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PubMed1990

MamI, a novel class-II restriction endonuclease from Microbacterium ammoniaphilum recognizing 5'-GATNN decreases NNATC-3'.

A new site-specific class-II restriction endonuclease, MamI, has been discovered in the nonsporulating Gram+ Microbacterium ammoniaphilum. MamI recognition sequence and cleavage positions were deduced using experimental and computer-assisted mapping and sequencing approaches. MamI cleavage specificity corresponds to: [formula: see text] The novel 43-kD enzyme recognizes a palindromic hexanucleotide interrupted by four ambiguous nucleotides. MamI cleavage positions are located in the center of the recognition sequence resulting in blunt-ended fragments after cleavage in the presence of Mg2+ ions. MamI is inhibited by N6-methyladenine residues. In case of overlapping sequences of MamI and Escherichia coli-coded DNA modification methyltransferase M.EcodamI (5'-[formula: see text]-3'), cleavage of DNA isolated from E. coli wild-type cells will be inhibited. By applying incubation conditions forcing star activity, relaxing of MamI sequence specificity is observed (MamI*).

Base Sequence↗

PubMed2004

Evolution: social selection for eccentricity.

The dress code of paper wasps, like that of humans, is related to their social habits: species with a flexible nest-founding strategy have highly variable black-and-yellow markings. This color polymorphism facilitates individual recognition and might have been selected to permit complex social interactions.

Animals↗

PubMed2005

A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984).

The phylogenetic relationships and historical biogeography of 10 currently described rainforest skinks in the genus Saproscincus were investigated using mitochondrial protein-coding ND4 and ribosomal RNA 16S genes. A robust phylogeny is inferred using both maximum likelihood and Bayesian analysis, with all inter-specific nodes strongly supported when datasets are combined. The phylogeny supports the recognition of two major lineages (northern and southern), each of which comprises two divergent clades. Both northern and southern lineages have comparably divergent representatives in mid-east Queensland (MEQ), providing further molecular evidence for the importance of two major biogeographic breaks, the St. Lawrence gap and Burdekin gap separating MEQ from southern and northern counterparts respectively. Vicariance associated with the fragmentation and contraction of temperate rainforest during the mid-late Miocene epoch underpins the deep divergence between morphologically conservative lineages in at least three instances. In contrast, one species, Saproscincus oriarus, shows very low sequence divergence but distinct morphological and ecological differentiation from its allopatric sister clade within Saproscincus mustelinus. These results suggest that while vicariance has played a prominent role in diversification and historical biogeography of Saproscincus, divergent selection may also be important.

Animals↗

PubMed1993

Identification of protein coding regions by database similarity search.

Sequence similarity between a translated nucleotide sequence and a known biological protein can provide strong evidence for the presence of a homologous coding region, even between distantly related genes. The computer program BLASTX performed conceptual translation of a nucleotide query sequence followed by a protein database search in one programmatic step. We characterized the sensitivity of BLASTX recognition to the presence of substitution, insertion and deletion errors in the query sequence and to sequence divergence. Reading frames were reliably identified in the presence of 1% query errors, a rate that is typical for primary sequence data. BLASTX is appropriate for use in moderate and large scale sequencing projects at the earliest opportunity, when the data are most prone to containing errors.

Algorithms↗

PubMed2002

The distinct methods by which manganese and iron regulate the Nramp transporters in yeast.

The bakers yeast Saccharomyces cerevisiae expresses three Smf metal transport proteins that are differentially regulated by metal ions. Smf1p and Smf2p are regulated at the post-translational level by manganese, whereas Smf3p is regulated by iron through a mechanism that, up until now, was unknown. Through promoter and protein-domain swapping experiments, we now demonstrate that the manganese regulation of Smf1p involves an internal protein-coding region that is separate from the N-terminal domain of this transporter. By comparison, iron regulation of Smf3p involves the upstream non-coding region of the gene. Using SMF3-lacZ reporter constructs, we identified two distinct regions of the SMF3 promoter that contribute to iron regulation: (1) approx. nt -435 to -350 that contain dual consensus recognition sites for the Aft1 iron transcription factor; and (2) nt -348 to -247 that do not contain obvious Aft1 binding sites. The -348 to -247 region by itself can confer strong iron regulation to the heterologous CYC1 core promoter, and therefore harbours a putative upstream activating sequence for iron. Iron regulation of SMF3 was dramatically reduced, but not completely eliminated, in strains lacking both the AFT1 and AFT2 iron regulatory factors. Together with the promoter mapping studies, these results suggest that both Aft-dependent and Aft-independent pathways may contribute to iron regulation of SMF3.

