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'Recognition units' at the top of a neuronal hierarchy? Prepacemaker neurons in Eigenmannia code the sign of frequency differences unambiguously.

The electric fish, Eigenmannia, is able to discriminate the sign of the frequency difference, Df, between a neighbor's electric organ discharges (EODs) and its own. The fish lowers its EOD frequency for positive Dfs and raises its frequency for negative Dfs to minimize jamming of its electrolocation ability by a neighbor's EODs of similar frequency. This jamming avoidance response (JAR) is controlled by a group of 'sign-selective' neurons in the prepacemaker nucleus (PPN) that is located at the boundary of the midbrain and the diencephalon (Fig. 1). Extracellular recordings from a total of 35 neurons revealed a great similarity between behavioral and neuronal response properties: 1. All neurons fired vigorously for negative Dfs and were almost silent for positive Dfs, regardless of the orientation of the jamming stimulus, and thus discriminated the sign of Df unambiguously (Fig. 2). 2. In accordance with behavioral observations, individual neurons failed to discriminate the sign of Df when the jamming stimulus had the same field geometry as the signal mimicking the animal's own EOD (Fig. 3). 3. Df magnitudes which evoke strongest JARs, usually 4 to 8 Hz, also induced most vigorous responses in sign-selective neurons (Fig. 5). 4. Behavioral and neuronal thresholds for the detection of small jamming signals were similar. Threshold for sign selectivity was reached when the amplitude ratio of the jamming signal to the EOD mimic, measured near the head surface, was 0.001. This value corresponds to a maximal temporal disparity (a necessary cue for performing a correct JAR) of 1 to 2 microseconds for signals received by the two sides of the body in a transverse jamming field (Fig. 7). 5. The effects of two jamming fields, offered orthogonally to each other, may interact nonlinearly at the behavioral as well as at the neuronal level. A positive Df presented in one field may suppress behavioral and neuronal responses to modulations of the sign of Df in the other field (Fig. 8c).

Animals

Nucleotide sequence of the gene encoding pilin of Bacteroides nodosus, the causal organism of ovine footrot.

The nucleotide sequence encoding pilin, the monomer protein subunit of the pilus from Bacteroides nodosus, has been determined. The sequence predicts a short, positively charged, amino-terminal segment which is absent from the amino acid sequence of mature pilin. The coding sequence is preceded upstream by a sequence of five nucleotides complementary to the 3' end of 16S rRNA of Escherichia coli--a potentially good ribosome binding site--and even further upstream by an AT-rich region preceding several potential recognition sites for RNA polymerase. The coding sequence is followed by a region of hyphenated dyad symmetry having the potential to act as a rho-independent terminator of transcription.

Amino Acid Sequence

Assessment of protein coding measures.

A number of methods for recognizing protein coding genes in DNA sequence have been published over the last 13 years, and new, more comprehensive algorithms, drawing on the repertoire of existing techniques, continue to be developed. To optimize continued development, it is valuable to systematically review and evaluate published techniques. At the core of most gene recognition algorithms is one or more coding measures--functions which produce, given any sample window of sequence, a number or vector intended to measure the degree to which a sample sequence resembles a window of 'typical' exonic DNA. In this paper we review and synthesize the underlying coding measures from published algorithms. A standardized benchmark is described, and each of the measures is evaluated according to this benchmark. Our main conclusion is that a very simple and obvious measure--counting oligomers--is more effective than any of the more sophisticated measures. Different measures contain different information. However there is a great deal of redundancy in the current suite of measures. We show that in future development of gene recognition algorithms, attention can probably be limited to six of the twenty or so measures proposed to date.

Algorithms

Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox.

