 16 tRNA entries relative to 25 higher plants, eight green algae, four red algae (RHODOPHYTAE:) and two STRAMENOPILES: The PLMItRNA database is accessible via the WWW at http://bio-www.ba.cnr.it:8000/PLMItRNA.

  3. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway.

    PubMed

    Saito, Yuichiro; Takeda, Jun; Adachi, Kousuke; Nobe, Yuko; Kobayashi, Junya; Hirota, Kouji; Oliveira, Douglas V; Taoka, Masato; Isobe, Toshiaki

    2014-01-01

    Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNA(Ser-Met). To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNA(Ser-Met), suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry-based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute "Domain 1" in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.

  4. RNase MRP Cleaves Pre-tRNASer-Met in the tRNA Maturation Pathway

    PubMed Central

    Adachi, Kousuke; Nobe, Yuko; Kobayashi, Junya; Hirota, Kouji; Oliveira, Douglas V.; Taoka, Masato; Isobe, Toshiaki

    2014-01-01

    Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNASer-Met. To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNASer-Met, suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry–based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute “Domain 1” in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP. PMID:25401760

  5. Cloning and characterization of LOS1, a Saccharomyces cerevisiae gene that affects tRNA splicing.

    PubMed Central

    Hurt, D J; Wang, S S; Lin, Y H; Hopper, A K

    1987-01-01

    Saccharomyces cerevisiae strains carrying los1-1 mutations are defective in tRNA processing; at 37 degrees C, such strains accumulate tRNA precursors which have mature 5' and 3' ends but contain intervening sequences. Strains bearing los1-1 and an intron-containing ochre-suppressing tRNA gene, SUP4(0), also fail to suppress the ochre mutations ade2-1(0) and can1-100(0) at 34 degrees C. To understand the role of the LOS1 product in tRNA splicing, we initiated a molecular study of the LOS1 gene. Two plasmids, YEpLOS1 and YCpLOS1, that complement the los1-1 phenotype were isolated from the YEp24 and YCp50 libraries, respectively. YEpLOS1 and YCpLOS1 had overlapping restriction maps, indicating that the DNA in the overlapping segment could complement los1-1 when present in multiple or single copy. Integration of plasmid DNA at the LOS1 locus confirmed that these clones contained authentic LOS1 sequences. Southern analyses showed that LOS1 is a single copy gene. The locations of the LOS1 gene within YEpLOS1 and YCpLOS1 were determined by deletion and gamma-delta mapping. Two genomic disruptions of the LOS1 gene were constructed, i.e., an insertion of a 1.2-kilobase fragment carrying the yeast URA3 gene, los1::URA3, and a 2.4-kilobase deletion from the LOS1 gene, los1-delta V. Disruption or deletion of most of the LOS1 gene was not lethal; cells carrying the disrupted los1 alleles were viable and had phenotypes similar to those of cells carrying the los1-1 allele. Thus, it appears that the los1 gene product expedites tRNA splicing at elevated temperatures but is not essential for this process. Images PMID:3031485

  6. Site-specific crosslinking of 4-thiouridine-modified human tRNA(3Lys) to reverse transcriptase from human immunodeficiency virus type I.

    PubMed Central

    Mishima, Y; Steitz, J A

    1995-01-01

    We have mapped specific RNA-protein contacts between human immunodeficiency virus (HIV) type I reverse transcriptase (RT) and its natural primer, human tRNA(3Lys), using a site-specific crosslinking strategy. Four different tRNA(3Lys) constructs with a single 32P-labeled 4-thiouridine (4-thioU) residue at positions -1, 16, 36 or 41 were synthesized. After incubation with RT followed by irradiation, crosslinks were localized to either the p66 or p51 subunit of RT by digestion with nuclease and SDS gel fractionation. 4-thioU at position -1 or 16 transferred label to the p66 subunit almost exclusively (> 90%), whereas position 36 labeled both p66 and p51 (3:1). Position 41 yielded no detectable crosslinks. The region of p66 contacted by position -1 of tRNA(3Lys) was localized to the 203 C-terminal amino acids of RT by CNBr cleavage, whereas a 127 amino acid-CNBr peptide (residues 230-357) from both p66 and p51 was labeled by position 36. Functionality of the 4-thioU-modified tRNA(3Lys)(-1) crosslinked to RT in the presence of an RNA but not a DNA template was demonstrated by the ability of the tRNA to be extended. These results localize the 5' half of the tRNA on the interface between the two RT subunits, closer to the RNase H domain than to the polymerase active site, in accord with previous suggestions. They argue further that a specific binding site for the 5' end of the primer tRNA(3Lys) may exist within the C-terminal portion of the p66 subunit, which could be important for the initiation of reverse transcription. Images PMID:7540137

  7. Life without tRNAIle-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA2Ile

    PubMed Central

    Köhrer, Caroline; Mandal, Debabrata; Gaston, Kirk W.; Grosjean, Henri; Limbach, Patrick A.; RajBhandary, Uttam L.

    2014-01-01

    Translation of the isoleucine codon AUA in most prokaryotes requires a modified C (lysidine or agmatidine) at the wobble position of tRNA2Ile to base pair specifically with the A of the AUA codon but not with the G of AUG. Recently, a Bacillus subtilis strain was isolated in which the essential gene encoding tRNAIle-lysidine synthetase was deleted for the first time. In such a strain, C34 at the wobble position of tRNA2Ile is expected to remain unmodified and cells depend on a mutant suppressor tRNA derived from tRNA1Ile, in which G34 has been changed to U34. An important question, therefore, is how U34 base pairs with A without also base pairing with G. Here, we show (i) that unlike U34 at the wobble position of all B. subtilis tRNAs of known sequence, U34 in the mutant tRNA is not modified, and (ii) that the mutant tRNA binds strongly to the AUA codon on B. subtilis ribosomes but only weakly to AUG. These in vitro data explain why the suppressor strain displays only a low level of misreading AUG codons in vivo and, as shown here, grows at a rate comparable to that of the wild-type strain. PMID:24194599

  8. Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment

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

    Ling, Jiqiang; Peterson, Kaitlyn M.; Simonovic, Ivana

    2014-03-12

    Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon sequences. Here, we show that in mitochondria of Saccharomyces cerevisiae, a single aaRS (MST1) recognizes and aminoacylates two natural tRNAs that contain anticodon loops of different size and sequence. Besides a regular ?? with a threonine (Thr) anticodon, MST1 also recognizes an unusual ??, which contains an enlarged anticodon loop and an anticodon triplet that reassigns the CUN codons from leucine to threonine. Our data show that MST1 recognizes the anticodon loop in both tRNAs, but employsmore » distinct recognition mechanisms. The size but not the sequence of the anticodon loop is critical for ?? recognition, whereas the anticodon sequence is essential for aminoacylation of ??. The crystal structure of MST1 reveals that, while lacking the N-terminal editing domain, the enzyme closely resembles the bacterial threonyl-tRNA synthetase (ThrRS). A detailed structural comparison with Escherichia coli ThrRS, which is unable to aminoacylate ??, reveals differences in the anticodon-binding domain that probably allow recognition of the distinct anticodon loops. Finally, our mutational and modeling analyses identify the structural elements in MST1 (e.g., helix {alpha}11) that define tRNA selectivity. Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria.« less

  9. MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery

    PubMed Central

    Li, Rongzhong; Macnamara, Lindsay M.; Leuchter, Jessica D.; Alexander, Rebecca W.; Cho, Samuel S.

    2015-01-01

    While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes. PMID:26184179

  10. Selective rescue of selenoprotein expression in mice lacking a highly specialized methyl group in selenocysteine tRNA.

    PubMed

    Carlson, Bradley A; Xu, Xue-Ming; Gladyshev, Vadim N; Hatfield, Dolph L

    2005-02-18

    Selenocysteine (Sec) is the 21st amino acid in the genetic code. Its tRNA is variably methylated on the 2'-O-hydroxyl site of the ribosyl moiety at position 34 (Um34). Herein, we identified a role of Um34 in regulating the expression of some, but not all, selenoproteins. A strain of knock-out transgenic mice was generated, wherein the Sec tRNA gene was replaced with either wild type or mutant Sec tRNA transgenes. The mutant transgene yielded a tRNA that lacked two base modifications, N(6)-isopentenyladenosine at position 37 (i(6)A37) and Um34. Several selenoproteins, including glutathione peroxidases 1 and 3, SelR, and SelT, were not detected in mice rescued with the mutant transgene, whereas other selenoproteins, including thioredoxin reductases 1 and 3 and glutathione peroxidase 4, were expressed in normal or reduced levels. Northern blot analysis suggested that other selenoproteins (e.g. SelW) were also poorly expressed. This novel regulation of protein expression occurred at the level of translation and manifested a tissue-specific pattern. The available data suggest that the Um34 modification has greater influence than the i(6)A37 modification in regulating the expression of various mammalian selenoproteins and Um34 is required for synthesis of several members of this protein class. Many proteins that were poorly rescued appear to be involved in responses to stress, and their expression is also highly dependent on selenium in the diet. Furthermore, their mRNA levels are regulated by selenium and are subject to nonsense-mediated decay. Overall, this study described a novel mechanism of regulation of protein expression by tRNA modification that is in turn regulated by levels of the trace element, selenium.

  11. Structure-Function Analysis of Rny1 in tRNA Cleavage and Growth Inhibition

    PubMed Central

    Luhtala, Natalie; Parker, Roy

    2012-01-01

    T2 ribonucleases are conserved nucleases that affect a variety of processes in eukaryotic cells including the regulation of self-incompatibility by S-RNases in plants, modulation of host immune cell responses by viral and schistosome T2 enzymes, and neurological development and tumor progression in humans. These roles for RNaseT2’s can be due to catalytic or catalytic-independent functions of the molecule. Despite this broad importance, the features of RNaseT2 proteins that modulate catalytic and catalytic-independent functions are poorly understood. Herein, we analyze the features of Rny1 in Saccharomyces cerevisiae to determine the requirements for cleaving tRNA in vivo and for inhibiting cellular growth in a catalytic-independent manner. We demonstrate that catalytic-independent inhibition of growth is a combinatorial property of the protein and is affected by a fungal-specific C-terminal extension, the conserved catalytic core, and the presence of a signal peptide. Catalytic functions of Rny1 are independent of the C-terminal extension, are affected by many mutations in the catalytic core, and also require a signal peptide. Biochemical flotation assays reveal that in rny1Δ cells, some tRNA molecules associate with membranes suggesting that cleavage of tRNAs by Rny1 can involve either tRNA association with, or uptake into, membrane compartments. PMID:22829915

  12. Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.

    PubMed

    Zhang, Yan; Hong, Samuel; Ruangprasert, Ajchareeya; Skiniotis, Georgios; Dunham, Christine M

    2018-03-06

    Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Biochemical and Structures Studies of tRNA Modificaton and Repair Enzymes

    ERIC Educational Resources Information Center

    Zhou, Chun

    2009-01-01

    RNA hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. We first determined the crystal structures of "Pseudomonas aeruginosa" DMATase.…

  14. Factors beyond Enolase 2 and Mitochondrial Lysyl-tRNA Synthetase Precursor Are Required for tRNA Import into Yeast Mitochondria.

    PubMed

    Baleva, M V; Meyer, M; Entelis, N; Tarassov, I; Kamenski, P; Masquida, B

    2017-11-01

    In yeast, the import of tRNA Lys with CUU anticodon (tRK1) relies on a complex mechanism where interaction with enolase 2 (Eno2p) dictates a deep conformational change of the tRNA. This event is believed to mask the tRNA from the cytosolic translational machinery to re-direct it towards the mitochondria. Once near the mitochondrial outer membrane, the precursor of the mitochondrial lysyl-tRNA synthetase (preMsk1p) takes over enolase to carry the tRNA within the mitochondrial matrix, where it is supposed to participate in translation following correct refolding. Biochemical data presented in this report focus on the role of enolase. They show that despite the inability of Eno2p alone to form a complex with tRK1, mitochondrial import can be recapitulated in vitro using fractions of yeast extracts sharing either recombinant or endogenous yeast Eno2p as one of the main components. Taken together, our data suggest the existence of a protein complex containing Eno2p that is involved in RNA mitochondrial import.

  15. DNA methyltransferase homologue TRDMT1 in Plasmodium falciparum specifically methylates endogenous aspartic acid tRNA.

    PubMed

    Govindaraju, Gayathri; Jabeena, C A; Sethumadhavan, Devadathan Valiyamangalath; Rajaram, Nivethika; Rajavelu, Arumugam

    2017-10-01

    In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro. We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum. Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Electrophysiological distinctions between recognition memory with and without awareness

    PubMed Central

    Ko, Philip C.; Duda, Bryant; Hussey, Erin P.; Ally, Brandon A.

    2013-01-01

    The influence of implicit memory representations on explicit recognition may help to explain cases of accurate recognition decisions made with high uncertainty. During a recognition task, implicit memory may enhance the fluency of a test item, biasing decision processes to endorse it as “old”. This model may help explain recognition-without-identification, a remarkable phenomenon in which participants make highly accurate recognition decisions despite the inability to identify the test item. The current study investigated whether recognition-without-identification for pictures elicits a similar pattern of neural activity as other types of accurate recognition decisions made with uncertainty. Further, this study also examined whether recognition-without-identification for pictures could be attained by the use of perceptual and conceptual information from memory. To accomplish this, participants studied pictures and then performed a recognition task under difficult viewing conditions while event-related potentials (ERPs) were recorded. Behavioral results showed that recognition was highly accurate even when test items could not be identified, demonstrating recognition-without identification. The behavioral performance also indicated that recognition-without-identification was mediated by both perceptual and conceptual information, independently of one another. The ERP results showed dramatically different memory related activity during the early 300 to 500 ms epoch for identified items that were studied compared to unidentified items that were studied. Similar to previous work highlighting accurate recognition without retrieval awareness, test items that were not identified, but correctly endorsed as “old,” elicited a negative posterior old/new effect (i.e., N300). In contrast, test items that were identified and correctly endorsed as “old,” elicited the classic positive frontal old/new effect (i.e., FN400). Importantly, both of these effects were

  17. RNA editing in the anticodon of tRNA Leu (CAA) occurs before group I intron splicing in plastids of a moss Takakia lepidozioides S. Hatt. & Inoue.

    PubMed

    Miyata, Y; Sugita, C; Maruyama, K; Sugita, M

    2008-03-01

    RNA editing of cytidine (C) to uridine (U) transitions occurs in plastids and mitochondria of most land plants. In this study, we amplified and sequenced the group I intron-containing tRNA Leu gene, trnL-CAA, from Takakia lepidozioides, a moss. DNA sequence analysis revealed that the T. lepidozioides tRNA Leu gene consisted of a 35-bp 5' exon, a 469-bp group I intron and a 50-bp 3' exon. The intron was inserted between the first and second position of the tRNA Leu anticodon. In general, plastid tRNA Leu genes with a group I intron code for a TAA anticodon in most land plants. This strongly suggests that the first nucleotide of the CAA anticodon could be edited in T. lepidozioides plastids. To investigate this possibility, we analysed cDNAs derived from the trnL-CAA transcripts. We demonstrated that the first nucleotide C of the anticodon was edited to create a canonical UAA anticodon in T. lepidozioides plastids. cDNA sequencing analyses of the spliced or unspliced tRNA Leu transcripts revealed that, while the spliced tRNA was completely edited, editing in the unspliced tRNAs were only partial. This is the first experimental evidence that the anticodon editing of tRNA occurs before RNA splicing in plastids. This suggests that this editing is a prerequisite to splicing of pre-tRNA Leu.

  18. Genome-wide investigation of the role of the tRNA nuclear-cytoplasmic trafficking pathway in regulation of the yeast Saccharomyces cerevisiae transcriptome and proteome.

    PubMed

    Chu, Hui-Yi; Hopper, Anita K

    2013-11-01

    In eukaryotic cells, tRNAs are transcribed and partially processed in the nucleus before they are exported to the cytoplasm, where they have an essential role in protein synthesis. Surprisingly, mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm, and tRNA subcellular distribution is nutrient dependent. At least three members of the β-importin family, Los1, Mtr10, and Msn5, function in tRNA nuclear-cytoplasmic intracellular movement. To test the hypothesis that the tRNA retrograde pathway regulates the translation of particular transcripts, we compared the expression profiles from nontranslating mRNAs and polyribosome-associated translating mRNAs collected from msn5Δ, mtr10Δ, and wild-type cells under fed or acute amino acid depletion conditions. Our microarray data revealed that the methionine, arginine, and leucine biosynthesis pathways are targets of the tRNA retrograde process. We confirmed the microarray data by Northern and Western blot analyses. The levels of some of the particular target mRNAs were reduced, while others appeared not to be affected. However, the protein levels of all tested targets in these pathways were greatly decreased when tRNA nuclear import or reexport to the cytoplasm was disrupted. This study provides information that tRNA nuclear-cytoplasmic dynamics is connected to the biogenesis of proteins involved in amino acid biosynthesis.

  19. Genome-Wide Investigation of the Role of the tRNA Nuclear-Cytoplasmic Trafficking Pathway in Regulation of the Yeast Saccharomyces cerevisiae Transcriptome and Proteome

    PubMed Central

    Chu, Hui-Yi

    2013-01-01

    In eukaryotic cells, tRNAs are transcribed and partially processed in the nucleus before they are exported to the cytoplasm, where they have an essential role in protein synthesis. Surprisingly, mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm, and tRNA subcellular distribution is nutrient dependent. At least three members of the β-importin family, Los1, Mtr10, and Msn5, function in tRNA nuclear-cytoplasmic intracellular movement. To test the hypothesis that the tRNA retrograde pathway regulates the translation of particular transcripts, we compared the expression profiles from nontranslating mRNAs and polyribosome-associated translating mRNAs collected from msn5Δ, mtr10Δ, and wild-type cells under fed or acute amino acid depletion conditions. Our microarray data revealed that the methionine, arginine, and leucine biosynthesis pathways are targets of the tRNA retrograde process. We confirmed the microarray data by Northern and Western blot analyses. The levels of some of the particular target mRNAs were reduced, while others appeared not to be affected. However, the protein levels of all tested targets in these pathways were greatly decreased when tRNA nuclear import or reexport to the cytoplasm was disrupted. This study provides information that tRNA nuclear-cytoplasmic dynamics is connected to the biogenesis of proteins involved in amino acid biosynthesis. PMID:23979602

  20. RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri

    PubMed Central

    Su, Andreas A. H.; Tripp, Vanessa; Randau, Lennart

    2013-01-01

    The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution. PMID:23620296

  1. Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop.

    PubMed

    Stephen, Preyesh; Ye, Sheng; Zhou, Ming; Song, Jian; Zhang, Rongguang; Wang, En-Duo; Giegé, Richard; Lin, Sheng-Xiang

    2018-05-25

    Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNA Arg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure-function understanding in prokaryotic tRNA Arg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNA Arg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNA Arg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding.

    PubMed

    Rezgui, Vanessa Anissa Nathalie; Tyagi, Kshitiz; Ranjan, Namit; Konevega, Andrey L; Mittelstaet, Joerg; Rodnina, Marina V; Peter, Matthias; Pedrioli, Patrick G A

    2013-07-23

    tRNA modifications are crucial to ensure translation efficiency and fidelity. In eukaryotes, the URM1 and ELP pathways increase cellular resistance to various stress conditions, such as nutrient starvation and oxidative agents, by promoting thiolation and methoxycarbonylmethylation, respectively, of the wobble uridine of cytoplasmic (tK(UUU)), (tQ(UUG)), and (tE(UUC)). Although in vitro experiments have implicated these tRNA modifications in modulating wobbling capacity and translation efficiency, their exact in vivo biological roles remain largely unexplored. Using a combination of quantitative proteomics and codon-specific translation reporters, we find that translation of a specific gene subset enriched for AAA, CAA, and GAA codons is impaired in the absence of URM1- and ELP-dependent tRNA modifications. Moreover, in vitro experiments using native tRNAs demonstrate that both modifications enhance binding of tK(UUU) to the ribosomal A-site. Taken together, our data suggest that tRNA thiolation and methoxycarbonylmethylation regulate translation of genes with specific codon content.

  3. “Ping-Pong” Interactions between Mitochondrial tRNA Import Receptors within a Multiprotein Complex

    PubMed Central

    Bhattacharyya, Subhendra Nath; Chatterjee, Saibal; Goswami, Srikanta; Tripathi, Gayatri; Dey, Sailendra Nath; Adhya, Samit

    2003-01-01

    The mitochondrial genomes of a wide variety of species contain an insufficient number of functional tRNA genes, and translation of mitochondrial mRNAs is sustained by import of nucleus-encoded tRNAs. In Leishmania, transfer of tRNAs across the inner membrane can be regulated by positive and negative interactions between them. To define the factors involved in such interactions, a large multisubunit complex (molecular mass, ∼640 kDa) from the inner mitochondrial membrane of the kinetoplastid protozoon Leishmania, consisting of ∼130-Å particles, was isolated. The complex, when incorporated into phospholipid vesicles, induced specific, ATP- and proton motive force-dependent transfer of Leishmania tRNATyr as well as of oligoribonucleotides containing the import signal YGGYAGAGC. Moreover, allosteric interactions between tRNATyr and tRNAIle were observed in the RNA import complex-reconstituted system, indicating the presence of primary and secondary tRNA binding sites within the complex. By a combination of antibody inhibition, photochemical cross-linking, and immunoprecipitation, it was shown that binding of tRNAIle to a 21-kDa component of the complex is dependent upon tRNATyr, while binding of tRNATyr to a 45-kDa component is inhibited by tRNAIle. This “ping-pong” mechanism may be an effective means to maintain a balanced tRNA pool for mitochondrial translation. PMID:12861008

  4. Guanosine 2-NH2 groups of Escherichia coli RNase P RNA involved in intramolecular tertiary contacts and direct interactions with tRNA.

    PubMed Central

    Heide, C; Pfeiffer, T; Nolan, J M; Hartmann, R K

    1999-01-01

    We have identified by nucleotide analog interference mapping (NAIM) exocyclic NH2 groups of guanosines in RNase P RNA from Escherichia coli that are important for tRNA binding. The majority of affected guanosines represent phylogenetically conserved nucleotides. Several sites of interference could be assigned to direct contacts with the tRNA moiety, whereas others were interpreted as reflecting indirect effects on tRNA binding due to the disruption of tertiary contacts within the catalytic RNA. Our results support the involvement of the 2-NH2 groups of G292/G293 in pairing with C74 and C75 of tRNA CCA-termini, as well as formation of two consecutive base triples involving C75 and A76 of CCA-ends interacting with G292/A258 and G291/G259, respectively. Moreover, we present first biochemical evidence for two tertiary contacts (L18/P8 and L8/P4) within the catalytic RNA, whose formation has been postulated previously on the basis of phylogenetic comparative analyses. The tRNA binding interference data obtained in this and our previous studies are consistent with the formation of a consecutive nucleotide triple and quadruple between the tetraloop L18 and helix P8. Formation of the nucleotide triple (G316 and A94:U104 in wild-type E. coli RNase P RNA) is also supported by mutational analysis. For the mutant RNase P RNA carrying a G94:C104 double mutation, an additional G316-to-A mutation resulted in a restoration of binding affinity for mature and precursor tRNA. PMID:9917070

  5. RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification

    PubMed Central

    Arimbasseri, Aneeshkumar G.; Blewett, Nathan H.; Iben, James R.; Lamichhane, Tek N.; Cherkasova, Vera; Hafner, Markus; Maraia, Richard J.

    2015-01-01

    Control of the differential abundance or activity of tRNAs can be important determinants of gene regulation. RNA polymerase (RNAP) III synthesizes all tRNAs in eukaryotes and it derepression is associated with cancer. Maf1 is a conserved general repressor of RNAP III under the control of the target of rapamycin (TOR) that acts to integrate transcriptional output and protein synthetic demand toward metabolic economy. Studies in budding yeast have indicated that the global tRNA gene activation that occurs with derepression of RNAP III via maf1-deletion is accompanied by a paradoxical loss of tRNA-mediated nonsense suppressor activity, manifested as an antisuppression phenotype, by an unknown mechanism. We show that maf1-antisuppression also occurs in the fission yeast S. pombe amidst general activation of RNAP III. We used tRNA-HydroSeq to document that little changes occurred in the relative levels of different tRNAs in maf1Δ cells. By contrast, the efficiency of N2,N2-dimethyl G26 (m2 2G26) modification on certain tRNAs was decreased in response to maf1-deletion and associated with antisuppression, and was validated by other methods. Over-expression of Trm1, which produces m2 2G26, reversed maf1-antisuppression. A model that emerges is that competition by increased tRNA levels in maf1Δ cells leads to m2 2G26 hypomodification due to limiting Trm1, reducing the activity of suppressor-tRNASerUCA and accounting for antisuppression. Consistent with this, we show that RNAP III mutations associated with hypomyelinating leukodystrophy decrease tRNA transcription, increase m2 2G26 efficiency and reverse antisuppression. Extending this more broadly, we show that a decrease in tRNA synthesis by treatment with rapamycin leads to increased m2 2G26 modification and that this response is conserved among highly divergent yeasts and human cells. PMID:26720005

  6. Mitochondrial genomes of praying mantises (Dictyoptera, Mantodea): rearrangement, duplication, and reassignment of tRNA genes.

    PubMed

    Ye, Fei; Lan, Xu-E; Zhu, Wen-Bo; You, Ping

    2016-05-09

    Insect mitochondrial genomes (mitogenomes) contain a conserved set of 37 genes for an extensive diversity of lineages. Previously reported dictyopteran mitogenomes share this conserved mitochondrial gene arrangement, although surprisingly little is known about the mitogenome of Mantodea. We sequenced eight mantodean mitogenomes including the first representatives of two families: Hymenopodidae and Liturgusidae. Only two of these genomes retain the typical insect gene arrangement. In three Liturgusidae species, the trnM genes have translocated. Four species of mantis (Creobroter gemmata, Mantis religiosa, Statilia sp., and Theopompa sp.-HN) have multiple identical tandem duplication of trnR, and Statilia sp. additionally includes five extra duplicate trnW. These extra trnR and trnW in Statilia sp. are erratically arranged and form another novel gene order. Interestingly, the extra trnW is converted from trnR by the process of point mutation at anticodon, which is the first case of tRNA reassignment for an insect. Furthermore, no significant differences were observed amongst mantodean mitogenomes with variable copies of tRNA according to comparative analysis of codon usage. Combined with phylogenetic analysis, the characteristics of tRNA only possess limited phylogenetic information in this research. Nevertheless, these features of gene rearrangement, duplication, and reassignment provide valuable information toward understanding mitogenome evolution in insects.

  7. Mitochondrial genomes of praying mantises (Dictyoptera, Mantodea): rearrangement, duplication, and reassignment of tRNA genes

    PubMed Central

    Ye, Fei; Lan, Xu-e; Zhu, Wen-bo; You, Ping

    2016-01-01

    Insect mitochondrial genomes (mitogenomes) contain a conserved set of 37 genes for an extensive diversity of lineages. Previously reported dictyopteran mitogenomes share this conserved mitochondrial gene arrangement, although surprisingly little is known about the mitogenome of Mantodea. We sequenced eight mantodean mitogenomes including the first representatives of two families: Hymenopodidae and Liturgusidae. Only two of these genomes retain the typical insect gene arrangement. In three Liturgusidae species, the trnM genes have translocated. Four species of mantis (Creobroter gemmata, Mantis religiosa, Statilia sp., and Theopompa sp.-HN) have multiple identical tandem duplication of trnR, and Statilia sp. additionally includes five extra duplicate trnW. These extra trnR and trnW in Statilia sp. are erratically arranged and form another novel gene order. Interestingly, the extra trnW is converted from trnR by the process of point mutation at anticodon, which is the first case of tRNA reassignment for an insect. Furthermore, no significant differences were observed amongst mantodean mitogenomes with variable copies of tRNA according to comparative analysis of codon usage. Combined with phylogenetic analysis, the characteristics of tRNA only possess limited phylogenetic information in this research. Nevertheless, these features of gene rearrangement, duplication, and reassignment provide valuable information toward understanding mitogenome evolution in insects. PMID:27157299

  8. tRNA Is the Source of Low-Level trans-Zeatin Production in Methylobacterium spp.†‡

    PubMed Central

    Koenig, Robbin L.; Morris, Roy O.; Polacco, Joe C.

    2002-01-01

    Pink-pigmented facultatively methylotrophic bacteria (PPFMs), classified as Methylobacterium spp., are persistent colonizers of plant leaf surfaces. Reports of PPFM-plant dialogue led us to examine cytokinin production by PPFMs. Using immunoaffinity and high-performance liquid chromatography (HPLC) purification, we obtained 22 to 111 ng of trans-zeatin per liter from culture filtrates of four PPFM leaf isolates (from Arabidopsis, barley, maize, and soybean) and of a Methylobacterium extorquens type culture originally recovered as a soil isolate. We identified the zeatin isolated as the trans isomer by HPLC and by a radioimmunoassay in which monoclonal antibodies specific for trans-hydroxylated cytokinins were used. Smaller and variable amounts of trans-zeatin riboside were also recovered. trans-Zeatin was recovered from tRNA hydrolysates in addition to the culture filtrates, suggesting that secreted trans-zeatin resulted from tRNA turnover rather than from de novo synthesis. The product of the miaA gene is responsible for isopentenylation of a specific adenine in some tRNAs. To confirm that the secreted zeatin originated from tRNA, we mutated the miaA gene of M. extorquens by single exchange of an internal miaA fragment into the chromosomal gene. Mutant exconjugants, confirmed by PCR, did not contain zeatin in their tRNAs and did not secrete zeatin into the medium, findings which are consistent with the hypothesis that all zeatin is tRNA derived rather than synthesized de novo. In germination studies performed with heat-treated soybean seeds, cytokinin-null (miaA) mutants stimulated germination as well as wild-type bacteria. While cytokinin production may play a role in the plant-PPFM interaction, it is not responsible for stimulation of germination by PPFMs. PMID:11889088

  9. Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality.

    PubMed

    Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A; Schimmel, Paul; Yang, Xiang-Lei

    2010-01-01

    Protein multifunctionality is an emerging explanation for the complexity of higher organisms. In this regard, aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, but some also act in pathways for inflammation, angiogenesis and apoptosis. It is unclear how these multiple functions evolved and how they relate to the active site. Here structural modeling analysis, mutagenesis and cell-based functional studies show that the potent angiostatic, natural fragment of human tryptophanyl-tRNA synthetase (TrpRS) associates via tryptophan side chains that protrude from its cognate cellular receptor vascular endothelial cadherin (VE-cadherin). VE-cadherin's tryptophan side chains fit into the tryptophan-specific active site of the synthetase. Thus, specific side chains of the receptor mimic amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multifunctionality of human tRNA synthetases and other proteins.

  10. 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

    PubMed

    Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka-Weng; Wang, Jinfan; Petrov, Alexey; Prabhakar, Arjun; Rechavi, Gideon; Dominissini, Dan; He, Chuan; Ehrenberg, Måns; Puglisi, Joseph D

    2018-03-01

    Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

  11. Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure

    PubMed Central

    Létoquart, Juliette; van Tran, Nhan; Caroline, Vonny; Aleksandrov, Alexey; Lazar, Noureddine; van Tilbeurgh, Herman; Liger, Dominique; Graille, Marc

    2015-01-01

    Most of the factors involved in translation (tRNA, rRNA and proteins) are subject to post-transcriptional and post-translational modifications, which participate in the fine-tuning and tight control of ribosome and protein synthesis processes. In eukaryotes, Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2). Trm112 is then at a nexus between ribosome synthesis and function. Here, we present a structure-function analysis of the Trm9-Trm112 complex, which is involved in the 5-methoxycarbonylmethyluridine (mcm5U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. We also compare the known crystal structures of various Trm112-MTase complexes, highlighting the structural plasticity allowing Trm112 to interact through a very similar mode with its MTase partners, although those share less than 20% sequence identity. PMID:26438534

  12. A mitochondrial locus is necessary for the synthesis of mitochondrial tRNA in the yeast Saccharomyces cerevisiae.

    PubMed Central

    Martin, N C; Underbrink-Lyon, K

    1981-01-01

    We have used a cloned yeast mitochondrial tRNAUCNSer gene as a probe to detect RNA species that are transcripts from this gene in wild-type Saccharomyces cerevisiae and in petite deletion mutants. In RNA from wild-type cells, the tRNA is the most prominent transcript of the gene. In RNA from deletion mutants that retain this gene but have lost other regions of mtDNA, high molecular weight transcripts containing the tRNAUCNSer sequences accumulate but tRNAUCNSer is not made. tRNAUCNSer synthesis can be restored in these mutants when they are mated to other deletion mutants that retain a different portion of the mitochondrial genome. Protein synthesis is not necessary for the restoration, and the restoration is not due to a nuclear effect or to an effect of mating alone, because strains without mtDNA are not able to restore tRNA synthesis. These results definitively demonstrate the existence of a yeast mitochondrial locus that is necessary for tRNA synthesis and, because the restoration of tRNAUCNSer synthesis appears to result from intergenic complementation, not recombination, indicate that this locus acts in trans. Images PMID:6795621

  13. Phosphorylation of Elp1 by Hrr25 Is Required for Elongator-Dependent tRNA Modification in Yeast

    PubMed Central

    Abdel-Fattah, Wael; Jablonowski, Daniel; Di Santo, Rachael; Thüring, Kathrin L.; Scheidt, Viktor; Hammermeister, Alexander; ten Have, Sara; Helm, Mark; Schaffrath, Raffael; Stark, Michael J. R.

    2015-01-01

    Elongator is a conserved protein complex comprising six different polypeptides that has been ascribed a wide range of functions, but which is now known to be required for modification of uridine residues in the wobble position of a subset of tRNAs in yeast, plants, worms and mammals. In previous work, we showed that Elongator's largest subunit (Elp1; also known as Iki3) was phosphorylated and implicated the yeast casein kinase I Hrr25 in Elongator function. Here we report identification of nine in vivo phosphorylation sites within Elp1 and show that four of these, clustered close to the Elp1 C-terminus and adjacent to a region that binds tRNA, are important for Elongator's tRNA modification function. Hrr25 protein kinase directly modifies Elp1 on two sites (Ser-1198 and Ser-1202) and through analyzing non-phosphorylatable (alanine) and acidic, phosphomimic substitutions at Ser-1198, Ser-1202 and Ser-1209, we provide evidence that phosphorylation plays a positive role in the tRNA modification function of Elongator and may regulate the interaction of Elongator both with its accessory protein Kti12 and with Hrr25 kinase. PMID:25569479

  14. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.

    PubMed

    Renalier, Marie-Hélène; Joseph, Nicole; Gaspin, Christine; Thebault, Patricia; Mougin, Annie

    2005-07-01

    We identified the first archaeal tRNA ribose 2'-O-methylase, aTrm56, belonging to the Cluster of Orthologous Groups (COG) 1303 that contains archaeal genes only. The corresponding protein exhibits a SPOUT S-adenosylmethionine (AdoMet)-dependent methyltransferase domain found in bacterial and yeast G18 tRNA 2'-O-methylases (SpoU, Trm3). We cloned the Pyrococcus abyssi PAB1040 gene belonging to this COG, expressed and purified the corresponding protein, and showed that in vitro, it specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of C at position 56 in tRNA transcripts. This tRNA methylation is present only in archaea, and the gene for this enzyme is present in all the archaeal genomes sequenced up to now, except in the crenarchaeon Pyrobaculum aerophilum. In this archaea, the C56 2'-O-methylation is provided by a C/D sRNP. Our work is the first demonstration that, within the same kingdom, two different mechanisms are used to modify the same nucleoside in tRNAs.

  15. Face Recognition Using Local Quantized Patterns and Gabor Filters

    NASA Astrophysics Data System (ADS)

    Khryashchev, V.; Priorov, A.; Stepanova, O.; Nikitin, A.

    2015-05-01

    The problem of face recognition in a natural or artificial environment has received a great deal of researchers' attention over the last few years. A lot of methods for accurate face recognition have been proposed. Nevertheless, these methods often fail to accurately recognize the person in difficult scenarios, e.g. low resolution, low contrast, pose variations, etc. We therefore propose an approach for accurate and robust face recognition by using local quantized patterns and Gabor filters. The estimation of the eye centers is used as a preprocessing stage. The evaluation of our algorithm on different samples from a standardized FERET database shows that our method is invariant to the general variations of lighting, expression, occlusion and aging. The proposed approach allows about 20% correct recognition accuracy increase compared with the known face recognition algorithms from the OpenCV library. The additional use of Gabor filters can significantly improve the robustness to changes in lighting conditions.

  16. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins

    PubMed Central

    Englert, Markus; Beier, Hildburg

    2005-01-01

    Pre-tRNA splicing is an essential process in all eukaryotes. It requires the concerted action of an endonuclease to remove the intron and a ligase for joining the resulting tRNA halves as studied best in the yeast Saccharomyces cerevisiae. Here, we report the first characterization of an RNA ligase protein and its gene from a higher eukaryotic organism that is an essential component of the pre-tRNA splicing process. Purification of tRNA ligase from wheat germ by successive column chromatographic steps has identified a protein of 125 kDa by its potentiality to covalently bind AMP, and by its ability to catalyse the ligation of tRNA halves and the circularization of linear introns. Peptide sequences obtained from the purified protein led to the elucidation of the corresponding proteins and their genes in Arabidopsis and Oryza databases. The plant tRNA ligases exhibit no overall sequence homologies to any known RNA ligases, however, they harbour a number of conserved motifs that indicate the presence of three intrinsic enzyme activities: an adenylyltransferase/ligase domain in the N-terminal region, a polynucleotide kinase in the centre and a cyclic phosphodiesterase domain at the C-terminal end. In vitro expression of the recombinant Arabidopsis tRNA ligase and functional analyses revealed all expected individual activities. Plant RNA ligases are active on a variety of substrates in vitro and are capable of inter- and intramolecular RNA joining. Hence, we conclude that their role in vivo might comprise yet unknown essential functions besides their involvement in pre-tRNA splicing. PMID:15653639

  17. On origin of genetic code and tRNA before translation

    PubMed Central

    2011-01-01

    Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental veto on "foresight evolution", 2) modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3) the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code) the anticodon(2-3)/codon(1-2) tetramers to their anticodon(1-2)/codon(2-3) counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other) needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator) to the eventual 76 base-long cloverleaf

  18. Children's Recognition of Cartoon Voices.

    ERIC Educational Resources Information Center

    Spence, Melanie J.; Rollins, Pamela R.; Jerger, Susan

    2002-01-01

    A study examined developmental changes in talker recognition skills by assessing 72 children's (ages 3-5) recognition of 20 cartoon characters' voices. Four- and 5-year-old children recognized more of the voices than did 3-year-olds. All children were more accurate at recognizing more familiar characters than less familiar characters. (Contains…

  19. Face Recognition Vendor Test 2000: Appendices

    DTIC Science & Technology

    2001-02-01

    DARPA), NAVSEA Crane Division and NAVSEA Dahlgren Division are sponsoring an evaluation of commercial off the shelf (COTS) facial recognition products...The purpose of these evaluations is to accurately gauge the capabilities of facial recognition biometric systems that are currently available for...or development efforts. Participation in these tests is open to all facial recognition systems on the US commercial market. The U.S. Government will

  20. tRNA1Ser(G34) with the anticodon GGA can recognize not only UCC and UCU codons but also UCA and UCG codons.

    PubMed

    Yamada, Yuko; Matsugi, Jitsuhiro; Ishikura, Hisayuki

    2003-04-15

    The tRNA1Ser (anticodon VGA, V=uridin-5-oxyacetic acid) is essential for translation of the UCA codon in Escherichia coli. Here, we studied the translational abilities of serine tRNA derivatives, which have different bases from wild type at the first positions of their anticodons, using synthetic mRNAs containing the UCN (N=A, G, C, or U) codon. The tRNA1Ser(G34) having the anticodon GGA was able to read not only UCC and UCU codons but also UCA and UCG codons. This means that the formation of G-A or G-G pair allowed at the wobble position and these base pairs are noncanonical. The translational efficiency of the tRNA1Ser(G34) for UCA or UCG codon depends on the 2'-O-methylation of the C32 (Cm). The 2'-O-methylation of C32 may give rise to the space necessary for G-A or G-G base pair formation between the first position of anticodon and the third position of codon.

  1. 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

  2. T box riboswitches in Actinobacteria: Translational regulation via novel tRNA interactions

    PubMed Central

    Sherwood, Anna V.; Grundy, Frank J.; Henkin, Tina M.

    2015-01-01

    The T box riboswitch regulates many amino acid-related genes in Gram-positive bacteria. T box riboswitch-mediated gene regulation was shown previously to occur at the level of transcription attenuation via structural rearrangements in the 5′ untranslated (leader) region of the mRNA in response to binding of a specific uncharged tRNA. In this study, a novel group of isoleucyl-tRNA synthetase gene (ileS) T box leader sequences found in organisms of the phylum Actinobacteria was investigated. The Stem I domains of these RNAs lack several highly conserved elements that are essential for interaction with the tRNA ligand in other T box RNAs. Many of these RNAs were predicted to regulate gene expression at the level of translation initiation through tRNA-dependent stabilization of a helix that sequesters a sequence complementary to the Shine–Dalgarno (SD) sequence, thus freeing the SD sequence for ribosome binding and translation initiation. We demonstrated specific binding to the cognate tRNAIle and tRNAIle-dependent structural rearrangements consistent with regulation at the level of translation initiation, providing the first biochemical demonstration, to our knowledge, of translational regulation in a T box riboswitch. PMID:25583497

  3. Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks.

    PubMed

    Wei, Fangping; Chen, Bowen

    2012-03-01

    To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.

  4. Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure.

    PubMed

    Létoquart, Juliette; van Tran, Nhan; Caroline, Vonny; Aleksandrov, Alexey; Lazar, Noureddine; van Tilbeurgh, Herman; Liger, Dominique; Graille, Marc

    2015-12-15

    Most of the factors involved in translation (tRNA, rRNA and proteins) are subject to post-transcriptional and post-translational modifications, which participate in the fine-tuning and tight control of ribosome and protein synthesis processes. In eukaryotes, Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2). Trm112 is then at a nexus between ribosome synthesis and function. Here, we present a structure-function analysis of the Trm9-Trm112 complex, which is involved in the 5-methoxycarbonylmethyluridine (mcm(5)U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. We also compare the known crystal structures of various Trm112-MTase complexes, highlighting the structural plasticity allowing Trm112 to interact through a very similar mode with its MTase partners, although those share less than 20% sequence identity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Division of Labor Among the Yeast Sol Proteins Implicated in tRNA Nuclear Export and Carbohydrate Metabolism

    PubMed Central

    Stanford, D. R.; Whitney, M. L.; Hurto, R. L.; Eisaman, D. M.; Shen, W.-C.; Hopper, A. K.

    2004-01-01

    SOL1, the founding member of the S. cerevisiae SOL family, was previously identified as a multi-copy suppressor of the los1 defect in tRNA-mediated nonsense suppression. Here we report that the four-member SOL family is not essential and that individual family members appear to have distinct functions. SOL1–SOL4 are homologous to genes encoding 6-phosphogluconolactonase (6Pgl) involved in the pentose phosphate pathway. Both Sol3p and Sol4p affect this activity. However, Sol4p does not act as a los1 multi-copy suppressor. In contrast, neither Sol1p nor Sol2p, both of which correct the los1 defect in nonsense suppression, possess detectable 6Pgl activity. Rather, Sol1p and Sol2p appear to function in tRNA nuclear export as sol1 and sol2 mutants possess elevated levels of nuclear tRNA. Members of the Sol protein family appear to have different subcellular distributions. Thus, Sol3p and Sol4p likely function in carbohydrate metabolism, while Sol1p and Sol2p appear to have roles in tRNA function and nuclear export, thereby defining an unusual protein family whose individual members are biochemically distinct and spatially dispersed. PMID:15454531

  6. Division of labor among the yeast Sol proteins implicated in tRNA nuclear export and carbohydrate metabolism.

    PubMed

    Stanford, D R; Whitney, M L; Hurto, R L; Eisaman, D M; Shen, W-C; Hopper, A K

    2004-09-01

    SOL1, the founding member of the S. cerevisiae SOL family, was previously identified as a multi-copy suppressor of the los1 defect in tRNA-mediated nonsense suppression. Here we report that the four-member SOL family is not essential and that individual family members appear to have distinct functions. SOL1-SOL4 are homologous to genes encoding 6-phosphogluconolactonase (6Pgl) involved in the pentose phosphate pathway. Both Sol3p and Sol4p affect this activity. However, Sol4p does not act as a los1 multi-copy suppressor. In contrast, neither Sol1p nor Sol2p, both of which correct the los1 defect in nonsense suppression, possess detectable 6Pgl activity. Rather, Sol1p and Sol2p appear to function in tRNA nuclear export as sol1 and sol2 mutants possess elevated levels of nuclear tRNA. Members of the Sol protein family appear to have different subcellular distributions. Thus, Sol3p and Sol4p likely function in carbohydrate metabolism, while Sol1p and Sol2p appear to have roles in tRNA function and nuclear export, thereby defining an unusual protein family whose individual members are biochemically distinct and spatially dispersed.

