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In this paper various aspects of codon usage and k-tuple correlations in the DNA are compared. It is shown that the correlation structures of the coding and the non-coding regions are very similar and that codon usage is reasonably specific for large groups of organisms. These results suggest that the origin of codon usage is related to the origin and structure of the DNA.
The genetic code is an instantaneous code i.e., each codon is deciphered out of ambiguities without knowing other symbols than the constituting nucleotides. Moreover entropy of the genetic source of information has a maximal value.
The 5' region of YP2 cDNA, a follicular epithelium yolk protein subunit in the moth, Plodia interpunctella, shows that the polypeptide contains an extended internal coding region. Partial cDNA clones for YP2 were isolated from a pharate adult female ovarian cDNA expression library in Lambda Zap II by screening with antigen selected YP2 antiserum. The 5' sequence of the YP2 transcript was determined by 5' RACE PCR of ovarian mRNA using YP2 sequence-specific nested primers. The combined cDNA and 5' RACE sequencing showed the YP2 transcript to be 1971 bp in length up to the poly(A) tail with a single open reading frame for a predicted polypeptide of 616 amino acids. Northern analysis showed a single YP2 transcript to be present in ovarian RNA that was approximately 2 kb in length. The predicted amino acid sequence for YP2 from P. interpunctella is most closely related to egg specific protein (ESP) from Bombyx mori and the partial YP2 sequence from Galleria mellonella. YP2 from P. interpunctella also is similar to vertebrate lipases and contains a conserved lipid binding region. However, the 5' coding region of YP2 from P. interpunctella contains an in-frame insert of approximately 438 bp that had replaced an approximately 270-bp region as compared with ESP from B. mori and YP2 of G. mellonella. This suggests that the insert occurred by a recombinational event internal to the YP2 structural gene of P. interpunctella.
The 'oscillations' which have been observed in the visual cortex of cats and monkeys in the case of moving targets are discussed in relation to a temporal coding based on the arrival times of spikes or bursts. A decoding process for this temporal coding is proposed in which neurons work in a correlator mode. In the case of motion analysis, periodic resetting is needed to avoid information jamming. This resetting is proposed to be responsible for the 'oscillations'. Good initial synchronization is required for the decoding process to be performed efficiently. A diffusive process based on interdendritic ionic currents is proposed and shown to operate efficiently, without any loss of spatial and temporal resolving powers.
The MXI1 gene encodes a protein interacting with Max, a regulatory factor of the Myc oncogene, and is located on chromosome 10q25, a region showing frequent loss of heterozygosity in malignant gliomas. We have reassessed the coding sequence of MXI1 and found that, at the 3' end, the open reading frame is 28 codons shorter than previously described. We have also found an AAAAC polymorphic repeat (two alleles, 45% heterozygosity) in the 3' non-coding region of the gene. Six anaplastic astrocytomas and nine glioblastomas, the most malignant form of glioma, were informative for this polymorphism. Loss of heterozygosity was demonstrated in all glioblastomas, but not in the remaining tumors.
Pemphigus vulgaris (PV) is a potentially lethal skin disease in which epidermal blisters occur as the result of the loss of cell-cell adhesion caused by the action of autoantibodies against a keratinocyte cell surface glycoprotein, the PV antigen (PVA). This latter protein is a member of the desmoglein subfamily of the cadherin superfamily of cell-cell adhesion molecules, present in the desmosome type of intercellular junction. The other two known desmogleins are DGI, which is a target antigen in another autoantibody-mediated blistering disease of the epidermis, pemphigus foliaceous, and HDGC, which is expressed in the basal layer of the epidermis and in the simple epithelium of, for example, the colon. Genes coding for DGI (DSG1) and HDGC (DSG2) have previously been assigned to human chromosome 18. We now present evidence, using a polymerase chain reaction assay, that DSG3, the gene coding for PVA, is assigned to the same chromosome.
Shand (Cognitive Psychology, 1982, 14, 1-12) hypothesized that strong reliance on a phonetic code by hearing individuals in short-term memory situations reflects their primary language experience. As support for this proposal, Shand reported an experiment in which deaf signers' recall of lists of printed English words was poorer when the American Sign Language translations of those words were structurally similar than when they were structurally unrelated. He interpreted this result as evidence that the deaf subjects were recoding the printed words into sign, reflecting their primary language experience. This primary language interpretation is challenged in the present article first by an experiment in which a group of hearing subjects showed a similar recall pattern on Shand's lists of words, and second by a review of the literature on short-term memory studies with deaf subjects. The literature survey reveals that whether or not deaf signers recode into sign depends on a variety of task and subject factors, and that, contrary to the primary language hypothesis, deaf signers may recode into a phonetic code in short-term recall.