The 40,000-fold variation in eukaryote haploid DNA content is unrelated to organismic complexity or to the numbers of protein-coding genes. In eukaryote microorganisms, as well as in animals and plants, DNA content is strongly correlated with cell volume and nuclear volume, and with cell cycle length and minimum generation time. These correlations are simply explained by postulating that DNA has 2 major functions unrelated to its protein-coding capacity: (1) the control of cell volume by the number of replicon origins, and (2) the determination of nuclear volume by the overall bulk of the DNA: cell growth rates are determined by the cell volume and by the area of the nuclear envelope available for nucleocytoplasmic transport of RNA, which in turn depends on the nuclear volume and therefore on the DNA content. During evolution nuclear volume, and therefore DNA content, has to be adjusted to the cell volume to allow reasonable growth rates. The great diversity of cell volumes and growth rates, and therefore of DNA contents, among eukaryotes results from a varying balance in different species between r-selection, which favours small cells and rapid growth rates and therefore low DNA C-values, and K-selection which favours large cells and slow growth rates and therefore high DNA C-values. In multicellular organisms cell size needs to vary in different tissues: size differences between somatic cells result from polyteny, endopolyploidy, or the synthesis of nucleoskeletal RNA. Conflict between the need for large ova and small somatic cells explains why lampbrush chromosomes, nurse cells, chromatin diminution and chromosome elimination evolved. Similar evolutionary considerations clarify the nature of polygenes, the significance of the distribution of haploidy, diploidy and dikaryosis in life cycles and of double fertilization in angiosperms, and of heteroploidy despite DNA constancy in cultured cells, and other puzzles in eukaryote chromosome biology. Eukaryote DNA can be divided into genic DNA (G-DNA), which codes for proteins (or serves as recognition sites for proteins involved in transcription, replication and recombination), and nucleoskeletal DNA (S-DNA) which exists only because of its nucleoskeletal role in determining the nuclear volume (which it shares with G-DNA, and performs not only directly, but also indirectly by coding for nucleoskeletal RNA). Mechanistic and evolutionary implications of this are discussed.

Animals

Structure of rat calmodulin processed genes with implications for a mRNA-mediated process of insertion.

Two distinct processed calmodulin genes of rat (lambda SC8 and lambda SC9) were identified, cloned and their DNA sequences determined. The existence of direct repeats of 19 base-pairs for lambda SC8 or 9 base-pairs for lambda SC9 at both ends of the coding plus non-coding regions suggested a possible involvement of a mRNA-mediated process of insertion. Total genomic Southern hybridization suggested the existence of at least three different calmodulin-related genes in the rat genome. The other gene was the bona fide calmodulin gene (lambda SC4) which was split into at least five exons. lambda SC9 contained insertions of one nucleotide and two 17 base-pair direct repeats in the coding region. These insertions cause frameshift mutations probably preventing it from encoding a functional calmodulin. It also carried an insertion of a rat middle repetitive sequence, identifier sequence (IDS: Sutcliffe et al., 1982) in the 3'-non-coding region. Otherwise, it consisted of an almost identical DNA sequence to that of the bona fide calmodulin gene (lambda SC4), including the 3'-non-coding region down to the poly(A) recognition signal, A-A-T-A-A-A. On the other hand, lambda SC8 did not possess frameshift mutations in the coding region, and hence was capable of encoding a functional protein. In fact, a probe specific to the lambda SC8 sequence identified a band in Northern blotting whose size was 300 nucleotides smaller than that of authentic calmodulin mRNA. Comparison of the nucleotide sequences showed that only the coding regions of these two processed genes were homologous, indicating that the divergence of these two processed genes from the common ancestor calmodulin was an ancient event.

Amino Acid Sequence

Animal lectins as cell adhesion molecules.

Protein-carbohydrate interaction is exploited in cell adhesion mechanisms besides the recognition of peptide motifs. The sugar code thus significantly contributes to the intriguing specificity of cellular selection of binding partners. Focusing on two classes of lectins (selectins and galectins), it is evident that their functionality for mediation of adhesive contacts is becoming increasingly appreciated, as is the integration of this type of interaction with other recognition modes to yield the noted specificity. The initial contact formation between leukocytes and activated endothelium makes use of selectins to guide lymphocyte trafficking. In addition to the three selectins which bind a distinct array of ligands, galectin-1 and galectin-3 and possibly other members of this family are involved in cell-cell or cell-matrix interactions. This review summarizes structural and functional aspects of these two classes of endogenous lectins relevant for cell adhesion.