  7. MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data

    PubMed Central

    Loher, Phillipe; Telonis, Aristeidis G.; Rigoutsos, Isidore

    2017-01-01

    Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license. PMID:28220888

  8. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.

    PubMed

    Sharma, Upasna; Conine, Colin C; Shea, Jeremy M; Boskovic, Ana; Derr, Alan G; Bing, Xin Y; Belleannee, Clemence; Kucukural, Alper; Serra, Ryan W; Sun, Fengyun; Song, Lina; Carone, Benjamin R; Ricci, Emiliano P; Li, Xin Z; Fauquier, Lucas; Moore, Melissa J; Sullivan, Robert; Mello, Craig C; Garber, Manuel; Rando, Oliver J

    2016-01-22

    Several recent studies link parental environments to phenotypes in subsequent generations. In this work, we investigate the mechanism by which paternal diet affects offspring metabolism. Protein restriction in mice affects small RNA (sRNA) levels in mature sperm, with decreased let-7 levels and increased amounts of 5' fragments of glycine transfer RNAs (tRNAs). In testicular sperm, tRNA fragments are scarce but increase in abundance as sperm mature in the epididymis. Epididymosomes (vesicles that fuse with sperm during epididymal transit) carry RNA payloads matching those of mature sperm and can deliver RNAs to immature sperm in vitro. Functionally, tRNA-glycine-GCC fragments repress genes associated with the endogenous retroelement MERVL, in both embryonic stem cells and embryos. Our results shed light on sRNA biogenesis and its dietary regulation during posttesticular sperm maturation, and they also link tRNA fragments to regulation of endogenous retroelements active in the preimplantation embryo. Copyright © 2016, American Association for the Advancement of Science.

  9. Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum

    PubMed Central

    Charles, Hubert; Calevro, Federica; Vinuelas, José; Fayard, Jean-Michel; Rahbe, Yvan

    2006-01-01

    Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in Buchnera: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon–anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of Buchnera. PMID:16963497

  10. Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum.

    PubMed

    Charles, Hubert; Calevro, Federica; Vinuelas, José; Fayard, Jean-Michel; Rahbe, Yvan

    2006-01-01

    Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in Buchnera: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon-anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of Buchnera.

  11. PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes.

    PubMed

    Rainaldi, Guglielmo; Volpicella, Mariateresa; Licciulli, Flavio; Liuni, Sabino; Gallerani, Raffaele; Ceci, Luigi R

    2003-01-01

    The updated version of PLMItRNA reports information and multialignments on 609 genes and 34 tRNA molecules active in the mitochondria of Viridiplantae (27 Embryophyta and 10 Chlorophyta), and photosynthetic algae (one Cryptophyta, four Rhodophyta and two Stramenopiles). Colour-code based tables reporting the different genetic origin of identified genes allow hyper-textual link to single entries. Promoter sequences identified for tRNA genes in the mitochondrial genomes of Angiospermae are also reported. The PLMItRNA database is accessible at http://bighost.area.ba.cnr.it/PLMItRNA/.

  12. Suppression of Murine Retrovirus Polypeptide Termination: Effect of Amber Suppressor tRNA on the Cell-Free Translation of Rauscher Murine Leukemia Virus, Moloney Murine Leukemia Virus, and Moloney Murine Sarcoma Virus 124 RNA

    PubMed Central

    Murphy, Edwin C.; Wills, Norma; Arlinghaus, Ralph B.

    1980-01-01

    The effect of suppressor tRNA's on the cell-free translation of several leukemia and sarcoma virus RNAs was examined. Yeast amber suppressor tRNA (amber tRNA) enhanced the synthesis of the Rauscher murine leukemia virus and clone 1 Moloney murine leukemia virus Pr200gag-pol polypeptides by 10- to 45-fold, but at the same time depressed the synthesis of Rauscher murine leukemia virus Pr65gag and Moloney murine leukemia virus Pr63gag. Under suppressor-minus conditions, Moloney murine leukemia virus Pr70gag was present as a closely spaced doublet. Amber tRNA stimulated the synthesis of the “upper” Moloney murine leukemia virus Pr70gag polypeptide. Yeast ochre suppressor tRNA appeared to be ineffective. Quantitative analyses of the kinetics of viral precursor polypeptide accumulation in the presence of amber tRNA showed that during linear protein synthesis, the increase in accumulated Moloney murine leukemia virus Pr200gag-pol coincided closely with the molar loss of Pr63gag. Enhancement of Pr200gag-pol and Pr70gag by amber tRNA persisted in the presence of pactamycin, a drug which blocks the initiation of protein synthesis, thus arguing for the addition of amino acids to the C terminus of Pr63gag as the mechanism behind the amber tRNA effect. Moloney murine sarcoma virus 124 30S RNA was translated into four major polypeptides, Pr63gag, P42, P38, and P23. In the presence of amber tRNA, a new polypeptide, Pr67gag, appeared, whereas Pr63gag synthesis was decreased. Quantitative estimates indicated that for every 1 mol of Pr67gag which appeared, 1 mol of Pr63gag was lost. Images PMID:7373716

  13. Mycobacterium tuberculosis Transfer RNA Induces IL-12p70 via Synergistic Activation of Pattern Recognition Receptors within a Cell Network.

    PubMed

    Keegan, Caroline; Krutzik, Stephan; Schenk, Mirjam; Scumpia, Philip O; Lu, Jing; Pang, Yan Ling Joy; Russell, Brandon S; Lim, Kok Seong; Shell, Scarlet; Prestwich, Erin; Su, Dan; Elashoff, David; Hershberg, Robert M; Bloom, Barry R; Belisle, John T; Fortune, Sarah; Dedon, Peter C; Pellegrini, Matteo; Modlin, Robert L

    2018-05-01

    Upon recognition of a microbial pathogen, the innate and adaptive immune systems are linked to generate a cell-mediated immune response against the foreign invader. The culture filtrate of Mycobacterium tuberculosis contains ligands, such as M. tuberculosis tRNA, that activate the innate immune response and secreted Ags recognized by T cells to drive adaptive immune responses. In this study, bioinformatics analysis of gene-expression profiles derived from human PBMCs treated with distinct microbial ligands identified a mycobacterial tRNA-induced innate immune network resulting in the robust production of IL-12p70, a cytokine required to instruct an adaptive Th1 response for host defense against intracellular bacteria. As validated by functional studies, this pathway contained a feed-forward loop, whereby the early production of IL-18, type I IFNs, and IL-12p70 primed NK cells to respond to IL-18 and produce IFN-γ, enhancing further production of IL-12p70. Mechanistically, tRNA activates TLR3 and TLR8, and this synergistic induction of IL-12p70 was recapitulated by the addition of a specific TLR8 agonist with a TLR3 ligand to PBMCs. These data indicate that M. tuberculosis tRNA activates a gene network involving the integration of multiple innate signals, including types I and II IFNs, as well as distinct cell types to induce IL-12p70. Copyright © 2018 by The American Association of Immunologists, Inc.

  14. Robotic CCD microscope for enhanced crystal recognition

    DOEpatents

    Segelke, Brent W.; Toppani, Dominique

    2007-11-06

    A robotic CCD microscope and procedures to automate crystal recognition. The robotic CCD microscope and procedures enables more accurate crystal recognition, leading to fewer false negative and fewer false positives, and enable detection of smaller crystals compared to other methods available today.

  15. Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.

    PubMed

    Seligmann, Hervé; Warthi, Ganesh

    2017-01-01

    A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').

  16. Possibility of cytoplasmic pre-tRNA splicing: the yeast tRNA splicing endonuclease mainly localizes on the mitochondria.

    PubMed

    Yoshihisa, Tohru; Yunoki-Esaki, Kaori; Ohshima, Chie; Tanaka, Nobuyuki; Endo, Toshiya

    2003-08-01

    Pre-tRNA splicing has been believed to occur in the nucleus. In yeast, the tRNA splicing endonuclease that cleaves the exon-intron junctions of pre-tRNAs consists of Sen54p, Sen2p, Sen34p, and Sen15p and was thought to be an integral membrane protein of the inner nuclear envelope. Here we show that the majority of Sen2p, Sen54p, and the endonuclease activity are not localized in the nucleus, but on the mitochondrial surface. The endonuclease is peripherally associated with the cytosolic surface of the outer mitochondrial membrane. A Sen54p derivative artificially fixed on the mitochondria as an integral membrane protein can functionally replace the authentic Sen54p, whereas mutant proteins defective in mitochondrial localization are not fully active. sen2 mutant cells accumulate unspliced pre-tRNAs in the cytosol under the restrictive conditions, and this export of the pre-tRNAs partly depends on Los1p, yeast exportin-t. It is difficult to explain these results from the view of tRNA splicing in the nucleus. We rather propose a new possibility that tRNA splicing occurs on the mitochondrial surface in yeast.

  17. A methods review on use of nonsense suppression to study 3′ end formation and other aspects of tRNA biogenesis

    PubMed Central

    Rijal, Keshab; Maraia, Richard J.; Arimbasseri, Aneeshkumar G.

    2014-01-01

    Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to S. pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5′ and 3′ processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3′ oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3′ oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a ‘technical approaches’ section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses. PMID:25447915

  18. Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome

    NASA Astrophysics Data System (ADS)

    Adio, Sarah; Senyushkina, Tamara; Peske, Frank; Fischer, Niels; Wintermeyer, Wolfgang; Rodnina, Marina V.

    2015-06-01

    The coupled translocation of transfer RNA and messenger RNA through the ribosome entails large-scale structural rearrangements, including step-wise movements of the tRNAs. Recent structural work has visualized intermediates of translocation induced by elongation factor G (EF-G) with tRNAs trapped in chimeric states with respect to 30S and 50S ribosomal subunits. The functional role of the chimeric states is not known. Here we follow the formation of translocation intermediates by single-molecule fluorescence resonance energy transfer. Using EF-G mutants, a non-hydrolysable GTP analogue, and fusidic acid, we interfere with either translocation or EF-G release from the ribosome and identify several rapidly interconverting chimeric tRNA states on the reaction pathway. EF-G engagement prevents backward transitions early in translocation and increases the fraction of ribosomes that rapidly fluctuate between hybrid, chimeric and posttranslocation states. Thus, the engagement of EF-G alters the energetics of translocation towards a flat energy landscape, thereby promoting forward tRNA movement.

  19. Specific replacement of Q base in the anticodon of tRNA by guanine catalyzed by a cell-free extract of rabbit reticulocytes.

    PubMed Central

    Okada, N; Harada, F; Nishimura, S

    1976-01-01

    Guanylation of tRNA by a lysate of rabbit reticulocytes was reported previously by Farkas and Singh. This reaction was investigated further using 18 purified E. coli tRNAs as acceptors.Results showed that only tRNATyr, tRNAHis, tRNAAsn and tRNAAsp which contain the modified nucleoside Q in the anticodon acted as acceptors. Analysis of the nucleotide sequences in the guanylated tRNA showed that guanine specifically replaced Q base in these tRNAs. Images PMID:792816

  20. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

    PubMed Central

    Zheng, Chenkang; Black, Katherine A.; Dos Santos, Patricia C.

    2017-01-01

    Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes. PMID:28327539

  1. Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.

    PubMed

    Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min

    2015-06-18

    Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Orthogonal use of a human tRNA synthetase active site to achieve multi-functionality

    PubMed Central

    Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B.; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A.; Schimmel, Paul; Yang, Xiang-Lei

    2011-01-01

    Protein multi-functionality is an emerging explanation for the complexity of higher organisms. In this regard, while aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, some also act in pathways for inflammation, angiogenesis, and apoptosis. How multiple functions evolved and their relationship to the active site is not clear. Here structural modeling analysis, mutagenesis, and cell-based functional studies show that the potent angiostatic, natural fragment of human TrpRS associates via Trp side chains that protrude from the cognate cellular receptor VE-cadherin. Modeling indicates that (I prefer the way it was because the conclusion was reached not only by modeling, but more so by experimental studies.)VE-cadherin Trp side chains fit into the Trp-specific active site of the synthetase. Thus, specific side chains of the receptor mimic (?) amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multi-functionality of human tRNA synthetases and other proteins. PMID:20010843

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

    PubMed

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

    2013-09-27

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

  4. Sudden Event Recognition: A Survey

    PubMed Central

    Suriani, Nor Surayahani; Hussain, Aini; Zulkifley, Mohd Asyraf

    2013-01-01

    Event recognition is one of the most active research areas in video surveillance fields. Advancement in event recognition systems mainly aims to provide convenience, safety and an efficient lifestyle for humanity. A precise, accurate and robust approach is necessary to enable event recognition systems to respond to sudden changes in various uncontrolled environments, such as the case of an emergency, physical threat and a fire or bomb alert. The performance of sudden event recognition systems depends heavily on the accuracy of low level processing, like detection, recognition, tracking and machine learning algorithms. This survey aims to detect and characterize a sudden event, which is a subset of an abnormal event in several video surveillance applications. This paper discusses the following in detail: (1) the importance of a sudden event over a general anomalous event; (2) frameworks used in sudden event recognition; (3) the requirements and comparative studies of a sudden event recognition system and (4) various decision-making approaches for sudden event recognition. The advantages and drawbacks of using 3D images from multiple cameras for real-time application are also discussed. The paper concludes with suggestions for future research directions in sudden event recognition. PMID:23921828

  5. Accurate, fast, and secure biometric fingerprint recognition system utilizing sensor fusion of fingerprint patterns

    NASA Astrophysics Data System (ADS)

    El-Saba, Aed; Alsharif, Salim; Jagapathi, Rajendarreddy

    2011-04-01

    Fingerprint recognition is one of the first techniques used for automatically identifying people and today it is still one of the most popular and effective biometric techniques. With this increase in fingerprint biometric uses, issues related to accuracy, security and processing time are major challenges facing the fingerprint recognition systems. Previous work has shown that polarization enhancementencoding of fingerprint patterns increase the accuracy and security of fingerprint systems without burdening the processing time. This is mainly due to the fact that polarization enhancementencoding is inherently a hardware process and does not have detrimental time delay effect on the overall process. Unpolarized images, however, posses a high visual contrast and when fused (without digital enhancement) properly with polarized ones, is shown to increase the recognition accuracy and security of the biometric system without any significant processing time delay.

  6. Episodic Short-Term Recognition Requires Encoding into Visual Working Memory: Evidence from Probe Recognition after Letter Report

    PubMed Central

    Poth, Christian H.; Schneider, Werner X.

    2016-01-01

    Human vision is organized in discrete processing episodes (e.g., eye fixations or task-steps). Object information must be transmitted across episodes to enable episodic short-term recognition: recognizing whether a current object has been seen in a previous episode. We ask whether episodic short-term recognition presupposes that objects have been encoded into capacity-limited visual working memory (VWM), which retains visual information for report. Alternatively, it could rely on the activation of visual features or categories that occurs before encoding into VWM. We assessed the dependence of episodic short-term recognition on VWM by a new paradigm combining letter report and probe recognition. Participants viewed displays of 10 letters and reported as many as possible after a retention interval (whole report). Next, participants viewed a probe letter and indicated whether it had been one of the 10 letters (probe recognition). In Experiment 1, probe recognition was more accurate for letters that had been encoded into VWM (reported letters) compared with non-encoded letters (non-reported letters). Interestingly, those letters that participants reported in their whole report had been near to one another within the letter displays. This suggests that the encoding into VWM proceeded in a spatially clustered manner. In Experiment 2, participants reported only one of 10 letters (partial report) and probes either referred to this letter, to letters that had been near to it, or far from it. Probe recognition was more accurate for near than for far letters, although none of these letters had to be reported. These findings indicate that episodic short-term recognition is constrained to a small number of simultaneously presented objects that have been encoded into VWM. PMID:27713722

  7. Episodic Short-Term Recognition Requires Encoding into Visual Working Memory: Evidence from Probe Recognition after Letter Report.

    PubMed

    Poth, Christian H; Schneider, Werner X

    2016-01-01

    Human vision is organized in discrete processing episodes (e.g., eye fixations or task-steps). Object information must be transmitted across episodes to enable episodic short-term recognition: recognizing whether a current object has been seen in a previous episode. We ask whether episodic short-term recognition presupposes that objects have been encoded into capacity-limited visual working memory (VWM), which retains visual information for report. Alternatively, it could rely on the activation of visual features or categories that occurs before encoding into VWM. We assessed the dependence of episodic short-term recognition on VWM by a new paradigm combining letter report and probe recognition. Participants viewed displays of 10 letters and reported as many as possible after a retention interval (whole report). Next, participants viewed a probe letter and indicated whether it had been one of the 10 letters (probe recognition). In Experiment 1, probe recognition was more accurate for letters that had been encoded into VWM (reported letters) compared with non-encoded letters (non-reported letters). Interestingly, those letters that participants reported in their whole report had been near to one another within the letter displays. This suggests that the encoding into VWM proceeded in a spatially clustered manner. In Experiment 2, participants reported only one of 10 letters (partial report) and probes either referred to this letter, to letters that had been near to it, or far from it. Probe recognition was more accurate for near than for far letters, although none of these letters had to be reported. These findings indicate that episodic short-term recognition is constrained to a small number of simultaneously presented objects that have been encoded into VWM.

  8. The development of cross-cultural recognition of vocal emotion during childhood and adolescence.

    PubMed

    Chronaki, Georgia; Wigelsworth, Michael; Pell, Marc D; Kotz, Sonja A

    2018-06-14

    Humans have an innate set of emotions recognised universally. However, emotion recognition also depends on socio-cultural rules. Although adults recognise vocal emotions universally, they identify emotions more accurately in their native language. We examined developmental trajectories of universal vocal emotion recognition in children. Eighty native English speakers completed a vocal emotion recognition task in their native language (English) and foreign languages (Spanish, Chinese, and Arabic) expressing anger, happiness, sadness, fear, and neutrality. Emotion recognition was compared across 8-to-10, 11-to-13-year-olds, and adults. Measures of behavioural and emotional problems were also taken. Results showed that although emotion recognition was above chance for all languages, native English speaking children were more accurate in recognising vocal emotions in their native language. There was a larger improvement in recognising vocal emotion from the native language during adolescence. Vocal anger recognition did not improve with age for the non-native languages. This is the first study to demonstrate universality of vocal emotion recognition in children whilst supporting an "in-group advantage" for more accurate recognition in the native language. Findings highlight the role of experience in emotion recognition, have implications for child development in modern multicultural societies and address important theoretical questions about the nature of emotions.

  9. An investigation of the effect of race-based social categorization on adults' recognition of emotion.

    PubMed

    Reyes, B Nicole; Segal, Shira C; Moulson, Margaret C

    2018-01-01

    Emotion recognition is important for social interaction and communication, yet previous research has identified a cross-cultural emotion recognition deficit: Recognition is less accurate for emotions expressed by individuals from a cultural group different than one's own. The current study examined whether social categorization based on race, in the absence of cultural differences, influences emotion recognition in a diverse context. South Asian and White Canadians in the Greater Toronto Area completed an emotion recognition task that required them to identify the seven basic emotional expressions when posed by members of the same two groups, allowing us to tease apart the contributions of culture and social group membership. Contrary to our hypothesis, there was no mutual in-group advantage in emotion recognition: Participants were not more accurate at recognizing emotions posed by their respective racial in-groups. Both groups were more accurate at recognizing expressions when posed by South Asian faces, and White participants were more accurate overall compared to South Asian participants. These results suggest that in a diverse environment, categorization based on race alone does not lead to the creation of social out-groups in a way that negatively impacts emotion recognition.

  10. An investigation of the effect of race-based social categorization on adults’ recognition of emotion

    PubMed Central

    Reyes, B. Nicole; Segal, Shira C.

    2018-01-01

    Emotion recognition is important for social interaction and communication, yet previous research has identified a cross-cultural emotion recognition deficit: Recognition is less accurate for emotions expressed by individuals from a cultural group different than one’s own. The current study examined whether social categorization based on race, in the absence of cultural differences, influences emotion recognition in a diverse context. South Asian and White Canadians in the Greater Toronto Area completed an emotion recognition task that required them to identify the seven basic emotional expressions when posed by members of the same two groups, allowing us to tease apart the contributions of culture and social group membership. Contrary to our hypothesis, there was no mutual in-group advantage in emotion recognition: Participants were not more accurate at recognizing emotions posed by their respective racial in-groups. Both groups were more accurate at recognizing expressions when posed by South Asian faces, and White participants were more accurate overall compared to South Asian participants. These results suggest that in a diverse environment, categorization based on race alone does not lead to the creation of social out-groups in a way that negatively impacts emotion recognition. PMID:29474367

  11. In vivo modification of tRNA with an artificial nucleobase leads to full disease remission in an animal model of multiple sclerosis.

    PubMed

    Varghese, Sreeja; Cotter, Michelle; Chevot, Franciane; Fergus, Claire; Cunningham, Colm; Mills, Kingston H; Connon, Stephen J; Southern, John M; Kelly, Vincent P

    2017-02-28

    Queuine is a modified pyrrolopyrimidine nucleobase derived exclusively from bacteria. It post-transcriptionally replaces guanine 34 in transfer RNA isoacceptors for Asp, Asn, His and Tyr, in almost all eukaryotic organisms, through the activity of the ancient tRNA guanine transglycosylase (TGT) enzyme. tRNA hypomodification with queuine is a characteristic of rapidly-proliferating, non-differentiated cells. Autoimmune diseases, including multiple sclerosis, are characterised by the rapid expansion of T cells directed to self-antigens. Here, we demonstrate the potential medicinal relevance of targeting the modification of tRNA in the treatment of a chronic multiple sclerosis model—murine experimental autoimmune encephalomyelitis. Administration of a de novo designed eukaryotic TGT substrate (NPPDAG) led to an unprecedented complete reversal of clinical symptoms and a dramatic reduction of markers associated with immune hyperactivation and neuronal damage after five daily doses. TGT is essential for the therapeutic effect, since animals deficient in TGT activity were refractory to therapy. The data suggest that exploitation of the eukaryotic TGT enzyme is a promising approach for the treatment of multiple sclerosis.

  12. Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

    NASA Astrophysics Data System (ADS)

    Kates-Harbeck, Julian; Tilloy, Antoine; Prentiss, Mara

    2013-07-01

    Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.

  13. Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism.

    PubMed

    Shaheen, Ranad; Abdel-Salam, Ghada M H; Guy, Michael P; Alomar, Rana; Abdel-Hamid, Mohamed S; Afifi, Hanan H; Ismail, Samira I; Emam, Bayoumi A; Phizicky, Eric M; Alkuraya, Fowzan S

    2015-09-28

    Primordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity. Two presumably unrelated consanguineous families presented with an apparently novel form of primordial dwarfism in which severe growth deficiency is accompanied by distinct facial dysmorphism, brain malformation (microcephaly, agenesis of corpus callosum, and simplified gyration), and severe encephalopathy with seizures. Combined autozygome/exome analysis revealed a novel missense mutation in WDR4 as the likely causal variant. WDR4 is the human ortholog of the yeast Trm82, an essential component of the Trm8/Trm82 holoenzyme that effects a highly conserved and specific (m(7)G46) methylation of tRNA. The human mutation and the corresponding yeast mutation result in a significant reduction of m(7)G46 methylation of specific tRNA species, which provides a potential mechanism for primordial dwarfism associated with this lesion, since reduced m(7)G46 modification causes a growth deficiency phenotype in yeast. Our study expands the number of biological pathways underlying primordial dwarfism and adds to a growing list of human diseases linked to abnormal tRNA modification.

  14. Varying face occlusion detection and iterative recovery for face recognition

    NASA Astrophysics Data System (ADS)

    Wang, Meng; Hu, Zhengping; Sun, Zhe; Zhao, Shuhuan; Sun, Mei

    2017-05-01

    In most sparse representation methods for face recognition (FR), occlusion problems were usually solved via removing the occlusion part of both query samples and training samples to perform the recognition process. This practice ignores the global feature of facial image and may lead to unsatisfactory results due to the limitation of local features. Considering the aforementioned drawback, we propose a method called varying occlusion detection and iterative recovery for FR. The main contributions of our method are as follows: (1) to detect an accurate occlusion area of facial images, an image processing and intersection-based clustering combination method is used for occlusion FR; (2) according to an accurate occlusion map, the new integrated facial images are recovered iteratively and put into a recognition process; and (3) the effectiveness on recognition accuracy of our method is verified by comparing it with three typical occlusion map detection methods. Experiments show that the proposed method has a highly accurate detection and recovery performance and that it outperforms several similar state-of-the-art methods against partial contiguous occlusion.

  15. Loss of the mitochondrial protein-only ribonuclease P complex causes aberrant tRNA processing and lethality in Drosophila.

    PubMed

    Sen, Aditya; Karasik, Agnes; Shanmuganathan, Aranganathan; Mirkovic, Elena; Koutmos, Markos; Cox, Rachel T

    2016-07-27

    Proteins encoded by mitochondrial DNA are translated using mitochondrially encoded tRNAs and rRNAs. As with nuclear encoded tRNAs, mitochondrial tRNAs must be processed to become fully functional. The mitochondrial form of ribonuclease P (mt:RNase P) is responsible for 5'-end maturation and is comprised of three proteins; mitochondrial RNase P protein (MRPP) 1 and 2 together with proteinaceous RNase P (PRORP). However, its mechanism and impact on development is not yet known. Using homology searches, we have identified the three proteins composing Drosophila mt:RNase P: Mulder (PRORP), Scully (MRPP2) and Roswell (MRPP1). Here, we show that each protein is essential and localizes with mitochondria. Furthermore, reducing levels of each causes mitochondrial deficits, which appear to be due at least in part to defective mitochondrial tRNA processing. Overexpressing two members of the complex, Mulder and Roswell, is also lethal, and in the case of Mulder, causes abnormal mitochondrial morphology. These data are the first evidence that defective mt:RNase P causes mitochondrial dysfunction, lethality and aberrant mitochondrial tRNA processing in vivo, underscoring its physiological importance. This in vivo mt:RNase P model will advance our understanding of how loss of mitochondrial tRNA processing causes tissue failure, an important aspect of human mitochondrial disease. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  16. Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains.

    PubMed

    Du, Meng-Ze; Wei, Wen; Qin, Lei; Liu, Shuo; Zhang, An-Ying; Zhang, Yong; Zhou, Hong; Guo, Feng-Biao

    2017-12-01

    Although more and more entangled participants of translation process were realized, how they cooperate and co-determine the final translation efficiency still lacks details. Here, we reasoned that the basic translation components, tRNAs and amino acids should be consistent to maximize the efficiency and minimize the cost. We firstly revealed that 310 out of 410 investigated genomes of three domains had significant co-adaptions between the tRNA gene copy numbers and amino acid compositions, indicating that maximum efficiency constitutes ubiquitous selection pressure on protein translation. Furthermore, fast-growing and larger bacteria are found to have significantly better co-adaption and confirmed the effect of this pressure. Within organism, highly expressed proteins and those connected to acute responses have higher co-adaption intensity. Thus, the better co-adaption probably speeds up the growing of cells through accelerating the translation of special proteins. Experimentally, manipulating the tRNA gene copy number to optimize co-adaption between enhanced green fluorescent protein (EGFP) and tRNA gene set of Escherichia coli indeed lifted the translation rate (speed). Finally, as a newly confirmed translation rate regulating mechanism, the co-adaption reflecting translation rate not only deepens our understanding on translation process but also provides an easy and practicable method to improve protein translation rates and productivity. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  17. Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains

    PubMed Central

    Du, Meng-Ze; Wei, Wen; Qin, Lei; Liu, Shuo; Zhang, An-Ying; Zhang, Yong; Zhou, Hong

    2017-01-01

    Abstract Although more and more entangled participants of translation process were realized, how they cooperate and co-determine the final translation efficiency still lacks details. Here, we reasoned that the basic translation components, tRNAs and amino acids should be consistent to maximize the efficiency and minimize the cost. We firstly revealed that 310 out of 410 investigated genomes of three domains had significant co-adaptions between the tRNA gene copy numbers and amino acid compositions, indicating that maximum efficiency constitutes ubiquitous selection pressure on protein translation. Furthermore, fast-growing and larger bacteria are found to have significantly better co-adaption and confirmed the effect of this pressure. Within organism, highly expressed proteins and those connected to acute responses have higher co-adaption intensity. Thus, the better co-adaption probably speeds up the growing of cells through accelerating the translation of special proteins. Experimentally, manipulating the tRNA gene copy number to optimize co-adaption between enhanced green fluorescent protein (EGFP) and tRNA gene set of Escherichia coli indeed lifted the translation rate (speed). Finally, as a newly confirmed translation rate regulating mechanism, the co-adaption reflecting translation rate not only deepens our understanding on translation process but also provides an easy and practicable method to improve protein translation rates and productivity. PMID:28992099

  18. In vitro selection of electrochemical peptide probes using bioorthogonal tRNA for influenza virus detection.

    PubMed

    K C, Tara Bahadur; Tada, Seiichi; Zhu, Liping; Uzawa, Takanori; Minagawa, Noriko; Luo, Shyh-Chyang; Zhao, Haichao; Yu, Hsiao-Hua; Aigaki, Toshiro; Ito, Yoshihiro

    2018-05-17

    An electrosensitive peptide probe has been developed from an in vitro selection technique using biorthogonal tRNA prepared with an electroreactive non-natural amino acid, 3,4-ethylenedioxythiophene-conjugated aminophenylalanine. The selected probe quantitatively detected the influenza virus based on a signal "turn-on" mechanism. The developed strategy could be used to develop electrochemical biosensors toward a variety of targets.

  19. Interaction of polyethyleneimine-anchored copper(II) complexes with tRNA studied by spectroscopy methods and biological activities.

    PubMed

    Lakshmipraba, Jagadeesan; Arunachalam, Sankaralingam; Gandi, Devadas A; Thirunalasundari, Thyagarajan; Vignesh, Sivanandham; James, Rathinam A

    2017-05-01

    Ultraviolet-visible, emission and circular dichroism spectroscopic methods were used in transfer RNA (tRNA) interaction studies performed for polyethyleneimine-copper(II) complexes [Cu(phen)(l-Tyr)BPEI]ClO 4 (where phen =1,10-phenanthroline, l-Tyr = l-tyrosine and BPEI = branched polyethyleneimine) with various degrees of coordination (x = 0.059, 0.149, 0.182) in the polymer chain. The results indicated that polyethyleneimine-copper(II) complexes bind with tRNA mostly through surface binding, although other binding modes, such as hydrogen bonding and van der Waals interactions, might also be present. Dye-exclusion, sulforhodamine B and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assays of a polyethyleneimine-copper(II) complex with a higher degree of coordination against different cancer cell lines proved that the complex exhibited cytotoxic specificity and a significant cancer cell inhibition rate. Antimicrobial screening showed activity against some human pathogens. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability.

    PubMed

    Morton, B R

    1993-09-01

    Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the psb A gene of all three genomes and other psb A sequences examined. In this gene, the codon use favors NNC over NNT for twofold degenerate amino acids. In each case the only tRNA coded by the genome is complementary to the NNC codon. This codon use is similar to the codon use by chloroplast genes examined from Chlamydomonas reinhardtii. Since psb A is the major translation product of the chloroplast, this suggests that selection is acting on the codon use of this gene to adapt codons to tRNA availability, as previously suggested for unicellular organisms.

  1. Utp22p acts in concert with Utp8p to channel aminoacyl-tRNA from the nucleolus to the nuclear tRNA export receptor Los1p but not Msn5p.

    PubMed

    Eswara, Manoja B K; Clayton, Ashley; Mangroo, Dev

    2012-12-01

    Utp8p is an essential nucleolar protein that channels aminoacyl-tRNAs from aminoacyl-tRNA synthetases in the nucleolus to the nuclear tRNA export receptors located in the nucleoplasm and nuclear pore complex in Saccharomyces cerevisiae. Utp8p is also part of the U3 snoRNA-associated protein complex involved in 18S rRNA biogenesis in the nucleolus. We report that Utp22p, which is another member of the U3 snoRNA-associated protein complex, is also an intranuclear component of the nuclear tRNA export machinery. Depletion of Utp22p results in nuclear retention of mature tRNAs derived from intron-containing and intronless precursors. Moreover, Utp22p copurifies with the nuclear tRNA export receptor Los1p, the aminoacyl-tRNA synthetase Tys1p and Utp8p, but not with the RanGTPase Gsp1p and the nuclear tRNA export receptor Msn5p. Utp22p interacts directly with Utp8p and Los1p in a tRNA-independent manner in vitro. Utp22p also interacts directly with Tys1p, but this binding is stimulated when Tys1p is bound to tRNA. However, Utp22p, unlike Utp8p, does not bind tRNA saturably. These data suggest that Utp22p recruits Utp8p to aminoacyl-tRNA synthetases in the nucleolus to collect aminoacyl-tRNA and then accompanies the Utp8p-tRNA complex to deliver the aminoacyl-tRNAs to Los1p but not Msn5p. It is possible that Nrap/Nol6, the mammalian orthologue of Utp22p, plays a role in channelling aminoacyl-tRNA to the nuclear tRNA export receptor exportin-t.

  2. Global translational impacts of the loss of the tRNA modification t6A in yeast.

    PubMed

    Thiaville, Patrick C; Legendre, Rachel; Rojas-Benítez, Diego; Baudin-Baillieu, Agnès; Hatin, Isabelle; Chalancon, Guilhem; Glavic, Alvaro; Namy, Olivier; de Crécy-Lagard, Valérie

    2016-01-01

    The universal tRNA modification t 6 A is found at position 37 of nearly all tRNAs decoding ANN codons. The absence of t 6 A 37 leads to severe growth defects in baker's yeast, phenotypes similar to those caused by defects in mcm 5 s 2 U 34 synthesis. Mutants in mcm 5 s 2 U 34 can be suppressed by overexpression of tRNA Lys UUU , but we show t 6 A phenotypes could not be suppressed by expressing any individual ANN decoding tRNA, and t 6 A and mcm 5 s 2 U are not determinants for each other's formation. Our results suggest that t 6 A deficiency, like mcm 5 s 2 U deficiency, leads to protein folding defects, and show that the absence of t 6 A led to stress sensitivities (heat, ethanol, salt) and sensitivity to TOR pathway inhibitors. Additionally, L-homoserine suppressed the slow growth phenotype seen in t 6 A-deficient strains, and proteins aggregates and Advanced Glycation End-products (AGEs) were increased in the mutants. The global consequences on translation caused by t 6 A absence were examined by ribosome profiling. Interestingly, the absence of t 6 A did not lead to global translation defects, but did increase translation initiation at upstream non-AUG codons and increased frame-shifting in specific genes. Analysis of codon occupancy rates suggests that one of the major roles of t 6 A is to homogenize the process of elongation by slowing the elongation rate at codons decoded by high abundance tRNAs and I 34 :C 3 pairs while increasing the elongation rate of rare tRNAs and G 34 :U 3 pairs. This work reveals that the consequences of t 6 A absence are complex and multilayered and has set the stage to elucidate the molecular basis of the observed phenotypes.

  3. Document recognition serving people with disabilities

    NASA Astrophysics Data System (ADS)

    Fruchterman, James R.

    2007-01-01

    Document recognition advances have improved the lives of people with print disabilities, by providing accessible documents. This invited paper provides perspectives on the author's career progression from document recognition professional to social entrepreneur applying this technology to help people with disabilities. Starting with initial thoughts about optical character recognition in college, it continues with the creation of accurate omnifont character recognition that did not require training. It was difficult to make a reading machine for the blind in a commercial setting, which led to the creation of a nonprofit social enterprise to deliver these devices around the world. This network of people with disabilities scanning books drove the creation of Bookshare.org, an online library of scanned books. Looking forward, the needs for improved document recognition technology to further lower the barriers to reading are discussed. Document recognition professionals should be proud of the positive impact their work has had on some of society's most disadvantaged communities.

  4. The Suitability of Cloud-Based Speech Recognition Engines for Language Learning

    ERIC Educational Resources Information Center

    Daniels, Paul; Iwago, Koji

    2017-01-01

    As online automatic speech recognition (ASR) engines become more accurate and more widely implemented with call software, it becomes important to evaluate the effectiveness and the accuracy of these recognition engines using authentic speech samples. This study investigates two of the most prominent cloud-based speech recognition engines--Apple's…

  5. Accurate label-free 3-part leukocyte recognition with single cell lens-free imaging flow cytometry.

    PubMed

    Li, Yuqian; Cornelis, Bruno; Dusa, Alexandra; Vanmeerbeeck, Geert; Vercruysse, Dries; Sohn, Erik; Blaszkiewicz, Kamil; Prodanov, Dimiter; Schelkens, Peter; Lagae, Liesbet

    2018-05-01

    Three-part white blood cell differentials which are key to routine blood workups are typically performed in centralized laboratories on conventional hematology analyzers operated by highly trained staff. With the trend of developing miniaturized blood analysis tool for point-of-need in order to accelerate turnaround times and move routine blood testing away from centralized facilities on the rise, our group has developed a highly miniaturized holographic imaging system for generating lens-free images of white blood cells in suspension. Analysis and classification of its output data, constitutes the final crucial step ensuring appropriate accuracy of the system. In this work, we implement reference holographic images of single white blood cells in suspension, in order to establish an accurate ground truth to increase classification accuracy. We also automate the entire workflow for analyzing the output and demonstrate clear improvement in the accuracy of the 3-part classification. High-dimensional optical and morphological features are extracted from reconstructed digital holograms of single cells using the ground-truth images and advanced machine learning algorithms are investigated and implemented to obtain 99% classification accuracy. Representative features of the three white blood cell subtypes are selected and give comparable results, with a focus on rapid cell recognition and decreased computational cost. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Mitochondrial tRNA 5'-editing in Dictyostelium discoideum and Polysphondylium pallidum.

    PubMed

    Abad, Maria G; Long, Yicheng; Kinchen, R Dimitri; Schindel, Elinor T; Gray, Michael W; Jackman, Jane E

    2014-05-30

    Mitochondrial tRNA (mt-tRNA) 5'-editing was first described more than 20 years ago; however, the first candidates for 5'-editing enzymes were only recently identified in a eukaryotic microbe (protist), the slime mold Dictyostelium discoideum. In this organism, eight of 18 mt-tRNAs are predicted to be edited based on the presence of genomically encoded mismatched nucleotides in their aminoacyl-acceptor stem sequences. Here, we demonstrate that mt-tRNA 5'-editing occurs at all predicted sites in D. discoideum as evidenced by changes in the sequences of isolated mt-tRNAs compared with the expected sequences encoded by the mitochondrial genome. We also identify two previously unpredicted editing events in which G-U base pairs are edited in the absence of any other genomically encoded mismatches. A comparison of 5'-editing in D. discoideum with 5'-editing in another slime mold, Polysphondylium pallidum, suggests organism-specific idiosyncrasies in the treatment of U-G/G-U pairs. In vitro activities of putative D. discoideum editing enzymes are consistent with the observed editing reactions and suggest an overall lack of tRNA substrate specificity exhibited by the repair component of the editing enzyme. Although the presence of terminal mismatches in mt-tRNA sequences is highly predictive of the occurrence of mt-tRNA 5'-editing, the variability in treatment of U-G/G-U base pairs observed here indicates that direct experimental evidence of 5'-editing must be obtained to understand the complete spectrum of mt-tRNA editing events in any species. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon.

    PubMed Central

    Yokoyama, S; Watanabe, T; Murao, K; Ishikura, H; Yamaizumi, Z; Nishimura, S; Miyazawa, T

    1985-01-01

    Proton NMR analyses have been made to elucidate the conformational characteristics of modified nucleotides as found in the first position of the anticodon of tRNA [derivatives of 5-methyl-2-thiouridine 5'-monophosphate (pxm5s2U) and derivatives of 5-hydroxyuridine 5'-monophosphate (pxo5U)]. In pxm5s2U, the C3'-endo form is extraordinarily more stable than the C2'-endo form for the ribose ring, because of the combined effects of the 2-thiocarbonyl group and the 5-substituent. By contrast, in pxo5U, the C2'-endo form is much more stable than the C3'-endo form, because of the interaction between the 5-substituent and the 5'-phosphate group. The enthalpy differences between the C2'-endo form and the C3'-endo form have been obtained as 1.1, -0.7, and 0.1 kcal/mol (1 cal = 4.184 J) for pxm5s2U, pxo5U, and unmodified uridine 5'-monophosphate, respectively. These findings lead to the conclusion that xm5s2U in the first position of the anticodon exclusively takes the C3'-endo form to recognize adenosine (but not uridine) as the third letter of the codon, whereas xo5U takes the C2'-endo form as well as the C3'-endo form to recognize adenosine, guanosine, and uridine as the third letter of the codon on ribosome. Accordingly, the biological significance of such modifications of uridine to xm5s2U/xo5U is in the regulation of the conformational rigidity/flexibility in the first position of the anticodon so as to guarantee the correct and efficient translation of codons in protein biosynthesis. PMID:3860833

  8. Neural network application for thermal image recognition of low-resolution objects

    NASA Astrophysics Data System (ADS)

    Fang, Yi-Chin; Wu, Bo-Wen

    2007-02-01

    In the ever-changing situation on a battle field, accurate recognition of a distant object is critical to a commander's decision-making and the general public's safety. Efficiently distinguishing between an enemy's armoured vehicles and ordinary civilian houses under all weather conditions has become an important research topic. This study presents a system for recognizing an armoured vehicle by distinguishing marks and contours. The characteristics of 12 different shapes and 12 characters are used to explore thermal image recognition under the circumstance of long distance and low resolution. Although the recognition capability of human eyes is superior to that of artificial intelligence under normal conditions, it tends to deteriorate substantially under long-distance and low-resolution scenarios. This study presents an effective method for choosing features and processing images. The artificial neural network technique is applied to further improve the probability of accurate recognition well beyond the limit of the recognition capability of human eyes.

  9. Structural insights into eRF3 and stop codon recognition by eRF1

    PubMed Central

    Cheng, Zhihong; Saito, Kazuki; Pisarev, Andrey V.; Wada, Miki; Pisareva, Vera P.; Pestova, Tatyana V.; Gajda, Michal; Round, Adam; Kong, Chunguang; Lim, Mengkiat; Nakamura, Yoshikazu; Svergun, Dmitri I.; Ito, Koichi; Song, Haiwei

    2009-01-01

    Eukaryotic translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act cooperatively to ensure efficient stop codon recognition and fast polypeptide release. The crystal structures of human and Schizosaccharomyces pombe full-length eRF1 in complex with eRF3 lacking the GTPase domain revealed details of the interaction between these two factors and marked conformational changes in eRF1 that occur upon binding to eRF3, leading eRF1 to resemble a tRNA molecule. Small-angle X-ray scattering analysis of the eRF1/eRF3/GTP complex suggested that eRF1's M domain contacts eRF3's GTPase domain. Consistently, mutation of Arg192, which is predicted to come in close contact with the switch regions of eRF3, revealed its important role for eRF1's stimulatory effect on eRF3's GTPase activity. An ATP molecule used as a crystallization additive was bound in eRF1's putative decoding area. Mutational analysis of the ATP-binding site shed light on the mechanism of stop codon recognition by eRF1. PMID:19417105

  10. Accurate Identification of Fear Facial Expressions Predicts Prosocial Behavior

    PubMed Central

    Marsh, Abigail A.; Kozak, Megan N.; Ambady, Nalini

    2009-01-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants’ ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale. PMID:17516803

  11. Accurate identification of fear facial expressions predicts prosocial behavior.

    PubMed

    Marsh, Abigail A; Kozak, Megan N; Ambady, Nalini

    2007-05-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants' ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale.

  12. Dynamics of the active site loops in catalyzing aminoacylation reaction in seryl and histidyl tRNA synthetases.

    PubMed

    Dutta, Saheb; Kundu, Soumya; Saha, Amrita; Nandi, Nilashis

    2018-03-01

    Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ( mk SerRS) and histidyl tRNA synthetases from Thermus thermophilus ( tt HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain. Catalytic residues of the loops form a network of interaction with the substrates to form a reactive state. The loops undergo transitions between closed state and open state and the relaxation of the constituent residues occurs in femtosecond to nanosecond time scale. Order parameters are higher for constituent catalytic residues which form a specific network of interaction with the substrates to form a reactive state compared to the Gly residues within the loop. The development of interaction is supported from mutation studies where the catalytic domain with mutated loop exhibits unfavorable binding energy with the substrates. During the open-close motion of the loops, the catalytic residues make relaxation by ultrafast librational motion as well as fast diffusive motion and subsequently relax rather slowly via slower diffusive motion. The Gly residues act as a hinge to facilitate the loop closing and opening by their faster relaxation behavior. The role of bound water is analyzed by comparing implicit solvent-based and explicit solvent-based simulations. Loops fail to form catalytically competent geometry in absence of water. The present result, for the first time reveals the nature of the active site loop dynamics in aaRS and their influence on catalysis.

