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At least 433 records · Page 24Linked to original sources
PubMed1985

Application of learning techniques to splicing site recognition.

Most genes of eukaryotic genomes are disrupted by introns. The application of a learning technique which uses both statistic and syntactic analysis lead to the establishment of logical rules enabling the recognition of intron/exon junctions between uncoding and coding sequences. The rules were tested on rat actin gene sequences containing some or all of the introns and 50 exon nucleotides on either side of the intron. The results show good recognition of the excision site. This recognition is more ambiguous when the sequence is short; for the acceptor sequence it presents a good selection. The learning achieved with both the donor and acceptor sequence does not lead to recognition. This result indicates that it is not the relationship between donor and acceptor sites in the same intron which determines sequence selection or the splicing mechanism.

Base Sequence↗
PubMed1982

Joining of immunoglobulin heavy chain gene segments: implications from a chromosome with evidence of three D-JH fusions.

A chromosomal segment with a unique structure around the immunoglobulin heavy chain joining region (JH) has been molecularly cloned from an Abelson murine leukemia virus-transformed cell line. Attached to JH3 in the cloned DNA, in inverted sequence, is the DNA from JH1 to the JH2 recognition sequence. The inverted segment is attached at its other end to the 5' recognition sequence of a diversity segment (D). To form this structure, three joining events must have occurred on the same chromosome. One of these events could have been a normal D-JH joining but the others must have been irregular events including ones that result in inversions. One of the joining events left fused recognition elements from JH2 and a D whose sequence shows that, during joining, reciprocal joinings of the recognition elements must occur to fuse the heptameric elements back to back. Because joined D and JH undergo deletion of terminal coding sequence during recombination but the joined heptameric recognition sequences do not contain the deleted sequence, joining must be a nonreciprocal event. Also, extra nucleotides are inserted between D and JH as part of the joining process; it is suggested that this added sequence is a product of the activity of terminal deoxynucleotidyltransferase at the D/JH (and probably the VH/D) joints and that it represents a new element of heavy chain gene structure, the N region.

Animals↗
PubMed2001

Differential cognitive processing of Kanji and Kana words: do orthographic and semantic codes function in parallel in word matching task.

Relative engagements of the orthographic and semantic codes in Kanji and Hiragana word recognition were investigated. In Exp. 1, subjects judged whether the pairs of Kanji words (prime and target) presented sequentially were physically identical to each other in the word condition. In the sentence condition, subjects decided whether the target word was valid for the prime sentence presented in advance. The results showed that the response times to the target swords orthographically similar (to the prime) were significantly slower than to semantically related target words in the word condition and that this was also the case in the sentence condition. In Exp. 2, subjects judged whether the target word written in Hiragana was physically identical to the prime word in the word condition. In the sentence condition, subjects decided if the target word was valid for the previously presented prime sentence. Analysis indicated that response times to orthographically similar words were slower than to semantically related words in the word condition but not in the sentence condition wherein the response times to the semantically and orthographically similar words were largely the same. Based on these results, differential contributions of orthographic and semantic codes in cognitive processing of Japanese Kanji and Hiragana words was discussed.

Adult↗
PubMed2002

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.

We investigate the conservation of amino acid residue sequences in 21 DNA-binding protein families and study the effects that mutations have on DNA-sequence recognition. The observations are best understood by assigning each protein family to one of three classes: (i) non-specific, where binding is independent of DNA sequence; (ii) highly specific, where binding is specific and all members of the family target the same DNA sequence; and (iii) multi-specific, where binding is also specific, but individual family members target different DNA sequences. Overall, protein residues in contact with the DNA are better conserved than the rest of the protein surface, but there is a complex underlying trend of conservation for individual residue positions. Amino acid residues that interact with the DNA backbone are well conserved across all protein families and provide a core of stabilising contacts for homologous protein-DNA complexes. In contrast, amino acid residues that interact with DNA bases have variable levels of conservation depending on the family classification. In non-specific families, base-contacting residues are well conserved and interactions are always found in the minor groove where there is little discrimination between base types. In highly specific families, base-contacting residues are highly conserved and allow member proteins to recognise the same target sequence. In multi-specific families, base-contacting residues undergo frequent mutations and enable different proteins to recognise distinct target sequences. Finally, we report that interactions with bases in the target sequence often follow (though not always) a universal code of amino acid-base recognition and the effects of amino acid mutations can be most easily understood for these interactions.

Amino Acid Sequence↗
PubMed2001

Towards defining the role of glycans as hardware in information storage and transfer: basic principles, experimental approaches and recent progress.