Cation Transport Proteins↗

PubMed1996

Repression of transcriptional enhancer factor-1 and activator protein-1-dependent enhancer activity by vascular actin single-stranded DNA binding factor 2.

Transcriptional repression of the murine vascular smooth muscle alpha-actin gene in fibroblasts results from the interaction of two sequence-specific single-stranded DNA binding activities (VACssBF1 and VACssBF2) with opposite strands of an essential transcriptional enhancer factor-1 (TEF-1) element (Sun, S., Stoflet, E. S., Cogan, J. G., Strauch, A. R., and Getz, M. J. (1995) Mol. Cell. Biol. 15, 2429-2436). Here, we identify a sequence element located within a protein-coding exon of the gene that bears structural similarity with the TEF-1 enhancer. This includes a 30-base pair region of purine-pyrimidine asymmetry encompassing a perfect 6-base pair GGAATG TEF-1 recognition motif. Unlike the enhancer, however, the exon sequence exhibits no TEF-1 binding activity nor does the pyrimidine-rich strand bind VACssBF1. However, VACssBF2 interacts equally well with the purine-rich strand of both the enhancer and the exon sequence. To test the ability of VACssBF2 to independently repress transcription, the exon sequence was placed upstream of a deletionally activated promoter containing an intact TEF-1 binding site. The exon sequence repressed promoter activity, whereas a mutant deficient in VACssBF2 binding did not. Moreover, VACssBF2 similarly repressed activator protein-1-dependent transcription of a heterologous tissue factor promoter. These results suggest that VACssBF2 possesses an intrinsic ability to disrupt enhancer function independently of the enhancer-binding proteins involved.

3T3 Cells↗

PubMed1995

A nuclear protein, synthesized in growth-arrested human hepatoblastoma cells, is a novel member of the short-chain alcohol dehydrogenase family.

We have described a protein (Hep27) [Donadel, G., Garzelli, C., Frank, R. & Gabrielli, F. (1991) Eur. J. Biochem. 195, 723-729] which is synthesized and accumulated in the nucleus of human hepatoblastoma (HepG2) cells, following growth arrest induced by butyrate treatment. The synthesis of Hep27 is inhibited in cells that, released from the butyrate block, have resumed DNA synthesis. This report describes the cloning and the characterization of the cDNA coding for the Hep27 protein. The translation of the Hep27 cDNA predicts an amino acid sequence that can be aligned with those of the known short-chain alcohol dehydrogenase enzymes (SCAD) family. Both the recognition of enzymic functional domains and the similarity with the SCAD family of proteins of several amino acid blocks throughout the molecule, strongly suggest that this protein is a new member of the SCAD family. In agreement with its nuclear localization Hep27 has a region similar to the bipartite nuclear-targeting sequence. The study of Hep27 mRNA expression and protein synthesis suggests the existence of a regulation at the post-transcriptional level. The possible nuclear role of the Hep27 protein is discussed.

11-beta-Hydroxysteroid Dehydrogenases↗

PubMed1991

Color Doppler artifact from metallic carotid clamp.

The presence of mirror artifacts in color Doppler has been noted by others. In that report, the artifact arose from scattering at the smooth vessel wall and appeared as signal outside the lumen of the vessel, but with no change in flow direction. As experience increases, recognition of the artifacts of color Doppler will lead to a better understanding and more precise evaluation. This case shows that a band of metal around the carotid artery causes registration errors in color-coded Doppler, and perhaps other metal foreign bodies in the soft tissues have similar potential. The specific appearance of the artifact will depend sensitively on the geometrical configuration of the metal body itself and on its orientation relative to the surrounding anatomy and the ultrasound probe. Appropriate placement of the transducer will reduce such artifact.