Animals

Recognition of follicle stimulating hormone (alpha-subunit) by a recombinant receptor protein domain coded by an alternately spliced mRNA and expressed in Escherichia coli.

To assess the functional significance of putative proteins encoded by alternately spliced mRNA of the sheep testicular FSH receptor, a short form cDNA comprising of the first four exons (117 residues mature protein) was engineered for expression in Escherichia coli. The expressed protein of molecular mass 15 kDa was purified to homogeneity and verified by reaction with an antibody against a synthetic peptide sequence unique to the amino (N)-terminal region FSH receptor. The purified FSH receptor domain protein bound 125I-labeled hFSH in a ligand blot on polyvinylidine difluoride membranes. Further analyses by slot blot revealed high affinity of the immobilized protein with significant reaction at 10 pmol. As the immobilized receptor protein also reacted with structurally related hormones (125I-labeled LH/125I-labeled human chorionic gonadotropin), we confirmed that interaction most probably occurred via the common alpha-subunit of these glycoprotein hormones. Our results reveal that this N-terminal portion of the FSH receptor contain(s) major site(s) for hormone recognition that could be mediated via the alpha-subunit. A rabbit antibody to the receptor inhibited FSH action in receptor bearing cells, revealing the utility of such recombinant FSH receptor protein(s) for modulation of hormone action.

Alternative Splicing

Cloning and sequencing of the yeast Saccharomyces cerevisiae SEC1 gene localized on chromosome IV.

The SEC1 gene of yeast Saccharomyces cerevisiae was cloned by complementing the temperature-sensitive mutation of sec1-1 at 37 degrees C, and its nucleotide sequence was determined. SEC1 is a single copy gene and encodes a protein of 724 amino acids and 83,490 daltons with a predicted pI value of 6.11. Hydrophobicity plotting showed no clearly hydrophobic regions suggesting a soluble nature for the protein. Amino acid sequence comparisons revealed no obvious homologies with the proteins in the SWISSPROT databank. Two consensus sequence for the cdc2 encoded protein kinase recognition site were revealed within Sec1p. The codon usage suggests a low expression level for SEC1. The 5' non-translated region contains two TATA-like sequences at -52 and -215 nucleotides from the translation start site. Two potential regulatory sequences for DNA binding proteins were found in the non-coding 5' region: a HAP2/HAP3 consensus recognition sequence at nucleotide-154 and a BAF1 consensus recognition sequence at nucleotide-136. The SEC1 specific probe detected a 2400 nucleotides long transcript, which was in reasonable agreement with the 2172 nucleotides long open reading frame.

Amino Acid Sequence

Avoidance of DNA methylation. A virus-encoded methylase inhibitor and evidence for counterselection of methylase recognition sites in viral genomes.

The ocr+ gene of bacterial virus T7 codes for the first protein recognized to inhibit a specific group of DNA methylases. The recognition sequences of several other DNA methylases, not susceptible to Ocr inhibition, are significantly suppressed in the virus genome. The bacterial virus T3 encodes an Ado-Met hydrolase, destroying the methyl donor and causing T3 DNA to be totally unmethylated. These observations could stimulate analogous investigations into the regulation of DNA methylation patterns of eukaryotic viruses and cells. For instance, an underrepresentation of methylation sites (5'-CG) is also true for animal DNA viruses. Moreover, we were able to disclose some novel properties of DNA restriction-modification enzymes concerning the protection of DNA recognition sequences in which only one strand can be methylated (e.g., type III enzyme EcoP15) and the primary resistance of (unmethylated) DNA recognition sites towards type II restriction endonuclease EcoRII.

Base Sequence

6-Phosphogluconate dehydrogenase activity variants in Musca domestica L.: A further allele at the Pgd locus as proved by densitometric assay.