The term 'code' in biological information transfer appears to be tightly and hitherto exclusively connected with the genetic code based on nucleotides and translated into functional activities via proteins. However, the recent appreciation of the enormous coding capacity of oligosaccharide chains of natural glycoconjugates has spurred to give heed to a new concept: versatile glycan assembly by the genetically encoded glycosyltransferases endows cells with a probably not yet fully catalogued array of meaningful messages. Enciphered by sugar receptors such as endogenous lectins the information of code words established by a series of covalently linked monosaccharides as letters for example guides correct intra- and intercellular routing of glycoproteins, modulates cell proliferation or migration and mediates cell adhesion. Evidently, the elucidation of the structural frameworks and the recognition strategies within the operation of the sugar code poses a fascinating conundrum. The far-reaching impact of this recognition mode on the level of cells, tissues and organs has fueled vigorous investigations to probe the subtleties of protein-carbohydrate interactions. This review presents information on the necessarily concerted approach using X-ray crystallography, molecular modeling, nuclear magnetic resonance spectroscopy, thermodynamic analysis and engineered ligands and receptors. This part of the treatise is flanked by exemplarily chosen insights made possible by these techniques.

Cell Communication↗
PubMed2006

Non-coding RNA in fly dosage compensation.

Dosage compensation modulates global expression of an X chromosome and is necessary to restore the balance between X-chromosome and autosome expression in both sexes. A central question in the field is how this regulation is directed. Large non-coding RNAs, such as Xist in mammals and roX in flies, have pivotal roles in targeting chromosome-wide modification for dosage compensation. Several recent studies in Drosophila provide new insight into the principles of X-chromosome recognition and the function of non-coding RNA in this process.

Animals↗
PubMed2004

Interaction of rat poly(A)-binding protein with poly(A)- and non-poly(A) sequences is preferentially mediated by RNA recognition motifs 3+4.

Vasopressin (VP) mRNA and the non-coding BC200 RNA are sorted to neuronal dendrites. Among proteins interacting specifically with both RNAs is the multifunctional poly(A)-binding protein (PABP) consisting of four RNA recognition motifs (RRMs) and a C-terminal auxiliary domain. The protein/RNA interaction studies presented here reveal that PABPs association with VP- and BC200 RNA is exclusively mediated by RRMs 3+4. Quantitative binding studies with PABP deletion mutants demonstrate preferential binding of RRMs 3+4 even to poly(A)-homopolymers, while RRMs 1+2 exhibit a lower affinity for those sequences. An optimal interaction with both poly(A)- and non-poly(A) sequences is only achieved by full-size PABP.

Animals↗
PubMed1987

Control of replication of plasmid R1: translation of the 7k reading frame in the RepA mRNA leader region counteracts the interaction between CopA RNA and CopT RNA.

Replication of IncFII plasmids is regulated through the expression of a gene, repA. The RepA protein is rate-limiting for initiation of replication. The main negative control is exerted by a countertranscript, CopA RNA, that binds to the complementary region of the RepA mRNA, thereby inhibiting the formation of the RepA protein. The target region for CopA RNA, CopT, is located upstream of the RepA coding region. An open reading frame for a putative 7k protein overlaps the CopT sequence. Here we show by using lacZ fusions that the 7k gene is expressed. We constructed a translation start mutation in order to abolish formation of the 7k protein. This resulted in a 10-fold decrease in repA expression. The 7k protein produced in trans did not reverse this effect, so the 7k protein per se does not control expression of repA. However, translation of the 7k coding sequence must influence CopA/CopT RNA recognition, since ribosomes will transiently disrupt the target hairpin. We propose here a novel mechanism that affects the level of gene expression: the 7k region of the RepA mRNA is a leader sequence that is involved in expression of the downstream gene; translation of the 7k region competes with a negative control system involving RNA-RNA interaction.

Amino Acid Sequence↗
PubMed2005

RNA binding motif (RBM) proteins: a novel family of apoptosis modulators?

RBM5 is a known modulator of apoptosis, an RNA binding protein, and a putative tumor suppressor. Originally identified as LUCA-15, and subsequently as H37, it was designated "RBM" (for RNA Binding Motif) due to the presence of two RRM (RNA Recognition Motif) domains within the protein coding sequence. Recently, a number of proteins have been attributed with this same RBM designation, based on the presence of one or more RRM consensus sequences. One such protein, RBM3, was also recently found to have apoptotic modulatory capabilities. The high sequence homology at the amino acid level between RBM5, RBM6, and particularly, RBM10 suggests that they, too, may play an important role in regulating apoptosis. It is the intent of this article to ammalgamate the data on the ten originally identified RBM proteins in order to question the existence of a novel family of RNA binding apoptosis regulators.