  13. Accurate Iris Recognition at a Distance Using Stabilized Iris Encoding and Zernike Moments Phase Features.

    PubMed

    Tan, Chun-Wei; Kumar, Ajay

    2014-07-10

    Accurate iris recognition from the distantly acquired face or eye images requires development of effective strategies which can account for significant variations in the segmented iris image quality. Such variations can be highly correlated with the consistency of encoded iris features and the knowledge that such fragile bits can be exploited to improve matching accuracy. A non-linear approach to simultaneously account for both local consistency of iris bit and also the overall quality of the weight map is proposed. Our approach therefore more effectively penalizes the fragile bits while simultaneously rewarding more consistent bits. In order to achieve more stable characterization of local iris features, a Zernike moment-based phase encoding of iris features is proposed. Such Zernike moments-based phase features are computed from the partially overlapping regions to more effectively accommodate local pixel region variations in the normalized iris images. A joint strategy is adopted to simultaneously extract and combine both the global and localized iris features. The superiority of the proposed iris matching strategy is ascertained by providing comparison with several state-of-the-art iris matching algorithms on three publicly available databases: UBIRIS.v2, FRGC, CASIA.v4-distance. Our experimental results suggest that proposed strategy can achieve significant improvement in iris matching accuracy over those competing approaches in the literature, i.e., average improvement of 54.3%, 32.7% and 42.6% in equal error rates, respectively for UBIRIS.v2, FRGC, CASIA.v4-distance.

  14. Iris Recognition: The Consequences of Image Compression

    NASA Astrophysics Data System (ADS)

    Ives, Robert W.; Bishop, Daniel A.; Du, Yingzi; Belcher, Craig

    2010-12-01

    Iris recognition for human identification is one of the most accurate biometrics, and its employment is expanding globally. The use of portable iris systems, particularly in law enforcement applications, is growing. In many of these applications, the portable device may be required to transmit an iris image or template over a narrow-bandwidth communication channel. Typically, a full resolution image (e.g., VGA) is desired to ensure sufficient pixels across the iris to be confident of accurate recognition results. To minimize the time to transmit a large amount of data over a narrow-bandwidth communication channel, image compression can be used to reduce the file size of the iris image. In other applications, such as the Registered Traveler program, an entire iris image is stored on a smart card, but only 4 kB is allowed for the iris image. For this type of application, image compression is also the solution. This paper investigates the effects of image compression on recognition system performance using a commercial version of the Daugman iris2pi algorithm along with JPEG-2000 compression, and links these to image quality. Using the ICE 2005 iris database, we find that even in the face of significant compression, recognition performance is minimally affected.

  15. Body Emotion Recognition Disproportionately Depends on Vertical Orientations during Childhood

    ERIC Educational Resources Information Center

    Balas, Benjamin; Auen, Amanda; Saville, Alyson; Schmidt, Jamie

    2018-01-01

    Children's ability to recognize emotional expressions from faces and bodies develops during childhood. However, the low-level features that support accurate body emotion recognition during development have not been well characterized. This is in marked contrast to facial emotion recognition, which is known to depend upon specific spatial frequency…

  16. Implicit recognition based on lateralized perceptual fluency.

    PubMed

    Vargas, Iliana M; Voss, Joel L; Paller, Ken A

    2012-02-06

    In some circumstances, accurate recognition of repeated images in an explicit memory test is driven by implicit memory. We propose that this "implicit recognition" results from perceptual fluency that influences responding without awareness of memory retrieval. Here we examined whether recognition would vary if images appeared in the same or different visual hemifield during learning and testing. Kaleidoscope images were briefly presented left or right of fixation during divided-attention encoding. Presentation in the same visual hemifield at test produced higher recognition accuracy than presentation in the opposite visual hemifield, but only for guess responses. These correct guesses likely reflect a contribution from implicit recognition, given that when the stimulated visual hemifield was the same at study and test, recognition accuracy was higher for guess responses than for responses with any level of confidence. The dramatic difference in guessing accuracy as a function of lateralized perceptual overlap between study and test suggests that implicit recognition arises from memory storage in visual cortical networks that mediate repetition-induced fluency increments.

  17. Vision-based object detection and recognition system for intelligent vehicles

    NASA Astrophysics Data System (ADS)

    Ran, Bin; Liu, Henry X.; Martono, Wilfung

    1999-01-01

    Recently, a proactive crash mitigation system is proposed to enhance the crash avoidance and survivability of the Intelligent Vehicles. Accurate object detection and recognition system is a prerequisite for a proactive crash mitigation system, as system component deployment algorithms rely on accurate hazard detection, recognition, and tracking information. In this paper, we present a vision-based approach to detect and recognize vehicles and traffic signs, obtain their information, and track multiple objects by using a sequence of color images taken from a moving vehicle. The entire system consist of two sub-systems, the vehicle detection and recognition sub-system and traffic sign detection and recognition sub-system. Both of the sub- systems consist of four models: object detection model, object recognition model, object information model, and object tracking model. In order to detect potential objects on the road, several features of the objects are investigated, which include symmetrical shape and aspect ratio of a vehicle and color and shape information of the signs. A two-layer neural network is trained to recognize different types of vehicles and a parameterized traffic sign model is established in the process of recognizing a sign. Tracking is accomplished by combining the analysis of single image frame with the analysis of consecutive image frames. The analysis of the single image frame is performed every ten full-size images. The information model will obtain the information related to the object, such as time to collision for the object vehicle and relative distance from the traffic sings. Experimental results demonstrated a robust and accurate system in real time object detection and recognition over thousands of image frames.

  18. Distinguishing highly confident accurate and inaccurate memory: insights about relevant and irrelevant influences on memory confidence.

    PubMed

    Chua, Elizabeth F; Hannula, Deborah E; Ranganath, Charan

    2012-01-01

    It is generally believed that accuracy and confidence in one's memory are related, but there are many instances when they diverge. Accordingly it is important to disentangle the factors that contribute to memory accuracy and confidence, especially those factors that contribute to confidence, but not accuracy. We used eye movements to separately measure fluent cue processing, the target recognition experience, and relative evidence assessment on recognition confidence and accuracy. Eye movements were monitored during a face-scene associative recognition task, in which participants first saw a scene cue, followed by a forced-choice recognition test for the associated face, with confidence ratings. Eye movement indices of the target recognition experience were largely indicative of accuracy, and showed a relationship to confidence for accurate decisions. In contrast, eye movements during the scene cue raised the possibility that more fluent cue processing was related to higher confidence for both accurate and inaccurate recognition decisions. In a second experiment we manipulated cue familiarity, and therefore cue fluency. Participants showed higher confidence for cue-target associations for when the cue was more familiar, especially for incorrect responses. These results suggest that over-reliance on cue familiarity and under-reliance on the target recognition experience may lead to erroneous confidence.

  19. Distinguishing highly confident accurate and inaccurate memory: insights about relevant and irrelevant influences on memory confidence

    PubMed Central

    Chua, Elizabeth F.; Hannula, Deborah E.; Ranganath, Charan

    2012-01-01

    It is generally believed that accuracy and confidence in one’s memory are related, but there are many instances when they diverge. Accordingly, it is important to disentangle the factors which contribute to memory accuracy and confidence, especially those factors that contribute to confidence, but not accuracy. We used eye movements to separately measure fluent cue processing, the target recognition experience, and relative evidence assessment on recognition confidence and accuracy. Eye movements were monitored during a face-scene associative recognition task, in which participants first saw a scene cue, followed by a forced-choice recognition test for the associated face, with confidence ratings. Eye movement indices of the target recognition experience were largely indicative of accuracy, and showed a relationship to confidence for accurate decisions. In contrast, eye movements during the scene cue raised the possibility that more fluent cue processing was related to higher confidence for both accurate and inaccurate recognition decisions. In a second experiment, we manipulated cue familiarity, and therefore cue fluency. Participants showed higher confidence for cue-target associations for when the cue was more familiar, especially for incorrect responses. These results suggest that over-reliance on cue familiarity and under-reliance on the target recognition experience may lead to erroneous confidence. PMID:22171810

  20. Escherichia coli tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA via S-geranylated-intermediate.

    PubMed

    Sierant, Malgorzata; Leszczynska, Grazyna; Sadowska, Klaudia; Komar, Patrycja; Radzikowska-Cieciura, Ewa; Sochacka, Elzbieta; Nawrot, Barbara

    2018-06-04

    To date the only tRNAs containing nucleosides modified with a selenium (5-carboxymethylaminomethyl-2-selenouridine and 5-methylaminomethyl-2-selenouridine) have been found in bacteria. By using tRNA anticodon-stem-loop fragments containing S2U, Se2U, or geS2U, we found that in vitro tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA in a two-step process involving S2U-RNA geranylation (with ppGe) and subsequent selenation of the resulting geS2U-RNA (with SePO 3 3- ). No 'direct' S2U-RNA→Se2U-RNA replacement is observed in the presence of SelU/SePO 3 3- only (without ppGe). These results suggest that the in vivo S2U→Se2U and S2U→geS2U transformations in tRNA, so far claimed to be the elementary reactions occurring independently in the same domain of the SelU enzyme, should be considered a combination of two consecutive events - geranylation (S2U→geS2U) and selenation (geS2U→Se2U). © 2018 Federation of European Biochemical Societies.

  1. Formation of tRNA granules in the nucleus of heat-induced human cells

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

    Miyagawa, Ryu; Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654; Mizuno, Rie

    Highlights: Black-Right-Pointing-Pointer tRNAs are tranlocated into the nucleus in heat-induced HeLa cells. Black-Right-Pointing-Pointer tRNAs form the unique granules in the nucleus. Black-Right-Pointing-Pointer tRNA ganules overlap with nuclear stress granules. -- Abstract: The stress response, which can trigger various physiological phenomena, is important for living organisms. For instance, a number of stress-induced granules such as P-body and stress granule have been identified. These granules are formed in the cytoplasm under stress conditions and are associated with translational inhibition and mRNA decay. In the nucleus, there is a focus named nuclear stress body (nSB) that distinguishes these structures from cytoplasmic stress granules.more » Many splicing factors and long non-coding RNA species localize in nSBs as a result of stress. Indeed, tRNAs respond to several kinds of stress such as heat, oxidation or starvation. Although nuclear accumulation of tRNAs occurs in starved Saccharomyces cerevisiae, this phenomenon is not found in mammalian cells. We observed that initiator tRNA{sup Met} (Meti) is actively translocated into the nucleus of human cells under heat stress. During this study, we identified unique granules of Meti that overlapped with nSBs. Similarly, elongator tRNA{sup Met} was translocated into the nucleus and formed granules during heat stress. Formation of tRNA granules is closely related to the translocation ratio. Then, all tRNAs may form the specific granules.« less

  2. Was there a universal tRNA before specialized tRNAs came into existence?

    NASA Technical Reports Server (NTRS)

    Lacey, James C., Jr.; Staves, Mark P.

    1990-01-01

    It is generally true that evolving systems begin simply and become more complex in the evolutionary process. For those who try to understand the origin of a biochemical system, what is required is the development of an idea as to what simpler system preceded the present one. A hypothesis is presented that a universal tRNA molecule, capable of reading many codons, may have preceded the appearance of individual tRNAs. Evidence seems to suggest that this molecule may have been derived from a common ancestor of the contemporary 5S rRNAs and tRNAs.

  3. Relationship between listeners' nonnative speech recognition and categorization abilities

    PubMed Central

    Atagi, Eriko; Bent, Tessa

    2015-01-01

    Enhancement of the perceptual encoding of talker characteristics (indexical information) in speech can facilitate listeners' recognition of linguistic content. The present study explored this indexical-linguistic relationship in nonnative speech processing by examining listeners' performance on two tasks: nonnative accent categorization and nonnative speech-in-noise recognition. Results indicated substantial variability across listeners in their performance on both the accent categorization and nonnative speech recognition tasks. Moreover, listeners' accent categorization performance correlated with their nonnative speech-in-noise recognition performance. These results suggest that having more robust indexical representations for nonnative accents may allow listeners to more accurately recognize the linguistic content of nonnative speech. PMID:25618098

  4. Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate.

    PubMed Central

    Ryals, J; Little, R; Bremer, H

    1982-01-01

    The expression of stable RNA (rRNA and tRNA) genes and the concentration of guanosine tetraphosphate (ppGpp) were measured in an isogenic pair of relA+ and relA derivatives of Escherichia coli B/r. The cells were either growing exponentially at different rates or subject to amino acid starvation when they were measured. The specific stable RNA gene activity (rs/rt, the rate of rRNA and tRNA synthesis relative to the total instantaneous rate of RNA synthesis) was found to decrease from 1.0 at a ppGpp concentration of 0 (extrapolated value) to 0.24 at saturating concentrations of ppGpp (above 100 pmoles per optical density at 460 nm unit of cell mass). The same relationship between the rs/rt ratio and ppGpp concentration was obtained independent of the physiological state of the bacteria (i.e., independent of the growth rate or of amino acid starvation) and independent of the relA allele. It can be concluded that ppGpp is an effector for stable RNA gene control and that stable RNA genes are not controlled by factors other than the ppGpp-mediated system. The results were shown to be qualitatively and quantitatively consistent with data on in vitro rRNA gene control by ppGpp, and they were interpreted in the light of reported ideas derived from those in vitro experiments. PMID:6179924

  5. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.

    PubMed

    Honda, Shozo; Loher, Phillipe; Shigematsu, Megumi; Palazzo, Juan P; Suzuki, Ryusuke; Imoto, Issei; Rigoutsos, Isidore; Kirino, Yohei

    2015-07-21

    Sex hormones and their receptors play critical roles in the development and progression of the breast and prostate cancers. Here we report that a novel type of transfer RNA (tRNA)-derived small RNA, termed Sex HOrmone-dependent TRNA-derived RNAs (SHOT-RNAs), are specifically and abundantly expressed in estrogen receptor (ER)-positive breast cancer and androgen receptor (AR)-positive prostate cancer cell lines. SHOT-RNAs are not abundantly present in ER(-) breast cancer, AR(-) prostate cancer, or other examined cancer cell lines from other tissues. ER-dependent accumulation of SHOT-RNAs is not limited to a cell culture system, but it also occurs in luminal-type breast cancer patient tissues. SHOT-RNAs are produced from aminoacylated mature tRNAs by angiogenin-mediated anticodon cleavage, which is promoted by sex hormones and their receptors. Resultant 5'- and 3'-SHOT-RNAs, corresponding to 5'- and 3'-tRNA halves, bear a cyclic phosphate (cP) and an amino acid at the 3'-end, respectively. By devising a "cP-RNA-seq" method that is able to exclusively amplify and sequence cP-containing RNAs, we identified the complete repertoire of 5'-SHOT-RNAs. Furthermore, 5'-SHOT-RNA, but not 3'-SHOT-RNA, has significant functional involvement in cell proliferation. These results have unveiled a novel tRNA-engaged pathway in tumorigenesis of hormone-dependent cancers and implicate SHOT-RNAs as potential candidates for biomarkers and therapeutic targets.

  6. Speech emotion recognition methods: A literature review

    NASA Astrophysics Data System (ADS)

    Basharirad, Babak; Moradhaseli, Mohammadreza

    2017-10-01

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

  7. Regulating recognition decisions through incremental reinforcement learning.

    PubMed

    Han, Sanghoon; Dobbins, Ian G

    2009-06-01

    Does incremental reinforcement learning influence recognition memory judgments? We examined this question by subtly altering the relative validity or availability of feedback in order to differentially reinforce old or new recognition judgments. Experiment 1 probabilistically and incorrectly indicated that either misses or false alarms were correct in the context of feedback that was otherwise accurate. Experiment 2 selectively withheld feedback for either misses or false alarms in the context of feedback that was otherwise present. Both manipulations caused prominent shifts of recognition memory decision criteria that remained for considerable periods even after feedback had been altogether removed. Overall, these data demonstrate that incremental reinforcement-learning mechanisms influence the degree of caution subjects exercise when evaluating explicit memories.

  8. Improving activity recognition using temporal coherence.

    PubMed

    Ataya, Abbas; Jallon, Pierre; Bianchi, Pascal; Doron, Maeva

    2013-01-01

    Assessment of daily physical activity using data from wearable sensors has recently become a prominent research area in the biomedical engineering field and a substantial application for pattern recognition. In this paper, we present an accelerometer-based activity recognition scheme on the basis of a hierarchical structured classifier. A first step consists of distinguishing static activities from dynamic ones in order to extract relevant features for each activity type. Next, a separate classifier is applied to detect more specific activities of the same type. On top of our activity recognition system, we introduce a novel approach to take into account the temporal coherence of activities. Inter-activity transition information is modeled by a directed graph Markov chain. Confidence measures in activity classes are then evaluated from conventional classifier's outputs and coupled with the graph to reinforce activity estimation. Accurate results and significant improvement of activity detection are obtained when applying our system for the recognition of 9 activities for 48 subjects.

  9. Impaired recognition of happy facial expressions in bipolar disorder.

    PubMed

    Lawlor-Savage, Linette; Sponheim, Scott R; Goghari, Vina M

    2014-08-01

    The ability to accurately judge facial expressions is important in social interactions. Individuals with bipolar disorder have been found to be impaired in emotion recognition; however, the specifics of the impairment are unclear. This study investigated whether facial emotion recognition difficulties in bipolar disorder reflect general cognitive, or emotion-specific, impairments. Impairment in the recognition of particular emotions and the role of processing speed in facial emotion recognition were also investigated. Clinically stable bipolar patients (n = 17) and healthy controls (n = 50) judged five facial expressions in two presentation types, time-limited and self-paced. An age recognition condition was used as an experimental control. Bipolar patients' overall facial recognition ability was unimpaired. However, patients' specific ability to judge happy expressions under time constraints was impaired. Findings suggest a deficit in happy emotion recognition impacted by processing speed. Given the limited sample size, further investigation with a larger patient sample is warranted.

  10. Associative recognition: a case of recall-to-reject processing.

    PubMed

    Rotello, C M; Heit, E

    2000-09-01

    Two-process accounts of recognition memory assume that memory judgments are based on both a rapidly available familiarity-based process and a slower, more accurate, recall-based mechanism. Past experiments on the time course of item recognition have not supported the recall-to-reject account of the second process, in which the retrieval of an old item is used to reject a similar foil (Rotello & Heit, 1999). In three new experiments, using analyses similar to those of Rotello and Heit, we found robust evidence for recall-to-reject processing in associative recognition, for word pairs, and for list-discrimination judgments. Put together, these results have implications for two-process accounts of recognition.

  11. Low-contrast underwater living fish recognition using PCANet

    NASA Astrophysics Data System (ADS)

    Sun, Xin; Yang, Jianping; Wang, Changgang; Dong, Junyu; Wang, Xinhua

    2018-04-01

    Quantitative and statistical analysis of ocean creatures is critical to ecological and environmental studies. And living fish recognition is one of the most essential requirements for fishery industry. However, light attenuation and scattering phenomenon are present in the underwater environment, which makes underwater images low-contrast and blurry. This paper tries to design a robust framework for accurate fish recognition. The framework introduces a two stage PCA Network to extract abstract features from fish images. On a real-world fish recognition dataset, we use a linear SVM classifier and set penalty coefficients to conquer data unbalanced issue. Feature visualization results show that our method can avoid the feature distortion in boundary regions of underwater image. Experiments results show that the PCA Network can extract discriminate features and achieve promising recognition accuracy. The framework improves the recognition accuracy of underwater living fishes and can be easily applied to marine fishery industry.

  12. The Recognition Heuristic: A Review of Theory and Tests

    PubMed Central

    Pachur, Thorsten; Todd, Peter M.; Gigerenzer, Gerd; Schooler, Lael J.; Goldstein, Daniel G.

    2011-01-01

    The recognition heuristic is a prime example of how, by exploiting a match between mind and environment, a simple mental strategy can lead to efficient decision making. The proposal of the heuristic initiated a debate about the processes underlying the use of recognition in decision making. We review research addressing four key aspects of the recognition heuristic: (a) that recognition is often an ecologically valid cue; (b) that people often follow recognition when making inferences; (c) that recognition supersedes further cue knowledge; (d) that its use can produce the less-is-more effect – the phenomenon that lesser states of recognition knowledge can lead to more accurate inferences than more complete states. After we contrast the recognition heuristic to other related concepts, including availability and fluency, we carve out, from the existing findings, some boundary conditions of the use of the recognition heuristic as well as key questions for future research. Moreover, we summarize developments concerning the connection of the recognition heuristic with memory models. We suggest that the recognition heuristic is used adaptively and that, compared to other cues, recognition seems to have a special status in decision making. Finally, we discuss how systematic ignorance is exploited in other cognitive mechanisms (e.g., estimation and preference). PMID:21779266

  13. The recognition heuristic: a review of theory and tests.

    PubMed

    Pachur, Thorsten; Todd, Peter M; Gigerenzer, Gerd; Schooler, Lael J; Goldstein, Daniel G

    2011-01-01

    The recognition heuristic is a prime example of how, by exploiting a match between mind and environment, a simple mental strategy can lead to efficient decision making. The proposal of the heuristic initiated a debate about the processes underlying the use of recognition in decision making. We review research addressing four key aspects of the recognition heuristic: (a) that recognition is often an ecologically valid cue; (b) that people often follow recognition when making inferences; (c) that recognition supersedes further cue knowledge; (d) that its use can produce the less-is-more effect - the phenomenon that lesser states of recognition knowledge can lead to more accurate inferences than more complete states. After we contrast the recognition heuristic to other related concepts, including availability and fluency, we carve out, from the existing findings, some boundary conditions of the use of the recognition heuristic as well as key questions for future research. Moreover, we summarize developments concerning the connection of the recognition heuristic with memory models. We suggest that the recognition heuristic is used adaptively and that, compared to other cues, recognition seems to have a special status in decision making. Finally, we discuss how systematic ignorance is exploited in other cognitive mechanisms (e.g., estimation and preference).

  14. An articulatorily constrained, maximum entropy approach to speech recognition and speech coding

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

    Hogden, J.

    Hidden Markov models (HMM`s) are among the most popular tools for performing computer speech recognition. One of the primary reasons that HMM`s typically outperform other speech recognition techniques is that the parameters used for recognition are determined by the data, not by preconceived notions of what the parameters should be. This makes HMM`s better able to deal with intra- and inter-speaker variability despite the limited knowledge of how speech signals vary and despite the often limited ability to correctly formulate rules describing variability and invariance in speech. In fact, it is often the case that when HMM parameter values aremore » constrained using the limited knowledge of speech, recognition performance decreases. However, the structure of an HMM has little in common with the mechanisms underlying speech production. Here, the author argues that by using probabilistic models that more accurately embody the process of speech production, he can create models that have all the advantages of HMM`s, but that should more accurately capture the statistical properties of real speech samples--presumably leading to more accurate speech recognition. The model he will discuss uses the fact that speech articulators move smoothly and continuously. Before discussing how to use articulatory constraints, he will give a brief description of HMM`s. This will allow him to highlight the similarities and differences between HMM`s and the proposed technique.« less

  15. The association between PTSD and facial affect recognition.

    PubMed

    Williams, Christian L; Milanak, Melissa E; Judah, Matt R; Berenbaum, Howard

    2018-05-05

    The major aims of this study were to examine how, if at all, having higher levels of PTSD would be associated with performance on a facial affect recognition task in which facial expressions of emotion are superimposed on emotionally valenced, non-face images. College students with trauma histories (N = 90) completed a facial affect recognition task as well as measures of exposure to traumatic events, and PTSD symptoms. When the face and context matched, participants with higher levels of PTSD were significantly more accurate. When the face and context were mismatched, participants with lower levels of PTSD were more accurate than were those with higher levels of PTSD. These findings suggest that PTSD is associated with how people process affective information. Furthermore, these results suggest that the enhanced attention of people with higher levels of PTSD to affective information can be either beneficial or detrimental to their ability to accurately identify facial expressions of emotion. Limitations, future directions and clinical implications are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Acquired prosopagnosia without word recognition deficits.

    PubMed

    Susilo, Tirta; Wright, Victoria; Tree, Jeremy J; Duchaine, Bradley

    2015-01-01

    It has long been suggested that face recognition relies on specialized mechanisms that are not involved in visual recognition of other object categories, including those that require expert, fine-grained discrimination at the exemplar level such as written words. But according to the recently proposed many-to-many theory of object recognition (MTMT), visual recognition of faces and words are carried out by common mechanisms [Behrmann, M., & Plaut, D. C. ( 2013 ). Distributed circuits, not circumscribed centers, mediate visual recognition. Trends in Cognitive Sciences, 17, 210-219]. MTMT acknowledges that face and word recognition are lateralized, but posits that the mechanisms that predominantly carry out face recognition still contribute to word recognition and vice versa. MTMT makes a key prediction, namely that acquired prosopagnosics should exhibit some measure of word recognition deficits. We tested this prediction by assessing written word recognition in five acquired prosopagnosic patients. Four patients had lesions limited to the right hemisphere while one had bilateral lesions with more pronounced lesions in the right hemisphere. The patients completed a total of seven word recognition tasks: two lexical decision tasks and five reading aloud tasks totalling more than 1200 trials. The performances of the four older patients (3 female, age range 50-64 years) were compared to those of 12 older controls (8 female, age range 56-66 years), while the performances of the younger prosopagnosic (male, 31 years) were compared to those of 14 younger controls (9 female, age range 20-33 years). We analysed all results at the single-patient level using Crawford's t-test. Across seven tasks, four prosopagnosics performed as quickly and accurately as controls. Our results demonstrate that acquired prosopagnosia can exist without word recognition deficits. These findings are inconsistent with a key prediction of MTMT. They instead support the hypothesis that face

  17. Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids.

    PubMed

    José, Marco V; Morgado, Eberto R; Guimarães, Romeu Cardoso; Zamudio, Gabriel S; de Farías, Sávio Torres; Bobadilla, Juan R; Sosa, Daniela

    2014-08-11

    Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state.

  18. Contour matching for a fish recognition and migration-monitoring system

    NASA Astrophysics Data System (ADS)

    Lee, Dah-Jye; Schoenberger, Robert B.; Shiozawa, Dennis; Xu, Xiaoqian; Zhan, Pengcheng

    2004-12-01

    Fish migration is being monitored year round to provide valuable information for the study of behavioral responses of fish to environmental variations. However, currently all monitoring is done by human observers. An automatic fish recognition and migration monitoring system is more efficient and can provide more accurate data. Such a system includes automatic fish image acquisition, contour extraction, fish categorization, and data storage. Shape is a very important characteristic and shape analysis and shape matching are studied for fish recognition. Previous work focused on finding critical landmark points on fish shape using curvature function analysis. Fish recognition based on landmark points has shown satisfying results. However, the main difficulty of this approach is that landmark points sometimes cannot be located very accurately. Whole shape matching is used for fish recognition in this paper. Several shape descriptors, such as Fourier descriptors, polygon approximation and line segments, are tested. A power cepstrum technique has been developed in order to improve the categorization speed using contours represented in tangent space with normalized length. Design and integration including image acquisition, contour extraction and fish categorization are discussed in this paper. Fish categorization results based on shape analysis and shape matching are also included.

  19. Apple S-RNase triggers inhibition of tRNA aminoacylation by interacting with a soluble inorganic pyrophosphatase in growing self-pollen tubes in vitro.

    PubMed

    Li, Wei; Meng, Dong; Gu, Zhaoyu; Yang, Qing; Yuan, Hui; Li, Yang; Chen, Qiuju; Yu, Jie; Liu, Chunsheng; Li, Tianzhong

    2018-04-01

    Apple exhibits S-RNase-based self-incompatibility (SI), in which S-RNase plays a central role in rejecting self-pollen. It has been proposed that the arrest of pollen growth in SI of Solanaceae plants is a consequence of the degradation of pollen rRNA by S-RNase; however, the underlying mechanism in Rosaceae is still unclear. Here, we used S 2 -RNase as a bait to screen an apple pollen cDNA library and characterized an apple soluble inorganic pyrophosphatase (MdPPa) that physically interacted with S-RNases. When treated with self S-RNases, apple pollen tubes showed a marked growth inhibition, as well as a decrease in endogenous soluble pyrophosphatase activity and elevated levels of inorganic pyrophosphate (PPi). In addition, S-RNase was found to bind to two variable regions of MdPPa, resulting in a noncompetitive inhibition of its activity. Silencing of MdPPa expression led to a reduction in pollen tube growth. Interestingly, tRNA aminoacylation was inhibited in self S-RNase-treated or MdPPa-silenced pollen tubes, resulting in the accumulation of uncharged tRNA. Furthermore, we provide evidence showing that this disturbance of tRNA aminoacylation is independent of RNase activity. We propose an alternative mechanism differing from RNA degradation to explain the cytotoxicity of the S-RNase apple SI process. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

  20. Hierarchical Recognition Scheme for Human Facial Expression Recognition Systems

    PubMed Central

    Siddiqi, Muhammad Hameed; Lee, Sungyoung; Lee, Young-Koo; Khan, Adil Mehmood; Truc, Phan Tran Ho

    2013-01-01

    Over the last decade, human facial expressions recognition (FER) has emerged as an important research area. Several factors make FER a challenging research problem. These include varying light conditions in training and test images; need for automatic and accurate face detection before feature extraction; and high similarity among different expressions that makes it difficult to distinguish these expressions with a high accuracy. This work implements a hierarchical linear discriminant analysis-based facial expressions recognition (HL-FER) system to tackle these problems. Unlike the previous systems, the HL-FER uses a pre-processing step to eliminate light effects, incorporates a new automatic face detection scheme, employs methods to extract both global and local features, and utilizes a HL-FER to overcome the problem of high similarity among different expressions. Unlike most of the previous works that were evaluated using a single dataset, the performance of the HL-FER is assessed using three publicly available datasets under three different experimental settings: n-fold cross validation based on subjects for each dataset separately; n-fold cross validation rule based on datasets; and, finally, a last set of experiments to assess the effectiveness of each module of the HL-FER separately. Weighted average recognition accuracy of 98.7% across three different datasets, using three classifiers, indicates the success of employing the HL-FER for human FER. PMID:24316568

  1. Towards discrete wavelet transform-based human activity recognition

    NASA Astrophysics Data System (ADS)

    Khare, Manish; Jeon, Moongu

    2017-06-01

    Providing accurate recognition of human activities is a challenging problem for visual surveillance applications. In this paper, we present a simple and efficient algorithm for human activity recognition based on a wavelet transform. We adopt discrete wavelet transform (DWT) coefficients as a feature of human objects to obtain advantages of its multiresolution approach. The proposed method is tested on multiple levels of DWT. Experiments are carried out on different standard action datasets including KTH and i3D Post. The proposed method is compared with other state-of-the-art methods in terms of different quantitative performance measures. The proposed method is found to have better recognition accuracy in comparison to the state-of-the-art methods.

  2. The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription.

    PubMed Central

    Ke, N; Gao, X; Keeney, J B; Boeke, J D; Voytas, D F

    1999-01-01

    Retrotransposons and retroviruses replicate by reverse transcription of an mRNA intermediate. Most retroelements initiate reverse transcription from a host-encoded tRNA primer. DNA synthesis typically extends from the 3'-OH of the acceptor stem, which is complementary to sequences on the retroelement mRNA (the primer binding site, PBS). However, for some retrotransposons, including the yeast Ty5 elements, sequences in the anticodon stem-loop of the initiator methionine tRNA (IMT) are complementary to the PBS. We took advantage of the genetic tractability of the yeast system to investigate the mechanism of Ty5 priming. We found that transposition frequencies decreased at least 800-fold for mutations in the Ty5 PBS that disrupt complementarity with the IMT. Similarly, transposition was reduced at least 200-fold for IMT mutations in the anticodon stem-loop. Base pairing between the Ty5 PBS and IMT is essential for transposition, as compensatory changes that restored base pairing between the two mutant RNAs restored transposition significantly. An analysis of 12 imt mutants with base changes outside of the region of complementarity failed to identify other tRNA residues important for transposition. In addition, assays carried out with heterologous IMTs from Schizosaccharomyces pombe and Arabidopsis thaliana indicated that residues outside of the anticodon stem-loop have at most a fivefold effect on transposition. Our genetic system should make it possible to further define the components required for priming and to understand the mechanism by which Ty5's novel primer is generated. PMID:10411136

  3. A Deafness- and Diabetes-associated tRNA Mutation Causes Deficient Pseudouridinylation at Position 55 in tRNAGlu and Mitochondrial Dysfunction*

    PubMed Central

    Wang, Meng; Liu, Hao; Zheng, Jing; Chen, Bobei; Zhou, Mi; Fan, Wenlu; Wang, Hen; Liang, Xiaoyang; Zhou, Xiaolong; Eriani, Gilbert; Jiang, Pingping; Guan, Min-Xin

    2016-01-01

    Several mitochondrial tRNA mutations have been associated with maternally inherited diabetes and deafness. However, the pathophysiology of these tRNA mutations remains poorly understood. In this report, we identified the novel homoplasmic 14692A→G mutation in the mitochondrial tRNAGlu gene among three Han Chinese families with maternally inherited diabetes and deafness. The m.14692A→G mutation affected a highly conserved uridine at position 55 of the TΨC loop of tRNAGlu. The uridine is modified to pseudouridine (Ψ55), which plays an important role in the structure and function of this tRNA. Using lymphoblastoid cell lines derived from a Chinese family, we demonstrated that the m.14692A→G mutation caused loss of Ψ55 modification and increased angiogenin-mediated endonucleolytic cleavage in mutant tRNAGlu. The destabilization of base-pairing (18A-Ψ55) caused by the m.14692A→G mutation perturbed the conformation and stability of tRNAGlu. An approximately 65% decrease in the steady-state level of tRNAGlu was observed in mutant cells compared with control cells. A failure in tRNAGlu metabolism impaired mitochondrial translation, especially for polypeptides with a high proportion of glutamic acid codons such as ND1, ND6, and CO2 in mutant cells. An impairment of mitochondrial translation caused defective respiratory capacity, especially reducing the activities of complexes I and IV. Furthermore, marked decreases in the levels of mitochondrial ATP and membrane potential were observed in mutant cells. These mitochondrial dysfunctions caused an increasing production of reactive oxygen species in the mutant cells. Our findings may provide new insights into the pathophysiology of maternally inherited diabetes and deafness, which is primarily manifested by the deficient nucleotide modification of mitochondrial tRNAGlu. PMID:27519417

  4. A Generalized Michaelis-Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon.

    PubMed

    Dutta, Annwesha; Chowdhury, Debashish

    2017-05-01

    The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a 'biologically motivated' generalization of the Michaelis-Menten formula for the average rate of enzymatic reactions. This generalized Michaelis-Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.

  5. Feature extraction for face recognition via Active Shape Model (ASM) and Active Appearance Model (AAM)

    NASA Astrophysics Data System (ADS)

    Iqtait, M.; Mohamad, F. S.; Mamat, M.

    2018-03-01

    Biometric is a pattern recognition system which is used for automatic recognition of persons based on characteristics and features of an individual. Face recognition with high recognition rate is still a challenging task and usually accomplished in three phases consisting of face detection, feature extraction, and expression classification. Precise and strong location of trait point is a complicated and difficult issue in face recognition. Cootes proposed a Multi Resolution Active Shape Models (ASM) algorithm, which could extract specified shape accurately and efficiently. Furthermore, as the improvement of ASM, Active Appearance Models algorithm (AAM) is proposed to extracts both shape and texture of specified object simultaneously. In this paper we give more details about the two algorithms and give the results of experiments, testing their performance on one dataset of faces. We found that the ASM is faster and gains more accurate trait point location than the AAM, but the AAM gains a better match to the texture.

  6. Automated smartphone audiometry: Validation of a word recognition test app.

    PubMed

    Dewyer, Nicholas A; Jiradejvong, Patpong; Henderson Sabes, Jennifer; Limb, Charles J

    2018-03-01

    Develop and validate an automated smartphone word recognition test. Cross-sectional case-control diagnostic test comparison. An automated word recognition test was developed as an app for a smartphone with earphones. English-speaking adults with recent audiograms and various levels of hearing loss were recruited from an audiology clinic and were administered the smartphone word recognition test. Word recognition scores determined by the smartphone app and the gold standard speech audiometry test performed by an audiologist were compared. Test scores for 37 ears were analyzed. Word recognition scores determined by the smartphone app and audiologist testing were in agreement, with 86% of the data points within a clinically acceptable margin of error and a linear correlation value between test scores of 0.89. The WordRec automated smartphone app accurately determines word recognition scores. 3b. Laryngoscope, 128:707-712, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  7. Violent video game players and non-players differ on facial emotion recognition.

    PubMed

    Diaz, Ruth L; Wong, Ulric; Hodgins, David C; Chiu, Carina G; Goghari, Vina M

    2016-01-01

    Violent video game playing has been associated with both positive and negative effects on cognition. We examined whether playing two or more hours of violent video games a day, compared to not playing video games, was associated with a different pattern of recognition of five facial emotions, while controlling for general perceptual and cognitive differences that might also occur. Undergraduate students were categorized as violent video game players (n = 83) or non-gamers (n = 69) and completed a facial recognition task, consisting of an emotion recognition condition and a control condition of gender recognition. Additionally, participants completed questionnaires assessing their video game and media consumption, aggression, and mood. Violent video game players recognized fearful faces both more accurately and quickly and disgusted faces less accurately than non-gamers. Desensitization to violence, constant exposure to fear and anxiety during game playing, and the habituation to unpleasant stimuli, are possible mechanisms that could explain these results. Future research should evaluate the effects of violent video game playing on emotion processing and social cognition more broadly. © 2015 Wiley Periodicals, Inc.

  8. Aging and solid shape recognition: Vision and haptics.

    PubMed

    Norman, J Farley; Cheeseman, Jacob R; Adkins, Olivia C; Cox, Andrea G; Rogers, Connor E; Dowell, Catherine J; Baxter, Michael W; Norman, Hideko F; Reyes, Cecia M

    2015-10-01

    The ability of 114 younger and older adults to recognize naturally-shaped objects was evaluated in three experiments. The participants viewed or haptically explored six randomly-chosen bell peppers (Capsicum annuum) in a study session and were later required to judge whether each of twelve bell peppers was "old" (previously presented during the study session) or "new" (not presented during the study session). When recognition memory was tested immediately after study, the younger adults' (Experiment 1) performance for vision and haptics was identical when the individual study objects were presented once. Vision became superior to haptics, however, when the individual study objects were presented multiple times. When 10- and 20-min delays (Experiment 2) were inserted in between study and test sessions, no significant differences occurred between vision and haptics: recognition performance in both modalities was comparable. When the recognition performance of older adults was evaluated (Experiment 3), a negative effect of age was found for visual shape recognition (younger adults' overall recognition performance was 60% higher). There was no age effect, however, for haptic shape recognition. The results of the present experiments indicate that the visual recognition of natural object shape is different from haptic recognition in multiple ways: visual shape recognition can be superior to that of haptics and is affected by aging, while haptic shape recognition is less accurate and unaffected by aging. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. MTO1 mediates tissue specificity of OXPHOS defects via tRNA modification and translation optimization, which can be bypassed by dietary intervention

    PubMed Central

    Tischner, Christin; Hofer, Annette; Wulff, Veronika; Stepek, Joanna; Dumitru, Iulia; Becker, Lore; Haack, Tobias; Kremer, Laura; Datta, Alexandre N.; Sperl, Wolfgang; Floss, Thomas; Wurst, Wolfgang; Chrzanowska-Lightowlers, Zofia; De Angelis, Martin Hrabe; Klopstock, Thomas; Prokisch, Holger; Wenz, Tina

    2015-01-01

    Mitochondrial diseases often exhibit tissue-specific pathologies, but this phenomenon is poorly understood. Here we present regulation of mitochondrial translation by the Mitochondrial Translation Optimization Factor 1, MTO1, as a novel player in this scenario. We demonstrate that MTO1 mediates tRNA modification and controls mitochondrial translation rate in a highly tissue-specific manner associated with tissue-specific OXPHOS defects. Activation of mitochondrial proteases, aberrant translation products, as well as defects in OXPHOS complex assembly observed in MTO1 deficient mice further imply that MTO1 impacts translation fidelity. In our mouse model, MTO1-related OXPHOS deficiency can be bypassed by feeding a ketogenic diet. This therapeutic intervention is independent of the MTO1-mediated tRNA modification and involves balancing of mitochondrial and cellular secondary stress responses. Our results thereby establish mammalian MTO1 as a novel factor in the tissue-specific regulation of OXPHOS and fine tuning of mitochondrial translation accuracy. PMID:25552653

  10. Defects in tRNA processing and nuclear export induce GCN4 translation independently of phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2.

    PubMed

    Qiu, H; Hu, C; Anderson, J; Björk, G R; Sarkar, S; Hopper, A K; Hinnebusch, A G

    2000-04-01

    Induction of GCN4 translation in amino acid-starved cells involves the inhibition of initiator tRNA(Met) binding to eukaryotic translation initiation factor 2 (eIF2) in response to eIF2 phosphorylation by protein kinase GCN2. It was shown previously that GCN4 translation could be induced independently of GCN2 by overexpressing a mutant tRNA(AAC)(Val) (tRNA(Val*)) or the RNA component of RNase MRP encoded by NME1. Here we show that overexpression of the tRNA pseudouridine 55 synthase encoded by PUS4 also leads to translational derepression of GCN4 (Gcd(-) phenotype) independently of eIF2 phosphorylation. Surprisingly, the Gcd(-) phenotype of high-copy-number PUS4 (hcPUS4) did not require PUS4 enzymatic activity, and several lines of evidence indicate that PUS4 overexpression did not diminish functional initiator tRNA(Met) levels. The presence of hcPUS4 or hcNME1 led to the accumulation of certain tRNA precursors, and their Gcd(-) phenotypes were reversed by overexpressing the RNA component of RNase P (RPR1), responsible for 5'-end processing of all tRNAs. Consistently, overexpression of a mutant pre-tRNA(Tyr) that cannot be processed by RNase P had a Gcd(-) phenotype. Interestingly, the Gcd(-) phenotype of hcPUS4 also was reversed by overexpressing LOS1, required for efficient nuclear export of tRNA, and los1Delta cells have a Gcd(-) phenotype. Overproduced PUS4 appears to impede 5'-end processing or export of certain tRNAs in the nucleus in a manner remedied by increased expression of RNase P or LOS1, respectively. The mutant tRNA(Val*) showed nuclear accumulation in otherwise wild-type cells, suggesting a defect in export to the cytoplasm. We propose that yeast contains a nuclear surveillance system that perceives defects in processing or export of tRNA and evokes a reduction in translation initiation at the step of initiator tRNA(Met) binding to the ribosome.

  11. Defects in tRNA Processing and Nuclear Export Induce GCN4 Translation Independently of Phosphorylation of the α Subunit of Eukaryotic Translation Initiation Factor 2

    PubMed Central

    Qiu, Hongfang; Hu, Cuihua; Anderson, James; Björk, Glenn R.; Sarkar, Srimonti; Hopper, Anita K.; Hinnebusch, Alan G.

