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PubMed1993

Restriction map and polymorphisms of nuclear ribosomal genes of Populus balsamifera.

Balsam poplar (Populus balsamifera) clones from five populations, which were collected along a transect from northern Wisconsin to the northern tree line, were evaluated for polymorphisms in nuclear ribosomal DNA. For this purpose, a restriction map was constructed using four six-cutter enzymes in single and double digests of genomic DNA. After electrophoretic separation on agarose gels and Southern transfer, blots were hybridized to non-radioactively labeled heterologous rDNA probes of soybean. Among populations, variation was detected in the length of the intergenic spacer between the tandem repeats of the coding regions and in the degree of methylation of one restriction enzyme recognition site. Based on a comparison of the derived restriction map of balsam poplar and other poplars, high homology was evident in the rDNA coding regions among species, whereas the intergenic spacer varied slightly in both length and number of restriction sites.

Journal Article↗

PubMed1994

PilR, a transcriptional regulator of piliation in Pseudomonas aeruginosa, binds to a cis-acting sequence upstream of the pilin gene promoter.

The PilR protein of Pseudomonas aeruginosa is a transcriptional activator of the pilin gene and belongs to a two-component sensor-regulator family. PilR was overproduced by fusing pilR to the gene for the maltose-binding protein (malE), yielding a MalE-PilR hybrid protein. The plasmid with the malE-pilR fusion, when introduced into a non-piliated pilR mutant strain of P. aeruginosa, restored piliation, indicating that the hybrid protein retains PilR function in vivo. The MalE-PilR protein was purified from Escherichia coli and used in a series of DNA-binding studies. A specific pilin promoter-binding activity of MalE-PilR was observed in a gel retardation assay. Subsequent DNase I footprinting analysis revealed a 40 bp PilR-binding site located at the -120 to -80 region, relative to the transcriptional start site of the pilin gene. This PilR-binding region consists of a nine-base sequence and three consensus sequences of 5'-(N)4-6C/GTGTC-3', in a tandem array in which the first 7-9 bp are bound by the PilR on the non-coding strand, leaving the last two nucleotides (TC) unbound. On the coding strand, PilR binds to sequences complementary to the two middle consensus sequences of the non-coding strand. A sequence similar to the NifA recognition site (5'-TGT-(N)11-ACA-3') is also found within the PilR-binding region. Deletion analysis and disruption of the individual consensus PilR-binding sequences by site-directed mutagenesis revealed that all four PilR-binding sites are absolutely required for the PilS/PilR-mediated pilin gene expression.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Outer Membrane Proteins↗

PubMed2001

V(D)J recombination: RAG proteins, repair factors, and regulation.

V(D)J recombination is the specialized DNA rearrangement used by cells of the immune system to assemble immunoglobulin and T-cell receptor genes from the preexisting gene segments. Because there is a large choice of segments to join, this process accounts for much of the diversity of the immune response. Recombination is initiated by the lymphoid-specific RAG1 and RAG2 proteins, which cooperate to make double-strand breaks at specific recognition sequences (recombination signal sequences, RSSs). The neighboring coding DNA is converted to a hairpin during breakage. Broken ends are then processed and joined with the help of several factors also involved in repair of radiation-damaged DNA, including the DNA-dependent protein kinase (DNA-PK) and the Ku, Artemis, DNA ligase IV, and Xrcc4 proteins, and possibly histone H2AX and the Mre11/Rad50/Nbs1 complex. There may be other factors not yet known. V(D)J recombination is strongly regulated by limiting access to RSS sites within chromatin, so that particular sites are available only in certain cell types and developmental stages. The roles of enhancers, histone acetylation, and chromatin remodeling factors in controlling accessibility are discussed. The RAG proteins are also capable of transposing RSS-ended fragments into new DNA sites. This transposition helps to explain the mechanism of RAG action and supports earlier proposals that V(D)J recombination evolved from an ancient mobile DNA element.

Amino Acid Motifs↗

PubMed1992

Preliminary results with the Clarion cochlear implant.

A new cochlear implant has become available. This device, called the Clarion Multichannel Cochlear Implant, is the result of collaborative efforts between the University of California, San Francisco (UCSF), the Research Triangle Institute (RTI), Research Triangle Park, North Carolina, and the device manufacturer and sponsor, MiniMed Technologies of Sylmar, California. The Clarion represents a new generation of multi-programmable cochlear implant systems. Options in waveform, the stimulation mode, and the temporal distribution of the signal permit the device to be optimally customized for each individual patient. The speech coding scheme offering the greatest opportunity for speech recognition can be selected. The first Clarion recipient has recently been implanted at UCSF, initiating the Clarion's investigational clinical trials. A description of the device and preliminary patient results are presented.