Alternative Splicing↗
PubMed1993

Inhibition of herpes simplex virus type 1 DNA replication by mutant forms of the origin-binding protein.

The herpes simplex virus type 1 (HSV-1) origin-binding protein (OBP) is a sequence-specific DNA binding protein encoded by gene UL9 which interacts with the viral origins of DNA replication and also exhibits DNA helicase activity. Sequence-specific DNA binding activity has previously been shown to reside within the C-terminal 317 amino acids, and when expressed alone, this domain exerts a dominant inhibitory effect on HSV-1 DNA synthesis. We have tested several UL9 gene mutants for ability to support or interfere with viral DNA replication. Mutants affected in an ATP binding motif presumed to be associated with DNA helicase activity (ATP-), or defective in origin binding (OBP-) were unable to support replication in a transient assay for HSV-1 origin-dependent DNA synthesis. When the products were screened for their ability to interfere with replication, the ATP- but not the OBP- mutant was inhibitory. Introduction of a mutation which abolished origin-binding activity into the isolated C-terminal fragment also removed the ability to interfere. The C-terminal fragment retained inhibitory activity when the wild-type (wt) protein was specified by a plasmid in which an OBP recognition site within the UL9 gene coding region had been mutated so as to prevent binding without affecting the encoded amino acids. These results suggest that in this assay inhibition of DNA synthesis probably results primarily from competition between mutant and wt forms of OBP for binding to the viral replication origins. The infectivity of HSV-1 DNA in co-transfection experiments was greatly reduced by mutant UL9 proteins which interfered with origin-dependent DNA replication and also by high level expression of the wt polypeptide.

Animals↗
PubMed1991

Expression in Escherichia coli of the genes coding for reaction center subunits from Rhodobacter sphaeroides: wild-type proteins and fusion proteins containing one or four truncated domains from Staphylococcus aureus protein A at the carboxy-terminus.

Gene cassettes were constructed containing Rhodobacter sphaeroides puhA, pufM and pufL sequences with synthetic 5' ends for production in Escherichia coli of the H, M and L subunits of the photosynthetic reaction center. In addition, gene cassettes coding for fusion proteins with proteinase recognition site(s) between the amino-terminal part of H, M or L subunits, and the carboxy-terminal part consisting of one (B') or four (D'ABC') domains of Staphylococcus aureus protein A were constructed. A modified expression vector pDS12/RBSII containing the T5 promoter PN25, the lac operator, and a newly inserted E. coli lipoprotein ribosome-binding site was used. Inducible synthesis of plasmid-encoded polypeptides was accompanied by reduced growth. The products comigrated with R. sphaeroides reaction center subunits H, M and L. They were identified by Western blot experiments using antibodies raised against reaction center proteins. The hybrid protein containing the reaction center H subunit fused to the single domain B' was not detected by nonspecific antisera. In contrast, the three fusion proteins containing domains D'ABC' were identified using nonspecific antisera. This indicated that domains D'ABC' were sufficient to bind to the Fc part of IgG molecules, whereas domain B' was not sufficient. This property was used to purify all three fusion proteins with domains D'ABC' by affinity chromatography from the membrane fraction of E. coli cells.

Amino Acid Sequence↗
PubMed2006

Neural evidence for intermediate representations in object recognition.

The lateral occipital complex (LOC), a cortical region critical for human object recognition, has been shown to primarily code the shape, rather than the surface properties, of an object. But what aspects of shape? Using an fMRI-adaptation (fMRI-a) paradigm in which subjects judged whether two contour-deleted images of objects were the same or different exemplars, virtually all the adaptation in LOC [especially in LOC's most anterior portion (pFs)] could be attributed to repetition of the parts, almost none to the repetition of local image features, such as lines or vertices, templates, or basic- or subordinate-level concepts of the object. These results support the hypothesis that the neural representation of shape in LOC is an intermediate one, encoding the parts of an object.

Adaptation, Psychological↗
PubMed1997

Distributed Learning, Recognition, and Prediction by ART and ARTMAP Neural Networks.