Artifacts↗

PubMed1998

Genetic and acquired predisposing factors and treatment of osteoporosis in thalassaemia major.

We have previously shown a high incidence of osteopenia and osteoporosis in patients with thalassaemia major. These bone changes, were more severe in males than females, in those with diabetes mellitus and with hypogonadal-hypogonadism. Our recent studies concern the relationship of erythroid activity, assessed by serum transferrin receptors as an overall measure of anaemia, to osteoporosis. Serum transferrin receptor levels correlated with the mean pre-transfusion haemoglobin level, but there was no correlation with the incidence of osteopenia and osteoporosis. As osteoporosis has a strong genetic component we have also studied the COLIA1 and COLIA2 genes which code for the major protein of bone (type 1 collagen). Studies by others have shown in non-thalassaemic patients that a polymorphism G-->T or TT in a regulatory region of COLIA1 at the recognition site for transcription factor Sp1 is associated with the presence of osteoporosis. Our studies suggest that Sp1 polymorphism is not specific to any one ethnic group; the polymorphism occurs more commonly in females (female to male ratio 2:1). In male thalassaemia major patients the presence of the Sp1 mutation was associated with more severe osteoporosis of the spine and the hip compared with female patients. There is failure of improvement in spinal osteoporosis with bisphosphonate therapy (intravenous Pamidronate) in male patients with the Sp1 mutation.

Adolescent↗

PubMed2004

Application of a diagnostic algorithm for inherited thrombocytopenias to 46 consecutive patients.

BACKGROUND AND OBJECTIVES: The Italian Gruppo di Studio delle Piastrine recently developed a diagnostic algorithm to assist clinicians in the diagnosis of inherited thrombocytopenias. This algorithm is based on the simplest possible diagnostic investigations and can also be used in centers that are not highly specialized. The aim of the present study was to validate this diagnostic algorithm by applying it to a case series of genetic thrombocytopenias. DESIGN AND METHODS: The diagnostic algorithm was applied retrospectively to 46 consecutive patients observed during the last five years at a single institution. Twenty-eight were affected by defined illnesses or their variants, while 18 had a disorder that did not fit the criteria for any known genetic thrombocytopenia. The study was based on the evaluation of clinical records and laboratory tests. RESULTS: The diagnostic algorithm recognized: 4 homozygous and 4 heterozygous Bernard-Soulier syndromes, 11 MYH9-related diseases, one von WillebrandOs disease type 2B, one gray platelet syndrome and one X-linked thrombocytopenia with thalassemia. Moreover, it identified 4 patients with the clinical and laboratory features of heterozygous Bernard-Soulier syndrome not caused by mutations in the coding region of the GPIbalpha, GPIbbeta, GPIX or GPV genes, and two patients with the clinical phenotype of MYH9-related disease but without MYH9 mutations. Since the diagnostic flow chart did not allow prompt recognition of two subjects with MYH9-related disease, we introduced a small change to the previously proposed flow chart to obviate this defect. INTERPRETATION AND CONCLUSIONS: The diagnostic algorithm correctly diagnosed 26 of 28 patients with known disorders or phenotypic variants of known disorders. By a simple modification of the investigation sequence, its sensitivity reached 100%. The algorithm also identified 18 patients with new, as yet uncharacterized forms of genetic thrombocytopenia.

Algorithms↗

PubMed1990

What should be implemented in future cochlear implants?

Cochlear-implant performance can be improved by focusing on: 1) psychophysical studies to determine hearing limitations; 2) speech perception to suggest the most effective speech-processing strategies; 3) aural rehabilitation to effectively train patients to use the new electrical stimuli. Basic psychophysical studies have shown only weak correlations with speech perception. Perhaps more speech-like stimuli should be explored in psychophysical tasks. Studies on vowel and consonant recognition suggest enhancing all speech features, but particularly frication and place of articulation should help most patients. Probably the feature that would be the most beneficial to enhance is place of articulation, which is poorly coded even in the best patients. Empirical studies are needed to determine the ways in which these cues can be enhanced. Certain types of auditory training are likely to be beneficial, particularly when the signal is new, incomplete or distorted. However, much more research in aural rehabilitation is needed.