Aged↗

PubMed2004

Planar-waveguide integrated spectral comparator.

A cost-effective yet robust and versatile dual-channel spectral comparator is presented. The silica-on-silicon planar-waveguide integrated device includes two holographic Bragg-grating reflectors (HBRs) with complementary spectral transfer functions. Output comprises projections of input signal spectra onto the complementary spectral channels. Spectral comparators may be useful in optical code-division multiplexing, optical packet decoding, spectral target recognition, and the identification of molecular spectra. HBRs may be considered to be mode-specific photonic crystals.

Journal Article↗

PubMed2004

Automated bioacoustic identification of species.

Research into the automated identification of animals by bioacoustics is becoming more widespread mainly due to difficulties in carrying out manual surveys. This paper describes automated recognition of insects (Orthoptera) using time domain signal coding and artificial neural networks. Results of field recordings made in the UK in 2002 are presented which show that it is possible to accurately recognize 4 British Orthoptera species in natural conditions under high levels of interference. Work is under way to increase the number of species recognized.

Acoustics↗

PubMedDate not supplied

[The use of filamentous phage M13 in protein engineering].

M13B1 vector based on the filamentous phage M13 has been constructed. M13B1 phage carries the gene of resistance to ampicillin and contains the unique site of recognition for BamHI restriction endonuclease in gene VIII coding for the major coat protein. BamHI restriction site has been inserted into the gene of the major coat protein by means of oligonucleotide directed mutagenesis. The synthetic DNA fragment coding for the model peptides has been inserted through BamHI site into the M13B1 DNA. The possibility of inserting foreign peptides into the N-terminus at maintaining the viability of hybrid phages has been shown. The differences in specificity of the recombinant phage maturation have been determined by analysing the amino acid sequence of B-protein.

Amino Acid Sequence↗

PubMed1985

Comparison of multiple HLA-A alleles at the DNA level by using Southern blotting and HLA-A-specific probes.

Numerous alleles of the HLA-A gene have been serologically identified. In this report we present a rapid and straightforward means to assess HLA-A polymorphism at the genomic level. Using 5' and 3' HLA-A-specific DNA probes and Southern blotting, we have placed the recognition sequences for five endonucleases relative to the coding regions of 15 HLA-A alleles. These data permit two interesting conclusions: four of the HLA-A alleles studied are associated with unique restriction fragments, and HLA-A alleles of a cross-reactive group are more closely related at the DNA level than are noncross-reactive alleles.

Alleles↗

PubMed1996

Cepstral representation of speech motivated by time-frequency masking: an application to speech recognition.

A new spectral representation incorporating time-frequency forward masking is proposed. This masked spectral representation is efficiently represented by a quefrency domain parameter called dynamic-cepstrum (DyC). Automatic speech recognition experiments have demonstrated that DyC powerfully improves performance in phoneme classification and phrase recognition. This new spectral representation simulates a perceived spectrum. It enhances formant transition, which provides relevant cues for phoneme perception, while suppressing temporally stationary spectral properties, such as the effect of microphone frequency characteristics or the speaker-dependent time-invariant spectral feature. These features are advantageous for speaker-independent speech recognition. DyC can efficiently represent both the instantaneous and transitional aspects of a running spectrum with a vector of the same size as a conventional cepstrum. DyC is calculated from a cepstrum time sequence using a matrix lifter. Each column vector of the matrix lifter performs spectral smoothing. Smoothing characteristics are a function of the time interval between a masker and a signal. DyC outperformed a conventional cepstrum parameter obtained through linear predictive coding (LPC) analysis for both phoneme classification and phrase recognition by using hidden Markov models (HMMs). Compared with speaker-dependent recognition, an even greater improvement over the cepstrum parameter was found in speaker-independent speech recognition. Furthermore, DyC with only 16 coefficients exhibited higher speech recognition performance than a combination of the cepstrum and a delta-cepstrum with 32 coefficients for the classification experiment of phonemes contaminated by noises.

Humans↗

PubMed2004

Frequent occurrence of recognition site-like sequences in the restriction endonucleases.