The nucleotide sequence from the 5' terminus to nucleotide 3822 has been determined for the genome of the enterovirus, coxsackievirus B3 (CB3). This region encompasses the 5'-terminal 738 nucleotide non-coding sequence and the region which codes for the four viral capsid proteins and for the initial products of the P2 region. Regions in the 5' non-translated RNA sequence which may be involved with a structural and/or regulatory role are discussed.
Desmoglein is a transmembrane glycoprotein of the cadherin superfamily present in the desmosomal junction in vertebrate epithelial cells. At least two variants of desmoglein are differentially expressed in human tissues: DGI, a characteristic desmosomal protein; and HDGC, which is, for example, expressed in the simple epithelium of the colon. Using a PCR assay, we were able to assign DSG2, the gene coding for desmoglein HDGC, to chromosome 18, the same chromosomal localization to which we have previously assigned DSG1 coding for desmoglein DGI.
Human L-ficolin (FCN) is a serum lectin characterized by a collagen-like and a fibrinogen-like domain that can activate the lectin pathway of complement. Structural and functional similarities to mannose-binding lectin (MBL) suggest a role for L-ficolin in innate immunity. Structural polymorphisms in the MBL2 gene lead to functional deficiency of MBL. Polymorphisms in the FCN2 gene have not been studied previously. We developed 10 denaturing gradient gel electrophoresis (DGGE) assays to screen a total of 188 Dutch Caucasians for polymorphisms in FCN2. Total gene screening in this large cohort revealed 10 single nucleotide polymorphisms (SNPs). Interestingly, two conserved coding SNPs were found in exon 8, leading to amino acid substitutions within the fibrinogen-like domain. Fibrinogen-like domains are highly conserved among several proteins in many species. As this domain is responsible for binding of L-ficolin, these newly found coding polymorphisms could alter the affinity of the protein for its substrates and possibly alter the ability of L-ficolin to recognize invading microorganisms.
CABYR is a highly polymorphic, sperm flagellar calcium-binding protein that is tyrosine as well as serine/threonine phosphorylated during capacitation. Six alternative splice variants of human CABYR (I-VI) have previously been identified, involving two coding regions, CR-A and CR-B, separated by an intervening stop codon. It is presently unknown if proteins encoded by the predicted coding region B of CABYR are translated during spermiogenesis, where they localize, or which CABYR isoforms bind calcium. Immunofluorescent and electron microscopic studies using polyclonal antibodies generated to the recombinant c-terminal 198 aa CABYR-B localized the isoforms containing CABYR-B to the ribs and longitudinal columns of the fibrous sheath in the principal piece of the flagellum. Antisera to recombinant CABYR-A and CABYR-B proteins recognized distinct populations of CABYR isoforms encoded by either CR-A alone and/or CR-B as well as a common population of CABYR isoforms. Only the recombinant CABYR-A and not the CABYR-B bound calcium in vitro, which is consistent with the hypothesis that CABYR-A is the only form that binds calcium in sperm. These observations confirmed that, despite the presence of the stop codon in CR-A, splice variants containing CR-B are expressed during spermiogenesis and assemble into the fibrous sheath of the principal piece; however, calcium binding occurs only to those CABYR isoforms containing CABYR-A.
An important approach in visual neuroscience considers how the function of the early visual system relates to the statistics of its natural input. Previous studies have shown how many basic properties of the primary visual cortex, such as the receptive fields of simple and complex cells and the spatial organization (topography) of the cells, can be understood as efficient coding of natural images. Here we extend the framework by considering how the responses of complex cells could be sparsely represented by a higher-order neural layer. This leads to contour coding and end-stopped receptive fields. In addition, contour integration could be interpreted as top-down inference in the presented model.