Cochlear Implants↗

PubMedDate not supplied

[Statistical characteristics in primary structures of functional regions of Escherichia coli genome. I. Frequency characteristics].

Analysis of the frequencies of occurrence of mono- and dinucleotides in sequenced E. coli DNA fragments was performed. The DNA sequences of total length 135 000 nucleotides were considered. It was demonstrated that the fragments of DNA which have different functional properties also have different parameters of neighbour nucleotides correlation. Moreover, periodical positional dependence of correlation parameters in coding regions was found. The evolution significance of stated observation is discussed, so as the opportunity of using them in the special model of nucleotide's sequences, which is needed for development of the computer recognition algorithms for genomic functional units.

Base Sequence↗

PubMed1990

Suppression and the code: beyond codons and anticodons.

Specificity and accuracy in the decoding of genetic information during mRNA-programmed, ribosome-dependent polypeptide synthesis (translation) involves more than just hydrogen bonding between two anti-parallel trinucleotides, the mRNA codon and the tRNA anticodon. Other macromolecules are also involved, and translational suppression has been and continues to be an appropriate and effective way to identify them, as well as other parts of mRNA and tRNA, and to elucidate the structural determinants of their functions and interactions. Experimental results are presented that bear upon codon context effects, the role of tRNA structural features in aminoacyl-tRNA selection and in codon selection (reading-frame maintenance), determinants of tRNA identity, elongation factor suppressor mutants, and termination codon recognition by the ribosomal RNA of the small subunit. The examples presented illustrate the complexity of the decoding process and the interconnectedness of translational macromolecules in achieving specificity and accuracy in polypeptide synthesis.

Anticodon↗

PubMed2026

Molecular Determinants and Therapeutic Targeting of Stop Codon Readthrough in Eukaryotic Translation.

Accurate translation termination is essential for proteome integrity and in eukaryotes is primarily governed by the release factors eRF1 and eRF3, which ensure precise recognition of stop codons and efficient release of nascent polypeptides. However, proteome integrity is challenged by mutations that generate premature termination codons (PTCs), leading to truncated, nonfunctional proteins and degradation of the aberrant transcript via nonsense-mediated mRNA decay (NMD). Collectively, these events account for ∼1800 human genetic diseases. Translational readthrough, the process by which near-cognate tRNAs decode stop codons and allow ribosomes to continue elongation beyond the stop codon, represents a possibility to suppress PTCs and restore full-length protein synthesis. Initially discovered in viruses as a mechanism to expand coding capacity, readthrough is now recognized as a regulated feature of eukaryotic gene expression influenced by both cis-acting sequence elements and trans-acting factors. Recent evidence highlights the remarkable context dependence of readthrough, revealing variation across transcripts, tissues, and developmental stages. In this review, we examine the molecular determinants that define stop codon recognition and readthrough efficiency, with particular emphasis on nucleotide context. We further discuss the mechanisms and binding sites of small molecules that promote PTC readthrough, and summarize the clinical development landscape of readthrough-inducing compounds for the treatment of diseases caused by nonsense mutations.

Humans↗

PubMed1991

RNA minihelices and the decoding of genetic information.

The rules of the genetic code are determined by the specific aminoacylation of transfer RNAs by aminoacyl transfer RNA synthetase. A straightforward analysis shows that a system of synthetase-tRNA interactions that relies on anticodons for specificity could, in principle, enable most synthetases to distinguish their cognate tRNA isoacceptors from all others. Although the anticodons of some tRNAs are recognition sites for the cognate aminoacyl tRNA synthetases, for other synthetases the anticodon is dispensable for specific aminoacylation. In particular, alanine and histidine tRNA synthetases aminoacylate small RNA minihelices that reconstruct the part of their cognate tRNAs that is proximate to the amino acid attachment site. Helices with as few as six base pairs can be efficiently aminoacylated. The specificity of aminoacylation is determined by a few nucleotides and can be converted from one amino acid to another by the change of only a few nucleotides. These findings suggest that, for a subgroup of the synthetases, there is a distinct code in the acceptor helix of transfer RNAs that determines aminoacylation specificity.

Amino Acyl-tRNA Synthetases↗

PubMed2003

The risks posed by the importation of animals vaccinated against foot and mouth disease and products derived from vaccinated animals: a review.