BACKGROUND: There are two different theories about the development of the genetic code. Woese suggested that it was developed in connection with the amino acid repertoire, while Crick argued that any connection between codons and amino acids is only the result of an "accident". This question is fundamental to understand the nature of specific protein-nucleic acid interactions. RESULTS: The nature of specific protein-nucleic acid interaction between restriction endonucleases (RE) and their recognition sequences (RS) was studied by bioinformatics methods. It was found that the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p < 0.001 respectively, n = 7). There is an extensive conservation of these RS-like sequences in RE isoschizomers. A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS.Fifty-five examples of this codon-amino acid co-localization are found and analyzed, which represents 41.5% of total 132 amino acids which are localized within 8 A distance to the C1' atoms in the DNA. The average distance between the closest atoms in the codons and amino acids is 5.5 +/- 0.2 A (mean +/- S.E.M, n = 55), while the distance between the nitrogen and oxygen atoms of the co-localized molecules is significantly shorter, (3.4 +/- 0.2 A, p < 0.001, n = 15), when positively charged amino acids are involved. This is indicating that an interaction between the nucleic- and amino acids might occur. CONCLUSION: We interpret these results in favor of Woese and suggest that the genetic code is "rational" and there is a stereospecific relationship between the codes and the amino acids.

Amino Acids↗

PubMed1982

New legal rules for an old art of healing: the case of Zairian Healers' Association.

Legitimacy of traditional medical practice could be recognized by modern legal codes in Africa through quite simple procedures. However, legal recognition of traditional medicine implies also the examination of more fundamental aspects of "laws regarding the art of healing': for example, what legal status can be given to cultural categories such as witchcraft, spirits and magic? To ritual therapeutics used concurrently with herbal remedies? To diagnostic procedures such as divination? This paper insists on the fact that both dimensions in traditional medicine, natural and meta-natural, must be assumed within the official legal framework. Western-oriented codes of law, such as they generally exist in African States, are limited in their capability to integrate the African medical conceptions. This limitation is discussed in this text.

Delivery of Health Care↗

PubMed1986

Understanding face recognition.

The aim of this paper is to develop a theoretical model and a set of terms for understanding and discussing how we recognize familiar faces, and the relationship between recognition and other aspects of face processing. It is suggested that there are seven distinct types of information that we derive from seen faces; these are labelled pictorial, structural, visually derived semantic, identity-specific semantic, name, expression and facial speech codes. A functional model is proposed in which structural encoding processes provide descriptions suitable for the analysis of facial speech, for analysis of expression and for face recognition units. Recognition of familiar faces involves a match between the products of structural encoding and previously stored structural codes describing the appearance of familiar faces, held in face recognition units. Identity-specific semantic codes are then accessed from person identity nodes, and subsequently name codes are retrieved. It is also proposed that the cognitive system plays an active role in deciding whether or not the initial match is sufficiently close to indicate true recognition or merely a 'resemblance'; several factors are seen as influencing such decisions. This functional model is used to draw together data from diverse sources including laboratory experiments, studies of everyday errors, and studies of patients with different types of cerebral injury. It is also used to clarify similarities and differences between processes for object, word and face recognition.

Attention↗

PubMed2005

Extending the imaging volume for biometric iris recognition.

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.

Algorithms↗

PubMed1993

Selection of a 'minimal' glutaminyl-tRNA synthetase and the evolution of class I synthetases.

The evolution of the aminoacyl-tRNA synthetases is intriguing in light of their elaborate relationship with tRNAs and their significance in the decoding process. Based on sequence motifs and structure determination, these enzymes have been assigned to two classes. The crystal structure of Escherichia coli glutaminyl-tRNA synthetase (GlnRS), a class I enzyme, complexed to tRNA(Gln) and ATP has been described. It is shown here that a 'minimal' GlnRS, i.e. a GlnRS from which domains interacting with the acceptor-end and the anticodon of the tRNA have been deleted, has enzymatic activity and can charge a tRNA(Tyr)-derived amber suppressor (supF) with glutamine. The catalytic core of GlnRS, which is structurally conserved in other class I synthetases, is therefore sufficient for the aminoacylation of tRNA substrates. Some of these truncated enzymes have lost their ability to discriminate against non-cognate tRNAs, implying a more specific role of the acceptor-end-binding domain in the recognition of tRNAs. Our results indicate that the catalytic and substrate recognition properties are carried by distinct domains of GlnRS, and support the notion that class I aminoacyl-tRNA synthetases evolved from a common ancestor, jointly with tRNAs and the genetic code, by the addition of non-catalytic domains conferring new recognition specificities.

Amino Acyl-tRNA Synthetases↗

PubMed2005

On beyond mirror neurons: internal representations subserving imitation and recognition of skilled object-related actions in humans.