    2000-01-01

    Induction of GCN4 translation in amino acid-starved cells involves the inhibition of initiator tRNAMet binding to eukaryotic translation initiation factor 2 (eIF2) in response to eIF2 phosphorylation by protein kinase GCN2. It was shown previously that GCN4 translation could be induced independently of GCN2 by overexpressing a mutant tRNAAACVal (tRNAVal*) or the RNA component of RNase MRP encoded by NME1. Here we show that overexpression of the tRNA pseudouridine 55 synthase encoded by PUS4 also leads to translational derepression of GCN4 (Gcd− phenotype) independently of eIF2 phosphorylation. Surprisingly, the Gcd− phenotype of high-copy-number PUS4 (hcPUS4) did not require PUS4 enzymatic activity, and several lines of evidence indicate that PUS4 overexpression did not diminish functional initiator tRNAMet levels. The presence of hcPUS4 or hcNME1 led to the accumulation of certain tRNA precursors, and their Gcd− phenotypes were reversed by overexpressing the RNA component of RNase P (RPR1), responsible for 5′-end processing of all tRNAs. Consistently, overexpression of a mutant pre-tRNATyr that cannot be processed by RNase P had a Gcd− phenotype. Interestingly, the Gcd− phenotype of hcPUS4 also was reversed by overexpressing LOS1, required for efficient nuclear export of tRNA, and los1Δ cells have a Gcd− phenotype. Overproduced PUS4 appears to impede 5′-end processing or export of certain tRNAs in the nucleus in a manner remedied by increased expression of RNase P or LOS1, respectively. The mutant tRNAVal* showed nuclear accumulation in otherwise wild-type cells, suggesting a defect in export to the cytoplasm. We propose that yeast contains a nuclear surveillance system that perceives defects in processing or export of tRNA and evokes a reduction in translation initiation at the step of initiator tRNAMet binding to the ribosome. PMID:10713174

  12. Page Recognition: Quantum Leap In Recognition Technology

    NASA Astrophysics Data System (ADS)

    Miller, Larry

    1989-07-01

    No milestone has proven as elusive as the always-approaching "year of the LAN," but the "year of the scanner" might claim the silver medal. Desktop scanners have been around almost as long as personal computers. And everyone thinks they are used for obvious desktop-publishing and business tasks like scanning business documents, magazine articles and other pages, and translating those words into files your computer understands. But, until now, the reality fell far short of the promise. Because it's true that scanners deliver an accurate image of the page to your computer, but the software to recognize this text has been woefully disappointing. Old optical-character recognition (OCR) software recognized such a limited range of pages as to be virtually useless to real users. (For example, one OCR vendor specified 12-point Courier font from an IBM Selectric typewriter: the same font in 10-point, or from a Diablo printer, was unrecognizable!) Computer dealers have told me the chasm between OCR expectations and reality is so broad and deep that nine out of ten prospects leave their stores in disgust when they learn the limitations. And this is a very important, very unfortunate gap. Because the promise of recognition -- what people want it to do -- carries with it tremendous improvements in our productivity and ability to get tons of written documents into our computers where we can do real work with it. The good news is that a revolutionary new development effort has led to the new technology of "page recognition," which actually does deliver the promise we've always wanted from OCR. I'm sure every reader appreciates the breakthrough represented by the laser printer and page-makeup software, a combination so powerful it created new reasons for buying a computer. A similar breakthrough is happening right now in page recognition: the Macintosh (and, I must admit, other personal computers) equipped with a moderately priced scanner and OmniPage software (from Caere

  13. Text recognition and correction for automated data collection by mobile devices

    NASA Astrophysics Data System (ADS)

    Ozarslan, Suleyman; Eren, P. Erhan

    2014-03-01

    Participatory sensing is an approach which allows mobile devices such as mobile phones to be used for data collection, analysis and sharing processes by individuals. Data collection is the first and most important part of a participatory sensing system, but it is time consuming for the participants. In this paper, we discuss automatic data collection approaches for reducing the time required for collection, and increasing the amount of collected data. In this context, we explore automated text recognition on images of store receipts which are captured by mobile phone cameras, and the correction of the recognized text. Accordingly, our first goal is to evaluate the performance of the Optical Character Recognition (OCR) method with respect to data collection from store receipt images. Images captured by mobile phones exhibit some typical problems, and common image processing methods cannot handle some of them. Consequently, the second goal is to address these types of problems through our proposed Knowledge Based Correction (KBC) method used in support of the OCR, and also to evaluate the KBC method with respect to the improvement on the accurate recognition rate. Results of the experiments show that the KBC method improves the accurate data recognition rate noticeably.

  14. A single base change in the acceptor stem of tRNA(3Leu) confers resistance upon Escherichia coli to the calmodulin inhibitor, 48/80.

    PubMed Central

    Chen, M X; Bouquin, N; Norris, V; Casarégola, S; Séror, S J; Holland, I B

    1991-01-01

    We have isolated several classes of spontaneous mutants resistant to the calmodulin inhibitor 48/80 which inhibits cell division in Escherichia coli K12. Several mutants were also temperature sensitive for growth and this property was exploited to clone a DNA fragment from an E. coli gene library restoring growth at 42 degrees C and drug sensitivity at 30 degrees C in one such mutant. Physical and genetic mapping confirmed that both the mutation and the cloned DNA were located at 15.5 min on the E. coli chromosome at a locus designated feeB. By subcloning, complementation analysis and sequencing, the feeB locus was identified as identical to the tRNA(CUALEU) gene. When the mutant locus was isolated and sequenced, the mutation was confirmed as a single base change, C to A, at position 77 in the acceptor stem of this rare Leu tRNA. In other studies we obtained evidence that this mutant tRNA, recognizing the rare Leu codon, CUA, was defective in translation at both permissive and non-permissive temperatures. The feeB1 mutant is defective in division and shows a reduced growth rate at non-permissive temperature. We discuss the possibility that the mutant tRNA(3Leu) is limiting for the synthesis of a polypeptide(s), requiring several CUA codons for translation which in turn regulates in some way the level or activity of the drug target, a putative cell cycle protein. Images PMID:1915285

  15. Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm.

    PubMed

    Nozawa, Kayo; Ishitani, Ryuichiro; Yoshihisa, Tohru; Sato, Mamoru; Arisaka, Fumio; Kanamaru, Shuji; Dohmae, Naoshi; Mangroo, Dev; Senger, Bruno; Becker, Hubert D; Nureki, Osamu

    2013-04-01

    In all eukaryotes, transcribed precursor tRNAs are maturated by processing and modification processes in nucleus and are transported to the cytoplasm. The cytoplasmic export protein (Cex1p) captures mature tRNAs from the nuclear export receptor (Los1p) on the cytoplasmic side of the nuclear pore complex, and it delivers them to eukaryotic elongation factor 1α. This conserved Cex1p function is essential for the quality control of mature tRNAs to ensure accurate translation. However, the structural basis of how Cex1p recognizes tRNAs and shuttles them to the translational apparatus remains unclear. Here, we solved the 2.2 Å resolution crystal structure of Saccharomyces cerevisiae Cex1p with C-terminal 197 disordered residues truncated. Cex1p adopts an elongated architecture, consisting of N-terminal kinase-like and a C-terminal α-helical HEAT repeat domains. Structure-based biochemical analyses suggested that Cex1p binds tRNAs on its inner side, using the positively charged HEAT repeat surface and the C-terminal disordered region. The N-terminal kinase-like domain acts as a scaffold to interact with the Ran-exportin (Los1p·Gsp1p) machinery. These results provide the structural basis of Los1p·Gsp1p·Cex1p·tRNA complex formation, thus clarifying the dynamic mechanism of tRNA shuttling from exportin to the translational apparatus.

  16. Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids

    PubMed Central

    José, Marco V.; Morgado, Eberto R.; Guimarães, Romeu Cardoso; Zamudio, Gabriel S.; de Farías, Sávio Torres; Bobadilla, Juan R.; Sosa, Daniela

    2014-01-01

    Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state. PMID:25370377

  17. Iris recognition in the presence of ocular disease

    PubMed Central

    Aslam, Tariq Mehmood; Tan, Shi Zhuan; Dhillon, Baljean

    2009-01-01

    Iris recognition systems are among the most accurate of all biometric technologies with immense potential for use in worldwide security applications. This study examined the effect of eye pathology on iris recognition and in particular whether eye disease could cause iris recognition systems to fail. The experiment involved a prospective cohort of 54 patients with anterior segment eye disease who were seen at the acute referral unit of the Princess Alexandra Eye Pavilion in Edinburgh. Iris camera images were obtained from patients before treatment was commenced and again at follow-up appointments after treatment had been given. The principal outcome measure was that of mathematical difference in the iris recognition templates obtained from patients' eyes before and after treatment of the eye disease. Results showed that the performance of iris recognition was remarkably resilient to most ophthalmic disease states, including corneal oedema, iridotomies (laser puncture of iris) and conjunctivitis. Problems were, however, encountered in some patients with acute inflammation of the iris (iritis/anterior uveitis). The effects of a subject developing anterior uveitis may cause current recognition systems to fail. Those developing and deploying iris recognition should be aware of the potential problems that this could cause to this key biometric technology. PMID:19324690

  18. Iris recognition in the presence of ocular disease.

    PubMed

    Aslam, Tariq Mehmood; Tan, Shi Zhuan; Dhillon, Baljean

    2009-05-06

    Iris recognition systems are among the most accurate of all biometric technologies with immense potential for use in worldwide security applications. This study examined the effect of eye pathology on iris recognition and in particular whether eye disease could cause iris recognition systems to fail. The experiment involved a prospective cohort of 54 patients with anterior segment eye disease who were seen at the acute referral unit of the Princess Alexandra Eye Pavilion in Edinburgh. Iris camera images were obtained from patients before treatment was commenced and again at follow-up appointments after treatment had been given. The principal outcome measure was that of mathematical difference in the iris recognition templates obtained from patients' eyes before and after treatment of the eye disease. Results showed that the performance of iris recognition was remarkably resilient to most ophthalmic disease states, including corneal oedema, iridotomies (laser puncture of iris) and conjunctivitis. Problems were, however, encountered in some patients with acute inflammation of the iris (iritis/anterior uveitis). The effects of a subject developing anterior uveitis may cause current recognition systems to fail. Those developing and deploying iris recognition should be aware of the potential problems that this could cause to this key biometric technology.

  19. Facial recognition deficits as a potential endophenotype in bipolar disorder.

    PubMed

    Vierck, Esther; Porter, Richard J; Joyce, Peter R

    2015-11-30

    Bipolar disorder (BD) is considered a highly heritable and genetically complex disorder. Several cognitive functions, such as executive functions and verbal memory have been suggested as promising candidates for endophenotypes. Although there is evidence for deficits in facial emotion recognition in individuals with BD, studies investigating these functions as endophenotypes are rare. The current study investigates emotion recognition as a potential endophenotype in BD by comparing 36 BD participants, 24 of their 1st degree relatives and 40 healthy control participants in a computerised facial emotion recognition task. Group differences were evaluated using repeated measurement analysis of co-variance with age as a covariate. Results revealed slowed emotion recognition for both BD and their relatives. Furthermore, BD participants were less accurate than healthy controls in their recognition of emotion expressions. We found no evidence of emotion specific differences between groups. Our results provide evidence for facial recognition as a potential endophenotype in BD. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  20. Sunspot drawings handwritten character recognition method based on deep learning

    NASA Astrophysics Data System (ADS)

    Zheng, Sheng; Zeng, Xiangyun; Lin, Ganghua; Zhao, Cui; Feng, Yongli; Tao, Jinping; Zhu, Daoyuan; Xiong, Li

    2016-05-01

    High accuracy scanned sunspot drawings handwritten characters recognition is an issue of critical importance to analyze sunspots movement and store them in the database. This paper presents a robust deep learning method for scanned sunspot drawings handwritten characters recognition. The convolution neural network (CNN) is one algorithm of deep learning which is truly successful in training of multi-layer network structure. CNN is used to train recognition model of handwritten character images which are extracted from the original sunspot drawings. We demonstrate the advantages of the proposed method on sunspot drawings provided by Chinese Academy Yunnan Observatory and obtain the daily full-disc sunspot numbers and sunspot areas from the sunspot drawings. The experimental results show that the proposed method achieves a high recognition accurate rate.

  1. Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.

    PubMed

    Song, Youngzee; Zhou, Huihao; Vo, My-Nuong; Shi, Yi; Nawaz, Mir Hussain; Vargas-Rodriguez, Oscar; Diedrich, Jolene K; Yates, John R; Kishi, Shuji; Musier-Forsyth, Karin; Schimmel, Paul

    2017-12-22

    Hundreds of non-proteinogenic (np) amino acids (AA) are found in plants and can in principle enter human protein synthesis through foods. While aminoacyl-tRNA synthetase (AARS) editing potentially provides a mechanism to reject np AAs, some have pathological associations. Co-crystal structures show that vegetable-sourced azetidine-2-carboxylic acid (Aze), a dual mimic of proline and alanine, is activated by both human prolyl- and alanyl-tRNA synthetases. However, it inserts into proteins as proline, with toxic consequences in vivo. Thus, dual mimicry increases odds for mistranslation through evasion of one but not both tRNA synthetase editing systems.

  2. Efficient local representations for three-dimensional palmprint recognition

    NASA Astrophysics Data System (ADS)

    Yang, Bing; Wang, Xiaohua; Yao, Jinliang; Yang, Xin; Zhu, Wenhua

    2013-10-01

    Palmprints have been broadly used for personal authentication because they are highly accurate and incur low cost. Most previous works have focused on two-dimensional (2-D) palmprint recognition in the past decade. Unfortunately, 2-D palmprint recognition systems lose the shape information when capturing palmprint images. Moreover, such 2-D palmprint images can be easily forged or affected by noise. Hence, three-dimensional (3-D) palmprint recognition has been regarded as a promising way to further improve the performance of palmprint recognition systems. We have developed a simple, but efficient method for 3-D palmprint recognition by using local features. We first utilize shape index representation to describe the geometry of local regions in 3-D palmprint data. Then, we extract local binary pattern and Gabor wavelet features from the shape index image. The two types of complementary features are finally fused at a score level for further improvements. The experimental results on the Hong Kong Polytechnic 3-D palmprint database, which contains 8000 samples from 400 palms, illustrate the effectiveness of the proposed method.

  3. Self- or familiar-face recognition advantage? New insight using ambient images.

    PubMed

    Bortolon, Catherine; Lorieux, Siméon; Raffard, Stéphane

    2018-06-01

    Self-face recognition has been widely explored in the past few years. Nevertheless, the current literature relies on the use of standardized photographs which do not represent daily-life face recognition. Therefore, we aim for the first time to evaluate self-face processing in healthy individuals using natural/ambient images which contain variations in the environment and in the face itself. In total, 40 undergraduate and graduate students performed a forced delayed-matching task, including images of one's own face, friend, famous and unknown individuals. For both reaction time and accuracy, results showed that participants were faster and more accurate when matching different images of their own face compared to both famous and unfamiliar faces. Nevertheless, no significant differences were found between self-face and friend-face and between friend-face and famous-face. They were also faster and more accurate when matching friend and famous faces compared to unfamiliar faces. Our results suggest that faster and more accurate responses to self-face might be better explained by a familiarity effect - that is, (1) the result of frequent exposition to one's own image through mirror and photos, (2) a more robust mental representation of one's own face and (3) strong face recognition units as for other familiar faces.

  4. Biosynthesis of Selenocysteine on Its tRNA in Eukaryotes

    PubMed Central

    Mix, Heiko; Zhang, Yan; Saira, Kazima; Glass, Richard S; Berry, Marla J; Gladyshev, Vadim N; Hatfield, Dolph L

    2007-01-01

    Selenocysteine (Sec) is cotranslationally inserted into protein in response to UGA codons and is the 21st amino acid in the genetic code. However, the means by which Sec is synthesized in eukaryotes is not known. Herein, comparative genomics and experimental analyses revealed that the mammalian Sec synthase (SecS) is the previously identified pyridoxal phosphate-containing protein known as the soluble liver antigen. SecS required selenophosphate and O-phosphoseryl-tRNA[Ser]Sec as substrates to generate selenocysteyl-tRNA[Ser]Sec. Moreover, it was found that Sec was synthesized on the tRNA scaffold from selenide, ATP, and serine using tRNA[Ser]Sec, seryl-tRNA synthetase, O-phosphoseryl-tRNA[Ser]Sec kinase, selenophosphate synthetase, and SecS. By identifying the pathway of Sec biosynthesis in mammals, this study not only functionally characterized SecS but also assigned the function of the O-phosphoseryl-tRNA[Ser]Sec kinase. In addition, we found that selenophosphate synthetase 2 could synthesize monoselenophosphate in vitro but selenophosphate synthetase 1 could not. Conservation of the overall pathway of Sec biosynthesis suggests that this pathway is also active in other eukaryotes and archaea that synthesize selenoproteins. PMID:17194211

  5. Retrieval Failure Contributes to Gist-Based False Recognition

    PubMed Central

    Guerin, Scott A.; Robbins, Clifford A.; Gilmore, Adrian W.; Schacter, Daniel L.

    2011-01-01

    People often falsely recognize items that are similar to previously encountered items. This robust memory error is referred to as gist-based false recognition. A widely held view is that this error occurs because the details fade rapidly from our memory. Contrary to this view, an initial experiment revealed that, following the same encoding conditions that produce high rates of gist-based false recognition, participants overwhelmingly chose the correct target rather than its related foil when given the option to do so. A second experiment showed that this result is due to increased access to stored details provided by reinstatement of the originally encoded photograph, rather than to increased attention to the details. Collectively, these results suggest that details needed for accurate recognition are, to a large extent, still stored in memory and that a critical factor determining whether false recognition will occur is whether these details can be accessed during retrieval. PMID:22125357

  6. Facial Recognition in a Group-Living Cichlid Fish.

    PubMed

    Kohda, Masanori; Jordan, Lyndon Alexander; Hotta, Takashi; Kosaka, Naoya; Karino, Kenji; Tanaka, Hirokazu; Taniyama, Masami; Takeyama, Tomohiro

    2015-01-01

    The theoretical underpinnings of the mechanisms of sociality, e.g. territoriality, hierarchy, and reciprocity, are based on assumptions of individual recognition. While behavioural evidence suggests individual recognition is widespread, the cues that animals use to recognise individuals are established in only a handful of systems. Here, we use digital models to demonstrate that facial features are the visual cue used for individual recognition in the social fish Neolamprologus pulcher. Focal fish were exposed to digital images showing four different combinations of familiar and unfamiliar face and body colorations. Focal fish attended to digital models with unfamiliar faces longer and from a further distance to the model than to models with familiar faces. These results strongly suggest that fish can distinguish individuals accurately using facial colour patterns. Our observations also suggest that fish are able to rapidly (≤ 0.5 sec) discriminate between familiar and unfamiliar individuals, a speed of recognition comparable to primates including humans.

  7. Protein synthesis editing by a DNA aptamer.

    PubMed Central

    Hale, S P; Schimmel, P

    1996-01-01

    Potential errors in decoding genetic information are corrected by tRNA-dependent amino acid recognition processes manifested through editing reactions. One example is the rejection of difficult-to-discriminate misactivated amino acids by tRNA synthetases through hydrolytic reactions. Although several crystal structures of tRNA synthetases and synthetase-tRNA complexes exist, none of them have provided insight into the editing reactions. Other work suggested that editing required active amino acid acceptor hydroxyl groups at the 3' end of a tRNA effector. We describe here the isolation of a DNA aptamer that specifically induced hydrolysis of a misactivated amino acid bound to a tRNA synthetase. The aptamer had no effect on the stability of the correctly activated amino acid and was almost as efficient as the tRNA for inducing editing activity. The aptamer has no sequence similarity to that of the tRNA effector and cannot be folded into a tRNA-like structure. These and additional data show that active acceptor hydroxyl groups in a tRNA effector and a tRNA-like structure are not essential for editing. Thus, specific bases in a nucleic acid effector trigger the editing response. Images Fig. 3 Fig. 4 PMID:8610114

  8. Recognition memory of newly learned faces.

    PubMed

    Ishai, Alumit; Yago, Elena

    2006-12-11

    We used event-related fMRI to study recognition memory of newly learned faces. Caucasian subjects memorized unfamiliar, neutral and happy South Korean faces and 4 days later performed a memory retrieval task in the MR scanner. We predicted that previously seen faces would be recognized faster and more accurately and would elicit stronger neural activation than novel faces. Consistent with our hypothesis, novel faces were recognized more slowly and less accurately than previously seen faces. We found activation in a distributed cortical network that included face-responsive regions in the visual cortex, parietal and prefrontal regions, and the hippocampus. Within all regions, correctly recognized, previously seen faces evoked stronger activation than novel faces. Additionally, in parietal and prefrontal cortices, stronger activation was observed during correct than incorrect trials. Finally, in the hippocampus, false alarms to happy faces elicited stronger responses than false alarms to neutral faces. Our findings suggest that face recognition memory is mediated by stimulus-specific representations stored in extrastriate regions; parietal and prefrontal regions where old and new items are classified; and the hippocampus where veridical memory traces are recovered.

  9. On the Time Course of Vocal Emotion Recognition

    PubMed Central

    Pell, Marc D.; Kotz, Sonja A.

    2011-01-01

    How quickly do listeners recognize emotions from a speaker's voice, and does the time course for recognition vary by emotion type? To address these questions, we adapted the auditory gating paradigm to estimate how much vocal information is needed for listeners to categorize five basic emotions (anger, disgust, fear, sadness, happiness) and neutral utterances produced by male and female speakers of English. Semantically-anomalous pseudo-utterances (e.g., The rivix jolled the silling) conveying each emotion were divided into seven gate intervals according to the number of syllables that listeners heard from sentence onset. Participants (n = 48) judged the emotional meaning of stimuli presented at each gate duration interval, in a successive, blocked presentation format. Analyses looked at how recognition of each emotion evolves as an utterance unfolds and estimated the “identification point” for each emotion. Results showed that anger, sadness, fear, and neutral expressions are recognized more accurately at short gate intervals than happiness, and particularly disgust; however, as speech unfolds, recognition of happiness improves significantly towards the end of the utterance (and fear is recognized more accurately than other emotions). When the gate associated with the emotion identification point of each stimulus was calculated, data indicated that fear (M = 517 ms), sadness (M = 576 ms), and neutral (M = 510 ms) expressions were identified from shorter acoustic events than the other emotions. These data reveal differences in the underlying time course for conscious recognition of basic emotions from vocal expressions, which should be accounted for in studies of emotional speech processing. PMID:22087275

  10. Visual Scanning Patterns and Executive Function in Relation to Facial Emotion Recognition in Aging

    PubMed Central

    Circelli, Karishma S.; Clark, Uraina S.; Cronin-Golomb, Alice

    2012-01-01

    Objective The ability to perceive facial emotion varies with age. Relative to younger adults (YA), older adults (OA) are less accurate at identifying fear, anger, and sadness, and more accurate at identifying disgust. Because different emotions are conveyed by different parts of the face, changes in visual scanning patterns may account for age-related variability. We investigated the relation between scanning patterns and recognition of facial emotions. Additionally, as frontal-lobe changes with age may affect scanning patterns and emotion recognition, we examined correlations between scanning parameters and performance on executive function tests. Methods We recorded eye movements from 16 OA (mean age 68.9) and 16 YA (mean age 19.2) while they categorized facial expressions and non-face control images (landscapes), and administered standard tests of executive function. Results OA were less accurate than YA at identifying fear (p<.05, r=.44) and more accurate at identifying disgust (p<.05, r=.39). OA fixated less than YA on the top half of the face for disgust, fearful, happy, neutral, and sad faces (p’s<.05, r’s≥.38), whereas there was no group difference for landscapes. For OA, executive function was correlated with recognition of sad expressions and with scanning patterns for fearful, sad, and surprised expressions. Conclusion We report significant age-related differences in visual scanning that are specific to faces. The observed relation between scanning patterns and executive function supports the hypothesis that frontal-lobe changes with age may underlie some changes in emotion recognition. PMID:22616800

  11. Process Demands of Rejection Mechanisms of Recognition Memory

    ERIC Educational Resources Information Center

    Odegard, Timothy N.; Koen, Joshua D.; Gama, Jorge M.

    2008-01-01

    A surge of research has been conducted to examine memory editing mechanisms that help distinguish accurate from inaccurate memories. In the present experiment, the authors examined the ability of participants to use novelty detection, recollection rejection, and plausibility judgments to reject lures presented on a recognition memory test.…

  12. Near-infrared face recognition utilizing open CV software

    NASA Astrophysics Data System (ADS)

    Sellami, Louiza; Ngo, Hau; Fowler, Chris J.; Kearney, Liam M.

    2014-06-01

    Commercially available hardware, freely available algorithms, and authors' developed software are synergized successfully to detect and recognize subjects in an environment without visible light. This project integrates three major components: an illumination device operating in near infrared (NIR) spectrum, a NIR capable camera and a software algorithm capable of performing image manipulation, facial detection and recognition. Focusing our efforts in the near infrared spectrum allows the low budget system to operate covertly while still allowing for accurate face recognition. In doing so a valuable function has been developed which presents potential benefits in future civilian and military security and surveillance operations.

  13. In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

    PubMed

    Czudnochowski, Nadine; Wang, Amy Liya; Finer-Moore, Janet; Stroud, Robert M

    2013-10-23

    Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications.

    PubMed

    Dewe, Joshua M; Whipple, Joseph M; Chernyakov, Irina; Jaramillo, Laura N; Phizicky, Eric M

    2012-10-01

    The structural and functional integrity of tRNA is crucial for translation. In the yeast Saccharomyces cerevisiae, certain aberrant pre-tRNA species are subject to nuclear surveillance, leading to 3' exonucleolytic degradation, and certain mature tRNA species are subject to rapid tRNA decay (RTD) if they are appropriately hypomodified or bear specific destabilizing mutations, leading to 5'-3' exonucleolytic degradation by Rat1 and Xrn1. Thus, trm8-Δ trm4-Δ strains are temperature sensitive due to lack of m(7)G(46) and m(5)C and the consequent RTD of tRNA(Val(AAC)), and tan1-Δ trm44-Δ strains are temperature sensitive due to lack of ac(4)C(12) and Um(44) and the consequent RTD of tRNA(Ser(CGA)) and tRNA(Ser(UGA)). It is unknown how the RTD pathway interacts with translation and other cellular processes, and how generally this pathway acts on hypomodified tRNAs. We provide evidence here that elongation factor 1A (EF-1A) competes with the RTD pathway for substrate tRNAs, since its overexpression suppresses the tRNA degradation and the growth defect of strains subject to RTD, whereas reduced levels of EF-1A have the opposite effect. We also provide evidence that RTD acts on a variety of tRNAs lacking one or more different modifications, since trm1-Δ trm4-Δ mutants are subject to RTD of tRNA(Ser(CGA)) and tRNA(Ser(UGA)) due to lack of m(2,2)G(26) and m(5)C, and since trm8-Δ, tan1-Δ, and trm1-Δ single mutants are each subject to RTD. These results demonstrate that RTD interacts with the translation machinery and acts widely on hypomodified tRNAs.

  15. Distractor Plausibility and Criterion Placement in Recognition

    ERIC Educational Resources Information Center

    Benjamin, Aaron S.; Bawa, Sameer

    2004-01-01

    To set an optimal decision criterion on a test of recognition, a subject must estimate the degree to which they can discriminate previously studied from unstudied stimuli. To do so accurately, the subject must assess not only their mastery of the material but also the extent to which the distractors yield mnemonic evidence that makes them…

  16. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection

    PubMed Central

    Au, Hilda H.; Cornilescu, Gabriel; Mouzakis, Kathryn D.; Ren, Qian; Burke, Jordan E.; Lee, Seonghoon; Butcher, Samuel E.; Jan, Eric

    2015-01-01

    The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame. PMID:26554019

  17. Structures and functions of proteins and nucleic acids in protein biosynthesis

    NASA Astrophysics Data System (ADS)

    Miyazawa, Tatsuo; Yokoyama, Shigeyuki

    Infrared and Raman spectroscopy is useful for studying helical conformations of polypeptides, which are determined by molecular structure parameters. Nuclear magnetic resonance spectroscopy, as well as X-ray analysis, is now established to be important for conformation studies of proteins and nucleic acids in solution. This article is mainly concerned with the conformational aspect and function regulation in protein biosynthesis. The strict recognition of transfer ribonucleic acid (tRNA) by aminoacyl-tRNA synthetase (ARS) is achieved by multi-step mutual adaptation. The conformations of ARS-bound amino acids have been elucidated by transferred nuclear Overhauser effect analysis. Aminoacyl-tRNA takes the 3‧-isomeric form in the polypeptide chain elongation cycle. The regulation of codon recognition by post-transcriptional modification is achieved by conversion of the conformational characteristic of the anticodon of tRNA. The cytidine → lysidine modification of the anticodon of minor isoleucine tRNA concurrently converts the amino acid specificity and the codon specificity. As novel protein engineering, a basic strategy has been established for in vivo biosynthesis of proteins that are substituted with unnatural amino acids (alloproteins).

  18. Empower multiplex cell and tissue-specific CRISPR-mediated gene manipulation with self-cleaving ribozymes and tRNA.

    PubMed

    Xu, Li; Zhao, Lixia; Gao, Yandi; Xu, Jing; Han, Renzhi

    2017-03-17

    Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) system has emerged in recent years as a highly efficient RNA-guided gene manipulation platform. Simultaneous editing or transcriptional activation/suppression of different genes becomes feasible with the co-delivery of multiple guide RNAs (gRNAs). Here, we report that multiple gRNAs linked with self-cleaving ribozymes and/or tRNA could be simultaneously expressed from a single U6 promoter to exert genome editing of dystrophin and myosin binding protein C3 in human and mouse cells. Moreover, this strategy allows the expression of multiple gRNAs for synergistic transcription activation of follistatin when used with catalytically inactive dCas9-VP64 or dCas9-p300core fusions. Finally, the gRNAs linked by the self-cleaving ribozymes and tRNA could be expressed from RNA polymerase type II (pol II) promoters such as generic CMV and muscle/heart-specific MHCK7. This is particularly useful for in vivo applications when the packaging capacity of recombinant adeno-associated virus is limited while tissue-specific delivery of gRNAs and Cas9 is desired. Taken together, this study provides a novel strategy to enable tissue-specific expression of more than one gRNAs for multiplex gene editing from a single pol II promoter. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. ASERA: A Spectrum Eye Recognition Assistant

    NASA Astrophysics Data System (ADS)

    Yuan, Hailong; Zhang, Haotong; Zhang, Yanxia; Lei, Yajuan; Dong, Yiqiao; Zhao, Yongheng

    2018-04-01

    ASERA, ASpectrum Eye Recognition Assistant, aids in quasar spectral recognition and redshift measurement and can also be used to recognize various types of spectra of stars, galaxies and AGNs (Active Galactic Nucleus). This interactive software allows users to visualize observed spectra, superimpose template spectra from the Sloan Digital Sky Survey (SDSS), and interactively access related spectral line information. ASERA is an efficient and user-friendly semi-automated toolkit for the accurate classification of spectra observed by LAMOST (the Large Sky Area Multi-object Fiber Spectroscopic Telescope) and is available as a standalone Java application and as a Java applet. The software offers several functions, including wavelength and flux scale settings, zoom in and out, redshift estimation, and spectral line identification.

  20. A Random Forest-based ensemble method for activity recognition.

    PubMed

    Feng, Zengtao; Mo, Lingfei; Li, Meng

    2015-01-01

    This paper presents a multi-sensor ensemble approach to human physical activity (PA) recognition, using random forest. We designed an ensemble learning algorithm, which integrates several independent Random Forest classifiers based on different sensor feature sets to build a more stable, more accurate and faster classifier for human activity recognition. To evaluate the algorithm, PA data collected from the PAMAP (Physical Activity Monitoring for Aging People), which is a standard, publicly available database, was utilized to train and test. The experimental results show that the algorithm is able to correctly recognize 19 PA types with an accuracy of 93.44%, while the training is faster than others. The ensemble classifier system based on the RF (Random Forest) algorithm can achieve high recognition accuracy and fast calculation.

  1. The level of cognitive function and recognition of emotions in older adults

    PubMed Central

    Singh-Manoux, Archana; Batty, G. David; Ebmeier, Klaus P.; Jokela, Markus; Harmer, Catherine J.; Kivimäki, Mika

    2017-01-01

    Background The association between cognitive decline and the ability to recognise emotions in interpersonal communication is not well understood. We aimed to investigate the association between cognitive function and the ability to recognise emotions in other people’s facial expressions across the full continuum of cognitive capacity. Methods Cross-sectional analysis of 4039 participants (3016 men, 1023 women aged 59 to 82 years) in the Whitehall II study. Cognitive function was assessed using a 30-item Mini-Mental State Examination (MMSE), further classified into 8 groups: 30, 29, 28, 27, 26, 25, 24, and <24 (possible dementia) MMSE points. The Facial Expression Recognition Task (FERT) was used to examine recognition of anger, fear, disgust, sadness, and happiness. Results The multivariable adjusted difference in the percentage of accurate recognition between the highest and lowest MMSE group was 14.9 (95%CI, 11.1–18.7) for anger, 15.5 (11.9–19.2) for fear, 18.5 (15.2–21.8) for disgust, 11.6 (7.3–16.0) for sadness, and 6.3 (3.1–9.4) for happiness. However, recognition of several emotions was reduced already after 1 to 2-point reduction in MMSE and with further points down in MMSE, the recognition worsened at an accelerated rate. Conclusions The ability to recognize emotion in facial expressions is affected at an early stage of cognitive impairment and might decline at an accelerated rate with the deterioration of cognitive function. Accurate recognition of happiness seems to be less affected by a severe decline in cognitive performance than recognition of negatively valued emotions. PMID:28977015

  2. The automaticity of emotion recognition.

    PubMed

    Tracy, Jessica L; Robins, Richard W

    2008-02-01

    Evolutionary accounts of emotion typically assume that humans evolved to quickly and efficiently recognize emotion expressions because these expressions convey fitness-enhancing messages. The present research tested this assumption in 2 studies. Specifically, the authors examined (a) how quickly perceivers could recognize expressions of anger, contempt, disgust, embarrassment, fear, happiness, pride, sadness, shame, and surprise; (b) whether accuracy is improved when perceivers deliberate about each expression's meaning (vs. respond as quickly as possible); and (c) whether accurate recognition can occur under cognitive load. Across both studies, perceivers quickly and efficiently (i.e., under cognitive load) recognized most emotion expressions, including the self-conscious emotions of pride, embarrassment, and shame. Deliberation improved accuracy in some cases, but these improvements were relatively small. Discussion focuses on the implications of these findings for the cognitive processes underlying emotion recognition.

  3. Altered nuclear tRNA metabolism in La-deleted Schizosaccharomyces pombe is accompanied by a nutritional stress response involving Atf1p and Pcr1p that is suppressible by Xpo-t/Los1p.

    PubMed

    Cherkasova, Vera; Maury, Luis Lopez; Bacikova, Dagmar; Pridham, Kevin; Bähler, Jürg; Maraia, Richard J

    2012-02-01

    Deletion of the sla1(+) gene, which encodes a homologue of the human RNA-binding protein La in Schizosaccharomyces pombe, causes irregularities in tRNA processing, with altered distribution of pre-tRNA intermediates. We show, using mRNA profiling, that cells lacking sla1(+) have increased mRNAs from amino acid metabolism (AAM) genes and, furthermore, exhibit slow growth in Edinburgh minimal medium. A subset of these AAM genes is under control of the AP-1-like, stress-responsive transcription factors Atf1p and Pcr1p. Although S. pombe growth is resistant to rapamycin, sla1-Δ cells are sensitive, consistent with deficiency of leucine uptake, hypersensitivity to NH4, and genetic links to the target of rapamycin (TOR) pathway. Considering that perturbed intranuclear pre-tRNA metabolism and apparent deficiency in tRNA nuclear export in sla1-Δ cells may trigger the AAM response, we show that modest overexpression of S. pombe los1(+) (also known as Xpo-t), encoding the nuclear exportin for tRNA, suppresses the reduction in pre-tRNA levels, AAM gene up-regulation, and slow growth of sla1-Δ cells. The conclusion that emerges is that sla1(+) regulates AAM mRNA production in S. pombe through its effects on nuclear tRNA processing and probably nuclear export. Finally, the results are discussed in the context of stress response programs in Saccharomyces cerevisiae.

  4. Altered nuclear tRNA metabolism in La-deleted Schizosaccharomyces pombe is accompanied by a nutritional stress response involving Atf1p and Pcr1p that is suppressible by Xpo-t/Los1p

    PubMed Central

    Cherkasova, Vera; Lopez Maury, Luis; Bacikova, Dagmar; Pridham, Kevin; Bähler, Jürg; Maraia, Richard J.

    2012-01-01

    Deletion of the sla1+ gene, which encodes a homologue of the human RNA-binding protein La in Schizosaccharomyces pombe, causes irregularities in tRNA processing, with altered distribution of pre-tRNA intermediates. We show, using mRNA profiling, that cells lacking sla1+ have increased mRNAs from amino acid metabolism (AAM) genes and, furthermore, exhibit slow growth in Edinburgh minimal medium. A subset of these AAM genes is under control of the AP-1–like, stress-responsive transcription factors Atf1p and Pcr1p. Although S. pombe growth is resistant to rapamycin, sla1-Δ cells are sensitive, consistent with deficiency of leucine uptake, hypersensitivity to NH4, and genetic links to the target of rapamycin (TOR) pathway. Considering that perturbed intranuclear pre-tRNA metabolism and apparent deficiency in tRNA nuclear export in sla1-Δ cells may trigger the AAM response, we show that modest overexpression of S. pombe los1+ (also known as Xpo-t), encoding the nuclear exportin for tRNA, suppresses the reduction in pre-tRNA levels, AAM gene up-regulation, and slow growth of sla1-Δ cells. The conclusion that emerges is that sla1+ regulates AAM mRNA production in S. pombe through its effects on nuclear tRNA processing and probably nuclear export. Finally, the results are discussed in the context of stress response programs in Saccharomyces cerevisiae. PMID:22160596

  5. Accuracy of computer-assisted navigation: significant augmentation by facial recognition software.

    PubMed

    Glicksman, Jordan T; Reger, Christine; Parasher, Arjun K; Kennedy, David W

    2017-09-01

    Over the past 20 years, image guidance navigation has been used with increasing frequency as an adjunct during sinus and skull base surgery. These devices commonly utilize surface registration, where varying pressure of the registration probe and loss of contact with the face during the skin tracing process can lead to registration inaccuracies, and the number of registration points incorporated is necessarily limited. The aim of this study was to evaluate the use of novel facial recognition software for image guidance registration. Consecutive adults undergoing endoscopic sinus surgery (ESS) were prospectively studied. Patients underwent image guidance registration via both conventional surface registration and facial recognition software. The accuracy of both registration processes were measured at the head of the middle turbinate (MTH), middle turbinate axilla (MTA), anterior wall of sphenoid sinus (SS), and nasal tip (NT). Forty-five patients were included in this investigation. Facial recognition was accurate to within a mean of 0.47 mm at the MTH, 0.33 mm at the MTA, 0.39 mm at the SS, and 0.36 mm at the NT. Facial recognition was more accurate than surface registration at the MTH by an average of 0.43 mm (p = 0.002), at the MTA by an average of 0.44 mm (p < 0.001), and at the SS by an average of 0.40 mm (p < 0.001). The integration of facial recognition software did not adversely affect registration time. In this prospective study, automated facial recognition software significantly improved the accuracy of image guidance registration when compared to conventional surface registration. © 2017 ARS-AAOA, LLC.

  6. Intelligent fault recognition strategy based on adaptive optimized multiple centers

    NASA Astrophysics Data System (ADS)

    Zheng, Bo; Li, Yan-Feng; Huang, Hong-Zhong

    2018-06-01

    For the recognition principle based optimized single center, one important issue is that the data with nonlinear separatrix cannot be recognized accurately. In order to solve this problem, a novel recognition strategy based on adaptive optimized multiple centers is proposed in this paper. This strategy recognizes the data sets with nonlinear separatrix by the multiple centers. Meanwhile, the priority levels are introduced into the multi-objective optimization, including recognition accuracy, the quantity of optimized centers, and distance relationship. According to the characteristics of various data, the priority levels are adjusted to ensure the quantity of optimized centers adaptively and to keep the original accuracy. The proposed method is compared with other methods, including support vector machine (SVM), neural network, and Bayesian classifier. The results demonstrate that the proposed strategy has the same or even better recognition ability on different distribution characteristics of data.

  7. Accurate recognition and effective treatment of ventricular fibrillation by automated external defibrillators in adolescents.

    PubMed

    Atkins, D L; Hartley, L L; York, D K

    1998-03-01

    To evaluate the accuracy and efficacy of automated external defibrillators (AEDs) in patients <16 years old. AEDs are standard therapy in out-of-hospital resuscitation of adults and have led to higher success rates. Their use in children and adolescents has never been evaluated, despite recommendations from the American Heart Association that they be used in children >8 years of age. This was a retrospective cohort study of children <16 years old who underwent out-of-hospital cardiac resuscitation and on whom an AED was used during the resuscitation. The setting was rural and urban prehospital emergency medical systems. Patients were identified by review of a database of cardiac arrests maintained by a large surveillance program of these services. AEDs were used to assess cardiac rhythm in 18 patients with a mean age of 12.1 +/- 3.7 years. The cardiac rhythms were analyzed 67 times and included ventricular fibrillation (25), asystole/pulseless electrical activity (32), sinus bradycardia (6), and sinus tachycardia (4). The AEDs recognized all nonshockable rhythms accurately and advised no shock. Ventricular fibrillation was recognized accurately in 22 (88%) of 25 episodes and advised or administered a shock 22 times. Sensitivity and specificity for accurate rhythm analysis were 88% and 100%, respectively. One patient with a nonshockable rhythm survived, whereas 3 of 9 patients with ventricular fibrillation survived. These data furnish evidence that AEDs provide accurate rhythm detection and shock delivery to children and young adolescents. AED use is potentially as effective for children as it is for adults.

  8. Exploring a Decrease in Recognition Performance for Non-Antecedents Following the Processing of Anaphors

    ERIC Educational Resources Information Center

    Dopkins, Stephen; Nordlie, Johanna

    2011-01-01

    Recognition judgments to the non-antecedents of a repeated-noun anaphor are slower and less accurate after than before the processing of the anaphor. Disagreement exists as to whether this pattern of performance reflects a bias shift carried out by a memory process associated with the recognition of a word that has previously occurred in the…

  9. Recognition memory is modulated by visual similarity.

    PubMed

    Yago, Elena; Ishai, Alumit

    2006-06-01

    We used event-related fMRI to test whether recognition memory depends on visual similarity between familiar prototypes and novel exemplars. Subjects memorized portraits, landscapes, and abstract compositions by six painters with a unique style, and later performed a memory recognition task. The prototypes were presented with new exemplars that were either visually similar or dissimilar. Behaviorally, novel, dissimilar items were detected faster and more accurately. We found activation in a distributed cortical network that included face- and object-selective regions in the visual cortex, where familiar prototypes evoked stronger responses than new exemplars; attention-related regions in parietal cortex, where responses elicited by new exemplars were reduced with decreased similarity to the prototypes; and the hippocampus and memory-related regions in parietal and prefrontal cortices, where stronger responses were evoked by the dissimilar exemplars. Our findings suggest that recognition memory is mediated by classification of novel exemplars as a match or a mismatch, based on their visual similarity to familiar prototypes.

  10. Recognition intent and visual word recognition.

    PubMed

    Wang, Man-Ying; Ching, Chi-Le

    2009-03-01

    This study adopted a change detection task to investigate whether and how recognition intent affects the construction of orthographic representation in visual word recognition. Chinese readers (Experiment 1-1) and nonreaders (Experiment 1-2) detected color changes in radical components of Chinese characters. Explicit recognition demand was imposed in Experiment 2 by an additional recognition task. When the recognition was implicit, a bias favoring the radical location informative of character identity was found in Chinese readers (Experiment 1-1), but not nonreaders (Experiment 1-2). With explicit recognition demands, the effect of radical location interacted with radical function and word frequency (Experiment 2). An estimate of identification performance under implicit recognition was derived in Experiment 3. These findings reflect the joint influence of recognition intent and orthographic regularity in shaping readers' orthographic representation. The implication for the role of visual attention in word recognition was also discussed.

  11. Domain Regeneration for Cross-Database Micro-Expression Recognition

    NASA Astrophysics Data System (ADS)

    Zong, Yuan; Zheng, Wenming; Huang, Xiaohua; Shi, Jingang; Cui, Zhen; Zhao, Guoying

    2018-05-01

    In this paper, we investigate the cross-database micro-expression recognition problem, where the training and testing samples are from two different micro-expression databases. Under this setting, the training and testing samples would have different feature distributions and hence the performance of most existing micro-expression recognition methods may decrease greatly. To solve this problem, we propose a simple yet effective method called Target Sample Re-Generator (TSRG) in this paper. By using TSRG, we are able to re-generate the samples from target micro-expression database and the re-generated target samples would share same or similar feature distributions with the original source samples. For this reason, we can then use the classifier learned based on the labeled source samples to accurately predict the micro-expression categories of the unlabeled target samples. To evaluate the performance of the proposed TSRG method, extensive cross-database micro-expression recognition experiments designed based on SMIC and CASME II databases are conducted. Compared with recent state-of-the-art cross-database emotion recognition methods, the proposed TSRG achieves more promising results.