The Terrestrial Animal Health Code of the OIE (World organisation for animal health) (the Terrestrial Code) makes recommendations for international movements of live animals and animal products because of a possible generic risk of foot and mouth disease (FMD) for these different commodities. For instance, international movement of vaccinated live animals or products of such animals is restricted due to the possible masking of clinical disease as a result of vaccination and to the perceived risk of persistently infected animals among vaccinated livestock. In addition, bilateral agreements between exporting and importing countries on the importation of animal products can be based on the 'equivalence' of the animal health conditions in both countries, or on formal or informal risk assessments in accordance with the norms and recommendations of the Terrestrial Code. In this regard, an exporting country may be required to prepare a complete and transparent document describing the animal health situation, including the factors required to assess the risk involved. Furthermore, expert committees of importing countries regularly evaluate and verify these conditions in exporting countries. The level of confidence in the information obtained by the expert committee can then be entered into the risk analysis equation. An important FMD risk reduction factor for the importation of animals and animal products is early recognition of the disease at the source of the commodity by alert stakeholders, such as official and private veterinarians and the chain of the livestock industry. This is true for all countries irrespective of their vaccination status. The risk posed by the importation of vaccinated animals becomes negligible when an adequate protocol--in compliance with the norms and recommendations of the Terrestrial Code--is applied. However, recently, export of live animals from countries that do not practise vaccination has also proven to pose a significant risk and the rules governing such transport may have to be reviewed. Disease surveillance, biosecurity at the farm level, traceability and control of the source cattle and slaughterhouse inspections are the main risk reduction measures for meat and meat products from vaccinated cattle. If these animals are slaughtered and processed under good management practice--in accordance with the norms and recommendations of the Terrestrial Code--these products present a negligible risk for the introduction of FMD. Risk reduction by maturation and deboning is an important procedure, but is probably overemphasised. Mechanical contamination of cattle carcasses with 'carrier virus' from the pharyngeal area during slaughter and processing is very unlikely. Risk assessments showed that the importation of milk products from countries or zones that practise vaccination of dairy herds poses a negligible risk. Risk assessments also demonstrated that the importation of bovine embryos from vaccinated cows--in accordance with the norms and recommendations of the Terrestrial Code--poses a negligible risk. Likewise, the risk from the importation of semen from vaccinated bulls is also negligible when an adequate test protocol is applied in accordance with the Terrestrial Code.

Abattoirs↗

PubMed2004

Automated identification of field-recorded songs of four British grasshoppers using bioacoustic signal recognition.

Recognition of Orthoptera species by means of their song is widely used in field work but requires expertise. It is now possible to develop computer-based systems to achieve the same task with a number of advantages including continuous long term unattended operation and automatic species logging. The system described here achieves automated discrimination between different species by utilizing a novel time domain signal coding technique and an artificial neural network. The system has previously been shown to recognize 25 species of British Orthoptera with 99% accuracy for good quality sounds. This paper tests the system on field recordings of four species of grasshopper in northern England in 2002 and shows that it is capable of not only correctly recognizing the target species under a range of acoustic conditions but also of recognizing other sounds such as birds and man-made sounds. Recognition accuracies for the four species of typically 70-100% are obtained for field recordings with varying sound intensities and background signals.

Acoustics↗

PubMed1991

Effects of preliminary information in a Go versus No-go task.

A series of studies using a Go versus No-go task examined the question of whether preliminary information available early in the recognition of a stimulus is made available to later processes before stimulus recognition is finished, a question relevant to the controversy between discrete and continuous models. Experiment 1 showed that a Go response is faster following a cue indicating that the response probably would be required than following a cue indicating it probably would not be required. Experiments 2-7 were conducted to find out whether analogous preparation occurred when probability of the Go response was signalled by easily discriminable features of a single stimulus rather than a separate cue. The effect was observed when the easily discriminable features uniquely determined the name of the stimulus letter, but not when they merely indicated that the stimulus name was one of two visually similar letters. These results are consistent with the Asynchronous Discrete Coding model, in which the perceptual system makes available to later processes only preliminary information corresponding to discretely activated stimulus attributes.

Attention↗