A considerable recent literature argues that the same representations, encoded by inferior prefrontal and parietal cells known as "mirror neurons", may be activated in both production and recognition of object-related actions. Here, we test several predictions derived from the contemporary literature on the parity between production and recognition and the putative emergence of the mirror neuron system from a system coding hand-object interactions. Forty-four patients with left-hemisphere stroke, 21 of whom exhibited ideomotor apraxia, performed a number of pantomime imitation and recognition tasks, and performance was scored with respect to hand posture, arm posture, amplitude, and timing. Consistent with predictions, there were strong relationships between object-related pantomime imitation and object-related pantomime recognition, and between imitation and recognition of the hand posture component of object-related actions. Skilled object-related gesture representations are likely to be closely tied to evolutionarily more primitive systems controlling object grasping, to emerge from a mapping between object and action information coded by ventral and dorsal streams, and to be lateralized to the left hemisphere in humans.

Adult↗

PubMed1980

Internal structure of the silk fibroin gene of Bombyx mori. II. Remarkable polymorphism of the organization of crystalline and amorphous coding sequences.

Alleles of the silk fibroin locus from 22 inbred stocks of Bombyx mori were compared. Nineteen alleles differing from one another in length and internal sequence organization were distinguished. Individuals from a single stock generaly are homozygous for a particular allele, as judged by their gene restriction pattern and the length of the fibroin protein produced. Restriction with endonucleases having four base recognition sequences revealed no variation with respect to these particular coding sequences among the alleles tested. Furthermore, digestion with endonucleases specific for amorphous coding sequences indicated that all the alleles tested had amorphous coding sequence domains alternating regularly with crystalline domains just as was found for the L allele. The stocks differed considerably in their fibroin length, and in the total length of the fibroin coding regions of their genes. These differences were accounted for by variation in the lengths of crystalline coding domains when compared to the ends of the genes. Several characteristics of the alleles indicates that this variation results from recombination between the highly repetitive coding sequences of misaligned genes (homologous unequal crossing-over). Polymorphism of the fibroin gene in B, mori appears to be greater than for any other gene for which data are available.

Alleles↗

PubMed2002

Parallel cascade recognition of exon and intron DNA sequences.

Many of the current procedures for detecting coding regions on human DNA sequences combine a number of individual techniques such as discriminant analysis and neural net methods. Recent papers have used techniques from nonlinear systems identification, in particular, parallel cascade identification (PCI), as one means for classifying protein sequences into their structure/function groups. In the present paper, PCI is used in a pilot study to distinguish exon (coding) from intron (noncoding; interspersed within genes) human DNA sequences. Only the first exon and first intron sequences with known boundaries in genomic DNA from the beta T-cell receptor locus were used for training. Then, the parallel cascade classifiers were able to achieve classification rates of about 89% on novel sequences in a test set, and averaged about 82% when results of a blind test were included. In testing over a much wider range of human nucleotide sequences, PCI classifiers averaged 83.6% correct classifications. These results indicate that parallel cascade classifiers may be useful components in future coding region detection programs.

Algorithms↗

PubMed2004

Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases.

Lysine insertion during coded protein synthesis requires lysyl-tRNA(Lys), which is synthesized by lysyl-tRNA synthetase (LysRS). Two unrelated forms of LysRS are known: LysRS2, which is found in eukaryotes, most bacteria, and a few archaea, and LysRS1, which is found in most archaea and a few bacteria. To compare amino acid recognition between the two forms of LysRS, the effects of l-lysine analogues on aminoacylation were investigated. Both enzymes showed stereospecificity toward the l-enantiomer of lysine and discriminated against noncognate amino acids with different R-groups (arginine, ornithine). Lysine analogues containing substitutions at other positions were generally most effective as inhibitors of LysRS2. For example, the K(i) values for aminoacylation of S-(2-aminoethyl)-l-cysteine and l-lysinamide were over 180-fold lower with LysRS2 than with LysRS1. Of the other analogues tested, only gamma-aminobutyric acid showed a significantly higher K(i) for LysRS2 than LysRS1. These data indicate that the lysine-binding site is more open in LysRS2 than in LysRS1, in agreement with previous structural studies. The physiological significance of divergent amino acid recognition was reflected by the in vivo resistance to growth inhibition imparted by LysRS1 against S-(2-aminoethyl)-l-cysteine and LysRS2 against gamma-aminobutyric acid. These differences in resistance to naturally occurring noncognate amino acids suggest the distribution of LysRS1 and LysRS2 contributes to quality control during protein synthesis. In addition, the specific inhibition of LysRS1 indicates it is a potential drug target.

Amino Acids↗