A new electrophoretic variant of 6-phosphogluconate dehydrogenase (6PGD) has been detected in flies of a laboratory Musca domestica strain. This variant is to be added to the two already described, PGD-A and PGD-B, identified by a fast-weak and a slow-thick electrophoretic band, respectively. The new variant, PGD-C, has the same mobility as PGD-A but provides a more intensely stained band; therefore it can be described as a fast-thick phenotype. The staining intensity of PGD-C is slightly lower than that of PGD-B. Genetic and densitometric tests have shown that the different levels of enzymatic activity of the two fast variants A and C are inherited as alternative genetic units, and they have been interpreted as one aspect of the phenotypic expression of two Pgd alleles, namely, PgdA and PgdC. These alleles determine both the rates of electrophoretic mobility (fast in both cases) and the levels of activity (low for A, strong for C; shown by weak or thick stained electrophoretic bands). Similarly, the two distinctive features of PGD-B, namely, slow mobility and high activity level, are always jointly inherited and appear as two pleiotropic aspects of the phenotype coded for by the PgdB allele. The PgdB/PgdC heterozygous flies provide a slightly asymmetrical three-banded zymogram, while the PgdA/PgdC combination leads to a single-banded pattern, showing the same mobility as the parents and an intermediate staining intensity. The quantitative analysis of enzyme activity of 6PGD zymograms, performed through densitometric methods, has led to the recognition of three different activity levels coded for by Pgd alleles, one of which, namely, PgdC, would not have been detected using electrophoretic methods alone.

Alleles

Analysis of WISC-R coding performance of normal and dyslexic readers.

WISC-R scores were examined for 25 normal readers and 25 dyslexic readers, with particular emphasis on the groups' performance on the Coding subtest. Subjects were also administered a series of experimental tasks assessing writing speed, copying speed, and recognition memory for the number/symbol associates of the Coding subtest. Dyslexics performed significantly more poorly than the normal readers on the Coding subtest and the writing speed task but showed no evidence of impaired memory for the number/symbol associates. These results are discussed in terms of their implication for profile analysis in general and in terms of their contribution to understanding the significance of the low Coding scores frequently observed among dyslexic readers.

Brain Damage, Chronic

Evolution of the major histocompatibility complex.

The major histocompatibility complex is a group of closely linked loci that code for molecules used by T-lymphocytes as context for the recognition of antigens. The loci fall into two classes: I, coding for molecules used as context by cytotoxic T-lymphocytes and II, used as context by helper and other regulatory T-cells. The Mhc is present in all mammals and perhaps all vertebrates. Some of the Mhc loci are highly polymorphic, while others are not. This article will summarize what is known about the genetic organization of the Mhc in different species and will discuss the selection pressures acting on the individual loci and the tempo and the mechanisms of their evolution.

Animals

Sensory and meaning features in stimulus recognition and associative retrieval.

Three experiments addressed the problem of isolating the effects of sensory similarity on subprocesses involved in coding paired associates. In the first, the standard recognition-recall procedure was used and stimulus similarity, concreteness, and frequency were varied. However, because of concern with the validity of this recognition procedure as a measure of functional stimulus contact, an alternative was developed. This alternative led to the second study in which only stimulus similarity was manipulated. In the third experiment, similarity was varied, and the pairs were either associatively compatible, unrelated, or incompatible. The results using the new procedure indicated that similarity consistently disrupted functional stimulus contact but not associative retrieval. By contrast, associative relatedness facilitated both subprocesses.

Adolescent

Speech recognition with a CIS strategy for the ineraid multichannel cochlear implant.