A class of adaptive resonance theory (ART) models for learning, recognition, and prediction with arbitrarily distributed code representations is introduced. Distributed ART neural networks combine the stable fast learning capabilities of winner-take-all ART systems with the noise tolerance and code compression capabilities of multilayer perceptrons. With a winner-take-all code, the unsupervised model dART reduces to fuzzy ART and the supervised model dARTMAP reduces to fuzzy ARTMAP. With a distributed code, these networks automatically apportion learned changes according to the degree of activation of each coding node, which permits fast as well as slow learning without catastrophic forgetting. Distributed ART models replace the traditional neural network path weight with a dynamic weight equal to the rectified difference between coding node activation and an adaptive threshold. Thresholds increase monotonically during learning according to a principle of atrophy due to disuse. However, monotonic change at the synaptic level manifests itself as bidirectional change at the dynamic level, where the result of adaptation resembles long-term potentiation (LTP) for single-pulse or low frequency test inputs but can resemble long-term depression (LTD) for higher frequency test inputs. This paradoxical behavior is traced to dual computational properties of phasic and tonic coding signal components. A parallel distributed match-reset-search process also helps stabilize memory. Without the match-reset-search system, dART becomes a type of distributed competitive learning network.

Journal Article↗
PubMed1982

Superattenuation in the tryptophan operon of Serratia marcescens.

Deletions were generated in vitro in the leader region of the tryptophan operon of Serratia marcescens and subsequently incorporated into the Escherichia coli chromosome in single copy form. Deletions which removed the translation start codon for the leader peptide or which ended in the ribosome recognition region preceding the leader peptide coding segment, caused superattenuation, that is, increased transcription termination at the attenuator. Apparently, the capacity to initiate translation of this coding region modulates expression of the operon.

Base Sequence↗
PubMed2005

Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes.

Rapid, multiplexed, sensitive and specific molecular detection is of great demand in gene profiling, drug screening, clinical diagnostics and environmental analysis. One of the major challenges in multiplexed analysis is to identify each specific reaction with a distinct label or 'code'. Two encoding strategies are currently used: positional encoding, in which every potential reaction is preassigned a particular position on a solid-phase support such as a DNA microarray, and reaction encoding, where every possible reaction is uniquely tagged with a code that is most often optical or particle based. The micrometer size, polydispersity, complex fabrication process and nonbiocompatibility of current codes limit their usability. Here we demonstrate the synthesis of dendrimer-like DNA-based, fluorescence-intensity-coded nanobarcodes, which contain a built-in code and a probe for molecular recognition. Their application to multiplexed detection of the DNA of several pathogens is first shown using fluorescence microscopy and dot blotting, and further demonstrated using flow cytometry that resulted in detection that was sensitive (attomole) and rapid.

Bacillus anthracis↗
PubMed2006

Performance and behaviour of rabbit does in a group-housing system with natural mating or artificial insemination.

This study compared reproductive performance and behaviour of does raised in a group-housing system and in a regular cage system. The group-housing pen was divided into different functional areas for suckling, resting, and eating and special hiding areas for kits when they had left the nest-boxes and does to favour the species specific behavioural traits. Does had access to their nest-box by means of an individual Electronic Nest-box Recognition System (ENRS) activated by a coded transponder placed in their eartags. Eight does were housed in each pen. Natural mating (NM, with a buck in the group) or artificial inseminations (AI) were applied. Litter size, kit mortality and kit weight at 14 d of age were similar for group-housing and cages when NM were applied. With a natural reproduction rhythm group-housing led to an increase of +38% of litters. However, from a management point of view, a cycled production system with AI is preferred. With AI and group-housing, a lower kindling rate and a lower kit weight at weaning were found. The lower kindling rate was partly caused by pseudo-pregnancies that were found in 23% (P < 0.01) of the does in the group-housing system against 0% in the control group. Sixteen to 20% of the does in the group-housing system had skin injuries, which is an indicator for aggression among does. Most of the injuries were seen on the body and most of them were superficial bites. Based on the results of this study, it can be concluded that group-housing of rabbit does seems possible, but more research is needed to solve the problems of the decreased kindling rate and occurrence of pseudo-pregnancies, the lower weight at weaning and aggressiveness among does.

Aggression↗
PubMed1999

Quantitative-trait locus for specific language and reading deficits on chromosome 6p.

Reading disability (RD), or dyslexia, is a complex cognitive disorder manifested by difficulties in learning to read, in otherwise normal individuals. Individuals with RD manifest deficits in several reading and language skills. Previous research has suggested the existence of a quantitative-trait locus (QTL) for RD on the short arm of chromosome 6. In the present study, RD subjects' performance in several measures of word recognition and component skills of orthographic coding, phonological decoding, and phoneme awareness were individually subjected to QTL analysis, with a new sample of 126 sib pairs, by means of a multipoint mapping method and eight informative DNA markers on chromosome 6 (D6S461, D6S276, D6S105, D6S306, D6S258, D6S439, D6S291, and D6S1019). The results indicate significant linkage across a distance of at least 5 cM for deficits in orthographic (LOD = 3.10) and phonological (LOD = 2.42) skills, confirming previous findings.

Adult↗