  12. Metacognitive Processes in Emotion Recognition: Are They Different in Adults with Asperger's Disorder?

    ERIC Educational Resources Information Center

    Sawyer, Alyssa C. P.; Williamson, Paul; Young, Robyn

    2014-01-01

    Deficits in emotion recognition and social interaction characterize individuals with Asperger's Disorder (AS). Moreover they also appear to be less able to accurately use confidence to gauge their emotion recognition accuracy (i.e., metacognitive monitoring). The aim of this study was to extend this finding by considering both monitoring and…

  13. Changing the criterion for memory conformity in free recall and recognition.

    PubMed

    Wright, Daniel B; Gabbert, Fiona; Memon, Amina; London, Kamala

    2008-02-01

    People's responses during memory studies are affected by what other people say. This memory conformity effect has been shown in both free recall and recognition. Here we examine whether accurate, inaccurate, and suggested answers are affected similarly when the response criterion is varied. In the first study, participants saw four pictures of detailed scenes and then discussed the content of these scenes with another participant who saw the same scenes, but with a couple of details changed. Participants were either told to recall everything they could and not to worry about making mistakes (lenient), or only to recall items if they were sure that they were accurate (strict). The strict instructions reduced the amount of inaccurate information reported that the other person suggested, but also reduced the number of accurate details recalled. In the second study, participants were shown a large set of faces and then their memory recognition was tested with a confederate on these and fillers. Here also, the criterion manipulation shifted both accurate and inaccurate responses, and those suggested by the confederate. The results are largely consistent with a shift in response criterion affecting accurate, inaccurate, and suggested information. In addition we varied the level of secrecy in the participants' responses. The effects of secrecy were complex and depended on the level of response criterion. Implications for interviewing eyewitnesses and line-ups are discussed.

  14. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.

    PubMed Central

    Marck, Christian; Grosjean, Henri

    2002-01-01

    From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria. PMID:12403461

  15. Molecular phylogeny for marine turtles based on sequences of the ND4-leucine tRNA and control regions of mitochondrial DNA.

    PubMed

    Dutton, P H; Davis, S K; Guerra, T; Owens, D

    1996-06-01

    Marine turtles are divided into two families, the Dermochelyidae and the Cheloniidae. The majority of species are currently placed within the two tribes of the Cheloniidae, the Chelonini and the Carettini, but debate continues over generic and tribal affinities as well as species boundaries. We used nucleotide sequences (907 bp) from the ND4-LEU tRNA region and the control region (526 bp) of mitochondrial DNA to resolve areas of uncertainty in marine turtle (Chelonioidae) systematics. The ND4-LEU tRNA fragment was more conserved than the fragment from the control region, with sequence divergences ranging from 0.026 to 0.148 and 0.067 to 0.267, respectively. Parsimony analysis based only on the ND4-LEU tRNA data suggests that the hawksbill, Eretmochelys imbricata, lies within the tribe Carettni and is closely related to the genus Caretta, but could not resolve the position of the flatback, Natator depressus. A similar analysis based only on the control region sequence data suggested that N. depressus is affiliated with the Chelonini, but failed to resolve the position of E. imbricata and the loggerhead, Caretta caretta. In contrast to these results, the combination of both data sets with published cytochrome b data produced a phylogeny based on 1924 bp of sequence data which resolves the position of E. imbricata relative to Caretta and Lepidochelys and joins N. depressus as sister to the Carettini. Based on the molecular data, the Chelonini contains the Chelonia species, while the Carettini contains the remaining species of Cheloniidae. The control region sequence divergence between Pacific and Atlantic populations of the leatherback, Dermochelys coriacea, was relatively low (0.0081) when compared with the green turtle, Chelonia mydas (0.071-0.074). Atlantic and Pacific populations of Ch. mydas were found to be paraphyletic with respect to the black turtle, Ch. agassizi, suggesting that the current taxonomic designations within the Pacific Chelonia are questionable

  16. Researching the Use of Voice Recognition Writing Software.

    ERIC Educational Resources Information Center

    Honeycutt, Lee

    2003-01-01

    Notes that voice recognition technology (VRT) has become accurate and fast enough to be useful in a variety of writing scenarios. Contends that little is known about how this technology might affect writing process or perceptions of silent writing. Explores future use of VRT by examining past research in the technology of dictation. (PM)

  17. Vision-based posture recognition using an ensemble classifier and a vote filter

    NASA Astrophysics Data System (ADS)

    Ji, Peng; Wu, Changcheng; Xu, Xiaonong; Song, Aiguo; Li, Huijun

    2016-10-01

    Posture recognition is a very important Human-Robot Interaction (HRI) way. To segment effective posture from an image, we propose an improved region grow algorithm which combining with the Single Gauss Color Model. The experiment shows that the improved region grow algorithm can get the complete and accurate posture than traditional Single Gauss Model and region grow algorithm, and it can eliminate the similar region from the background at the same time. In the posture recognition part, and in order to improve the recognition rate, we propose a CNN ensemble classifier, and in order to reduce the misjudgments during a continuous gesture control, a vote filter is proposed and applied to the sequence of recognition results. Comparing with CNN classifier, the CNN ensemble classifier we proposed can yield a 96.27% recognition rate, which is better than that of CNN classifier, and the proposed vote filter can improve the recognition result and reduce the misjudgments during the consecutive gesture switch.

  18. Recognition and context memory for faces from own and other ethnic groups: a remember-know investigation.

    PubMed

    Horry, Ruth; Wright, Daniel B; Tredoux, Colin G

    2010-03-01

    People are more accurate at recognizing faces from their own ethnic group than at recognizing faces from other ethnic groups. This other-ethnicity effect (OEE) in recognition may be produced by a deficit in recollective memory for other-ethnicity faces. In a single study, White and Black participants saw White and Black faces presented within several different visual contexts. The participants were then given an old/new recognition task. Old responses were followed by remember-know-guess judgments and context judgments. Own-ethnicity faces were recognized more accurately, were given more remember responses, and produced more accurate context judgments than did other-ethnicity faces. These results are discussed in a dual-process framework, and implications for eyewitness memory are considered.

  19. Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing

    PubMed Central

    Jones, Christopher P.; Saadatmand, Jenan; Kleiman, Lawrence; Musier-Forsyth, Karin

    2013-01-01

    The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNALys3. Host cell tRNALys is selectively packaged into HIV-1 through a specific interaction between the major tRNALys-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNALys3 is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNALys and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNALys3 in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNALys to increase the efficiency of tRNALys3 annealing to viral RNA. PMID:23264568

  20. The effect of comorbid depression on facial and prosody emotion recognition in first-episode schizophrenia spectrum.

    PubMed

    Herniman, Sarah E; Allott, Kelly A; Killackey, Eóin; Hester, Robert; Cotton, Sue M

    2017-01-15

    Comorbid depression is common in first-episode schizophrenia spectrum (FES) disorders. Both depression and FES are associated with significant deficits in facial and prosody emotion recognition performance. However, it remains unclear whether people with FES and comorbid depression, compared to those without comorbid depression, have overall poorer emotion recognition, or instead, a different pattern of emotion recognition deficits. The aim of this study was to compare facial and prosody emotion recognition performance between those with and without comorbid depression in FES. This study involved secondary analysis of baseline data from a randomized controlled trial of vocational intervention for young people with first-episode psychosis (N=82; age range: 15-25 years). Those with comorbid depression (n=24) had more accurate recognition of sadness in faces compared to those without comorbid depression. Severity of depressive symptoms was also associated with more accurate recognition of sadness in faces. Such results did not recur for prosody emotion recognition. In addition to the cross-sectional design, limitations of this study include the absence of facial and prosodic recognition of neutral emotions. Findings indicate a mood congruent negative bias in facial emotion recognition in those with comorbid depression and FES, and provide support for cognitive theories of depression that emphasise the role of such biases in the development and maintenance of depression. Longitudinal research is needed to determine whether mood-congruent negative biases are implicated in the development and maintenance of depression in FES, or whether such biases are simply markers of depressed state. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. A Survey on Banknote Recognition Methods by Various Sensors

    PubMed Central

    Lee, Ji Woo; Hong, Hyung Gil; Kim, Ki Wan; Park, Kang Ryoung

    2017-01-01

    Despite a decrease in the use of currency due to the recent growth in the use of electronic financial transactions, real money transactions remain very important in the global market. While performing transactions with real money, touching and counting notes by hand, is still a common practice in daily life, various types of automated machines, such as ATMs and banknote counters, are essential for large-scale and safe transactions. This paper presents studies that have been conducted in four major areas of research (banknote recognition, counterfeit banknote detection, serial number recognition, and fitness classification) in the accurate banknote recognition field by various sensors in such automated machines, and describes the advantages and drawbacks of the methods presented in those studies. While to a limited extent some surveys have been presented in previous studies in the areas of banknote recognition or counterfeit banknote recognition, this paper is the first of its kind to review all four areas. Techniques used in each of the four areas recognize banknote information (denomination, serial number, authenticity, and physical condition) based on image or sensor data, and are actually applied to banknote processing machines across the world. This study also describes the technological challenges faced by such banknote recognition techniques and presents future directions of research to overcome them. PMID:28208733

  2. Changing predictions, stable recognition: Children's representations of downward incline motion.

    PubMed

    Hast, Michael; Howe, Christine

    2017-11-01

    Various studies to-date have demonstrated children hold ill-conceived expressed beliefs about the physical world such as that one ball will fall faster than another because it is heavier. At the same time, they also demonstrate accurate recognition of dynamic events. How these representations relate is still unresolved. This study examined 5- to 11-year-olds' (N = 130) predictions and recognition of motion down inclines. Predictions were typically in error, matching previous work, but children largely recognized correct events as correct and rejected incorrect ones. The results also demonstrate while predictions change with increasing age, recognition shows signs of stability. The findings provide further support for a hybrid model of object representations and argue in favour of stable core cognition existing alongside developmental changes. Statement of contribution What is already known on this subject? Children's predictions of physical events show limitations in accuracy Their recognition of such events suggests children may use different knowledge sources in their reasoning What the present study adds? Predictions fluctuate more strongly than recognition, suggesting stable core cognition But recognition also shows some fluctuation, arguing for a hybrid model of knowledge representation. © 2017 The British Psychological Society.

  3. Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics.

    PubMed

    Yang, Andrew C; du Bois, Haley; Olsson, Niclas; Gate, David; Lehallier, Benoit; Berdnik, Daniela; Brewer, Kyle D; Bertozzi, Carolyn R; Elias, Joshua E; Wyss-Coray, Tony

    2018-06-13

    Bioorthogonal tools enable cell-type-specific proteomics, a prerequisite to understanding biological processes in multicellular organisms. Here we report two engineered aminoacyl-tRNA synthetases for mammalian bioorthogonal labeling: a tyrosyl ( ScTyr Y43G ) and a phenylalanyl ( MmPhe T413G ) tRNA synthetase that incorporate azide-bearing noncanonical amino acids specifically into the nascent proteomes of host cells. Azide-labeled proteins are chemoselectively tagged via azide-alkyne cycloadditions with fluorophores for imaging or affinity resins for mass spectrometric characterization. Both mutant synthetases label human, hamster, and mouse cell line proteins and selectively activate their azido-bearing amino acids over 10-fold above the canonical. ScTyr Y43G and MmPhe T413G label overlapping but distinct proteomes in human cell lines, with broader proteome coverage upon their coexpression. In mice, ScTyr Y43G and MmPhe T413G label the melanoma tumor proteome and plasma secretome. This work furnishes new tools for mammalian residue-specific bioorthogonal chemistry, and enables more robust and comprehensive cell-type-specific proteomics in live mammals.

  4. An observational study of implicit motor imagery using laterality recognition of the hand after stroke.

    PubMed

    Amesz, Sarah; Tessari, Alessia; Ottoboni, Giovanni; Marsden, Jon

    2016-01-01

    To explore the relationship between laterality recognition after stroke and impairments in attention, 3D object rotation and functional ability. Observational cross-sectional study. Acute care teaching hospital. Thirty-two acute and sub-acute people with stroke and 36 healthy, age-matched controls. Laterality recognition, attention and mental rotation of objects. Within the stroke group, the relationship between laterality recognition and functional ability, neglect, hemianopia and dyspraxia were further explored. People with stroke were significantly less accurate (69% vs 80%) and showed delayed reaction times (3.0 vs 1.9 seconds) when determining the laterality of a pictured hand. Deficits either in accuracy or reaction times were seen in 53% of people with stroke. The accuracy of laterality recognition was associated with reduced functional ability (R(2) = 0.21), less accurate mental rotation of objects (R(2) = 0.20) and dyspraxia (p = 0.03). Implicit motor imagery is affected in a significant number of patients after stroke with these deficits related to lesions to the motor networks as well as other deficits seen after stroke. This research provides new insights into how laterality recognition is related to a number of other deficits after stroke, including the mental rotation of 3D objects, attention and dyspraxia. Further research is required to determine if treatment programmes can improve deficits in laterality recognition and impact functional outcomes after stroke.

  5. Semantic Ambiguity Effects in L2 Word Recognition

    ERIC Educational Resources Information Center

    Ishida, Tomomi

    2018-01-01

    The present study examined the ambiguity effects in second language (L2) word recognition. Previous studies on first language (L1) lexical processing have observed that ambiguous words are recognized faster and more accurately than unambiguous words on lexical decision tasks. In this research, L1 and L2 speakers of English were asked whether a…

  6. Current trends in small vocabulary speech recognition for equipment control

    NASA Astrophysics Data System (ADS)

    Doukas, Nikolaos; Bardis, Nikolaos G.

    2017-09-01

    Speech recognition systems allow human - machine communication to acquire an intuitive nature that approaches the simplicity of inter - human communication. Small vocabulary speech recognition is a subset of the overall speech recognition problem, where only a small number of words need to be recognized. Speaker independent small vocabulary recognition can find significant applications in field equipment used by military personnel. Such equipment may typically be controlled by a small number of commands that need to be given quickly and accurately, under conditions where delicate manual operations are difficult to achieve. This type of application could hence significantly benefit by the use of robust voice operated control components, as they would facilitate the interaction with their users and render it much more reliable in times of crisis. This paper presents current challenges involved in attaining efficient and robust small vocabulary speech recognition. These challenges concern feature selection, classification techniques, speaker diversity and noise effects. A state machine approach is presented that facilitates the voice guidance of different equipment in a variety of situations.

  7. Does aging impair first impression accuracy? Differentiating emotion recognition from complex social inferences.

    PubMed

    Krendl, Anne C; Rule, Nicholas O; Ambady, Nalini

    2014-09-01

    Young adults can be surprisingly accurate at making inferences about people from their faces. Although these first impressions have important consequences for both the perceiver and the target, it remains an open question whether first impression accuracy is preserved with age. Specifically, could age differences in impressions toward others stem from age-related deficits in accurately detecting complex social cues? Research on aging and impression formation suggests that young and older adults show relative consensus in their first impressions, but it is unknown whether they differ in accuracy. It has been widely shown that aging disrupts emotion recognition accuracy, and that these impairments may predict deficits in other social judgments, such as detecting deceit. However, it is unclear whether general impression formation accuracy (e.g., emotion recognition accuracy, detecting complex social cues) relies on similar or distinct mechanisms. It is important to examine this question to evaluate how, if at all, aging might affect overall accuracy. Here, we examined whether aging impaired first impression accuracy in predicting real-world outcomes and categorizing social group membership. Specifically, we studied whether emotion recognition accuracy and age-related cognitive decline (which has been implicated in exacerbating deficits in emotion recognition) predict first impression accuracy. Our results revealed that emotion recognition accuracy did not predict first impression accuracy, nor did age-related cognitive decline impair it. These findings suggest that domains of social perception outside of emotion recognition may rely on mechanisms that are relatively unimpaired by aging. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  8. Memory evaluation in mild cognitive impairment using recall and recognition tests.

    PubMed

    Bennett, Ilana J; Golob, Edward J; Parker, Elizabeth S; Starr, Arnold

    2006-11-01

    Amnestic mild cognitive impairment (MCI) is a selective episodic memory deficit that often indicates early Alzheimer's disease. Episodic memory function in MCI is typically defined by deficits in free recall, but can also be tested using recognition procedures. To assess both recall and recognition in MCI, MCI (n = 21) and older comparison (n = 30) groups completed the USC-Repeatable Episodic Memory Test. Subjects memorized two verbally presented 15-item lists. One list was used for three free recall trials, immediately followed by yes/no recognition. The second list was used for three-alternative forced-choice recognition. Relative to the comparison group, MCI had significantly fewer hits and more false alarms in yes/no recognition, and were less accurate in forced-choice recognition. Signal detection analysis showed that group differences were not due to response bias. Discriminant function analysis showed that yes/no recognition was a better predictor of group membership than free recall or forced-choice measures. MCI subjects recalled fewer items than comparison subjects, with no group differences in repetitions, intrusions, serial position effects, or measures of recall strategy (subjective organization, recall consistency). Performance deficits on free recall and recognition in MCI suggest a combination of both tests may be useful for defining episodic memory impairment associated with MCI and early Alzheimer's disease.

  9. Generalization between canonical and non-canonical views in object recognition

    PubMed Central

    Ghose, Tandra; Liu, Zili

    2013-01-01

    Viewpoint generalization in object recognition is the process that allows recognition of a given 3D object from many different viewpoints despite variations in its 2D projections. We used the canonical view effects as a foundation to empirically test the validity of a major theory in object recognition, the view-approximation model (Poggio & Edelman, 1990). This model predicts that generalization should be better when an object is first seen from a non-canonical view and then a canonical view than when seen in the reversed order. We also manipulated object similarity to study the degree to which this view generalization was constrained by shape details and task instructions (object vs. image recognition). Old-new recognition performance for basic and subordinate level objects was measured in separate blocks. We found that for object recognition, view generalization between canonical and non-canonical views was comparable for basic level objects. For subordinate level objects, recognition performance was more accurate from non-canonical to canonical views than the other way around. When the task was changed from object recognition to image recognition, the pattern of the results reversed. Interestingly, participants responded “old” to “new” images of “old” objects with a substantially higher rate than to “new” objects, despite instructions to the contrary, thereby indicating involuntary view generalization. Our empirical findings are incompatible with the prediction of the view-approximation theory, and argue against the hypothesis that views are stored independently. PMID:23283692

  10. End-to-end system of license plate localization and recognition

    NASA Astrophysics Data System (ADS)

    Zhu, Siyu; Dianat, Sohail; Mestha, Lalit K.

    2015-03-01

    An end-to-end license plate recognition system is proposed. It is composed of preprocessing, detection, segmentation, and character recognition to find and recognize plates from camera-based still images. The system utilizes connected component (CC) properties to quickly extract the license plate region. A two-stage CC filtering is utilized to address both shape and spatial relationship information to produce high precision and to recall values for detection. Floating peak and valleys of projection profiles are used to cut the license plates into individual characters. A turning function-based method is proposed to quickly and accurately recognize each character. It is further accelerated using curvature histogram-based support vector machine. The INFTY dataset is used to train the recognition system, and MediaLab license plate dataset is used for testing. The proposed system achieved 89.45% F-measure for detection and 87.33% accuracy for overall recognition rate which is comparable to current state-of-the-art systems.

  11. Two areas for familiar face recognition in the primate brain.

    PubMed

    Landi, Sofia M; Freiwald, Winrich A

    2017-08-11

    Familiarity alters face recognition: Familiar faces are recognized more accurately than unfamiliar ones and under difficult viewing conditions when unfamiliar face recognition fails. The neural basis for this fundamental difference remains unknown. Using whole-brain functional magnetic resonance imaging, we found that personally familiar faces engage the macaque face-processing network more than unfamiliar faces. Familiar faces also recruited two hitherto unknown face areas at anatomically conserved locations within the perirhinal cortex and the temporal pole. These two areas, but not the core face-processing network, responded to familiar faces emerging from a blur with a characteristic nonlinear surge, akin to the abruptness of familiar face recognition. In contrast, responses to unfamiliar faces and objects remained linear. Thus, two temporal lobe areas extend the core face-processing network into a familiar face-recognition system. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  12. An evolutionary ‘intermediate state’ of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu

    PubMed Central

    Arita, Masashi; Suematsu, Takuma; Osanai, Arihiro; Inaba, Takashi; Kamiya, Haruo; Kita, Kiyoshi; Sisido, Masahiko; Watanabe, Yoh-ichi; Ohtsuki, Takashi

    2006-01-01

    EF-Tu delivers aminoacyl-tRNAs to ribosomes in the translation system. However, unusual truncations found in some animal mitochondrial tRNAs seem to prevent recognition by a canonical EF-Tu. We showed previously that the chromadorean nematode has two distinct EF-Tus, one of which (EF-Tu1) binds only to T-armless aminoacyl-tRNAs and the other (EF-Tu2) binds to D-armless Ser-tRNAs. Neither of the EF-Tus can bind to canonical cloverleaf tRNAs. In this study, by analyzing the translation system of enoplean nematode Trichinella species, we address how EF-Tus and tRNAs have evolved from the canonical structures toward those of the chromadorean translation system. Trichinella mitochondria possess three types of tRNAs: cloverleaf tRNAs, which do not exist in chromadorean nematode mitochondria; T-armless tRNAs; and D-armless tRNAs. We found two mitochondrial EF-Tu species, EF-Tu1 and EF-Tu2, in Trichinella britovi. T.britovi EF-Tu2 could bind to only D-armless Ser-tRNA, as Caenorhabditis elegans EF-Tu2 does. In contrast to the case of C.elegans EF-Tu1, however, T.britovi EF-Tu1 bound to all three types of tRNA present in Trichinella mitochondria. These results suggest that Trichinella mitochondrial translation system, and particularly the tRNA-binding specificity of EF-Tu1, could be an intermediate state between the canonical system and the chromadorean nematode mitochondrial system. PMID:17012285

  13. A Spatial Frequency Account of the Detriment that Local Processing of Navon Letters Has on Face Recognition

    ERIC Educational Resources Information Center

    Hills, Peter J.; Lewis, Michael B.

    2009-01-01

    Five minutes of processing the local features of a Navon letter causes a detriment in subsequent face-recognition performance (Macrae & Lewis, 2002). We hypothesize a perceptual after effect explanation of this effect in which face recognition is less accurate after adapting to high-spatial frequencies at high contrasts. Five experiments were…

  14. Orientation estimation of anatomical structures in medical images for object recognition

    NASA Astrophysics Data System (ADS)

    Bağci, Ulaş; Udupa, Jayaram K.; Chen, Xinjian

    2011-03-01

    Recognition of anatomical structures is an important step in model based medical image segmentation. It provides pose estimation of objects and information about "where" roughly the objects are in the image and distinguishing them from other object-like entities. In,1 we presented a general method of model-based multi-object recognition to assist in segmentation (delineation) tasks. It exploits the pose relationship that can be encoded, via the concept of ball scale (b-scale), between the binary training objects and their associated grey images. The goal was to place the model, in a single shot, close to the right pose (position, orientation, and scale) in a given image so that the model boundaries fall in the close vicinity of object boundaries in the image. Unlike position and scale parameters, we observe that orientation parameters require more attention when estimating the pose of the model as even small differences in orientation parameters can lead to inappropriate recognition. Motivated from the non-Euclidean nature of the pose information, we propose in this paper the use of non-Euclidean metrics to estimate orientation of the anatomical structures for more accurate recognition and segmentation. We statistically analyze and evaluate the following metrics for orientation estimation: Euclidean, Log-Euclidean, Root-Euclidean, Procrustes Size-and-Shape, and mean Hermitian metrics. The results show that mean Hermitian and Cholesky decomposition metrics provide more accurate orientation estimates than other Euclidean and non-Euclidean metrics.

  15. Dance recognition system using lower body movement.

    PubMed

    Simpson, Travis T; Wiesner, Susan L; Bennett, Bradford C

    2014-02-01

    The current means of locating specific movements in film necessitate hours of viewing, making the task of conducting research into movement characteristics and patterns tedious and difficult. This is particularly problematic for the research and analysis of complex movement systems such as sports and dance. While some systems have been developed to manually annotate film, to date no automated way of identifying complex, full body movement exists. With pattern recognition technology and knowledge of joint locations, automatically describing filmed movement using computer software is possible. This study used various forms of lower body kinematic analysis to identify codified dance movements. We created an algorithm that compares an unknown move with a specified start and stop against known dance moves. Our recognition method consists of classification and template correlation using a database of model moves. This system was optimized to include nearly 90 dance and Tai Chi Chuan movements, producing accurate name identification in over 97% of trials. In addition, the program had the capability to provide a kinematic description of either matched or unmatched moves obtained from classification recognition.

  16. A new method of edge detection for object recognition

    USGS Publications Warehouse

    Maddox, Brian G.; Rhew, Benjamin

    2004-01-01

    Traditional edge detection systems function by returning every edge in an input image. This can result in a large amount of clutter and make certain vectorization algorithms less accurate. Accuracy problems can then have a large impact on automated object recognition systems that depend on edge information. A new method of directed edge detection can be used to limit the number of edges returned based on a particular feature. This results in a cleaner image that is easier for vectorization. Vectorized edges from this process could then feed an object recognition system where the edge data would also contain information as to what type of feature it bordered.

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

    ERIC Educational Resources Information Center

    Wixted, John T.

    2007-01-01

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

  18. Automatic Recognition of Road Signs

    NASA Astrophysics Data System (ADS)

    Inoue, Yasuo; Kohashi, Yuuichirou; Ishikawa, Naoto; Nakajima, Masato

    2002-11-01

    The increase in traffic accidents is becoming a serious social problem with the recent rapid traffic increase. In many cases, the driver"s carelessness is the primary factor of traffic accidents, and the driver assistance system is demanded for supporting driver"s safety. In this research, we propose the new method of automatic detection and recognition of road signs by image processing. The purpose of this research is to prevent accidents caused by driver"s carelessness, and call attention to a driver when the driver violates traffic a regulation. In this research, high accuracy and the efficient sign detecting method are realized by removing unnecessary information except for a road sign from an image, and detect a road sign using shape features. At first, the color information that is not used in road signs is removed from an image. Next, edges except for circular and triangle ones are removed to choose sign shape. In the recognition process, normalized cross correlation operation is carried out to the two-dimensional differentiation pattern of a sign, and the accurate and efficient method for detecting the road sign is realized. Moreover, the real-time operation in a software base was realized by holding down calculation cost, maintaining highly precise sign detection and recognition. Specifically, it becomes specifically possible to process by 0.1 sec(s)/frame using a general-purpose PC (CPU: Pentium4 1.7GHz). As a result of in-vehicle experimentation, our system could process on real time and has confirmed that detection and recognition of a sign could be performed correctly.

  19. Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing.

    PubMed

    Jones, Christopher P; Saadatmand, Jenan; Kleiman, Lawrence; Musier-Forsyth, Karin

    2013-02-01

    The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNA(Lys3). Host cell tRNA(Lys) is selectively packaged into HIV-1 through a specific interaction between the major tRNA(Lys)-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNA(Lys3) is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNA(Lys) and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNA(Lys3) in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNA(Lys) to increase the efficiency of tRNA(Lys3) annealing to viral RNA.

  20. Structural insights into translational fidelity.

    PubMed

    Ogle, James M; Ramakrishnan, V

    2005-01-01

    The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.

  1. Age-related differences in emotion recognition ability: a cross-sectional study.

    PubMed

    Mill, Aire; Allik, Jüri; Realo, Anu; Valk, Raivo

    2009-10-01

    Experimental studies indicate that recognition of emotions, particularly negative emotions, decreases with age. However, there is no consensus at which age the decrease in emotion recognition begins, how selective this is to negative emotions, and whether this applies to both facial and vocal expression. In the current cross-sectional study, 607 participants ranging in age from 18 to 84 years (mean age = 32.6 +/- 14.9 years) were asked to recognize emotions expressed either facially or vocally. In general, older participants were found to be less accurate at recognizing emotions, with the most distinctive age difference pertaining to a certain group of negative emotions. Both modalities revealed an age-related decline in the recognition of sadness and -- to a lesser degree -- anger, starting at about 30 years of age. Although age-related differences in the recognition of expression of emotion were not mediated by personality traits, 2 of the Big 5 traits, openness and conscientiousness, made an independent contribution to emotion-recognition performance. Implications of age-related differences in facial and vocal emotion expression and early onset of the selective decrease in emotion recognition are discussed in terms of previous findings and relevant theoretical models.

  2. Neural system for heartbeats recognition using genetically integrated ensemble of classifiers.

    PubMed

    Osowski, Stanislaw; Siwek, Krzysztof; Siroic, Robert

    2011-03-01

    This paper presents the application of genetic algorithm for the integration of neural classifiers combined in the ensemble for the accurate recognition of heartbeat types on the basis of ECG registration. The idea presented in this paper is that using many classifiers arranged in the form of ensemble leads to the increased accuracy of the recognition. In such ensemble the important problem is the integration of all classifiers into one effective classification system. This paper proposes the use of genetic algorithm. It was shown that application of the genetic algorithm is very efficient and allows to reduce significantly the total error of heartbeat recognition. This was confirmed by the numerical experiments performed on the MIT BIH Arrhythmia Database. Copyright © 2011 Elsevier Ltd. All rights reserved.

  3. Probabilistic Open Set Recognition

    NASA Astrophysics Data System (ADS)

    Jain, Lalit Prithviraj

    Real-world tasks in computer vision, pattern recognition and machine learning often touch upon the open set recognition problem: multi-class recognition with incomplete knowledge of the world and many unknown inputs. An obvious way to approach such problems is to develop a recognition system that thresholds probabilities to reject unknown classes. Traditional rejection techniques are not about the unknown; they are about the uncertain boundary and rejection around that boundary. Thus traditional techniques only represent the "known unknowns". However, a proper open set recognition algorithm is needed to reduce the risk from the "unknown unknowns". This dissertation examines this concept and finds existing probabilistic multi-class recognition approaches are ineffective for true open set recognition. We hypothesize the cause is due to weak adhoc assumptions combined with closed-world assumptions made by existing calibration techniques. Intuitively, if we could accurately model just the positive data for any known class without overfitting, we could reject the large set of unknown classes even under this assumption of incomplete class knowledge. For this, we formulate the problem as one of modeling positive training data by invoking statistical extreme value theory (EVT) near the decision boundary of positive data with respect to negative data. We provide a new algorithm called the PI-SVM for estimating the unnormalized posterior probability of class inclusion. This dissertation also introduces a new open set recognition model called Compact Abating Probability (CAP), where the probability of class membership decreases in value (abates) as points move from known data toward open space. We show that CAP models improve open set recognition for multiple algorithms. Leveraging the CAP formulation, we go on to describe the novel Weibull-calibrated SVM (W-SVM) algorithm, which combines the useful properties of statistical EVT for score calibration with one-class and binary

  4. Facial Emotion Recognition: A Survey and Real-World User Experiences in Mixed Reality

    PubMed Central

    Mehta, Dhwani; Siddiqui, Mohammad Faridul Haque

    2018-01-01

    Extensive possibilities of applications have made emotion recognition ineluctable and challenging in the field of computer science. The use of non-verbal cues such as gestures, body movement, and facial expressions convey the feeling and the feedback to the user. This discipline of Human–Computer Interaction places reliance on the algorithmic robustness and the sensitivity of the sensor to ameliorate the recognition. Sensors play a significant role in accurate detection by providing a very high-quality input, hence increasing the efficiency and the reliability of the system. Automatic recognition of human emotions would help in teaching social intelligence in the machines. This paper presents a brief study of the various approaches and the techniques of emotion recognition. The survey covers a succinct review of the databases that are considered as data sets for algorithms detecting the emotions by facial expressions. Later, mixed reality device Microsoft HoloLens (MHL) is introduced for observing emotion recognition in Augmented Reality (AR). A brief introduction of its sensors, their application in emotion recognition and some preliminary results of emotion recognition using MHL are presented. The paper then concludes by comparing results of emotion recognition by the MHL and a regular webcam. PMID:29389845

  5. Facial Emotion Recognition: A Survey and Real-World User Experiences in Mixed Reality.

    PubMed

    Mehta, Dhwani; Siddiqui, Mohammad Faridul Haque; Javaid, Ahmad Y

    2018-02-01

    Extensive possibilities of applications have made emotion recognition ineluctable and challenging in the field of computer science. The use of non-verbal cues such as gestures, body movement, and facial expressions convey the feeling and the feedback to the user. This discipline of Human-Computer Interaction places reliance on the algorithmic robustness and the sensitivity of the sensor to ameliorate the recognition. Sensors play a significant role in accurate detection by providing a very high-quality input, hence increasing the efficiency and the reliability of the system. Automatic recognition of human emotions would help in teaching social intelligence in the machines. This paper presents a brief study of the various approaches and the techniques of emotion recognition. The survey covers a succinct review of the databases that are considered as data sets for algorithms detecting the emotions by facial expressions. Later, mixed reality device Microsoft HoloLens (MHL) is introduced for observing emotion recognition in Augmented Reality (AR). A brief introduction of its sensors, their application in emotion recognition and some preliminary results of emotion recognition using MHL are presented. The paper then concludes by comparing results of emotion recognition by the MHL and a regular webcam.

  6. Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications.

    PubMed

    Iddamalgoda, Lahiru; Das, Partha S; Aponso, Achala; Sundararajan, Vijayaraghava S; Suravajhala, Prashanth; Valadi, Jayaraman K

    2016-01-01

    Data mining and pattern recognition methods reveal interesting findings in genetic studies, especially on how the genetic makeup is associated with inherited diseases. Although researchers have proposed various data mining models for biomedical approaches, there remains a challenge in accurately prioritizing the single nucleotide polymorphisms (SNP) associated with the disease. In this commentary, we review the state-of-art data mining and pattern recognition models for identifying inherited diseases and deliberate the need of binary classification- and scoring-based prioritization methods in determining causal variants. While we discuss the pros and cons associated with these methods known, we argue that the gene prioritization methods and the protein interaction (PPI) methods in conjunction with the K nearest neighbors' could be used in accurately categorizing the genetic factors in disease causation.

  7. Facial and prosodic emotion recognition in social anxiety disorder.

    PubMed

    Tseng, Huai-Hsuan; Huang, Yu-Lien; Chen, Jian-Ting; Liang, Kuei-Yu; Lin, Chao-Cheng; Chen, Sue-Huei

    2017-07-01

    Patients with social anxiety disorder (SAD) have a cognitive preference to negatively evaluate emotional information. In particular, the preferential biases in prosodic emotion recognition in SAD have been much less explored. The present study aims to investigate whether SAD patients retain negative evaluation biases across visual and auditory modalities when given sufficient response time to recognise emotions. Thirty-one SAD patients and 31 age- and gender-matched healthy participants completed a culturally suitable non-verbal emotion recognition task and received clinical assessments for social anxiety and depressive symptoms. A repeated measures analysis of variance was conducted to examine group differences in emotion recognition. Compared to healthy participants, SAD patients were significantly less accurate at recognising facial and prosodic emotions, and spent more time on emotion recognition. The differences were mainly driven by the lower accuracy and longer reaction times for recognising fearful emotions in SAD patients. Within the SAD patients, lower accuracy of sad face recognition was associated with higher severity of depressive and social anxiety symptoms, particularly with avoidance symptoms. These findings may represent a cross-modality pattern of avoidance in the later stage of identifying negative emotions in SAD. This pattern may be linked to clinical symptom severity.

  8. Exhibits Recognition System for Combining Online Services and Offline Services

    NASA Astrophysics Data System (ADS)

    Ma, He; Liu, Jianbo; Zhang, Yuan; Wu, Xiaoyu

    2017-10-01

    In order to achieve a more convenient and accurate digital museum navigation, we have developed a real-time and online-to-offline museum exhibits recognition system using image recognition method based on deep learning. In this paper, the client and server of the system are separated and connected through the HTTP. Firstly, by using the client app in the Android mobile phone, the user can take pictures and upload them to the server. Secondly, the features of the picture are extracted using the deep learning network in the server. With the help of the features, the pictures user uploaded are classified with a well-trained SVM. Finally, the classification results are sent to the client and the detailed exhibition’s introduction corresponding to the classification results are shown in the client app. Experimental results demonstrate that the recognition accuracy is close to 100% and the computing time from the image uploading to the exhibit information show is less than 1S. By means of exhibition image recognition algorithm, our implemented exhibits recognition system can combine online detailed exhibition information to the user in the offline exhibition hall so as to achieve better digital navigation.

  9. The review and results of different methods for facial recognition

    NASA Astrophysics Data System (ADS)

    Le, Yifan

    2017-09-01

    In recent years, facial recognition draws much attention due to its wide potential applications. As a unique technology in Biometric Identification, facial recognition represents a significant improvement since it could be operated without cooperation of people under detection. Hence, facial recognition will be taken into defense system, medical detection, human behavior understanding, etc. Several theories and methods have been established to make progress in facial recognition: (1) A novel two-stage facial landmark localization method is proposed which has more accurate facial localization effect under specific database; (2) A statistical face frontalization method is proposed which outperforms state-of-the-art methods for face landmark localization; (3) It proposes a general facial landmark detection algorithm to handle images with severe occlusion and images with large head poses; (4) There are three methods proposed on Face Alignment including shape augmented regression method, pose-indexed based multi-view method and a learning based method via regressing local binary features. The aim of this paper is to analyze previous work of different aspects in facial recognition, focusing on concrete method and performance under various databases. In addition, some improvement measures and suggestions in potential applications will be put forward.

  10. Integration trumps selection in object recognition.

    PubMed

    Saarela, Toni P; Landy, Michael S

    2015-03-30

    Finding and recognizing objects is a fundamental task of vision. Objects can be defined by several "cues" (color, luminance, texture, etc.), and humans can integrate sensory cues to improve detection and recognition [1-3]. Cortical mechanisms fuse information from multiple cues [4], and shape-selective neural mechanisms can display cue invariance by responding to a given shape independent of the visual cue defining it [5-8]. Selective attention, in contrast, improves recognition by isolating a subset of the visual information [9]. Humans can select single features (red or vertical) within a perceptual dimension (color or orientation), giving faster and more accurate responses to items having the attended feature [10, 11]. Attention elevates neural responses and sharpens neural tuning to the attended feature, as shown by studies in psychophysics and modeling [11, 12], imaging [13-16], and single-cell and neural population recordings [17, 18]. Besides single features, attention can select whole objects [19-21]. Objects are among the suggested "units" of attention because attention to a single feature of an object causes the selection of all of its features [19-21]. Here, we pit integration against attentional selection in object recognition. We find, first, that humans can integrate information near optimally from several perceptual dimensions (color, texture, luminance) to improve recognition. They cannot, however, isolate a single dimension even when the other dimensions provide task-irrelevant, potentially conflicting information. For object recognition, it appears that there is mandatory integration of information from multiple dimensions of visual experience. The advantage afforded by this integration, however, comes at the expense of attentional selection. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Integration trumps selection in object recognition

    PubMed Central

    Saarela, Toni P.; Landy, Michael S.

    2015-01-01

    Summary Finding and recognizing objects is a fundamental task of vision. Objects can be defined by several “cues” (color, luminance, texture etc.), and humans can integrate sensory cues to improve detection and recognition [1–3]. Cortical mechanisms fuse information from multiple cues [4], and shape-selective neural mechanisms can display cue-invariance by responding to a given shape independent of the visual cue defining it [5–8]. Selective attention, in contrast, improves recognition by isolating a subset of the visual information [9]. Humans can select single features (red or vertical) within a perceptual dimension (color or orientation), giving faster and more accurate responses to items having the attended feature [10,11]. Attention elevates neural responses and sharpens neural tuning to the attended feature, as shown by studies in psychophysics and modeling [11,12], imaging [13–16], and single-cell and neural population recordings [17,18]. Besides single features, attention can select whole objects [19–21]. Objects are among the suggested “units” of attention because attention to a single feature of an object causes the selection of all of its features [19–21]. Here, we pit integration against attentional selection in object recognition. We find, first, that humans can integrate information near-optimally from several perceptual dimensions (color, texture, luminance) to improve recognition. They cannot, however, isolate a single dimension even when the other dimensions provide task-irrelevant, potentially conflicting information. For object recognition, it appears that there is mandatory integration of information from multiple dimensions of visual experience. The advantage afforded by this integration, however, comes at the expense of attentional selection. PMID:25802154

  12. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.

    PubMed

    Lowe, Todd M; Chan, Patricia P

    2016-07-08

    High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database. Previously, web-server tRNA detection was isolated from knowledge of existing tRNAs and their annotation. In this update of the tRNAscan-SE On-line resource, we tie together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers. The tRNAscan-SE On-line web server can be accessed at http://trna.ucsc.edu/tRNAscan-SE/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Holistic face processing can inhibit recognition of forensic facial composites.

    PubMed

    McIntyre, Alex H; Hancock, Peter J B; Frowd, Charlie D; Langton, Stephen R H

    2016-04-01

    Facial composite systems help eyewitnesses to show the appearance of criminals. However, likenesses created by unfamiliar witnesses will not be completely accurate, and people familiar with the target can find them difficult to identify. Faces are processed holistically; we explore whether this impairs identification of inaccurate composite images and whether recognition can be improved. In Experiment 1 (n = 64) an imaging technique was used to make composites of celebrity faces more accurate and identification was contrasted with the original composite images. Corrected composites were better recognized, confirming that errors in production of the likenesses impair identification. The influence of holistic face processing was explored by misaligning the top and bottom parts of the composites (cf. Young, Hellawell, & Hay, 1987). Misalignment impaired recognition of corrected composites but identification of the original, inaccurate composites significantly improved. This effect was replicated with facial composites of noncelebrities in Experiment 2 (n = 57). We conclude that, like real faces, facial composites are processed holistically: recognition is impaired because unlike real faces, composites contain inaccuracies and holistic face processing makes it difficult to perceive identifiable features. This effect was consistent across composites of celebrities and composites of people who are personally familiar. Our findings suggest that identification of forensic facial composites can be enhanced by presenting composites in a misaligned format. (c) 2016 APA, all rights reserved).

  14. Dual-process theory and signal-detection theory of recognition memory.

    PubMed

    Wixted, John T

    2007-01-01

    Two influential models of recognition memory, the unequal-variance signal-detection model and a dual-process threshold/detection model, accurately describe the receiver operating characteristic, but only the latter model can provide estimates of recollection and familiarity. Such estimates often accord with those provided by the remember-know procedure, and both methods are now widely used in the neuroscience literature to identify the brain correlates of recollection and familiarity. However, in recent years, a substantial literature has accumulated directly contrasting the signal-detection model against the threshold/detection model, and that literature is almost unanimous in its endorsement of signal-detection theory. A dual-process version of signal-detection theory implies that individual recognition decisions are not process pure, and it suggests new ways to investigate the brain correlates of recognition memory. ((c) 2007 APA, all rights reserved).

  15. Collaborative Efforts to Promote Emergent Literacy and Efficient Word Recognition Skills

    ERIC Educational Resources Information Center

    Roth, Froma P.; Troia, Gary A.

    2006-01-01

    In this article, 3 models of collaboration between speech-language pathologists and classroom teachers are discussed to promote emergent literacy and accurate and fluent word recognition. These models are demonstration lessons, team teaching, and consultation. A number of instructional principles are presented for emergent literacy and decoding…

  16. 8 CFR 1292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. 1292.2...; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. (a) Qualifications of organizations. A non-profit religious, charitable, social service, or similar organization...

  17. Mollusk genes encoding lysine tRNA (UUU) contain introns.

    PubMed

    Matsuo, M; Abe, Y; Saruta, Y; Okada, N

    1995-11-20

    New intron-containing genes encoding tRNAs were discovered when genomic DNA isolated from various animal species was amplified by the polymerase chain reaction (PCR) with primers based on sequences of rabbit tRNA(Lys). From sequencing analysis of the products of PCR, we found that introns are present in several genes encoding tRNA(Lys) in mollusks, such as Loligo bleekeri (squid) and Octopus vulgaris (octopus). These introns were specific to genes encoding tRNA(Lys)(CUU) and were not present in genes encoding tRNA(Lys)(CUU). In addition, the sequences of the introns were different from one another. To confirm the results of our initial experiments, we isolated and sequenced genes encoding tRNA(Lys)(CUU) and tRNA(Lys)(UUU). The gene for tRNA(Lys)(UUU) from squid contained an intron, whose sequence was the same as that identified by PCR, and the gene formed a cluster with a corresponding pseudogene. Several DNA regions of 2.1 kb containing this cluster appeared to be tandemly arrayed in the squid genome. By contrast, the gene encoding tRNA(Lys)(CUU) did not contain an intron, as shown also by PCR. The tRNA(Lys)(UUU) that corresponded to the analyzed gene was isolated and characterized. The present study provides the first example of an intron-containing gene encoding a tRNA in mollusks and suggests the universality of introns in such genes in higher eukaryotes.

  18. Inhibition of selenocysteine tRNA[Ser]Sec aminoacylation provides evidence that aminoacylation is required for regulatory methylation of this tRNA

    PubMed Central

    Kim, Jin Young; Carlson, Bradley A.; Xu, Xue-Ming; Zeng, Yu; Chen, Shawn; Gladyshev, Vadim N.; Lee, Byeong Jae; Hatfield, Dolph L.