Wilson et al. proposed a new sound-processing strategy for multichannel cochlear implants, the Continuous Interleaved Sampling (CIS) strategy. Their study was performed on seven American patients, selected for their excellent performance with the Ineraid multichannel cochlear implant, and involved refined testing of several parameter modifications of the CIS strategy during a 1-week period. At the end of the week, the CIS strategy produced large improvements in speech-recognition tests for all subjects. To evaluate the generality of this promising result, the goal of this study was to assess whether similar improvements of performance could be observed in a typical population of Ineraid users and implemented as a clinical protocol. Therefore we designed one unique, predetermined CIS processor that could be temporarily fitted to the patients in < 2 h, and we evaluated speech recognition with consonant-and vowel-identification tests in a group of patients with performances ranging from star to almost chance levels and speaking six different native languages. Scores of vowel and consonant identifications obtained with this predetermined CIS processor and with the standard processor of the Ineraid system were compared in 15 Ineraid users. Fourteen of 15 patients had significantly better scores of consonant identification with the new CIS strategy. The group mean scores of vowel identification with either strategy were not statistically different. In agreement with these observations, most patients immediately reported that the CIS strategy sounded subjectively "more clear" for real-time speech recognition. It is now possible to implement a CIS speech-coding strategy as a standard clinical procedure to improve speech-recognition performances of all Ineraid users.

Adolescent

A cluster of mutations in HLA-A2 alpha 2 helix abolishes peptide recognition by T cells.

In order to investigate the regions of HLA-A2 that control peptide-specific cytotoxic T lymphocyte (CTL) recognition, 37 HLA-A2 genes coding for 50 point mutations that span the alpha 2 helix were synthesized by the technique of saturation mutagenesis. Twenty-nine of these genes, which code for 41 point mutations, were transfected into C1R cells and used as targets in cytotoxicity assays, in the presence of influenza-A matrix peptide 58-68 with specific CTL as effectors. All the transfectants were recognized fully by matrix peptide-specific CTL apart from those with amino acid substitutions at positions 152, 154, 155, 156, or 161, which led to a total loss of recognition and those with mutations at residue 27 or a double mutation at 138 and 150, which were recognized in an intermediate manner. The clustering of the crucial residues that emerges may reflect direct interaction of their side-chains with peptide or the CTL receptor.

Cell Line

The major histocompatibility complex determines susceptibility to cytotoxic T cells directed against minor histocompatibility antigens.

Cytotoxic cells were generated by immunizing one strain of mouse with cells from an allogeneic strain which carries the same H-2 region. The effector cells assayed in a 4 h 51Cr release assay were shown to be T cells and indistinguishable, except in specificity, from cytotoxic T cells directed at H-2 alloantigens. Although the genetic differences between responder and stimulator cells responsible for the immunization did not code in H-2, the H-2 complex did restrict susceptibility of target cells. For example, BALB.B cytotoxic cells (H-2b) immunized against and capable of lysing C57BL/6 cells (H-2b) would not lyse B6.C/H-2d target cells. C57BL/6 and B6.C/H-2d are congenic and differ in the H-2 region. Two hypotheses are considered to explain the H-2 restriction of susceptibility to cytotoxic T cells generated by an H-2 identical alloimmunization. (a) The dual (self) recognition hypothesis states that the cytotoxic cell has two recognition units, one for H-2-coded structures and another clonally restricted receptor for the minor alloantigen. (b) The interaction antigen hypothesis states that all the surface alloantigenic determinants recognized by cytotoxic T cells are the result of interaction between H-2- and non-H-2-coded gene products. Two lines of evidence, one with F1 effector cells and the other a cold target competition experiment, are presented which argue strongly in favor of the interaction antigen hypothesis. The regions of H-2 required to be histocompatible were mapped to the D region and to the left of IC, probably the K region. These results, and recent work on the response to virus-infected and TNP-modified syngeneic cells, suggest that cytotoxic cells are restricted in specificity to preferentially recognizing alterations in structures that are coded in the major histocompatibility complex.

Animals

[The HLA system. An introduction].

The cellular identity is determined by the cell surface antigens. The recognition of self and non-self in vertebrates is mainly controlled by antigens and coded for by the major histocompatibility complex (MHC). Upon recognition of a foreign antigen, the immune system does not only initiate a reaction with the help of cytotoxic T-cells, phagocytes and humoral antibodies; memory cells are also generated, enabling a very swift and powerful response after repeated exposure to the same foreign antigens. These characteristics, although essential for the survival of the organism in a hostile environment, can markedly limit the life of useful and potentially lifesaving organ transplants.

Graft Rejection