The experiments presented here were designed to determine the origin of the temporally complex activity of antennal lobe projection neurons in the cockroach olfactory system. We determined this through the use of complex chemical stimuli that evoked neural activity recorded extracellularly from olfactory sensory neurons and intracellularly from antennal lobe projection neurons in the cockroach Periplaneta americana. Olfactory information was represented by a simple, short time-scale rate code in the olfactory sensory neurons. This rate code input from the sensory neurons was processed by the antennal lobe and transformed into a longer time-scale, temporally encoded output expressed across a smaller population of antennal lobe projection neurons. The projection neuron responses comprised temporal patterns of increases and decreases in spike frequency that differed among projection neurons and were consistent among repeated presentations of the same stimulus. Presentation of simple and complex chemical stimuli showed that the complexity of projection neuron activity was a product of the antennal lobes and was not associated with the chemical complexity of the stimulus. To characterize the encoding schemes used by each class of neurons, the responses were decomposed into their principal components. The stimulus was correlated with only the first principal component of the activity of sensory neurons, which is consistent with a rate encoding scheme. The stimulus was correlated with higher order principal components of the activity of projection neurons, which is consistent with a temporal encoding scheme.
Extracellular matrix proteins are a diverse family of secreted proteins and glycoproteins that are responsible for a variety of critical functions in different tissues. A large number of multiexon genes encode these proteins of the extracellular matrix. Over the last few years, it has become evident that the processing of the pre-mRNA from several of these genes involves alternative splicing. This review summarizes the known examples of alternative splicing in genes coding for the extracellular matrix and attempts to relate the increase in coding diversity generated by alternate exon usage to the function(s) of individual extracellular matrix proteins.
Echinococcus multilocularis, a vulpine intestinal tapeworm, is the causative agent of alveolar echinococosis in humans, one of the most severe and lethal parasitic infections in man. To date, there is very little knowledge about the genetical polymorphism of this parasite. To assess sequence polymorphism, we analysed a sample of 33 E. multilocularis isolates from Europe, North America and Asia by PCR-SSCP followed by nucleotide sequencing. This assessment was performed comparatively to sheep, cattle and pig E. granulosus strains. Coding (nuclear antigen B and mitochondrial NADH dehydrogenase genes) and non-coding (introns of actin and homeobox-containing genes) regions of the parasite genome were chosen as targets. Since the estimated nucleotide diversity among genotypes of E. multilocularis were, in general, 10 times lower than among the recognized different strains of E. granulosus, we suggest that the conventional classification of the former species in 2 separated strains (European and North American) should be reviewed.
The "International Statistical Classification of Diseases and Related Health Problems", Tenth Revision (ICD-10), has to be used by all social security funds in Germany since Jan. 1, 2000. For purposes of the official statistical classification of causes of death, it has been used since 1998. There are a number of fundamental differences between the ICD-10 and the ninth revision. In particular, a considerably higher degree of specification and differentiation warrant a thorough look at the ICD-10 in numerous respects. The Unified diagnoses code of the statutory pension insurance is an extract from the ICD-10 referring specifically to diseases occurring in medical rehabilitation and early retirement contexts. Several new four- and five-digit codes were added for statutory pension insurance purposes, hence are not contained in the original ICD-10. This extract will only turn out a practical tool if the physician is well-qualified in his particular field and is familiar with the sometimes very complex differentiations within the systematical register in volume I of the ICD-10. The article provides an overview of the structure of the ICD-10; deals with major novelties and alterations as well as practical problems; uses various exemplary diagnoses to illustrate a systematical approach in possibly problematical encoding; and recalls several general rules for diagnoses encoding in social medicine.
Nucleotide sequence analysis was performed with the Maxam--Gilbert method on a cloned woodchuck hepatitis virus DNA (Eco WHV DNA). The structural gene coding for the envelope protein of the virus was localized on the viral genome in the partially single-stranded region between map positions 91.2 and 71. This gene is composed of 669 nucleotides and can code for a polypeptide of 25,645 daltons. The DNA sequence and the deduced amino acid sequence were compared with those of the corresponding gene and surface antigen of the related hepatitis B virus, allowing some insight into the localization of the antigenic site.
A bitmap display of the Fourier spectra has been developed which allows convenient whole chromosome scanning for genes and other features. Use of a limited sliding window gives rapid visualization and localization of coding regions in the chromosomes, as well as non-coding features such as repetitive DNA. The method works particularly well on organisms with a skewed base composition, to provide an overview of genomic features.