    2011-01-01

    There are two isoforms of selenocysteine (Sec) tRNA[Ser]Sec that differ by a single methyl group, Um34. The non-Um34 isoform supports the synthesis of a subclass of selenoproteins, designated housekeeping, while the Um34 isoform supports the expression of another subclass, designated stress-related selenoproteins. Herein, we investigated the relationship between tRNA[Ser]Sec aminoacylation and Um34 synthesis which is the last step in the maturation of this tRNA. Mutation of the discriminator base at position 73 in tRNA[Ser]Sec dramatically reduced aminoacylation with serine, as did an inhibitor of seryl-tRNA synthetase, SB-217452. Although both the mutation and the inhibitor prevented Um34 synthesis, neither precluded the synthesis of any other of the known base modifications on tRNA[Ser]Sec following microinjection and incubation of the mutant tRNA[Ser]Sec transcript, or the wild type transcript along with inhibitor, in Xenopus oocytes. The data demonstrate that Sec tRNA[Ser]Sec must be aminoacylated for Um34 addition. The fact that selenium is required for Um34 methylation suggests that Sec must be attached to its tRNA for Um34 methylation. This would explain why selenium is essential for the function of Um34 methylase and provides further insights into the hierarchy of selenoprotein expression. PMID:21624347

  19. Recognition of Arabic Sign Language Alphabet Using Polynomial Classifiers

    NASA Astrophysics Data System (ADS)

    Assaleh, Khaled; Al-Rousan, M.

    2005-12-01

    Building an accurate automatic sign language recognition system is of great importance in facilitating efficient communication with deaf people. In this paper, we propose the use of polynomial classifiers as a classification engine for the recognition of Arabic sign language (ArSL) alphabet. Polynomial classifiers have several advantages over other classifiers in that they do not require iterative training, and that they are highly computationally scalable with the number of classes. Based on polynomial classifiers, we have built an ArSL system and measured its performance using real ArSL data collected from deaf people. We show that the proposed system provides superior recognition results when compared with previously published results using ANFIS-based classification on the same dataset and feature extraction methodology. The comparison is shown in terms of the number of misclassified test patterns. The reduction in the rate of misclassified patterns was very significant. In particular, we have achieved a 36% reduction of misclassifications on the training data and 57% on the test data.

  20. Improving Protein Fold Recognition by Deep Learning Networks

    NASA Astrophysics Data System (ADS)

    Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin

    2015-12-01

    For accurate recognition of protein folds, a deep learning network method (DN-Fold) was developed to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features extracted from the protein pair. We evaluated the performance of DN-Fold along with 18 different methods on Lindahl’s benchmark dataset and on a large benchmark set extracted from SCOP 1.75 consisting of about one million protein pairs, at three different levels of fold recognition (i.e., protein family, superfamily, and fold) depending on the evolutionary distance between protein sequences. The correct recognition rate of ensembled DN-Fold for Top 1 predictions is 84.5%, 61.5%, and 33.6% and for Top 5 is 91.2%, 76.5%, and 60.7% at family, superfamily, and fold levels, respectively. We also evaluated the performance of single DN-Fold (DN-FoldS), which showed the comparable results at the level of family and superfamily, compared to ensemble DN-Fold. Finally, we extended the binary classification problem of fold recognition to real-value regression task, which also show a promising performance. DN-Fold is freely available through a web server at http://iris.rnet.missouri.edu/dnfold.

  1. Improving Protein Fold Recognition by Deep Learning Networks.

    PubMed

    Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin

    2015-12-04

    For accurate recognition of protein folds, a deep learning network method (DN-Fold) was developed to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features extracted from the protein pair. We evaluated the performance of DN-Fold along with 18 different methods on Lindahl's benchmark dataset and on a large benchmark set extracted from SCOP 1.75 consisting of about one million protein pairs, at three different levels of fold recognition (i.e., protein family, superfamily, and fold) depending on the evolutionary distance between protein sequences. The correct recognition rate of ensembled DN-Fold for Top 1 predictions is 84.5%, 61.5%, and 33.6% and for Top 5 is 91.2%, 76.5%, and 60.7% at family, superfamily, and fold levels, respectively. We also evaluated the performance of single DN-Fold (DN-FoldS), which showed the comparable results at the level of family and superfamily, compared to ensemble DN-Fold. Finally, we extended the binary classification problem of fold recognition to real-value regression task, which also show a promising performance. DN-Fold is freely available through a web server at http://iris.rnet.missouri.edu/dnfold.

  2. Face recognition based on two-dimensional discriminant sparse preserving projection

    NASA Astrophysics Data System (ADS)

    Zhang, Dawei; Zhu, Shanan

    2018-04-01

    In this paper, a supervised dimensionality reduction algorithm named two-dimensional discriminant sparse preserving projection (2DDSPP) is proposed for face recognition. In order to accurately model manifold structure of data, 2DDSPP constructs within-class affinity graph and between-class affinity graph by the constrained least squares (LS) and l1 norm minimization problem, respectively. Based on directly operating on image matrix, 2DDSPP integrates graph embedding (GE) with Fisher criterion. The obtained projection subspace preserves within-class neighborhood geometry structure of samples, while keeping away samples from different classes. The experimental results on the PIE and AR face databases show that 2DDSPP can achieve better recognition performance.

  3. The Effects of Musical and Linguistic Components in Recognition of Real-World Musical Excerpts by Cochlear Implant Recipients and Normal-Hearing Adults

    PubMed Central

    Gfeller, Kate; Jiang, Dingfeng; Oleson, Jacob; Driscoll, Virginia; Olszewski, Carol; Knutson, John F.; Turner, Christopher; Gantz, Bruce

    2011-01-01

    Background Cochlear implants (CI) are effective in transmitting salient features of speech, especially in quiet, but current CI technology is not well suited in transmission of key musical structures (e.g., melody, timbre). It is possible, however, that sung lyrics, which are commonly heard in real-world music may provide acoustical cues that support better music perception. Objective The purpose of this study was to examine how accurately adults who use CIs (n=87) and those with normal hearing (NH) (n=17) are able to recognize real-world music excerpts based upon musical and linguistic (lyrics) cues. Results CI recipients were significantly less accurate than NH listeners on recognition of real-world music with or, in particular, without lyrics; however, CI recipients whose devices transmitted acoustic plus electric stimulation were more accurate than CI recipients reliant upon electric stimulation alone (particularly items without linguistic cues). Recognition by CI recipients improved as a function of linguistic cues. Methods Participants were tested on melody recognition of complex melodies (pop, country, classical styles). Results were analyzed as a function of: hearing status and history, device type (electric only or acoustic plus electric stimulation), musical style, linguistic and musical cues, speech perception scores, cognitive processing, music background, age, and in relation to self-report on listening acuity and enjoyment. Age at time of testing was negatively correlated with recognition performance. Conclusions These results have practical implications regarding successful participation of CI users in music-based activities that include recognition and accurate perception of real-world songs (e.g., reminiscence, lyric analysis, listening for enjoyment). PMID:22803258

  4. The effects of musical and linguistic components in recognition of real-world musical excerpts by cochlear implant recipients and normal-hearing adults.

    PubMed

    Gfeller, Kate; Jiang, Dingfeng; Oleson, Jacob J; Driscoll, Virginia; Olszewski, Carol; Knutson, John F; Turner, Christopher; Gantz, Bruce

    2012-01-01

    Cochlear implants (CI) are effective in transmitting salient features of speech, especially in quiet, but current CI technology is not well suited in transmission of key musical structures (e.g., melody, timbre). It is possible, however, that sung lyrics, which are commonly heard in real-world music may provide acoustical cues that support better music perception. The purpose of this study was to examine how accurately adults who use CIs (n = 87) and those with normal hearing (NH) (n = 17) are able to recognize real-world music excerpts based upon musical and linguistic (lyrics) cues. CI recipients were significantly less accurate than NH listeners on recognition of real-world music with or, in particular, without lyrics; however, CI recipients whose devices transmitted acoustic plus electric stimulation were more accurate than CI recipients reliant upon electric stimulation alone (particularly items without linguistic cues). Recognition by CI recipients improved as a function of linguistic cues. Participants were tested on melody recognition of complex melodies (pop, country, & classical styles). Results were analyzed as a function of: hearing status and history, device type (electric only or acoustic plus electric stimulation), musical style, linguistic and musical cues, speech perception scores, cognitive processing, music background, age, and in relation to self-report on listening acuity and enjoyment. Age at time of testing was negatively correlated with recognition performance. These results have practical implications regarding successful participation of CI users in music-based activities that include recognition and accurate perception of real-world songs (e.g., reminiscence, lyric analysis, & listening for enjoyment).

  5. Leigh syndrome caused by a novel m.4296G>A mutation in mitochondrial tRNA isoleucine.

    PubMed

    Cox, Rachel; Platt, Julia; Chen, Li Chieh; Tang, Sha; Wong, Lee-Jun; Enns, Gregory M

    2012-03-01

    Leigh syndrome is a severe neurodegenerative disease with heterogeneous genetic etiology. We report a novel m.4296G>A variant in the mitochondrial tRNA isoleucine gene in a child with Leigh syndrome, mitochondrial proliferation, lactic acidosis, and abnormal respiratory chain enzymology. The variant is present at >75% heteroplasmy in blood and cultured fibroblasts from the proband, <5% in asymptomatic maternal relatives, and is absent in 3000 controls. It is located in the highly conserved anticodon region of tRNA(Ile) where three other pathogenic changes have been described. We conclude that there is strong evidence to classify m.4296G>A as a pathogenic mutation causing Leigh syndrome. Copyright © 2011 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  6. Genomic characteristics comparisons of 12 food-related filamentous fungi in tRNA gene set, codon usage and amino acid composition.

    PubMed

    Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

    2012-04-10

    Filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. The recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. In this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were Aspergillus clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus, Monascus ruber, Neurospora crassa, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma reesei, and did the comparative studies of their genomic characteristics of tRNA gene distribution, codon usage pattern and amino acid composition. The results showed that the copy numbers greatly differed among isoaccepting tRNA genes and the distribution seemed to be related with translation process. The results also revealed that genome compositional variation probably constrained the base choice at the third codon, and affected the overall amino acid composition but seemed to have little effect on the integrated physicochemical characteristics of overall amino acids. The further analysis suggested that the wobble pairing and base modification were the important mechanisms in codon-anticodon interaction. In the scope of authors' knowledge, it is the first report about the genomic characteristics analysis of food-related filamentous fungi, which would be informative for the analysis of filamentous fungal genome evolution and their practical application in food industry. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo

    PubMed Central

    Rijal, Keshab; Maraia, Richard J.

    2016-01-01

    The ability of RNA polymerase (RNAP) III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC); they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT) mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease. PMID:27518095

  8. Super-resolution method for face recognition using nonlinear mappings on coherent features.

    PubMed

    Huang, Hua; He, Huiting

    2011-01-01

    Low-resolution (LR) of face images significantly decreases the performance of face recognition. To address this problem, we present a super-resolution method that uses nonlinear mappings to infer coherent features that favor higher recognition of the nearest neighbor (NN) classifiers for recognition of single LR face image. Canonical correlation analysis is applied to establish the coherent subspaces between the principal component analysis (PCA) based features of high-resolution (HR) and LR face images. Then, a nonlinear mapping between HR/LR features can be built by radial basis functions (RBFs) with lower regression errors in the coherent feature space than in the PCA feature space. Thus, we can compute super-resolved coherent features corresponding to an input LR image according to the trained RBF model efficiently and accurately. And, face identity can be obtained by feeding these super-resolved features to a simple NN classifier. Extensive experiments on the Facial Recognition Technology, University of Manchester Institute of Science and Technology, and Olivetti Research Laboratory databases show that the proposed method outperforms the state-of-the-art face recognition algorithms for single LR image in terms of both recognition rate and robustness to facial variations of pose and expression.

  9. A Vision-Based Counting and Recognition System for Flying Insects in Intelligent Agriculture.

    PubMed

    Zhong, Yuanhong; Gao, Junyuan; Lei, Qilun; Zhou, Yao

    2018-05-09

    Rapid and accurate counting and recognition of flying insects are of great importance, especially for pest control. Traditional manual identification and counting of flying insects is labor intensive and inefficient. In this study, a vision-based counting and classification system for flying insects is designed and implemented. The system is constructed as follows: firstly, a yellow sticky trap is installed in the surveillance area to trap flying insects and a camera is set up to collect real-time images. Then the detection and coarse counting method based on You Only Look Once (YOLO) object detection, the classification method and fine counting based on Support Vector Machines (SVM) using global features are designed. Finally, the insect counting and recognition system is implemented on Raspberry PI. Six species of flying insects including bee, fly, mosquito, moth, chafer and fruit fly are selected to assess the effectiveness of the system. Compared with the conventional methods, the test results show promising performance. The average counting accuracy is 92.50% and average classifying accuracy is 90.18% on Raspberry PI. The proposed system is easy-to-use and provides efficient and accurate recognition data, therefore, it can be used for intelligent agriculture applications.

  10. Application of image recognition-based automatic hyphae detection in fungal keratitis.

    PubMed

    Wu, Xuelian; Tao, Yuan; Qiu, Qingchen; Wu, Xinyi

    2018-03-01

    the conventional artificial identification of confocal microscope corneal images, of being accurate, stable and does not rely on human expertise. It was the most useful to the medical experts who are not familiar with fungal keratitis. The technology of automatic hyphae detection based on image recognition can quantify the hyphae density and grade this property. Being noninvasive, it can provide an evaluation criterion to fungal keratitis in a timely, accurate, objective and quantitative manner.

  11. Individual Differences in Visual Word Recognition: Insights from the English Lexicon Project

    PubMed Central

    Yap, Melvin J.; Balota, David A.; Sibley, Daragh E.; Ratcliff, Roger

    2011-01-01

    Empirical work and models of visual word recognition have traditionally focused on group-level performance. Despite the emphasis on the prototypical reader, there is clear evidence that variation in reading skill modulates word recognition performance. In the present study, we examined differences between individuals who contributed to the English Lexicon Project (http://elexicon.wustl.edu), an online behavioral database containing nearly four million word recognition (speeded pronunciation and lexical decision) trials from over 1,200 participants. We observed considerable within- and between-session reliability across distinct sets of items, in terms of overall mean response time (RT), RT distributional characteristics, diffusion model parameters (Ratcliff, Gomez, & McKoon, 2004), and sensitivity to underlying lexical dimensions. This indicates reliably detectable individual differences in word recognition performance. In addition, higher vocabulary knowledge was associated with faster, more accurate word recognition performance, attenuated sensitivity to stimuli characteristics, and more efficient accumulation of information. Finally, in contrast to suggestions in the literature, we did not find evidence that individuals were trading-off in their utilization of lexical and nonlexical information. PMID:21728459

  12. Human Activity Recognition from Body Sensor Data using Deep Learning.

    PubMed

    Hassan, Mohammad Mehedi; Huda, Shamsul; Uddin, Md Zia; Almogren, Ahmad; Alrubaian, Majed

    2018-04-16

    In recent years, human activity recognition from body sensor data or wearable sensor data has become a considerable research attention from academia and health industry. This research can be useful for various e-health applications such as monitoring elderly and physical impaired people at Smart home to improve their rehabilitation processes. However, it is not easy to accurately and automatically recognize physical human activity through wearable sensors due to the complexity and variety of body activities. In this paper, we address the human activity recognition problem as a classification problem using wearable body sensor data. In particular, we propose to utilize a Deep Belief Network (DBN) model for successful human activity recognition. First, we extract the important initial features from the raw body sensor data. Then, a kernel principal component analysis (KPCA) and linear discriminant analysis (LDA) are performed to further process the features and make them more robust to be useful for fast activity recognition. Finally, the DBN is trained by these features. Various experiments were performed on a real-world wearable sensor dataset to verify the effectiveness of the deep learning algorithm. The results show that the proposed DBN outperformed other algorithms and achieves satisfactory activity recognition performance.

  13. Emotion recognition abilities across stimulus modalities in schizophrenia and the role of visual attention.

    PubMed

    Simpson, Claire; Pinkham, Amy E; Kelsven, Skylar; Sasson, Noah J

    2013-12-01

    Emotion can be expressed by both the voice and face, and previous work suggests that presentation modality may impact emotion recognition performance in individuals with schizophrenia. We investigated the effect of stimulus modality on emotion recognition accuracy and the potential role of visual attention to faces in emotion recognition abilities. Thirty-one patients who met DSM-IV criteria for schizophrenia (n=8) or schizoaffective disorder (n=23) and 30 non-clinical control individuals participated. Both groups identified emotional expressions in three different conditions: audio only, visual only, combined audiovisual. In the visual only and combined conditions, time spent visually fixating salient features of the face were recorded. Patients were significantly less accurate than controls in emotion recognition during both the audio and visual only conditions but did not differ from controls on the combined condition. Analysis of visual scanning behaviors demonstrated that patients attended less than healthy individuals to the mouth in the visual condition but did not differ in visual attention to salient facial features in the combined condition, which may in part explain the absence of a deficit for patients in this condition. Collectively, these findings demonstrate that patients benefit from multimodal stimulus presentations of emotion and support hypotheses that visual attention to salient facial features may serve as a mechanism for accurate emotion identification. © 2013.

  14. A standardization model based on image recognition for performance evaluation of an oral scanner.

    PubMed

    Seo, Sang-Wan; Lee, Wan-Sun; Byun, Jae-Young; Lee, Kyu-Bok

    2017-12-01

    Accurate information is essential in dentistry. The image information of missing teeth is used in optically based medical equipment in prosthodontic treatment. To evaluate oral scanners, the standardized model was examined from cases of image recognition errors of linear discriminant analysis (LDA), and a model that combines the variables with reference to ISO 12836:2015 was designed. The basic model was fabricated by applying 4 factors to the tooth profile (chamfer, groove, curve, and square) and the bottom surface. Photo-type and video-type scanners were used to analyze 3D images after image capture. The scans were performed several times according to the prescribed sequence to distinguish the model from the one that did not form, and the results confirmed it to be the best. In the case of the initial basic model, a 3D shape could not be obtained by scanning even if several shots were taken. Subsequently, the recognition rate of the image was improved with every variable factor, and the difference depends on the tooth profile and the pattern of the floor surface. Based on the recognition error of the LDA, the recognition rate decreases when the model has a similar pattern. Therefore, to obtain the accurate 3D data, the difference of each class needs to be provided when developing a standardized model.

  15. Recognition of neural brain activity patterns correlated with complex motor activity

    NASA Astrophysics Data System (ADS)

    Kurkin, Semen; Musatov, Vyacheslav Yu.; Runnova, Anastasia E.; Grubov, Vadim V.; Efremova, Tatyana Yu.; Zhuravlev, Maxim O.

    2018-04-01

    In this paper, based on the apparatus of artificial neural networks, a technique for recognizing and classifying patterns corresponding to imaginary movements on electroencephalograms (EEGs) obtained from a group of untrained subjects was developed. The works on the selection of the optimal type, topology, training algorithms and neural network parameters were carried out from the point of view of the most accurate and fast recognition and classification of patterns on multi-channel EEGs associated with the imagination of movements. The influence of the number and choice of the analyzed channels of a multichannel EEG on the quality of recognition of imaginary movements was also studied, and optimal configurations of electrode arrangements were obtained. The effect of pre-processing of EEG signals is analyzed from the point of view of improving the accuracy of recognition of imaginary movements.

  16. An effective approach for iris recognition using phase-based image matching.

    PubMed

    Miyazawa, Kazuyuki; Ito, Koichi; Aoki, Takafumi; Kobayashi, Koji; Nakajima, Hiroshi

    2008-10-01

    This paper presents an efficient algorithm for iris recognition using phase-based image matching--an image matching technique using phase components in 2D Discrete Fourier Transforms (DFTs) of given images. Experimental evaluation using CASIA iris image databases (versions 1.0 and 2.0) and Iris Challenge Evaluation (ICE) 2005 database clearly demonstrates that the use of phase components of iris images makes possible to achieve highly accurate iris recognition with a simple matching algorithm. This paper also discusses major implementation issues of our algorithm. In order to reduce the size of iris data and to prevent the visibility of iris images, we introduce the idea of 2D Fourier Phase Code (FPC) for representing iris information. The 2D FPC is particularly useful for implementing compact iris recognition devices using state-of-the-art Digital Signal Processing (DSP) technology.

  17. Can Changes in Eye Movement Scanning Alter the Age-Related Deficit in Recognition Memory?

    PubMed Central

    Chan, Jessica P. K.; Kamino, Daphne; Binns, Malcolm A.; Ryan, Jennifer D.

    2011-01-01

    Older adults typically exhibit poorer face recognition compared to younger adults. These recognition differences may be due to underlying age-related changes in eye movement scanning. We examined whether older adults’ recognition could be improved by yoking their eye movements to those of younger adults. Participants studied younger and older faces, under free viewing conditions (bases), through a gaze-contingent moving window (own), or a moving window which replayed the eye movements of a base participant (yoked). During the recognition test, participants freely viewed the faces with no viewing restrictions. Own-age recognition biases were observed for older adults in all viewing conditions, suggesting that this effect occurs independently of scanning. Participants in the bases condition had the highest recognition accuracy, and participants in the yoked condition were more accurate than participants in the own condition. Among yoked participants, recognition did not depend on age of the base participant. These results suggest that successful encoding for all participants requires the bottom-up contribution of peripheral information, regardless of the locus of control of the viewer. Although altering the pattern of eye movements did not increase recognition, the amount of sampling of the face during encoding predicted subsequent recognition accuracy for all participants. Increased sampling may confer some advantages for subsequent recognition, particularly for people who have declining memory abilities. PMID:21687460

  18. Crop species recognition and mensuration in the Sacramento Valley

    NASA Technical Reports Server (NTRS)

    Thomson, F. J.

    1973-01-01

    The goal of the second recognition map was to delineate various crop species in a portion of the Sacramento Valley, and at the same time to determine how accurately each could be classified and measured from ERTS-1 data. The new recognition map, a new and concise display of the old map, and classification and mensuration accuracy data are presented and discussed. The mensuration accuracy, in particular, is affected by the presence of an edge effect one resolution wide surrounding nearly all fields. Points on the edge are misclassified because they contain a mixture of, crop and bare soil. Using a processing technique to estimate the proportions of unresolved objects in this edge region, a much improved mensuration capability will be demonstrated.

  19. Exploring a recognition-induced recognition decrement

    PubMed Central

    Dopkins, Stephen; Ngo, Catherine Trinh; Sargent, Jesse

    2007-01-01

    Four experiments explored a recognition decrement that is associated with the recognition of a word from a short list. The stimulus material for demonstrating the phenomenon was a list of words of different syntactic types. A word from the list was recognized less well following a decision that a word of the same type had occurred in the list than following a decision that such a word had not occurred in the list. A recognition decrement did not occur for a word of a given type following a positive recognition decision to a word of a different type. A recognition decrement did not occur when the list consisted exclusively of nouns. It was concluded that the phenomenon may reflect a criterion shift but probably does not reflect a list strength effect, suppression, or familiarity attribution consequent to a perceived discrepancy between actual and expected fluency. PMID:17063915

  20. Multimodal Emotion Recognition Is Resilient to Insufficient Sleep: Results From Cross-Sectional and Experimental Studies.

    PubMed

    Holding, Benjamin C; Laukka, Petri; Fischer, Håkan; Bänziger, Tanja; Axelsson, John; Sundelin, Tina

    2017-11-01

    Insufficient sleep has been associated with impaired recognition of facial emotions. However, previous studies have found inconsistent results, potentially stemming from the type of static picture task used. We therefore examined whether insufficient sleep was associated with decreased emotion recognition ability in two separate studies using a dynamic multimodal task. Study 1 used a cross-sectional design consisting of 291 participants with questionnaire measures assessing sleep duration and self-reported sleep quality for the previous night. Study 2 used an experimental design involving 181 participants where individuals were quasi-randomized into either a sleep-deprivation (N = 90) or a sleep-control (N = 91) condition. All participants from both studies were tested on the same forced-choice multimodal test of emotion recognition to assess the accuracy of emotion categorization. Sleep duration, self-reported sleep quality (study 1), and sleep deprivation (study 2) did not predict overall emotion recognition accuracy or speed. Similarly, the responses to each of the twelve emotions tested showed no evidence of impaired recognition ability, apart from one positive association suggesting that greater self-reported sleep quality could predict more accurate recognition of disgust (study 1). The studies presented here involve considerably larger samples than previous studies and the results support the null hypotheses. Therefore, we suggest that the ability to accurately categorize the emotions of others is not associated with short-term sleep duration or sleep quality and is resilient to acute periods of insufficient sleep. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

  1. Tolerance for distorted faces: challenges to a configural processing account of familiar face recognition.

    PubMed

    Sandford, Adam; Burton, A Mike

    2014-09-01

    Face recognition is widely held to rely on 'configural processing', an analysis of spatial relations between facial features. We present three experiments in which viewers were shown distorted faces, and asked to resize these to their correct shape. Based on configural theories appealing to metric distances between features, we reason that this should be an easier task for familiar than unfamiliar faces (whose subtle arrangements of features are unknown). In fact, participants were inaccurate at this task, making between 8% and 13% errors across experiments. Importantly, we observed no advantage for familiar faces: in one experiment participants were more accurate with unfamiliars, and in two experiments there was no difference. These findings were not due to general task difficulty - participants were able to resize blocks of colour to target shapes (squares) more accurately. We also found an advantage of familiarity for resizing other stimuli (brand logos). If configural processing does underlie face recognition, these results place constraints on the definition of 'configural'. Alternatively, familiar face recognition might rely on more complex criteria - based on tolerance to within-person variation rather than highly specific measurement. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Unaware person recognition from the body when face identification fails.

    PubMed

    Rice, Allyson; Phillips, P Jonathon; Natu, Vaidehi; An, Xiaobo; O'Toole, Alice J

    2013-11-01

    How does one recognize a person when face identification fails? Here, we show that people rely on the body but are unaware of doing so. State-of-the-art face-recognition algorithms were used to select images of people with almost no useful identity information in the face. Recognition of the face alone in these cases was near chance level, but recognition of the person was accurate. Accuracy in identifying the person without the face was identical to that in identifying the whole person. Paradoxically, people reported relying heavily on facial features over noninternal face and body features in making their identity decisions. Eye movements indicated otherwise, with gaze duration and fixations shifting adaptively toward the body and away from the face when the body was a better indicator of identity than the face. This shift occurred with no cost to accuracy or response time. Human identity processing may be partially inaccessible to conscious awareness.

  3. Use of terbium as a probe of tRNA tertiary structure and folding.

    PubMed Central

    Hargittai, M R; Musier-Forsyth, K

    2000-01-01

    Lanthanide metals such as terbium have previously been shown to be useful for mapping metal-binding sites in RNA. Terbium binds to the same sites on RNA as magnesium, however, with a much higher affinity. Thus, low concentrations of terbium ions can easily displace magnesium and promote phosphodiester backbone scission. At higher concentrations, terbium cleaves RNA in a sequence-independent manner, with a preference for single-stranded, non-Watson-Crick base-paired regions. Here, we show that terbium is a sensitive probe of human tRNALys,3 tertiary structure and folding. When 1 microM tRNA is used, the optimal terbium ion concentration for detecting Mg2+-induced tertiary structural changes is 50-60 microM. Using these concentrations of RNA and terbium, a magnesium-dependent folding transition with a midpoint (KMg) of 2.6 mM is observed for unmodified human tRNALys,3. At lower Tb3+ concentrations, cleavage is restricted to nucleotides that constitute specific metal-binding pockets. This small chemical probe should also be useful for detecting protein induced structural changes in RNA. PMID:11105765

  4. TRMT5 Mutations Cause a Defect in Post-transcriptional Modification of Mitochondrial tRNA Associated with Multiple Respiratory-Chain Deficiencies.

    PubMed

    Powell, Christopher A; Kopajtich, Robert; D'Souza, Aaron R; Rorbach, Joanna; Kremer, Laura S; Husain, Ralf A; Dallabona, Cristina; Donnini, Claudia; Alston, Charlotte L; Griffin, Helen; Pyle, Angela; Chinnery, Patrick F; Strom, Tim M; Meitinger, Thomas; Rodenburg, Richard J; Schottmann, Gudrun; Schuelke, Markus; Romain, Nadine; Haller, Ronald G; Ferrero, Ileana; Haack, Tobias B; Taylor, Robert W; Prokisch, Holger; Minczuk, Michal

    2015-08-06

    Deficiencies in respiratory-chain complexes lead to a variety of clinical phenotypes resulting from inadequate energy production by the mitochondrial oxidative phosphorylation system. Defective expression of mtDNA-encoded genes, caused by mutations in either the mitochondrial or nuclear genome, represents a rapidly growing group of human disorders. By whole-exome sequencing, we identified two unrelated individuals carrying compound heterozygous variants in TRMT5 (tRNA methyltransferase 5). TRMT5 encodes a mitochondrial protein with strong homology to members of the class I-like methyltransferase superfamily. Both affected individuals presented with lactic acidosis and evidence of multiple mitochondrial respiratory-chain-complex deficiencies in skeletal muscle, although the clinical presentation of the two affected subjects was remarkably different; one presented in childhood with failure to thrive and hypertrophic cardiomyopathy, and the other was an adult with a life-long history of exercise intolerance. Mutations in TRMT5 were associated with the hypomodification of a guanosine residue at position 37 (G37) of mitochondrial tRNA; this hypomodification was particularly prominent in skeletal muscle. Deficiency of the G37 modification was also detected in human cells subjected to TRMT5 RNAi. The pathogenicity of the detected variants was further confirmed in a heterologous yeast model and by the rescue of the molecular phenotype after re-expression of wild-type TRMT5 cDNA in cells derived from the affected individuals. Our study highlights the importance of post-transcriptional modification of mitochondrial tRNAs for faithful mitochondrial function. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Sign Perception and Recognition in Non-Native Signers of ASL

    PubMed Central

    Morford, Jill P.; Carlson, Martina L.

    2011-01-01

    Past research has established that delayed first language exposure is associated with comprehension difficulties in non-native signers of American Sign Language (ASL) relative to native signers. The goal of the current study was to investigate potential explanations of this disparity: do non-native signers have difficulty with all aspects of comprehension, or are their comprehension difficulties restricted to some aspects of processing? We compared the performance of deaf non-native, hearing L2, and deaf native signers on a handshape and location monitoring and a sign recognition task. The results indicate that deaf non-native signers are as rapid and accurate on the monitoring task as native signers, with differences in the pattern of relative performance across handshape and location parameters. By contrast, non-native signers differ significantly from native signers during sign recognition. Hearing L2 signers, who performed almost as well as the two groups of deaf signers on the monitoring task, resembled the deaf native signers more than the deaf non-native signers on the sign recognition task. The combined results indicate that delayed exposure to a signed language leads to an overreliance on handshape during sign recognition. PMID:21686080

  6. 8 CFR 292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. 292.2...; withdrawal of recognition; accreditation of representatives; roster. (a) Qualifications of organizations. A non-profit religious, charitable, social service, or similar organization established in the United...

  7. Adaptive optics to enhance target recognition

    NASA Astrophysics Data System (ADS)

    McAulay, Alastair D.

    2012-06-01

    Target recognition can be enhanced by reducing image degradation due to atmospheric turbulence. This is accomplished by an adaptive optic system. We discuss the forms of degradation when a target is viewed through the atmosphere1: scintillation from ground targets on a hot day in visible or infrared light; beam spreading and wavering around in time; atmospheric turbulence caused by motion of the target or by weather. In the case of targets we can use a beacon laser that reflects back from the target into a wavefront detector to measure the effects of turbulence on propagation to and from the target before imaging.1 A deformable mirror then corrects the wavefront shape of the transmitted, reflected or scattered data for enhanced imaging. Further, recognition of targets is enhanced by performing accurate distance measurements to localized parts of the target using lidar. Distance is obtained by sending a short pulse to the target and measuring the time for the pulse to return. There is inadequate time to scan the complete field of view so that the beam must be steered to regions of interest such as extremities of the image during image recognition. Distance is particularly valuable to recognize fine features in range along the target or when segmentation is required to separate a target from background or from other targets. We discuss the issues involved.

  8. Rational protein engineering in action: The first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus

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

    Evdokimov, Artem G.; Mekel, Marlene; Hutchings, Kim

    2008-07-08

    In this article, we describe for the first time the high-resolution crystal structure of a phenylalanine tRNA synthetase from the pathogenic bacterium Staphylococcus haemolyticus. We demonstrate the subtle yet important structural differences between this enzyme and the previously described Thermus thermophilus ortholog. We also explain the structure-activity relationship of several recently reported inhibitors. The native enzyme crystals were of poor quality -- they only diffracted X-rays to 3--5 {angstrom} resolution. Therefore, we have executed a rational surface mutagenesis strategy that has yielded crystals of this 2300-amino acid multidomain protein, diffracting to 2 {angstrom} or better. This methodology is discussed andmore » contrasted with the more traditional domain truncation approach.« less

  9. A Vision-Based Counting and Recognition System for Flying Insects in Intelligent Agriculture

    PubMed Central

    Zhong, Yuanhong; Gao, Junyuan; Lei, Qilun; Zhou, Yao

    2018-01-01

    Rapid and accurate counting and recognition of flying insects are of great importance, especially for pest control. Traditional manual identification and counting of flying insects is labor intensive and inefficient. In this study, a vision-based counting and classification system for flying insects is designed and implemented. The system is constructed as follows: firstly, a yellow sticky trap is installed in the surveillance area to trap flying insects and a camera is set up to collect real-time images. Then the detection and coarse counting method based on You Only Look Once (YOLO) object detection, the classification method and fine counting based on Support Vector Machines (SVM) using global features are designed. Finally, the insect counting and recognition system is implemented on Raspberry PI. Six species of flying insects including bee, fly, mosquito, moth, chafer and fruit fly are selected to assess the effectiveness of the system. Compared with the conventional methods, the test results show promising performance. The average counting accuracy is 92.50% and average classifying accuracy is 90.18% on Raspberry PI. The proposed system is easy-to-use and provides efficient and accurate recognition data, therefore, it can be used for intelligent agriculture applications. PMID:29747429

  10. NetVLAD: CNN Architecture for Weakly Supervised Place Recognition.

    PubMed

    Arandjelovic, Relja; Gronat, Petr; Torii, Akihiko; Pajdla, Tomas; Sivic, Josef

    2018-06-01

    We tackle the problem of large scale visual place recognition, where the task is to quickly and accurately recognize the location of a given query photograph. We present the following four principal contributions. First, we develop a convolutional neural network (CNN) architecture that is trainable in an end-to-end manner directly for the place recognition task. The main component of this architecture, NetVLAD, is a new generalized VLAD layer, inspired by the "Vector of Locally Aggregated Descriptors" image representation commonly used in image retrieval. The layer is readily pluggable into any CNN architecture and amenable to training via backpropagation. Second, we create a new weakly supervised ranking loss, which enables end-to-end learning of the architecture's parameters from images depicting the same places over time downloaded from Google Street View Time Machine. Third, we develop an efficient training procedure which can be applied on very large-scale weakly labelled tasks. Finally, we show that the proposed architecture and training procedure significantly outperform non-learnt image representations and off-the-shelf CNN descriptors on challenging place recognition and image retrieval benchmarks.

  11. Prediction of consonant recognition in quiet for listeners with normal and impaired hearing using an auditory model.

    PubMed

    Jürgens, Tim; Ewert, Stephan D; Kollmeier, Birger; Brand, Thomas

    2014-03-01

    Consonant recognition was assessed in normal-hearing (NH) and hearing-impaired (HI) listeners in quiet as a function of speech level using a nonsense logatome test. Average recognition scores were analyzed and compared to recognition scores of a speech recognition model. In contrast to commonly used spectral speech recognition models operating on long-term spectra, a "microscopic" model operating in the time domain was used. Variations of the model (accounting for hearing impairment) and different model parameters (reflecting cochlear compression) were tested. Using these model variations this study examined whether speech recognition performance in quiet is affected by changes in cochlear compression, namely, a linearization, which is often observed in HI listeners. Consonant recognition scores for HI listeners were poorer than for NH listeners. The model accurately predicted the speech reception thresholds of the NH and most HI listeners. A partial linearization of the cochlear compression in the auditory model, while keeping audibility constant, produced higher recognition scores and improved the prediction accuracy. However, including listener-specific information about the exact form of the cochlear compression did not improve the prediction further.

  12. Personal recognition using hand shape and texture.

    PubMed

    Kumar, Ajay; Zhang, David

    2006-08-01

    This paper proposes a new bimodal biometric system using feature-level fusion of hand shape and palm texture. The proposed combination is of significance since both the palmprint and hand-shape images are proposed to be extracted from the single hand image acquired from a digital camera. Several new hand-shape features that can be used to represent the hand shape and improve the performance are investigated. The new approach for palmprint recognition using discrete cosine transform coefficients, which can be directly obtained from the camera hardware, is demonstrated. None of the prior work on hand-shape or palmprint recognition has given any attention on the critical issue of feature selection. Our experimental results demonstrate that while majority of palmprint or hand-shape features are useful in predicting the subjects identity, only a small subset of these features are necessary in practice for building an accurate model for identification. The comparison and combination of proposed features is evaluated on the diverse classification schemes; naive Bayes (normal, estimated, multinomial), decision trees (C4.5, LMT), k-NN, SVM, and FFN. Although more work remains to be done, our results to date indicate that the combination of selected hand-shape and palmprint features constitutes a promising addition to the biometrics-based personal recognition systems.

  13. Segment-based acoustic models for continuous speech recognition

    NASA Astrophysics Data System (ADS)

    Ostendorf, Mari; Rohlicek, J. R.

    1993-07-01

    This research aims to develop new and more accurate stochastic models for speaker-independent continuous speech recognition, by extending previous work in segment-based modeling and by introducing a new hierarchical approach to representing intra-utterance statistical dependencies. These techniques, which are more costly than traditional approaches because of the large search space associated with higher order models, are made feasible through rescoring a set of HMM-generated N-best sentence hypotheses. We expect these different modeling techniques to result in improved recognition performance over that achieved by current systems, which handle only frame-based observations and assume that these observations are independent given an underlying state sequence. In the fourth quarter of the project, we have completed the following: (1) ported our recognition system to the Wall Street Journal task, a standard task in the ARPA community; (2) developed an initial dependency-tree model of intra-utterance observation correlation; and (3) implemented baseline language model estimation software. Our initial results on the Wall Street Journal task are quite good and represent significantly improved performance over most HMM systems reporting on the Nov. 1992 5k vocabulary test set.

  14. Real-time image restoration for iris recognition systems.

    PubMed

    Kang, Byung Jun; Park, Kang Ryoung

    2007-12-01

    In the field of biometrics, it has been reported that iris recognition techniques have shown high levels of accuracy because unique patterns of the human iris, which has very many degrees of freedom, are used. However, because conventional iris cameras have small depth-of-field (DOF) areas, input iris images can easily be blurred, which can lead to lower recognition performance, since iris patterns are transformed by the blurring caused by optical defocusing. To overcome these problems, an autofocusing camera can be used. However, this inevitably increases the cost, size, and complexity of the system. Therefore, we propose a new real-time iris image-restoration method, which can increase the camera's DOF without requiring any additional hardware. This paper presents five novelties as compared to previous works: 1) by excluding eyelash and eyelid regions, it is possible to obtain more accurate focus scores from input iris images; 2) the parameter of the point spread function (PSF) can be estimated in terms of camera optics and measured focus scores; therefore, parameter estimation is more accurate than it has been in previous research; 3) because the PSF parameter can be obtained by using a predetermined equation, iris image restoration can be done in real-time; 4) by using a constrained least square (CLS) restoration filter that considers noise, performance can be greatly enhanced; and 5) restoration accuracy can also be enhanced by estimating the weight value of the noise-regularization term of the CLS filter according to the amount of image blurring. Experimental results showed that iris recognition errors when using the proposed restoration method were greatly reduced as compared to those results achieved without restoration or those achieved using previous iris-restoration methods.

  15. Macromolecular recognition: Structural aspects of the origin of the genetic system

    NASA Technical Reports Server (NTRS)

    Rein, Robert; Sokalski, W. Andrzej; Barak, Dov; Luo, Ning; Zielinski, Theresa Julia; Shibata, Masayuki

    1991-01-01

    Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

  16. Action recognition using mined hierarchical compound features.

    PubMed

    Gilbert, Andrew; Illingworth, John; Bowden, Richard

    2011-05-01

    The field of Action Recognition has seen a large increase in activity in recent years. Much of the progress has been through incorporating ideas from single-frame object recognition and adapting them for temporal-based action recognition. Inspired by the success of interest points in the 2D spatial domain, their 3D (space-time) counterparts typically form the basic components used to describe actions, and in action recognition the features used are often engineered to fire sparsely. This is to ensure that the problem is tractable; however, this can sacrifice recognition accuracy as it cannot be assumed that the optimum features in terms of class discrimination are obtained from this approach. In contrast, we propose to initially use an overcomplete set of simple 2D corners in both space and time. These are grouped spatially and temporally using a hierarchical process, with an increasing search area. At each stage of the hierarchy, the most distinctive and descriptive features are learned efficiently through data mining. This allows large amounts of data to be searched for frequently reoccurring patterns of features. At each level of the hierarchy, the mined compound features become more complex, discriminative, and sparse. This results in fast, accurate recognition with real-time performance on high-resolution video. As the compound features are constructed and selected based upon their ability to discriminate, their speed and accuracy increase at each level of the hierarchy. The approach is tested on four state-of-the-art data sets, the popular KTH data set to provide a comparison with other state-of-the-art approaches, the Multi-KTH data set to illustrate performance at simultaneous multiaction classification, despite no explicit localization information provided during training. Finally, the recent Hollywood and Hollywood2 data sets provide challenging complex actions taken from commercial movie sequences. For all four data sets, the proposed hierarchical

  17. Multi-task learning with group information for human action recognition

    NASA Astrophysics Data System (ADS)

    Qian, Li; Wu, Song; Pu, Nan; Xu, Shulin; Xiao, Guoqiang

    2018-04-01

    Human action recognition is an important and challenging task in computer vision research, due to the variations in human motion performance, interpersonal differences and recording settings. In this paper, we propose a novel multi-task learning framework with group information (MTL-GI) for accurate and efficient human action recognition. Specifically, we firstly obtain group information through calculating the mutual information according to the latent relationship between Gaussian components and action categories, and clustering similar action categories into the same group by affinity propagation clustering. Additionally, in order to explore the relationships of related tasks, we incorporate group information into multi-task learning. Experimental results evaluated on two popular benchmarks (UCF50 and HMDB51 datasets) demonstrate the superiority of our proposed MTL-GI framework.

  18. Providing information about diagnostic features at retrieval reduces false recognition.

    PubMed

    Lane, Sean M; Roussel, Cristine C; Starns, Jeffrey J; Villa, Diane; Alonzo, Jill D

    2008-11-01

    In the following study, participants encoded blocked DRM word lists and we varied whether they received information before test about the utility of mnemonic features that potentially discriminate between veridical and false memories. The results of three experiments revealed that this manipulation successfully reduced false recognition of critical theme words. We also found that this manipulation was effective for younger but not older adults. Furthermore, calling attention to the features in test instructions alone was sufficient for reducing false recognition and its effectiveness was not enhanced by also asking participants to rate their phenomenal experience. We argue that providing diagnostic information before test allows participants to establish more accurate expectations about the task and thus improves the efficacy of retrieval and monitoring processes that are subsequently engaged.

  19. Memory Asymmetry of Forward and Backward Associations in Recognition Tasks

    PubMed Central

    Yang, Jiongjiong; Zhu, Zijian; Mecklinger, Axel; Fang, Zhiyong; Li, Han

    2013-01-01

    There is an intensive debate on whether memory for serial order is symmetric. The objective of this study was to explore whether associative asymmetry is modulated by memory task (recognition vs. cued recall). Participants were asked to memorize word triples (Experiment 1–2) or pairs (Experiment 3–6) during the study phase. They then recalled the word by a cue during a cued recall task (Experiment 1–4), and judged whether the presented two words were in the same or in a different order compared to the study phase during a recognition task (Experiment 1–6). To control for perceptual matching between the study and test phase, participants were presented with vertical test pairs when they made directional judgment in Experiment 5. In Experiment 6, participants also made associative recognition judgments for word pairs presented at the same or the reversed position. The results showed that forward associations were recalled at similar levels as backward associations, and that the correlations between forward and backward associations were high in the cued recall tasks. On the other hand, the direction of forward associations was recognized more accurately (and more quickly) than backward associations, and their correlations were comparable to the control condition in the recognition tasks. This forward advantage was also obtained for the associative recognition task. Diminishing positional information did not change the pattern of associative asymmetry. These results suggest that associative asymmetry is modulated by cued recall and recognition manipulations, and that direction as a constituent part of a memory trace can facilitate associative memory. PMID:22924326

  20. One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

    PubMed Central

    Rodin, Andrei S; Szathmáry, Eörs; Rodin, Sergei N

    2009-01-01

    Background The genetic code is brought into action by 20 aminoacyl-tRNA synthetases. These enzymes are evenly divided into two classes (I and II) that recognize tRNAs from the minor and major groove sides of the acceptor stem, respectively. We have reported recently that: (1) ribozymic precursors of the synthetases seem to have used the same two sterically mirror modes of tRNA recognition, (2) having these two modes might have helped in preventing erroneous aminoacylation of ancestral tRNAs with complementary anticodons, yet (3) the risk of confusion for the presumably earliest pairs of complementarily encoded amino acids had little to do with anticodons. Accordingly, in this communication we focus on the acceptor stem. Results Our main result is the emergence of a palindrome structure for the acceptor stem's common ancestor, reconstructed from the phylogenetic trees of Bacteria, Archaea and Eukarya. In parallel, for pairs of ancestral tRNAs with complementary anticodons, we present updated evidence of concerted complementarity of the second bases in the acceptor stems. These two results suggest that the first pairs of "complementary" amino acids that were engaged in primordial coding, such as Gly and Ala, could have avoided erroneous aminoacylation if and only if the acceptor stems of their adaptors were recognized from the same, major groove, side. The class II protein synthetases then inherited this "primary preference" from isofunctional ribozymes. Conclusion Taken together, our results support the hypothesis that the genetic code per se (the one associated with the anticodons) and the operational code of aminoacylation (associated with the acceptor) diverged from a common ancestor that probably began developing before translation. The primordial advantage of linking some amino acids (most likely glycine and alanine) to the ancestral acceptor stem may have been selective retention in a protocell surrounded by a leaky membrane for use in nucleotide and coenzyme

  1. Invariant recognition drives neural representations of action sequences

    PubMed Central

    Poggio, Tomaso

    2017-01-01

    Recognizing the actions of others from visual stimuli is a crucial aspect of human perception that allows individuals to respond to social cues. Humans are able to discriminate between similar actions despite transformations, like changes in viewpoint or actor, that substantially alter the visual appearance of a scene. This ability to generalize across complex transformations is a hallmark of human visual intelligence. Advances in understanding action recognition at the neural level have not always translated into precise accounts of the computational principles underlying what representations of action sequences are constructed by human visual cortex. Here we test the hypothesis that invariant action discrimination might fill this gap. Recently, the study of artificial systems for static object perception has produced models, Convolutional Neural Networks (CNNs), that achieve human level performance in complex discriminative tasks. Within this class, architectures that better support invariant object recognition also produce image representations that better match those implied by human and primate neural data. However, whether these models produce representations of action sequences that support recognition across complex transformations and closely follow neural representations of actions remains unknown. Here we show that spatiotemporal CNNs accurately categorize video stimuli into action classes, and that deliberate model modifications that improve performance on an invariant action recognition task lead to data representations that better match human neural recordings. Our results support our hypothesis that performance on invariant discrimination dictates the neural representations of actions computed in the brain. These results broaden the scope of the invariant recognition framework for understanding visual intelligence from perception of inanimate objects and faces in static images to the study of human perception of action sequences. PMID:29253864

  2. Eye-Gaze Analysis of Facial Emotion Recognition and Expression in Adolescents with ASD.

    PubMed

    Wieckowski, Andrea Trubanova; White, Susan W

    2017-01-01

    Impaired emotion recognition and expression in individuals with autism spectrum disorder (ASD) may contribute to observed social impairment. The aim of this study was to examine the role of visual attention directed toward nonsocial aspects of a scene as a possible mechanism underlying recognition and expressive ability deficiency in ASD. One recognition and two expression tasks were administered. Recognition was assessed in force-choice paradigm, and expression was assessed during scripted and free-choice response (in response to emotional stimuli) tasks in youth with ASD (n = 20) and an age-matched sample of typically developing youth (n = 20). During stimulus presentation prior to response in each task, participants' eye gaze was tracked. Youth with ASD were less accurate at identifying disgust and sadness in the recognition task. They fixated less to the eye region of stimuli showing surprise. A group difference was found during the free-choice response task, such that those with ASD expressed emotion less clearly but not during the scripted task. Results suggest altered eye gaze to the mouth region but not the eye region as a candidate mechanism for decreased ability to recognize or express emotion. Findings inform our understanding of the association between social attention and emotion recognition and expression deficits.

  3. Visual scanning behavior is related to recognition performance for own- and other-age faces

    PubMed Central

    Proietti, Valentina; Macchi Cassia, Viola; dell’Amore, Francesca; Conte, Stefania; Bricolo, Emanuela

    2015-01-01

    It is well-established that our recognition ability is enhanced for faces belonging to familiar categories, such as own-race faces and own-age faces. Recent evidence suggests that, for race, the recognition bias is also accompanied by different visual scanning strategies for own- compared to other-race faces. Here, we tested the hypothesis that these differences in visual scanning patterns extend also to the comparison between own and other-age faces and contribute to the own-age recognition advantage. Participants (young adults with limited experience with infants) were tested in an old/new recognition memory task where they encoded and subsequently recognized a series of adult and infant faces while their eye movements were recorded. Consistent with findings on the other-race bias, we found evidence of an own-age bias in recognition which was accompanied by differential scanning patterns, and consequently differential encoding strategies, for own-compared to other-age faces. Gaze patterns for own-age faces involved a more dynamic sampling of the internal features and longer viewing time on the eye region compared to the other regions of the face. This latter strategy was extensively employed during learning (vs. recognition) and was positively correlated to discriminability. These results suggest that deeply encoding the eye region is functional for recognition and that the own-age bias is evident not only in differential recognition performance, but also in the employment of different sampling strategies found to be effective for accurate recognition. PMID:26579056

  4. Levels-of-Processing Effect on Frontotemporal Function in Schizophrenia During Word Encoding and Recognition

    PubMed Central

    Ragland, J. Daniel; Gur, Ruben C.; Valdez, Jeffrey N.; Loughead, James; Elliott, Mark; Kohler, Christian; Kanes, Stephen; Siegel, Steven J.; Moelter, Stephen T.; Gur, Raquel E.

    2015-01-01

    Objective Patients with schizophrenia improve episodic memory accuracy when given organizational strategies through levels-of-processing paradigms. This study tested if improvement is accompanied by normalized frontotemporal function. Method Event-related blood-oxygen-level-dependent functional magnetic resonance imaging (fMRI) was used to measure activation during shallow (perceptual) and deep (semantic) word encoding and recognition in 14 patients with schizophrenia and 14 healthy comparison subjects. Results Despite slower and less accurate overall word classification, the patients showed normal levels-of-processing effects, with faster and more accurate recognition of deeply processed words. These effects were accompanied by left ventrolateral prefrontal activation during encoding in both groups, although the thalamus, hippocampus, and lingual gyrus were overactivated in the patients. During word recognition, the patients showed overactivation in the left frontal pole and had a less robust right prefrontal response. Conclusions Evidence of normal levels-of-processing effects and left prefrontal activation suggests that patients with schizophrenia can form and maintain semantic representations when they are provided with organizational cues and can improve their word encoding and retrieval. Areas of overactivation suggest residual inefficiencies. Nevertheless, the effect of teaching organizational strategies on episodic memory and brain function is a worthwhile topic for future interventional studies. PMID:16199830

  5. Speech recognition training for enhancing written language generation by a traumatic brain injury survivor.

    PubMed

    Manasse, N J; Hux, K; Rankin-Erickson, J L

    2000-11-01

    Impairments in motor functioning, language processing, and cognitive status may impact the written language performance of traumatic brain injury (TBI) survivors. One strategy to minimize the impact of these impairments is to use a speech recognition system. The purpose of this study was to explore the effect of mild dysarthria and mild cognitive-communication deficits secondary to TBI on a 19-year-old survivor's mastery and use of such a system-specifically, Dragon Naturally Speaking. Data included the % of the participant's words accurately perceived by the system over time, the participant's accuracy over time in using commands for navigation and error correction, and quantitative and qualitative changes in the participant's written texts generated with and without the use of the speech recognition system. Results showed that Dragon NaturallySpeaking was approximately 80% accurate in perceiving words spoken by the participant, and the participant quickly and easily mastered all navigation and error correction commands presented. Quantitatively, the participant produced a greater amount of text using traditional word processing and a standard keyboard than using the speech recognition system. Minimal qualitative differences appeared between writing samples. Discussion of factors that may have contributed to the obtained results and that may affect the generalization of the findings to other TBI survivors is provided.

  6. Levels-of-processing effect on frontotemporal function in schizophrenia during word encoding and recognition.

    PubMed

    Ragland, J Daniel; Gur, Ruben C; Valdez, Jeffrey N; Loughead, James; Elliott, Mark; Kohler, Christian; Kanes, Stephen; Siegel, Steven J; Moelter, Stephen T; Gur, Raquel E

    2005-10-01

    Patients with schizophrenia improve episodic memory accuracy when given organizational strategies through levels-of-processing paradigms. This study tested if improvement is accompanied by normalized frontotemporal function. Event-related blood-oxygen-level-dependent functional magnetic resonance imaging (fMRI) was used to measure activation during shallow (perceptual) and deep (semantic) word encoding and recognition in 14 patients with schizophrenia and 14 healthy comparison subjects. Despite slower and less accurate overall word classification, the patients showed normal levels-of-processing effects, with faster and more accurate recognition of deeply processed words. These effects were accompanied by left ventrolateral prefrontal activation during encoding in both groups, although the thalamus, hippocampus, and lingual gyrus were overactivated in the patients. During word recognition, the patients showed overactivation in the left frontal pole and had a less robust right prefrontal response. Evidence of normal levels-of-processing effects and left prefrontal activation suggests that patients with schizophrenia can form and maintain semantic representations when they are provided with organizational cues and can improve their word encoding and retrieval. Areas of overactivation suggest residual inefficiencies. Nevertheless, the effect of teaching organizational strategies on episodic memory and brain function is a worthwhile topic for future interventional studies.

  7. Probing binding hot spots at protein-RNA recognition sites.

    PubMed

    Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

    2016-01-29

    We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Codebook-based electrooculography data analysis towards cognitive activity recognition.

    PubMed

    Lagodzinski, P; Shirahama, K; Grzegorzek, M

    2018-04-01

    With the advancement in mobile/wearable technology, people started to use a variety of sensing devices to track their daily activities as well as health and fitness conditions in order to improve the quality of life. This work addresses an idea of eye movement analysis, which due to the strong correlation with cognitive tasks can be successfully utilized in activity recognition. Eye movements are recorded using an electrooculographic (EOG) system built into the frames of glasses, which can be worn more unobtrusively and comfortably than other devices. Since the obtained information is low-level sensor data expressed as a sequence representing values in constant intervals (100 Hz), the cognitive activity recognition problem is formulated as sequence classification. However, it is unclear what kind of features are useful for accurate cognitive activity recognition. Thus, a machine learning algorithm like a codebook approach is applied, which instead of focusing on feature engineering is using a distribution of characteristic subsequences (codewords) to describe sequences of recorded EOG data, where the codewords are obtained by clustering a large number of subsequences. Further, statistical analysis of the codeword distribution results in discovering features which are characteristic to a certain activity class. Experimental results demonstrate good accuracy of the codebook-based cognitive activity recognition reflecting the effective usage of the codewords. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Can blind persons accurately assess body size from the voice?

    PubMed

    Pisanski, Katarzyna; Oleszkiewicz, Anna; Sorokowska, Agnieszka

    2016-04-01

    Vocal tract resonances provide reliable information about a speaker's body size that human listeners use for biosocial judgements as well as speech recognition. Although humans can accurately assess men's relative body size from the voice alone, how this ability is acquired remains unknown. In this study, we test the prediction that accurate voice-based size estimation is possible without prior audiovisual experience linking low frequencies to large bodies. Ninety-one healthy congenitally or early blind, late blind and sighted adults (aged 20-65) participated in the study. On the basis of vowel sounds alone, participants assessed the relative body sizes of male pairs of varying heights. Accuracy of voice-based body size assessments significantly exceeded chance and did not differ among participants who were sighted, or congenitally blind or who had lost their sight later in life. Accuracy increased significantly with relative differences in physical height between men, suggesting that both blind and sighted participants used reliable vocal cues to size (i.e. vocal tract resonances). Our findings demonstrate that prior visual experience is not necessary for accurate body size estimation. This capacity, integral to both nonverbal communication and speech perception, may be present at birth or may generalize from broader cross-modal correspondences. © 2016 The Author(s).

  10. Can blind persons accurately assess body size from the voice?

    PubMed Central

    Oleszkiewicz, Anna; Sorokowska, Agnieszka

    2016-01-01

    Vocal tract resonances provide reliable information about a speaker's body size that human listeners use for biosocial judgements as well as speech recognition. Although humans can accurately assess men's relative body size from the voice alone, how this ability is acquired remains unknown. In this study, we test the prediction that accurate voice-based size estimation is possible without prior audiovisual experience linking low frequencies to large bodies. Ninety-one healthy congenitally or early blind, late blind and sighted adults (aged 20–65) participated in the study. On the basis of vowel sounds alone, participants assessed the relative body sizes of male pairs of varying heights. Accuracy of voice-based body size assessments significantly exceeded chance and did not differ among participants who were sighted, or congenitally blind or who had lost their sight later in life. Accuracy increased significantly with relative differences in physical height between men, suggesting that both blind and sighted participants used reliable vocal cues to size (i.e. vocal tract resonances). Our findings demonstrate that prior visual experience is not necessary for accurate body size estimation. This capacity, integral to both nonverbal communication and speech perception, may be present at birth or may generalize from broader cross-modal correspondences. PMID:27095264

  11. A Diffusion Model Analysis of the Effects of Aging on Recognition Memory

    ERIC Educational Resources Information Center

    Ratcliff, Roger; Thapar, Anjali; McKoon, Gail

    2004-01-01

    The effects of aging on response time were examined in a recognition memory experiment with young, college age subjects and older, 60-75 year old subjects. The older subjects were slower than the young subjects but almost as accurate. Ratcliff's (1978) diffusion model was fit to the data and it provided a good account of response times, their…

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

    PubMed Central

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

    2013-01-01

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

  13. Anodal tDCS targeting the right orbitofrontal cortex enhances facial expression recognition

    PubMed Central

    Murphy, Jillian M.; Ridley, Nicole J.; Vercammen, Ans

    2015-01-01

    The orbitofrontal cortex (OFC) has been implicated in the capacity to accurately recognise facial expressions. The aim of the current study was to determine if anodal transcranial direct current stimulation (tDCS) targeting the right OFC in healthy adults would enhance facial expression recognition, compared with a sham condition. Across two counterbalanced sessions of tDCS (i.e. anodal and sham), 20 undergraduate participants (18 female) completed a facial expression labelling task comprising angry, disgusted, fearful, happy, sad and neutral expressions, and a control (social judgement) task comprising the same expressions. Responses on the labelling task were scored for accuracy, median reaction time and overall efficiency (i.e. combined accuracy and reaction time). Anodal tDCS targeting the right OFC enhanced facial expression recognition, reflected in greater efficiency and speed of recognition across emotions, relative to the sham condition. In contrast, there was no effect of tDCS to responses on the control task. This is the first study to demonstrate that anodal tDCS targeting the right OFC boosts facial expression recognition. This finding provides a solid foundation for future research to examine the efficacy of this technique as a means to treat facial expression recognition deficits, particularly in individuals with OFC damage or dysfunction. PMID:25971602

  14. Early effects of duloxetine on emotion recognition in healthy volunteers

    PubMed Central

    Bamford, Susan; Penton-Voak, Ian; Pinkney, Verity; Baldwin, David S; Munafò, Marcus R; Garner, Matthew

    2015-01-01

    The serotonin-noradrenaline reuptake inhibitor (SNRI) duloxetine is an effective treatment for major depression and generalised anxiety disorder. Neuropsychological models of antidepressant drug action suggest therapeutic effects might be mediated by the early correction of maladaptive biases in emotion processing, including the recognition of emotional expressions. Sub-chronic administration of duloxetine (for two weeks) produces adaptive changes in neural circuitry implicated in emotion processing; however, its effects on emotional expression recognition are unknown. Forty healthy participants were randomised to receive either 14 days of duloxetine (60 mg/day, titrated from 30 mg after three days) or matched placebo (with sham titration) in a double-blind, between-groups, repeated-measures design. On day 0 and day 14 participants completed a computerised emotional expression recognition task that measured sensitivity to the six primary emotions. Thirty-eight participants (19 per group) completed their course of tablets and were included in the analysis. Results provide evidence that duloxetine, compared to placebo, may reduce the accurate recognition of sadness. Drug effects were driven by changes in participants’ ability to correctly detect subtle expressions of sadness, with greater change observed in the placebo relative to the duloxetine group. These effects occurred in the absence of changes in mood. Our preliminary findings require replication, but complement recent evidence that sadness recognition is a therapeutic target in major depression, and a mechanism through which SNRIs could resolve negative biases in emotion processing to achieve therapeutic effects. PMID:25759400

  15. Autonomous learning in gesture recognition by using lobe component analysis

    NASA Astrophysics Data System (ADS)

    Lu, Jian; Weng, Juyang

    2007-02-01

    Gesture recognition is a new human-machine interface method implemented by pattern recognition(PR).In order to assure robot safety when gesture is used in robot control, it is required to implement the interface reliably and accurately. Similar with other PR applications, 1) feature selection (or model establishment) and 2) training from samples, affect the performance of gesture recognition largely. For 1), a simple model with 6 feature points at shoulders, elbows, and hands, is established. The gestures to be recognized are restricted to still arm gestures, and the movement of arms is not considered. These restrictions are to reduce the misrecognition, but are not so unreasonable. For 2), a new biological network method, called lobe component analysis(LCA), is used in unsupervised learning. Lobe components, corresponding to high-concentrations in probability of the neuronal input, are orientation selective cells follow Hebbian rule and lateral inhibition. Due to the advantage of LCA method for balanced learning between global and local features, large amount of samples can be used in learning efficiently.

  16. Higher-order neural network software for distortion invariant object recognition

    NASA Technical Reports Server (NTRS)

    Reid, Max B.; Spirkovska, Lilly

    1991-01-01

    The state-of-the-art in pattern recognition for such applications as automatic target recognition and industrial robotic vision relies on digital image processing. We present a higher-order neural network model and software which performs the complete feature extraction-pattern classification paradigm required for automatic pattern recognition. Using a third-order neural network, we demonstrate complete, 100 percent accurate invariance to distortions of scale, position, and in-plate rotation. In a higher-order neural network, feature extraction is built into the network, and does not have to be learned. Only the relatively simple classification step must be learned. This is key to achieving very rapid training. The training set is much smaller than with standard neural network software because the higher-order network only has to be shown one view of each object to be learned, not every possible view. The software and graphical user interface run on any Sun workstation. Results of the use of the neural software in autonomous robotic vision systems are presented. Such a system could have extensive application in robotic manufacturing.

  17. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

    PubMed

    Whitford, Paul C; Blanchard, Scott C; Cate, Jamie H D; Sanbonmatsu, Karissa Y

    2013-01-01

    Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

  18. Sensitivity and specificity of a digit symbol recognition trial in the identification of response bias.

    PubMed

    Kim, Nancy; Boone, Kyle B; Victor, Tara; Lu, Po; Keatinge, Carolyn; Mitchell, Cary

    2010-08-01

    Recently published practice standards recommend that multiple effort indicators be interspersed throughout neuropsychological evaluations to assess for response bias, which is most efficiently accomplished through use of effort indicators from standard cognitive tests already included in test batteries. The present study examined the utility of a timed recognition trial added to standard administration of the WAIS-III Digit Symbol subtest in a large sample of "real world" noncredible patients (n=82) as compared with credible neuropsychology clinic patients (n=89). Scores from the recognition trial were more sensitive in identifying poor effort than were standard Digit Symbol scores, and use of an equation incorporating Digit Symbol Age-Corrected Scaled Scores plus accuracy and time scores from the recognition trial was associated with nearly 80% sensitivity at 88.7% specificity. Thus, inclusion of a brief recognition trial to Digit Symbol administration has the potential to provide accurate assessment of response bias.

  19. Expression intensity, gender and facial emotion recognition: Women recognize only subtle facial emotions better than men.

    PubMed

    Hoffmann, Holger; Kessler, Henrik; Eppel, Tobias; Rukavina, Stefanie; Traue, Harald C

    2010-11-01

    Two experiments were conducted in order to investigate the effect of expression intensity on gender differences in the recognition of facial emotions. The first experiment compared recognition accuracy between female and male participants when emotional faces were shown with full-blown (100% emotional content) or subtle expressiveness (50%). In a second experiment more finely grained analyses were applied in order to measure recognition accuracy as a function of expression intensity (40%-100%). The results show that although women were more accurate than men in recognizing subtle facial displays of emotion, there was no difference between male and female participants when recognizing highly expressive stimuli. Copyright © 2010 Elsevier B.V. All rights reserved.

  20. Optical Pattern Recognition

    NASA Astrophysics Data System (ADS)

    Yu, Francis T. S.; Jutamulia, Suganda

    2008-10-01

    Contributors; Preface; 1. Pattern recognition with optics Francis T. S. Yu and Don A. Gregory; 2. Hybrid neural networks for nonlinear pattern recognition Taiwei Lu; 3. Wavelets, optics, and pattern recognition Yao Li and Yunglong Sheng; 4. Applications of the fractional Fourier transform to optical pattern recognition David Mendlovic, Zeev Zalesky and Haldum M. Oxaktas; 5. Optical implementation of mathematical morphology Tien-Hsin Chao; 6. Nonlinear optical correlators with improved discrimination capability for object location and recognition Leonid P. Yaroslavsky; 7. Distortion-invariant quadratic filters Gregory Gheen; 8. Composite filter synthesis as applied to pattern recognition Shizhou Yin and Guowen Lu; 9. Iterative procedures in electro-optical pattern recognition Joseph Shamir; 10. Optoelectronic hybrid system for three-dimensional object pattern recognition Guoguang Mu, Mingzhe Lu and Ying Sun; 11. Applications of photrefractive devices in optical pattern recognition Ziangyang Yang; 12. Optical pattern recognition with microlasers Eung-Gi Paek; 13. Optical properties and applications of bacteriorhodopsin Q. Wang Song and Yu-He Zhang; 14. Liquid-crystal spatial light modulators Aris Tanone and Suganda Jutamulia; 15. Representations of fully complex functions on real-time spatial light modulators Robert W. Cohn and Laurence G. Hassbrook; Index.

  1. The relationship between change detection and recognition of centrally attended objects in motion pictures.

    PubMed

    Angelone, Bonnie L; Levin, Daniel T; Simons, Daniel J

    2003-01-01

    Observers typically detect changes to central objects more readily than changes to marginal objects, but they sometimes miss changes to central, attended objects as well. However, even if observers do not report such changes, they may be able to recognize the changed object. In three experiments we explored change detection and recognition memory for several types of changes to central objects in motion pictures. Observers who failed to detect a change still performed at above chance levels on a recognition task in almost all conditions. In addition, observers who detected the change were no more accurate in their recognition than those who did not detect the change. Despite large differences in the detectability of changes across conditions, those observers who missed the change did not vary in their ability to recognize the changing object.

  2. Automatic anatomy recognition in whole-body PET/CT images

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

    Wang, Huiqian; Udupa, Jayaram K., E-mail: jay@mail.med.upenn.edu; Odhner, Dewey

    Purpose: Whole-body positron emission tomography/computed tomography (PET/CT) has become a standard method of imaging patients with various disease conditions, especially cancer. Body-wide accurate quantification of disease burden in PET/CT images is important for characterizing lesions, staging disease, prognosticating patient outcome, planning treatment, and evaluating disease response to therapeutic interventions. However, body-wide anatomy recognition in PET/CT is a critical first step for accurately and automatically quantifying disease body-wide, body-region-wise, and organwise. This latter process, however, has remained a challenge due to the lower quality of the anatomic information portrayed in the CT component of this imaging modality and the paucity ofmore » anatomic details in the PET component. In this paper, the authors demonstrate the adaptation of a recently developed automatic anatomy recognition (AAR) methodology [Udupa et al., “Body-wide hierarchical fuzzy modeling, recognition, and delineation of anatomy in medical images,” Med. Image Anal. 18, 752–771 (2014)] to PET/CT images. Their goal was to test what level of object localization accuracy can be achieved on PET/CT compared to that achieved on diagnostic CT images. Methods: The authors advance the AAR approach in this work in three fronts: (i) from body-region-wise treatment in the work of Udupa et al. to whole body; (ii) from the use of image intensity in optimal object recognition in the work of Udupa et al. to intensity plus object-specific texture properties, and (iii) from the intramodality model-building-recognition strategy to the intermodality approach. The whole-body approach allows consideration of relationships among objects in different body regions, which was previously not possible. Consideration of object texture allows generalizing the previous optimal threshold-based fuzzy model recognition method from intensity images to any derived fuzzy membership image, and in the

  3. Adults' strategies for simple addition and multiplication: verbal self-reports and the operand recognition paradigm.

    PubMed

    Metcalfe, Arron W S; Campbell, Jamie I D

    2011-05-01

    Accurate measurement of cognitive strategies is important in diverse areas of psychological research. Strategy self-reports are a common measure, but C. Thevenot, M. Fanget, and M. Fayol (2007) proposed a more objective method to distinguish different strategies in the context of mental arithmetic. In their operand recognition paradigm, speed of recognition memory for problem operands after solving a problem indexes strategy (e.g., direct memory retrieval vs. a procedural strategy). Here, in 2 experiments, operand recognition time was the same following simple addition or multiplication, but, consistent with a wide variety of previous research, strategy reports indicated much greater use of procedures (e.g., counting) for addition than multiplication. Operation, problem size (e.g., 2 + 3 vs. 8 + 9), and operand format (digits vs. words) had interactive effects on reported procedure use that were not reflected in recognition performance. Regression analyses suggested that recognition time was influenced at least as much by the relative difficulty of the preceding problem as by the strategy used. The findings indicate that the operand recognition paradigm is not a reliable substitute for strategy reports and highlight the potential impact of difficulty-related carryover effects in sequential cognitive tasks.

  4. A new selective developmental deficit: Impaired object recognition with normal face recognition.

    PubMed

    Germine, Laura; Cashdollar, Nathan; Düzel, Emrah; Duchaine, Bradley

    2011-05-01

    Studies of developmental deficits in face recognition, or developmental prosopagnosia, have shown that individuals who have not suffered brain damage can show face recognition impairments coupled with normal object recognition (Duchaine and Nakayama, 2005; Duchaine et al., 2006; Nunn et al., 2001). However, no developmental cases with the opposite dissociation - normal face recognition with impaired object recognition - have been reported. The existence of a case of non-face developmental visual agnosia would indicate that the development of normal face recognition mechanisms does not rely on the development of normal object recognition mechanisms. To see whether a developmental variant of non-face visual object agnosia exists, we conducted a series of web-based object and face recognition tests to screen for individuals showing object recognition memory impairments but not face recognition impairments. Through this screening process, we identified AW, an otherwise normal 19-year-old female, who was then tested in the lab on face and object recognition tests. AW's performance was impaired in within-class visual recognition memory across six different visual categories (guns, horses, scenes, tools, doors, and cars). In contrast, she scored normally on seven tests of face recognition, tests of memory for two other object categories (houses and glasses), and tests of recall memory for visual shapes. Testing confirmed that her impairment was not related to a general deficit in lower-level perception, object perception, basic-level recognition, or memory. AW's results provide the first neuropsychological evidence that recognition memory for non-face visual object categories can be selectively impaired in individuals without brain damage or other memory impairment. These results indicate that the development of recognition memory for faces does not depend on intact object recognition memory and provide further evidence for category-specific dissociations in visual

  5. Further insight into self-face recognition in schizophrenia patients: Why ambiguity matters.

    PubMed

    Bortolon, Catherine; Capdevielle, Delphine; Salesse, Robin N; Raffard, Stephane

    2016-03-01

    Although some studies reported specifically self-face processing deficits in patients with schizophrenia disorder (SZ), it remains unclear whether these deficits rather reflect a more global face processing deficit. Contradictory results are probably due to the different methodologies employed and the lack of control of other confounding factors. Moreover, no study has so far evaluated possible daily life self-face recognition difficulties in SZ. Therefore, our primary objective was to investigate self-face recognition in patients suffering from SZ compared to healthy controls (HC) using an "objective measure" (reaction time and accuracy) and a "subjective measure" (self-report of daily self-face recognition difficulties). Twenty-four patients with SZ and 23 HC performed a self-face recognition task and completed a questionnaire evaluating daily difficulties in self-face recognition. Recognition task material consisted in three different faces (the own, a famous and an unknown) being morphed in steps of 20%. Results showed that SZ were overall slower than HC regardless of the face identity, but less accurate only for the faces containing 60%-40% morphing. Moreover, SZ and HC reported a similar amount of daily problems with self/other face recognition. No significant correlations were found between objective and subjective measures (p > 0.05). The small sample size and relatively mild severity of psychopathology does not allow us to generalize our results. These results suggest that: (1) patients with SZ are as capable of recognizing their own face as HC, although they are susceptible to ambiguity; (2) there are far less self recognition deficits in schizophrenia patients than previously postulated. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Ordinal feature selection for iris and palmprint recognition.

    PubMed

    Sun, Zhenan; Wang, Libin; Tan, Tieniu

    2014-09-01

    Ordinal measures have been demonstrated as an effective feature representation model for iris and palmprint recognition. However, ordinal measures are a general concept of image analysis and numerous variants with different parameter settings, such as location, scale, orientation, and so on, can be derived to construct a huge feature space. This paper proposes a novel optimization formulation for ordinal feature selection with successful applications to both iris and palmprint recognition. The objective function of the proposed feature selection method has two parts, i.e., misclassification error of intra and interclass matching samples and weighted sparsity of ordinal feature descriptors. Therefore, the feature selection aims to achieve an accurate and sparse representation of ordinal measures. And, the optimization subjects to a number of linear inequality constraints, which require that all intra and interclass matching pairs are well separated with a large margin. Ordinal feature selection is formulated as a linear programming (LP) problem so that a solution can be efficiently obtained even on a large-scale feature pool and training database. Extensive experimental results demonstrate that the proposed LP formulation is advantageous over existing feature selection methods, such as mRMR, ReliefF, Boosting, and Lasso for biometric recognition, reporting state-of-the-art accuracy on CASIA and PolyU databases.

  7. Fashioning the Face: Sensorimotor Simulation Contributes to Facial Expression Recognition.

    PubMed

    Wood, Adrienne; Rychlowska, Magdalena; Korb, Sebastian; Niedenthal, Paula

    2016-03-01

    When we observe a facial expression of emotion, we often mimic it. This automatic mimicry reflects underlying sensorimotor simulation that supports accurate emotion recognition. Why this is so is becoming more obvious: emotions are patterns of expressive, behavioral, physiological, and subjective feeling responses. Activation of one component can therefore automatically activate other components. When people simulate a perceived facial expression, they partially activate the corresponding emotional state in themselves, which provides a basis for inferring the underlying emotion of the expresser. We integrate recent evidence in favor of a role for sensorimotor simulation in emotion recognition. We then connect this account to a domain-general understanding of how sensory information from multiple modalities is integrated to generate perceptual predictions in the brain. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Double-Windows-Based Motion Recognition in Multi-Floor Buildings Assisted by a Built-In Barometer.

    PubMed

    Liu, Maolin; Li, Huaiyu; Wang, Yuan; Li, Fei; Chen, Xiuwan

    2018-04-01

    Accelerometers, gyroscopes and magnetometers in smartphones are often used to recognize human motions. Since it is difficult to distinguish between vertical motions and horizontal motions in the data provided by these built-in sensors, the vertical motion recognition accuracy is relatively low. The emergence of a built-in barometer in smartphones improves the accuracy of motion recognition in the vertical direction. However, there is a lack of quantitative analysis and modelling of the barometer signals, which is the basis of barometer's application to motion recognition, and a problem of imbalanced data also exists. This work focuses on using the barometers inside smartphones for vertical motion recognition in multi-floor buildings through modelling and feature extraction of pressure signals. A novel double-windows pressure feature extraction method, which adopts two sliding time windows of different length, is proposed to balance recognition accuracy and response time. Then, a random forest classifier correlation rule is further designed to weaken the impact of imbalanced data on recognition accuracy. The results demonstrate that the recognition accuracy can reach 95.05% when pressure features and the improved random forest classifier are adopted. Specifically, the recognition accuracy of the stair and elevator motions is significantly improved with enhanced response time. The proposed approach proves effective and accurate, providing a robust strategy for increasing accuracy of vertical motions.

  9. Temporal Sensitivity Measured Shortly After Cochlear Implantation Predicts 6-Month Speech Recognition Outcome.

    PubMed

    Erb, Julia; Ludwig, Alexandra Annemarie; Kunke, Dunja; Fuchs, Michael; Obleser, Jonas

    2018-04-24

    Psychoacoustic tests assessed shortly after cochlear implantation are useful predictors of the rehabilitative speech outcome. While largely independent, both spectral and temporal resolution tests are important to provide an accurate prediction of speech recognition. However, rapid tests of temporal sensitivity are currently lacking. Here, we propose a simple amplitude modulation rate discrimination (AMRD) paradigm that is validated by predicting future speech recognition in adult cochlear implant (CI) patients. In 34 newly implanted patients, we used an adaptive AMRD paradigm, where broadband noise was modulated at the speech-relevant rate of ~4 Hz. In a longitudinal study, speech recognition in quiet was assessed using the closed-set Freiburger number test shortly after cochlear implantation (t0) as well as the open-set Freiburger monosyllabic word test 6 months later (t6). Both AMRD thresholds at t0 (r = -0.51) and speech recognition scores at t0 (r = 0.56) predicted speech recognition scores at t6. However, AMRD and speech recognition at t0 were uncorrelated, suggesting that those measures capture partially distinct perceptual abilities. A multiple regression model predicting 6-month speech recognition outcome with deafness duration and speech recognition at t0 improved from adjusted R = 0.30 to adjusted R = 0.44 when AMRD threshold was added as a predictor. These findings identify AMRD thresholds as a reliable, nonredundant predictor above and beyond established speech tests for CI outcome. This AMRD test could potentially be developed into a rapid clinical temporal-resolution test to be integrated into the postoperative test battery to improve the reliability of speech outcome prognosis.

  10. 3D palmprint data fast acquisition and recognition

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoxu; Huang, Shujun; Gao, Nan; Zhang, Zonghua

    2014-11-01

    This paper presents a fast 3D (Three-Dimension) palmprint capturing system and develops an efficient 3D palmprint feature extraction and recognition method. In order to fast acquire accurate 3D shape and texture of palmprint, a DLP projector triggers a CCD camera to realize synchronization. By generating and projecting green fringe pattern images onto the measured palm surface, 3D palmprint data are calculated from the fringe pattern images. The periodic feature vector can be derived from the calculated 3D palmprint data, so undistorted 3D biometrics is obtained. Using the obtained 3D palmprint data, feature matching test have been carried out by Gabor filter, competition rules and the mean curvature. Experimental results on capturing 3D palmprint show that the proposed acquisition method can fast get 3D shape information of palmprint. Some initial experiments on recognition show the proposed method is efficient by using 3D palmprint data.

  11. Gender Differences in the Recognition of Vocal Emotions

    PubMed Central

    Lausen, Adi; Schacht, Annekathrin

    2018-01-01

    The conflicting findings from the few studies conducted with regard to gender differences in the recognition of vocal expressions of emotion have left the exact nature of these differences unclear. Several investigators have argued that a comprehensive understanding of gender differences in vocal emotion recognition can only be achieved by replicating these studies while accounting for influential factors such as stimulus type, gender-balanced samples, number of encoders, decoders, and emotional categories. This study aimed to account for these factors by investigating whether emotion recognition from vocal expressions differs as a function of both listeners' and speakers' gender. A total of N = 290 participants were randomly and equally allocated to two groups. One group listened to words and pseudo-words, while the other group listened to sentences and affect bursts. Participants were asked to categorize the stimuli with respect to the expressed emotions in a fixed-choice response format. Overall, females were more accurate than males when decoding vocal emotions, however, when testing for specific emotions these differences were small in magnitude. Speakers' gender had a significant impact on how listeners' judged emotions from the voice. The group listening to words and pseudo-words had higher identification rates for emotions spoken by male than by female actors, whereas in the group listening to sentences and affect bursts the identification rates were higher when emotions were uttered by female than male actors. The mixed pattern for emotion-specific effects, however, indicates that, in the vocal channel, the reliability of emotion judgments is not systematically influenced by speakers' gender and the related stereotypes of emotional expressivity. Together, these results extend previous findings by showing effects of listeners' and speakers' gender on the recognition of vocal emotions. They stress the importance of distinguishing these factors to explain

  12. Examining Event-Related Potential (ERP) correlates of decision bias in recognition memory judgments.

    PubMed

    Hill, Holger; Windmann, Sabine

    2014-01-01

    Memory judgments can be based on accurate memory information or on decision bias (the tendency to report that an event is part of episodic memory when one is in fact unsure). Event related potentials (ERP) correlates are important research tools for elucidating the dynamics underlying memory judgments but so far have been established only for investigations of accurate old/new discrimination. To identify the ERP correlates of bias, and observe how these interact with ERP correlates of memory, we conducted three experiments that manipulated decision bias within participants via instructions during recognition memory tests while their ERPs were recorded. In Experiment 1, the bias manipulation was performed between blocks of trials (automatized bias) and compared to trial-by-trial shifts of bias in accord with an external cue (flexibly controlled bias). In Experiment 2, the bias manipulation was performed at two different levels of accurate old/new discrimination as the memory strength of old (studied) items was varied. In Experiment 3, the bias manipulation was added to another, bottom-up driven manipulation of bias induced via familiarity. In the first two Experiments, and in the low familiarity condition of Experiment 3, we found evidence of an early frontocentral ERP component at 320 ms poststimulus (the FN320) that was sensitive to the manipulation of bias via instruction, with more negative amplitudes indexing more liberal bias. By contrast, later during the trial (500-700 ms poststimulus), bias effects interacted with old/new effects across all three experiments. Results suggest that the decision criterion is typically activated early during recognition memory trials, and is integrated with retrieved memory signals and task-specific processing demands later during the trial. More generally, the findings demonstrate how ERPs can help to specify the dynamics of recognition memory processes under top-down and bottom-up controlled retrieval conditions.

  13. Examining Event-Related Potential (ERP) Correlates of Decision Bias in Recognition Memory Judgments

    PubMed Central

    Hill, Holger; Windmann, Sabine

    2014-01-01

    Memory judgments can be based on accurate memory information or on decision bias (the tendency to report that an event is part of episodic memory when one is in fact unsure). Event related potentials (ERP) correlates are important research tools for elucidating the dynamics underlying memory judgments but so far have been established only for investigations of accurate old/new discrimination. To identify the ERP correlates of bias, and observe how these interact with ERP correlates of memory, we conducted three experiments that manipulated decision bias within participants via instructions during recognition memory tests while their ERPs were recorded. In Experiment 1, the bias manipulation was performed between blocks of trials (automatized bias) and compared to trial-by-trial shifts of bias in accord with an external cue (flexibly controlled bias). In Experiment 2, the bias manipulation was performed at two different levels of accurate old/new discrimination as the memory strength of old (studied) items was varied. In Experiment 3, the bias manipulation was added to another, bottom-up driven manipulation of bias induced via familiarity. In the first two Experiments, and in the low familiarity condition of Experiment 3, we found evidence of an early frontocentral ERP component at 320 ms poststimulus (the FN320) that was sensitive to the manipulation of bias via instruction, with more negative amplitudes indexing more liberal bias. By contrast, later during the trial (500–700 ms poststimulus), bias effects interacted with old/new effects across all three experiments. Results suggest that the decision criterion is typically activated early during recognition memory trials, and is integrated with retrieved memory signals and task-specific processing demands later during the trial. More generally, the findings demonstrate how ERPs can help to specify the dynamics of recognition memory processes under top-down and bottom-up controlled retrieval conditions. PMID

  14. Quick acquisition and recognition method for the beacon in deep space optical communications.

    PubMed

    Wang, Qiang; Liu, Yuefei; Ma, Jing; Tan, Liying; Yu, Siyuan; Li, Changjiang

    2016-12-01

    In deep space optical communications, it is very difficult to acquire the beacon given the long communication distance. Acquisition efficiency is essential for establishing and holding the optical communication link. Here we proposed a quick acquisition and recognition method for the beacon in deep optical communications based on the characteristics of the deep optical link. To identify the beacon from the background light efficiently, we utilized the maximum similarity between the collecting image and the reference image for accurate recognition and acquisition of the beacon in the area of uncertainty. First, the collecting image and the reference image were processed by Fourier-Mellin. Second, image sampling and image matching were applied for the accurate positioning of the beacon. Finally, the field programmable gate array (FPGA)-based system was used to verify and realize this method. The experimental results showed that the acquisition time for the beacon was as fast as 8.1s. Future application of this method in the system design of deep optical communication will be beneficial.

  15. Do people have insight into their face recognition abilities?

    PubMed

    Palermo, Romina; Rossion, Bruno; Rhodes, Gillian; Laguesse, Renaud; Tez, Tolga; Hall, Bronwyn; Albonico, Andrea; Malaspina, Manuela; Daini, Roberta; Irons, Jessica; Al-Janabi, Shahd; Taylor, Libby C; Rivolta, Davide; McKone, Elinor

    2017-02-01

    Diagnosis of developmental or congenital prosopagnosia (CP) involves self-report of everyday face recognition difficulties, which are corroborated with poor performance on behavioural tests. This approach requires accurate self-evaluation. We examine the extent to which typical adults have insight into their face recognition abilities across four experiments involving nearly 300 participants. The experiments used five tests of face recognition ability: two that tap into the ability to learn and recognize previously unfamiliar faces [the Cambridge Face Memory Test, CFMT; Duchaine, B., & Nakayama, K. (2006). The Cambridge Face Memory Test: Results for neurologically intact individuals and an investigation of its validity using inverted face stimuli and prosopagnosic participants. Neuropsychologia, 44(4), 576-585. doi:10.1016/j.neuropsychologia.2005.07.001; and a newly devised test based on the CFMT but where the study phases involve watching short movies rather than viewing static faces-the CFMT-Films] and three that tap face matching [Benton Facial Recognition Test, BFRT; Benton, A., Sivan, A., Hamsher, K., Varney, N., & Spreen, O. (1983). Contribution to neuropsychological assessment. New York: Oxford University Press; and two recently devised sequential face matching tests]. Self-reported ability was measured with the 15-item Kennerknecht et al. questionnaire [Kennerknecht, I., Ho, N. Y., & Wong, V. C. (2008). Prevalence of hereditary prosopagnosia (HPA) in Hong Kong Chinese population. American Journal of Medical Genetics Part A, 146A(22), 2863-2870. doi:10.1002/ajmg.a.32552]; two single-item questions assessing face recognition ability; and a new 77-item meta-cognition questionnaire. Overall, we find that adults with typical face recognition abilities have only modest insight into their ability to recognize faces on behavioural tests. In a fifth experiment, we assess self-reported face recognition ability in people with CP and find that some people who expect to

  16. Gender differences in emotion recognition: Impact of sensory modality and emotional category.

    PubMed

    Lambrecht, Lena; Kreifelts, Benjamin; Wildgruber, Dirk

    2014-04-01

    Results from studies on gender differences in emotion recognition vary, depending on the types of emotion and the sensory modalities used for stimulus presentation. This makes comparability between different studies problematic. This study investigated emotion recognition of healthy participants (N = 84; 40 males; ages 20 to 70 years), using dynamic stimuli, displayed by two genders in three different sensory modalities (auditory, visual, audio-visual) and five emotional categories. The participants were asked to categorise the stimuli on the basis of their nonverbal emotional content (happy, alluring, neutral, angry, and disgusted). Hit rates and category selection biases were analysed. Women were found to be more accurate in recognition of emotional prosody. This effect was partially mediated by hearing loss for the frequency of 8,000 Hz. Moreover, there was a gender-specific selection bias for alluring stimuli: Men, as compared to women, chose "alluring" more often when a stimulus was presented by a woman as compared to a man.

  17. Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

    PubMed Central

    Ishida, Hisashi; Matsumoto, Atsushi

    2014-01-01

    To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

  18. Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.

    PubMed

    Ishida, Hisashi; Matsumoto, Atsushi

    2014-01-01

    To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.

  19. Sad people are more accurate at expression identification with a smaller own-ethnicity bias than happy people.

    PubMed

    Hills, Peter J; Hill, Dominic M

    2017-07-12

    Sad individuals perform more accurately at face identity recognition (Hills, Werno, & Lewis, 2011), possibly because they scan more of the face during encoding. During expression identification tasks, sad individuals do not fixate on the eyes as much as happier individuals (Wu, Pu, Allen, & Pauli, 2012). Fixating on features other than the eyes leads to a reduced own-ethnicity bias (Hills & Lewis, 2006). This background indicates that sad individuals would not view the eyes as much as happy individuals and this would result in improved expression recognition and a reduced own-ethnicity bias. This prediction was tested using an expression identification task, with eye tracking. We demonstrate that sad-induced participants show enhanced expression recognition and a reduced own-ethnicity bias than happy-induced participants due to scanning more facial features. We conclude that mood affects eye movements and face encoding by causing a wider sampling strategy and deeper encoding of facial features diagnostic for expression identification.

  20. Emotion recognition in preschool children: associations with maternal depression and early parenting.

    PubMed

    Kujawa, Autumn; Dougherty, Lea; Durbin, C Emily; Laptook, Rebecca; Torpey, Dana; Klein, Daniel N

    2014-02-01

    Emotion knowledge in childhood has been shown to predict social functioning and psychological well-being, but relatively little is known about parental factors that influence its development in early childhood. There is some evidence that both parenting behavior and maternal depression are associated with emotion recognition, but previous research has only examined these factors independently. The current study assessed auditory and visual emotion recognition ability among a large sample of preschool children to examine typical emotion recognition skills in children of this age, as well as the independent and interactive effects of maternal and paternal depression and negative parenting (i.e., hostility and intrusiveness). Results indicated that children were most accurate at identifying happy emotional expressions. The lowest accuracy was observed for neutral expressions. A significant interaction was found between maternal depression and negative parenting behavior: children with a maternal history of depression were particularly sensitive to the negative effects of maladaptive parenting behavior on emotion recognition ability. No significant effects were found for paternal depression. These results highlight the importance of examining the effects of multiple interacting factors on children's emotional development and provide suggestions for identifying children for targeted preventive interventions.

  1. Predicting the Accuracy of Facial Affect Recognition: The Interaction of Child Maltreatment and Intellectual Functioning

    ERIC Educational Resources Information Center

    Shenk, Chad E.; Putnam, Frank W.; Noll, Jennie G.

    2013-01-01

    Previous research demonstrates that both child maltreatment and intellectual performance contribute uniquely to the accurate identification of facial affect by children and adolescents. The purpose of this study was to extend this research by examining whether child maltreatment affects the accuracy of facial recognition differently at varying…

  2. Postencoding cognitive processes in the cross-race effect: Categorization and individuation during face recognition.

    PubMed

    Ho, Michael R; Pezdek, Kathy

    2016-06-01

    The cross-race effect (CRE) describes the finding that same-race faces are recognized more accurately than cross-race faces. According to social-cognitive theories of the CRE, processes of categorization and individuation at encoding account for differential recognition of same- and cross-race faces. Recent face memory research has suggested that similar but distinct categorization and individuation processes also occur postencoding, at recognition. Using a divided-attention paradigm, in Experiments 1A and 1B we tested and confirmed the hypothesis that distinct postencoding categorization and individuation processes occur during the recognition of same- and cross-race faces. Specifically, postencoding configural divided-attention tasks impaired recognition accuracy more for same-race than for cross-race faces; on the other hand, for White (but not Black) participants, postencoding featural divided-attention tasks impaired recognition accuracy more for cross-race than for same-race faces. A social categorization paradigm used in Experiments 2A and 2B tested the hypothesis that the postencoding in-group or out-group social orientation to faces affects categorization and individuation processes during the recognition of same-race and cross-race faces. Postencoding out-group orientation to faces resulted in categorization for White but not for Black participants. This was evidenced by White participants' impaired recognition accuracy for same-race but not for cross-race out-group faces. Postencoding in-group orientation to faces had no effect on recognition accuracy for either same-race or cross-race faces. The results of Experiments 2A and 2B suggest that this social orientation facilitates White but not Black participants' individuation and categorization processes at recognition. Models of recognition memory for same-race and cross-race faces need to account for processing differences that occur at both encoding and recognition.

  3. [Application of image recognition technology in census of national traditional Chinese medicine resources].

    PubMed

    Zhang, Xiao-Bo; Ge, Xiao-Guang; Jin, Yan; Shi, Ting-Ting; Wang, Hui; Li, Meng; Jing, Zhi-Xian; Guo, Lan-Ping; Huang, Lu-Qi

    2017-11-01

    With the development of computer and image processing technology, image recognition technology has been applied to the national medicine resources census work at all stages.Among them: ①In the preparatory work, in order to establish a unified library of traditional Chinese medicine resources, using text recognition technology based on paper materials, be the assistant in the digitalization of various categories related to Chinese medicine resources; to determine the representative area and plots of the survey from each census team, based on the satellite remote sensing image and vegetation map and other basic data, using remote sensing image classification and other technical methods to assist in determining the key investigation area. ②In the process of field investigation, to obtain the planting area of Chinese herbal medicine was accurately, we use the decision tree model, spectral feature and object-oriented method were used to assist the regional identification and area estimation of Chinese medicinal materials.③In the process of finishing in the industry, in order to be able to relatively accurately determine the type of Chinese medicine resources in the region, based on the individual photos of the plant, the specimens and the name of the use of image recognition techniques, to assist the statistical summary of the types of traditional Chinese medicine resources. ④In the application of the results of transformation, based on the pharmaceutical resources and individual samples of medicinal herbs, the development of Chinese medicine resources to identify APP and authentic herbs 3D display system, assisted the identification of Chinese medicine resources and herbs identification characteristics. The introduction of image recognition technology in the census of Chinese medicine resources, assisting census personnel to carry out related work, not only can reduce the workload of the artificial, improve work efficiency, but also improve the census results

  4. Cognitive mechanisms of false facial recognition in older adults.

    PubMed

    Edmonds, Emily C; Glisky, Elizabeth L; Bartlett, James C; Rapcsak, Steven Z

    2012-03-01

    Older adults show elevated false alarm rates on recognition memory tests involving faces in comparison to younger adults. It has been proposed that this age-related increase in false facial recognition reflects a deficit in recollection and a corresponding increase in the use of familiarity when making memory decisions. To test this hypothesis, we examined the performance of 40 older adults and 40 younger adults on a face recognition memory paradigm involving three different types of lures with varying levels of familiarity. A robust age effect was found, with older adults demonstrating a markedly heightened false alarm rate in comparison to younger adults for "familiarized lures" that were exact repetitions of faces encountered earlier in the experiment, but outside the study list, and therefore required accurate recollection of contextual information to reject. By contrast, there were no age differences in false alarms to "conjunction lures" that recombined parts of study list faces, or to entirely new faces. Overall, the pattern of false recognition errors observed in older adults was consistent with excessive reliance on a familiarity-based response strategy. Specifically, in the absence of recollection older adults appeared to base their memory decisions on item familiarity, as evidenced by a linear increase in false alarm rates with increasing familiarity of the lures. These findings support the notion that automatic memory processes such as familiarity remain invariant with age, while more controlled memory processes such as recollection show age-related decline.

  5. Recognition errors suggest fast familiarity and slow recollection in rhesus monkeys

    PubMed Central

    Basile, Benjamin M.; Hampton, Robert R.

    2013-01-01

    One influential model of recognition posits two underlying memory processes: recollection, which is detailed but relatively slow, and familiarity, which is quick but lacks detail. Most of the evidence for this dual-process model in nonhumans has come from analyses of receiver operating characteristic (ROC) curves in rats, but whether ROC analyses can demonstrate dual processes has been repeatedly challenged. Here, we present independent converging evidence for the dual-process model from analyses of recognition errors made by rhesus monkeys. Recognition choices were made in three different ways depending on processing duration. Short-latency errors were disproportionately false alarms to familiar lures, suggesting control by familiarity. Medium-latency responses were less likely to be false alarms and were more accurate, suggesting onset of a recollective process that could correctly reject familiar lures. Long-latency responses were guesses. A response deadline increased false alarms, suggesting that limiting processing time weakened the contribution of recollection and strengthened the contribution of familiarity. Together, these findings suggest fast familiarity and slow recollection in monkeys, that monkeys use a “recollect to reject” strategy to countermand false familiarity, and that primate recognition performance is well-characterized by a dual-process model consisting of recollection and familiarity. PMID:23864646

  6. Impairment in the recognition of emotion across different media following traumatic brain injury.

    PubMed

    Williams, Claire; Wood, Rodger Ll

    2010-02-01

    The current study examined emotion recognition following traumatic brain injury (TBI) and examined whether performance differed according to the affective valence and type of media presentation of the stimuli. A total of 64 patients with TBI and matched controls completed the Emotion Evaluation Test (EET) and Ekman 60 Faces Test (E-60-FT). Patients with TBI also completed measures of information processing and verbal ability. Results revealed that the TBI group were significantly impaired compared to controls when recognizing emotion on the EET and E-60-FT. A significant main effect of valence was found in both groups, with poor recognition of negative emotions. However, the difference between the recognition of positive and negative emotions was larger in the TBI group. The TBI group were also more accurate recognizing emotion displayed in audiovisual media (EET) than that displayed in still media (E-60-FT). No significant relationship was obtained between emotion recognition tasks and information-processing speed. A significant positive relationship was found between the E-60-FT and one measure of verbal ability. These findings support models of emotion that specify separate neurological pathways for certain emotions and different media and confirm that patients with TBI are vulnerable to experiencing emotion recognition difficulties.

  7. A unified framework for gesture recognition and spatiotemporal gesture segmentation.

    PubMed

    Alon, Jonathan; Athitsos, Vassilis; Yuan, Quan; Sclaroff, Stan

    2009-09-01

    Within the context of hand gesture recognition, spatiotemporal gesture segmentation is the task of determining, in a video sequence, where the gesturing hand is located and when the gesture starts and ends. Existing gesture recognition methods typically assume either known spatial segmentation or known temporal segmentation, or both. This paper introduces a unified framework for simultaneously performing spatial segmentation, temporal segmentation, and recognition. In the proposed framework, information flows both bottom-up and top-down. A gesture can be recognized even when the hand location is highly ambiguous and when information about when the gesture begins and ends is unavailable. Thus, the method can be applied to continuous image streams where gestures are performed in front of moving, cluttered backgrounds. The proposed method consists of three novel contributions: a spatiotemporal matching algorithm that can accommodate multiple candidate hand detections in every frame, a classifier-based pruning framework that enables accurate and early rejection of poor matches to gesture models, and a subgesture reasoning algorithm that learns which gesture models can falsely match parts of other longer gestures. The performance of the approach is evaluated on two challenging applications: recognition of hand-signed digits gestured by users wearing short-sleeved shirts, in front of a cluttered background, and retrieval of occurrences of signs of interest in a video database containing continuous, unsegmented signing in American Sign Language (ASL).

  8. Age, gender, and puberty influence the development of facial emotion recognition.

    PubMed

    Lawrence, Kate; Campbell, Ruth; Skuse, David

    2015-01-01

    Our ability to differentiate between simple facial expressions of emotion develops between infancy and early adulthood, yet few studies have explored the developmental trajectory of emotion recognition using a single methodology across a wide age-range. We investigated the development of emotion recognition abilities through childhood and adolescence, testing the hypothesis that children's ability to recognize simple emotions is modulated by chronological age, pubertal stage and gender. In order to establish norms, we assessed 478 children aged 6-16 years, using the Ekman-Friesen Pictures of Facial Affect. We then modeled these cross-sectional data in terms of competence in accurate recognition of the six emotions studied, when the positive correlation between emotion recognition and IQ was controlled. Significant linear trends were seen in children's ability to recognize facial expressions of happiness, surprise, fear, and disgust; there was improvement with increasing age. In contrast, for sad and angry expressions there is little or no change in accuracy over the age range 6-16 years; near-adult levels of competence are established by middle-childhood. In a sampled subset, pubertal status influenced the ability to recognize facial expressions of disgust and anger; there was an increase in competence from mid to late puberty, which occurred independently of age. A small female advantage was found in the recognition of some facial expressions. The normative data provided in this study will aid clinicians and researchers in assessing the emotion recognition abilities of children and will facilitate the identification of abnormalities in a skill that is often impaired in neurodevelopmental disorders. If emotion recognition abilities are a good model with which to understand adolescent development, then these results could have implications for the education, mental health provision and legal treatment of teenagers.

  9. Age, gender, and puberty influence the development of facial emotion recognition

    PubMed Central

    Lawrence, Kate; Campbell, Ruth; Skuse, David

    2015-01-01

    Our ability to differentiate between simple facial expressions of emotion develops between infancy and early adulthood, yet few studies have explored the developmental trajectory of emotion recognition using a single methodology across a wide age-range. We investigated the development of emotion recognition abilities through childhood and adolescence, testing the hypothesis that children’s ability to recognize simple emotions is modulated by chronological age, pubertal stage and gender. In order to establish norms, we assessed 478 children aged 6–16 years, using the Ekman-Friesen Pictures of Facial Affect. We then modeled these cross-sectional data in terms of competence in accurate recognition of the six emotions studied, when the positive correlation between emotion recognition and IQ was controlled. Significant linear trends were seen in children’s ability to recognize facial expressions of happiness, surprise, fear, and disgust; there was improvement with increasing age. In contrast, for sad and angry expressions there is little or no change in accuracy over the age range 6–16 years; near-adult levels of competence are established by middle-childhood. In a sampled subset, pubertal status influenced the ability to recognize facial expressions of disgust and anger; there was an increase in competence from mid to late puberty, which occurred independently of age. A small female advantage was found in the recognition of some facial expressions. The normative data provided in this study will aid clinicians and researchers in assessing the emotion recognition abilities of children and will facilitate the identification of abnormalities in a skill that is often impaired in neurodevelopmental disorders. If emotion recognition abilities are a good model with which to understand adolescent development, then these results could have implications for the education, mental health provision and legal treatment of teenagers. PMID:26136697

  10. Pattern Recognition Algorithm for High-Sensitivity Odorant Detection in Unknown Environments

    NASA Technical Reports Server (NTRS)

    Duong, Tuan A.

    2012-01-01

    In a realistic odorant detection application environment, the collected sensory data is a mix of unknown chemicals with unknown concentrations and noise. The identification of the odorants among these mixtures is a challenge in data recognition. In addition, deriving their individual concentrations in the mix is also a challenge. A deterministic analytical model was developed to accurately identify odorants and calculate their concentrations in a mixture with noisy data.

  11. An ERP study of recognition memory for concrete and abstract pictures in school-aged children

    PubMed Central

    Boucher, Olivier; Chouinard-Leclaire, Christine; Muckle, Gina; Westerlund, Alissa; Burden, Matthew J.; Jacobson, Sandra W.; Jacobson, Joseph L.

    2016-01-01

    Recognition memory for concrete, nameable pictures is typically faster and more accurate than for abstract pictures. A dual-coding account for these findings suggests that concrete pictures are processed into verbal and image codes, whereas abstract pictures are encoded in image codes only. Recognition memory relies on two successive and distinct processes, namely familiarity and recollection. Whether these two processes are similarly or differently affected by stimulus concreteness remains unknown. This study examined the effect of picture concreteness on visual recognition memory processes using event-related potentials (ERPs). In a sample of children involved in a longitudinal study, participants (N = 96; mean age = 11.3 years) were assessed on a continuous visual recognition memory task in which half the pictures were easily nameable, everyday concrete objects, and the other half were three-dimensional abstract, sculpture-like objects. Behavioral performance and ERP correlates of familiarity and recollection (respectively, the FN400 and P600 repetition effects) were measured. Behavioral results indicated faster and more accurate identification of concrete pictures as “new” or “old” (i.e., previously displayed) compared to abstract pictures. ERPs were characterised by a larger repetition effect, on the P600 amplitude, for concrete than for abstract images, suggesting a graded recollection process dependant on the type of material to be recollected. Topographic differences were observed within the FN400 latency interval, especially over anterior-inferior electrodes, with the repetition effect more pronounced and localized over the left hemisphere for concrete stimuli, potentially reflecting different neural processes underlying early processing of verbal/semantic and visual material in memory. PMID:27329352

  12. Robust representation and recognition of facial emotions using extreme sparse learning.

    PubMed

    Shojaeilangari, Seyedehsamaneh; Yau, Wei-Yun; Nandakumar, Karthik; Li, Jun; Teoh, Eam Khwang

    2015-07-01

    Recognition of natural emotions from human faces is an interesting topic with a wide range of potential applications, such as human-computer interaction, automated tutoring systems, image and video retrieval, smart environments, and driver warning systems. Traditionally, facial emotion recognition systems have been evaluated on laboratory controlled data, which is not representative of the environment faced in real-world applications. To robustly recognize the facial emotions in real-world natural situations, this paper proposes an approach called extreme sparse learning, which has the ability to jointly learn a dictionary (set of basis) and a nonlinear classification model. The proposed approach combines the discriminative power of extreme learning machine with the reconstruction property of sparse representation to enable accurate classification when presented with noisy signals and imperfect data recorded in natural settings. In addition, this paper presents a new local spatio-temporal descriptor that is distinctive and pose-invariant. The proposed framework is able to achieve the state-of-the-art recognition accuracy on both acted and spontaneous facial emotion databases.

  13. Action and emotion recognition from point light displays: an investigation of gender differences.

    PubMed

    Alaerts, Kaat; Nackaerts, Evelien; Meyns, Pieter; Swinnen, Stephan P; Wenderoth, Nicole

    2011-01-01

    Folk psychology advocates the existence of gender differences in socio-cognitive functions such as 'reading' the mental states of others or discerning subtle differences in body-language. A female advantage has been demonstrated for emotion recognition from facial expressions, but virtually nothing is known about gender differences in recognizing bodily stimuli or body language. The aim of the present study was to investigate potential gender differences in a series of tasks, involving the recognition of distinct features from point light displays (PLDs) depicting bodily movements of a male and female actor. Although recognition scores were considerably high at the overall group level, female participants were more accurate than males in recognizing the depicted actions from PLDs. Response times were significantly higher for males compared to females on PLD recognition tasks involving (i) the general recognition of 'biological motion' versus 'non-biological' (or 'scrambled' motion); or (ii) the recognition of the 'emotional state' of the PLD-figures. No gender differences were revealed for a control test (involving the identification of a color change in one of the dots) and for recognizing the gender of the PLD-figure. In addition, previous findings of a female advantage on a facial emotion recognition test (the 'Reading the Mind in the Eyes Test' (Baron-Cohen, 2001)) were replicated in this study. Interestingly, a strong correlation was revealed between emotion recognition from bodily PLDs versus facial cues. This relationship indicates that inter-individual or gender-dependent differences in recognizing emotions are relatively generalized across facial and bodily emotion perception. Moreover, the tight correlation between a subject's ability to discern subtle emotional cues from PLDs and the subject's ability to basically discriminate biological from non-biological motion provides indications that differences in emotion recognition may - at least to some degree

  14. A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs.

    PubMed

    Diroma, Maria Angela; Lubisco, Paolo; Attimonelli, Marcella

    2016-11-08

    The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Nevertheless, many aspects are still unclear, specifically about the variability of the 22 human mitochondrial transfer RNA (tRNA) genes and their involvement in diseases. The complex enrichment and isolation of tRNAs in vitro leads to an incomplete knowledge of their post-transcriptional modifications and three-dimensional folding, essential for correct tRNA functioning. An accurate annotation of mitochondrial tRNA variants would be definitely useful and appreciated by mitochondrial researchers and clinicians since the most of bioinformatics tools for variant annotation and prioritization available so far cannot shed light on the functional role of tRNA variations. To this aim, we updated our MToolBox pipeline for mitochondrial DNA analysis of high throughput and Sanger sequencing data by integrating tRNA variant annotations in order to identify and characterize relevant variants not only in protein coding regions, but also in tRNA genes. The annotation step in the pipeline now provides detailed information for variants mapping onto the 22 mitochondrial tRNAs. For each mt-tRNA position along the entire genome, the relative tRNA numbering, tRNA type, cloverleaf secondary domains (loops and stems), mature nucleotide and interactions in the three-dimensional folding were reported. Moreover, pathogenicity predictions for tRNA and rRNA variants were retrieved from the literature and integrated within the annotations provided by MToolBox, both in the stand-alone version and web-based tool at the Mitochondrial Disease Sequence Data Resource (MSeqDR) website. All the information available in the annotation step of MToolBox were exploited to generate custom tracks which can be displayed in the GBrowse instance at MSeqDR website. To the best of our knowledge, specific data regarding mitochondrial variants in tRNA genes were

  15. Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

    DOE PAGES

    Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P.

    2014-11-05

    Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islandsmore » in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.« less

  16. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification

    PubMed Central

    Fang, Pengfei; Guo, Min

    2015-01-01

    Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories. PMID:26670257

  17. State Recognition and Visualization of Hoisting Motor of Quayside Container Crane Based on SOFM

    NASA Astrophysics Data System (ADS)

    Yang, Z. Q.; He, P.; Tang, G.; Hu, X.

    2017-07-01

    The neural network structure and algorithm of self-organizing feature map (SOFM) are researched and analysed. The method is applied to state recognition and visualization of the quayside container crane hoisting motor. By using SOFM, the clustering and visualization of attribute reduction of data are carried out, and three kinds motor states are obtained with Root Mean Square(RMS), Impulse Index and Margin Index, and the simulation visualization interface is realized by MATLAB. Through the processing of the sample data, it can realize the accurate identification of the motor state, thus provide better monitoring of the quayside container crane hoisting motor and a new way for the mechanical state recognition.

  18. Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

    PubMed Central

    Whitford, Paul C.; Blanchard, Scott C.; Cate, Jamie H. D.; Sanbonmatsu, Karissa Y.

    2013-01-01

    Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states. PMID:23555233

  19. Speech Recognition for Medical Dictation: Overview in Quebec and Systematic Review.

    PubMed

    Poder, Thomas G; Fisette, Jean-François; Déry, Véronique

    2018-04-03

    Speech recognition is increasingly used in medical reporting. The aim of this article is to identify in the literature the strengths and weaknesses of this technology, as well as barriers to and facilitators of its implementation. A systematic review of systematic reviews was performed using PubMed, Scopus, the Cochrane Library and the Center for Reviews and Dissemination through August 2017. The gray literature has also been consulted. The quality of systematic reviews has been assessed with the AMSTAR checklist. The main inclusion criterion was use of speech recognition for medical reporting (front-end or back-end). A survey has also been conducted in Quebec, Canada, to identify the dissemination of this technology in this province, as well as the factors leading to the success or failure of its implementation. Five systematic reviews were identified. These reviews indicated a high level of heterogeneity across studies. The quality of the studies reported was generally poor. Speech recognition is not as accurate as human transcription, but it can dramatically reduce turnaround times for reporting. In front-end use, medical doctors need to spend more time on dictation and correction than required with human transcription. With speech recognition, major errors occur up to three times more frequently. In back-end use, a potential increase in productivity of transcriptionists was noted. In conclusion, speech recognition offers several advantages for medical reporting. However, these advantages are countered by an increased burden on medical doctors and by risks of additional errors in medical reports. It is also hard to identify for which medical specialties and which clinical activities the use of speech recognition will be the most beneficial.

  20. Talker and accent variability effects on spoken word recognition

    NASA Astrophysics Data System (ADS)

    Nyang, Edna E.; Rogers, Catherine L.; Nishi, Kanae

    2003-04-01

    A number of studies have shown that words in a list are recognized less accurately in noise and with longer response latencies when they are spoken by multiple talkers, rather than a single talker. These results have been interpreted as support for an exemplar-based model of speech perception, in which it is assumed that detailed information regarding the speaker's voice is preserved in memory and used in recognition, rather than being eliminated via normalization. In the present study, the effects of varying both accent and talker are investigated using lists of words spoken by (a) a single native English speaker, (b) six native English speakers, (c) three native English speakers and three Japanese-accented English speakers. Twelve /hVd/ words were mixed with multi-speaker babble at three signal-to-noise ratios (+10, +5, and 0 dB) to create the word lists. Native English-speaking listeners' percent-correct recognition for words produced by native English speakers across the three talker conditions (single talker native, multi-talker native, and multi-talker mixed native and non-native) and three signal-to-noise ratios will be compared to determine whether sources of speaker variability other than voice alone add to the processing demands imposed by simple (i.e., single accent) speaker variability in spoken word recognition.

  1. How Accurately Can the Google Web Speech API Recognize and Transcribe Japanese L2 English Learners' Oral Production?

    ERIC Educational Resources Information Center

    Ashwell, Tim; Elam, Jesse R.

    2017-01-01

    The ultimate aim of our research project was to use the Google Web Speech API to automate scoring of elicited imitation (EI) tests. However, in order to achieve this goal, we had to take a number of preparatory steps. We needed to assess how accurate this speech recognition tool is in recognizing native speakers' production of the test items; we…

  2. Dissociation between recognition and detection advantage for facial expressions: a meta-analysis.

    PubMed

    Nummenmaa, Lauri; Calvo, Manuel G

    2015-04-01

    Happy facial expressions are recognized faster and more accurately than other expressions in categorization tasks, whereas detection in visual search tasks is widely believed to be faster for angry than happy faces. We used meta-analytic techniques for resolving this categorization versus detection advantage discrepancy for positive versus negative facial expressions. Effect sizes were computed on the basis of the r statistic for a total of 34 recognition studies with 3,561 participants and 37 visual search studies with 2,455 participants, yielding a total of 41 effect sizes for recognition accuracy, 25 for recognition speed, and 125 for visual search speed. Random effects meta-analysis was conducted to estimate effect sizes at population level. For recognition tasks, an advantage in recognition accuracy and speed for happy expressions was found for all stimulus types. In contrast, for visual search tasks, moderator analysis revealed that a happy face detection advantage was restricted to photographic faces, whereas a clear angry face advantage was found for schematic and "smiley" faces. Robust detection advantage for nonhappy faces was observed even when stimulus emotionality was distorted by inversion or rearrangement of the facial features, suggesting that visual features primarily drive the search. We conclude that the recognition advantage for happy faces is a genuine phenomenon related to processing of facial expression category and affective valence. In contrast, detection advantages toward either happy (photographic stimuli) or nonhappy (schematic) faces is contingent on visual stimulus features rather than facial expression, and may not involve categorical or affective processing. (c) 2015 APA, all rights reserved).

  3. Sex differences in facial emotion recognition across varying expression intensity levels from videos.

    PubMed

    Wingenbach, Tanja S H; Ashwin, Chris; Brosnan, Mark

    2018-01-01

    There has been much research on sex differences in the ability to recognise facial expressions of emotions, with results generally showing a female advantage in reading emotional expressions from the face. However, most of the research to date has used static images and/or 'extreme' examples of facial expressions. Therefore, little is known about how expression intensity and dynamic stimuli might affect the commonly reported female advantage in facial emotion recognition. The current study investigated sex differences in accuracy of response (Hu; unbiased hit rates) and response latencies for emotion recognition using short video stimuli (1sec) of 10 different facial emotion expressions (anger, disgust, fear, sadness, surprise, happiness, contempt, pride, embarrassment, neutral) across three variations in the intensity of the emotional expression (low, intermediate, high) in an adolescent and adult sample (N = 111; 51 male, 60 female) aged between 16 and 45 (M = 22.2, SD = 5.7). Overall, females showed more accurate facial emotion recognition compared to males and were faster in correctly recognising facial emotions. The female advantage in reading expressions from the faces of others was unaffected by expression intensity levels and emotion categories used in the study. The effects were specific to recognition of emotions, as males and females did not differ in the recognition of neutral faces. Together, the results showed a robust sex difference favouring females in facial emotion recognition using video stimuli of a wide range of emotions and expression intensity variations.

  4. Sex differences in facial emotion recognition across varying expression intensity levels from videos

    PubMed Central

    2018-01-01

    There has been much research on sex differences in the ability to recognise facial expressions of emotions, with results generally showing a female advantage in reading emotional expressions from the face. However, most of the research to date has used static images and/or ‘extreme’ examples of facial expressions. Therefore, little is known about how expression intensity and dynamic stimuli might affect the commonly reported female advantage in facial emotion recognition. The current study investigated sex differences in accuracy of response (Hu; unbiased hit rates) and response latencies for emotion recognition using short video stimuli (1sec) of 10 different facial emotion expressions (anger, disgust, fear, sadness, surprise, happiness, contempt, pride, embarrassment, neutral) across three variations in the intensity of the emotional expression (low, intermediate, high) in an adolescent and adult sample (N = 111; 51 male, 60 female) aged between 16 and 45 (M = 22.2, SD = 5.7). Overall, females showed more accurate facial emotion recognition compared to males and were faster in correctly recognising facial emotions. The female advantage in reading expressions from the faces of others was unaffected by expression intensity levels and emotion categories used in the study. The effects were specific to recognition of emotions, as males and females did not differ in the recognition of neutral faces. Together, the results showed a robust sex difference favouring females in facial emotion recognition using video stimuli of a wide range of emotions and expression intensity variations. PMID:29293674

  5. Always on My Mind? Recognition of Attractive Faces May Not Depend on Attention

    PubMed Central

    Silva, André; Macedo, António F.; Albuquerque, Pedro B.; Arantes, Joana

    2016-01-01

    Little research has examined what happens to attention and memory as a whole when humans see someone attractive. Hence, we investigated whether attractive stimuli gather more attention and are better remembered than unattractive stimuli. Participants took part in an attention task – in which matrices containing attractive and unattractive male naturalistic photographs were presented to 54 females, and measures of eye-gaze location and fixation duration using an eye-tracker were taken – followed by a recognition task. Eye-gaze was higher for the attractive stimuli compared to unattractive stimuli. Also, attractive photographs produced more hits and false recognitions than unattractive photographs which may indicate that regardless of attention allocation, attractive photographs produce more correct but also more false recognitions. We present an evolutionary explanation for this, as attending to more attractive faces but not always remembering them accurately and differentially compared with unseen attractive faces, may help females secure mates with higher reproductive value. PMID:26858683

  6. Always on My Mind? Recognition of Attractive Faces May Not Depend on Attention.

    PubMed

    Silva, André; Macedo, António F; Albuquerque, Pedro B; Arantes, Joana

    2016-01-01

    Little research has examined what happens to attention and memory as a whole when humans see someone attractive. Hence, we investigated whether attractive stimuli gather more attention and are better remembered than unattractive stimuli. Participants took part in an attention task - in which matrices containing attractive and unattractive male naturalistic photographs were presented to 54 females, and measures of eye-gaze location and fixation duration using an eye-tracker were taken - followed by a recognition task. Eye-gaze was higher for the attractive stimuli compared to unattractive stimuli. Also, attractive photographs produced more hits and false recognitions than unattractive photographs which may indicate that regardless of attention allocation, attractive photographs produce more correct but also more false recognitions. We present an evolutionary explanation for this, as attending to more attractive faces but not always remembering them accurately and differentially compared with unseen attractive faces, may help females secure mates with higher reproductive value.

  7. The own-age face recognition bias is task dependent.

    PubMed

    Proietti, Valentina; Macchi Cassia, Viola; Mondloch, Catherine J

    2015-08-01

    The own-age bias (OAB) in face recognition (more accurate recognition of own-age than other-age faces) is robust among young adults but not older adults. We investigated the OAB under two different task conditions. In Experiment 1 young and older adults (who reported more recent experience with own than other-age faces) completed a match-to-sample task with young and older adult faces; only young adults showed an OAB. In Experiment 2 young and older adults completed an identity detection task in which we manipulated the identity strength of target and distracter identities by morphing each face with an average face in 20% steps. Accuracy increased with identity strength and facial age influenced older adults' (but not younger adults') strategy, but there was no evidence of an OAB. Collectively, these results suggest that the OAB depends on task demands and may be absent when searching for one identity. © 2014 The British Psychological Society.

  8. Target Recognition Using Neural Networks for Model Deformation Measurements

    NASA Technical Reports Server (NTRS)

    Ross, Richard W.; Hibler, David L.

    1999-01-01

    Optical measurements provide a non-invasive method for measuring deformation of wind tunnel models. Model deformation systems use targets mounted or painted on the surface of the model to identify known positions, and photogrammetric methods are used to calculate 3-D positions of the targets on the model from digital 2-D images. Under ideal conditions, the reflective targets are placed against a dark background and provide high-contrast images, aiding in target recognition. However, glints of light reflecting from the model surface, or reduced contrast caused by light source or model smoothness constraints, can compromise accurate target determination using current algorithmic methods. This paper describes a technique using a neural network and image processing technologies which increases the reliability of target recognition systems. Unlike algorithmic methods, the neural network can be trained to identify the characteristic patterns that distinguish targets from other objects of similar size and appearance and can adapt to changes in lighting and environmental conditions.

  9. Performance evaluation of MLP and RBF feed forward neural network for the recognition of off-line handwritten characters

    NASA Astrophysics Data System (ADS)

    Rishi, Rahul; Choudhary, Amit; Singh, Ravinder; Dhaka, Vijaypal Singh; Ahlawat, Savita; Rao, Mukta

    2010-02-01

    In this paper we propose a system for classification problem of handwritten text. The system is composed of preprocessing module, supervised learning module and recognition module on a very broad level. The preprocessing module digitizes the documents and extracts features (tangent values) for each character. The radial basis function network is used in the learning and recognition modules. The objective is to analyze and improve the performance of Multi Layer Perceptron (MLP) using RBF transfer functions over Logarithmic Sigmoid Function. The results of 35 experiments indicate that the Feed Forward MLP performs accurately and exhaustively with RBF. With the change in weight update mechanism and feature-drawn preprocessing module, the proposed system is competent with good recognition show.

  10. Rate and onset cues can improve cochlear implant synthetic vowel recognition in noise

    PubMed Central

    Mc Laughlin, Myles; Reilly, Richard B.; Zeng, Fan-Gang

    2013-01-01

    Understanding speech-in-noise is difficult for most cochlear implant (CI) users. Speech-in-noise segregation cues are well understood for acoustic hearing but not for electric hearing. This study investigated the effects of stimulation rate and onset delay on synthetic vowel-in-noise recognition in CI subjects. In experiment I, synthetic vowels were presented at 50, 145, or 795 pulse/s and noise at the same three rates, yielding nine combinations. Recognition improved significantly if the noise had a lower rate than the vowel, suggesting that listeners can use temporal gaps in the noise to detect a synthetic vowel. This hypothesis is supported by accurate prediction of synthetic vowel recognition using a temporal integration window model. Using lower rates a similar trend was observed in normal hearing subjects. Experiment II found that for CI subjects, a vowel onset delay improved performance if the noise had a lower or higher rate than the synthetic vowel. These results show that differing rates or onset times can improve synthetic vowel-in-noise recognition, indicating a need to develop speech processing strategies that encode or emphasize these cues. PMID:23464025

  11. Getting the Gist of Events: Recognition of Two-Participant Actions from Brief Displays

    PubMed Central

    Hafri, Alon; Papafragou, Anna; Trueswell, John C.

    2013-01-01

    Unlike rapid scene and object recognition from brief displays, little is known about recognition of event categories and event roles from minimal visual information. In three experiments, we displayed naturalistic photographs of a wide range of two-participant event scenes for 37 ms and 73 ms followed by a mask, and found that event categories (the event gist, e.g., ‘kicking’, ‘pushing’, etc.) and event roles (i.e., Agent and Patient) can be recognized rapidly, even with various actor pairs and backgrounds. Norming ratings from a subsequent experiment revealed that certain physical features (e.g., outstretched extremities) that correlate with Agent-hood could have contributed to rapid role recognition. In a final experiment, using identical twin actors, we then varied these features in two sets of stimuli, in which Patients had Agent-like features or not. Subjects recognized the roles of event participants less accurately when Patients possessed Agent-like features, with this difference being eliminated with two-second durations. Thus, given minimal visual input, typical Agent-like physical features are used in role recognition but, with sufficient input from multiple fixations, people categorically determine the relationship between event participants. PMID:22984951

  12. A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

    PubMed Central

    Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

    2016-01-01

    The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including “codon capture,” “genome streamlining,” and “ambiguous intermediate” theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNAAla containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. PMID:27197221

  13. Exercise recognition for Kinect-based telerehabilitation.

    PubMed

    Antón, D; Goñi, A; Illarramendi, A

    2015-01-01

    An aging population and people's higher survival to diseases and traumas that leave physical consequences are challenging aspects in the context of an efficient health management. This is why telerehabilitation systems are being developed, to allow monitoring and support of physiotherapy sessions at home, which could reduce healthcare costs while also improving the quality of life of the users. Our goal is the development of a Kinect-based algorithm that provides a very accurate real-time monitoring of physical rehabilitation exercises and that also provides a friendly interface oriented both to users and physiotherapists. The two main constituents of our algorithm are the posture classification method and the exercises recognition method. The exercises consist of series of movements. Each movement is composed of an initial posture, a final posture and the angular trajectories of the limbs involved in the movement. The algorithm was designed and tested with datasets of real movements performed by volunteers. We also explain in the paper how we obtained the optimal values for the trade-off values for posture and trajectory recognition. Two relevant aspects of the algorithm were evaluated in our tests, classification accuracy and real-time data processing. We achieved 91.9% accuracy in posture classification and 93.75% accuracy in trajectory recognition. We also checked whether the algorithm was able to process the data in real-time. We found that our algorithm could process more than 20,000 postures per second and all the required trajectory data-series in real-time, which in practice guarantees no perceptible delays. Later on, we carried out two clinical trials with real patients that suffered shoulder disorders. We obtained an exercise monitoring accuracy of 95.16%. We present an exercise recognition algorithm that handles the data provided by Kinect efficiently. The algorithm has been validated in a real scenario where we have verified its suitability. Moreover

  14. Use of the recognition heuristic depends on the domain's recognition validity, not on the recognition validity of selected sets of objects.

    PubMed

    Pohl, Rüdiger F; Michalkiewicz, Martha; Erdfelder, Edgar; Hilbig, Benjamin E

    2017-07-01

    According to the recognition-heuristic theory, decision makers solve paired comparisons in which one object is recognized and the other not by recognition alone, inferring that recognized objects have higher criterion values than unrecognized ones. However, success-and thus usefulness-of this heuristic depends on the validity of recognition as a cue, and adaptive decision making, in turn, requires that decision makers are sensitive to it. To this end, decision makers could base their evaluation of the recognition validity either on the selected set of objects (the set's recognition validity), or on the underlying domain from which the objects were drawn (the domain's recognition validity). In two experiments, we manipulated the recognition validity both in the selected set of objects and between domains from which the sets were drawn. The results clearly show that use of the recognition heuristic depends on the domain's recognition validity, not on the set's recognition validity. In other words, participants treat all sets as roughly representative of the underlying domain and adjust their decision strategy adaptively (only) with respect to the more general environment rather than the specific items they are faced with.

  15. Extending the imaging volume for biometric iris recognition.

    PubMed

    Narayanswamy, Ramkumar; Johnson, Gregory E; Silveira, Paulo E X; Wach, Hans B

    2005-02-10

    The use of the human iris as a biometric has recently attracted significant interest in the area of security applications. The need to capture an iris without active user cooperation places demands on the optical system. Unlike a traditional optical design, in which a large imaging volume is traded off for diminished imaging resolution and capacity for collecting light, Wavefront Coded imaging is a computational imaging technology capable of expanding the imaging volume while maintaining an accurate and robust iris identification capability. We apply Wavefront Coded imaging to extend the imaging volume of the iris recognition application.

  16. What Type of Vocabulary Knowledge Predicts Reading Comprehension: Word Meaning Recall or Word Meaning Recognition?

    ERIC Educational Resources Information Center

    Laufer, Batia; Aviad-Levitzky, Tami

    2017-01-01

    This study examined how well second language (L2) recall and recognition vocabulary tests correlated with a reading test, how well each vocabulary test discriminated between reading proficiency levels, and how accurate each test was in predicting reading proficiency when compared with corpus studies. A total of 116 college-level learners of…

  17. Emotion Recognition in Preschool Children: Associations with Maternal Depression and Early Parenting

    PubMed Central

    Kujawa, Autumn; Dougherty, Lea; Durbin, C. Emily; Laptook, Rebecca; Torpey, Dana; Klein, Daniel N.

    2013-01-01

    Emotion knowledge in childhood has been shown to predict social functioning and psychological well-being, but relatively little is known about parental factors that influence its development in early childhood. There is some evidence that both parenting behavior and maternal depression are associated with emotion recognition, but previous research has only examined these factors independently. The current study assessed auditory and visual emotion recognition ability among a large sample of preschool children to examine typical emotion recognition skills in children of this age, as well as the independent and interactive effects of maternal and paternal depression and negative parenting (i.e., hostility and intrusiveness). Results indicated that children were most accurate at identifying happy emotional expressions, followed by other basic emotions. The lowest accuracy was observed for neutral expressions. A significant interaction was found between maternal depression and negative parenting behavior, such that children with a maternal history of depression were particularly sensitive to the negative effects of maladaptive parenting behavior on emotion recognition ability. No significant effects were found for paternal depression. These results highlight the importance of examining the effects of multiple interacting factors on children’s emotional development, and provide suggestions for identifying children for targeted preventive interventions. PMID:24444174

  18. Impaired recognition of facial emotions from low-spatial frequencies in Asperger syndrome.

    PubMed

    Kätsyri, Jari; Saalasti, Satu; Tiippana, Kaisa; von Wendt, Lennart; Sams, Mikko

    2008-01-01

    The theory of 'weak central coherence' [Happe, F., & Frith, U. (2006). The weak coherence account: Detail-focused cognitive style in autism spectrum disorders. Journal of Autism and Developmental Disorders, 36(1), 5-25] implies that persons with autism spectrum disorders (ASDs) have a perceptual bias for local but not for global stimulus features. The recognition of emotional facial expressions representing various different levels of detail has not been studied previously in ASDs. We analyzed the recognition of four basic emotional facial expressions (anger, disgust, fear and happiness) from low-spatial frequencies (overall global shapes without local features) in adults with an ASD. A group of 20 participants with Asperger syndrome (AS) was compared to a group of non-autistic age- and sex-matched controls. Emotion recognition was tested from static and dynamic facial expressions whose spatial frequency contents had been manipulated by low-pass filtering at two levels. The two groups recognized emotions similarly from non-filtered faces and from dynamic vs. static facial expressions. In contrast, the participants with AS were less accurate than controls in recognizing facial emotions from very low-spatial frequencies. The results suggest intact recognition of basic facial emotions and dynamic facial information, but impaired visual processing of global features in ASDs.

  19. Gene conversion as a mechanism for divergence of a chloroplast tRNA gene inserted in the mitochondrial genome of Brassica oleracea.

    PubMed Central

    Dron, M; Hartmann, C; Rode, A; Sevignac, M

    1985-01-01

    We have characterized a 1.7 kb sequence, containing a tRNA Leu2 gene shared by the ct and mt genomes of Brassica oleracea. The two sequences are completely homologous except in two short regions where two distinct gene conversion events have occurred between two sets of direct repeats leading to the insertion of 5 bp in the T loop of the mt copy of the ct gene. This is the first evidence that gene conversion represents the initial evolutionary step in inactivation of transferred ct genes in the mt genome. We also indicate that organelle DNA transfer by organelle fusion is an ongoing process which could be useful in genetic engineering. PMID:4080548

  20. Identification of Alfalfa Leaf Diseases Using Image Recognition Technology

    PubMed Central

    Qin, Feng; Liu, Dongxia; Sun, Bingda; Ruan, Liu; Ma, Zhanhong; Wang, Haiguang

    2016-01-01

    Common leaf spot (caused by Pseudopeziza medicaginis), rust (caused by Uromyces striatus), Leptosphaerulina leaf spot (caused by Leptosphaerulina briosiana) and Cercospora leaf spot (caused by Cercospora medicaginis) are the four common types of alfalfa leaf diseases. Timely and accurate diagnoses of these diseases are critical for disease management, alfalfa quality control and the healthy development of the alfalfa industry. In this study, the identification and diagnosis of the four types of alfalfa leaf diseases were investigated using pattern recognition algorithms based on image-processing technology. A sub-image with one or multiple typical lesions was obtained by artificial cutting from each acquired digital disease image. Then the sub-images were segmented using twelve lesion segmentation methods integrated with clustering algorithms (including K_means clustering, fuzzy C-means clustering and K_median clustering) and supervised classification algorithms (including logistic regression analysis, Naive Bayes algorithm, classification and regression tree, and linear discriminant analysis). After a comprehensive comparison, the segmentation method integrating the K_median clustering algorithm and linear discriminant analysis was chosen to obtain lesion images. After the lesion segmentation using this method, a total of 129 texture, color and shape features were extracted from the lesion images. Based on the features selected using three methods (ReliefF, 1R and correlation-based feature selection), disease recognition models were built using three supervised learning methods, including the random forest, support vector machine (SVM) and K-nearest neighbor methods. A comparison of the recognition results of the models was conducted. The results showed that when the ReliefF method was used for feature selection, the SVM model built with the most important 45 features (selected from a total of 129 features) was the optimal model. For this SVM model, the