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PubMed2001

Investigating the hows and whys of DNA endoreduplication.

Endoreduplication is a form of nuclear polyploidization that results in multiple, uniform copies of chromosomes. This process is common in plants and animals, especially in tissues with high metabolic activity, and it generally occurs in cells that are terminally differentiated. In plants, endoreduplication is well documented in the endosperm and cotyledons of developing seeds, but it also occurs in many tissues throughout the plant. It is thought that endoreduplication provides a mechanism to increase the level of gene expression, but the function of this process has not been thoroughly investigated. Numerous observations have been made of endoreduplication, or at least extra cycles of S-phase, as a consequence of mutations in genes controlling several aspects of cell cycle regulation. However, until recently there were few studies directed at the molecular mechanisms responsible for this specialized cell cycle. It is suggested that endoreduplication requires nothing more elaborate than a loss of M-phase cyclin-dependent kinase activity and oscillations in the activity of S-phase cyclin-dependent kinase.

Cell Cycle↗

PubMed1976

MEDLINE services to the developing countries.

Supplying MEDLINE services to a widely dispersed user population in the developing countries creates numerous problems not encountered by other MEDLINE centres. The inability to interact with the user complicates system promotion and makes search formulation sometimes a gamble. Nevertheless, an evaluation survey has shown high user satisfaction. Of great concern is the still inadequate solution of document delivery. Near-term objectives are the broadening of geographic coverage and the integration of search processing with supporting hard copy supply.

Developing Countries↗

PubMed1988

[Digital radiography using light-emitting detectors. Operative principles and characteristics of images].

This paper briefly describes the technical features of a digital radiographic system based on the principle of scanning laser stimulated luminescence. Such aspects as the physics of the stimulable phosphor detector are dealt with, and image acquisition, processing, and hard-copy output. Automatic analysis of pixel histograms is described, in a qualitative way, together with contrast modifications and spatial filtering. Physical image characteristics are reported. The overall performance of digital radiography is examined, together with the current requirements and its eventual developments.

Humans↗

PubMed1986

A model for DNA sequence evolution within transposable element families.

A quantitative model is proposed for the expected degree of relationship between copies of a family of transposable elements in a finite population of hosts. Special cases of the model (in which the process of homogenization of element copies either is or is not limited by transposition rate) are presented and illustrated, using data on mobile sequences from different species. It is shown that transposition will be expected, in large populations, to result in only a rather distant relationship between transposable elements at different genomic sites. Possible inadequacies of the model are suggested and quantified.

Animals↗

PubMed1997

Dissociation between word reading and word copying in a patient with left visual neglect.

A patient with left visual neglect following a right hemisphere infarction is described. When presented with isolated words and nonwords, she made left neglect errors in reading aloud, but not in direct copying. This finding suggests a distinction between two ways of processing orthographic stimuli: depending on the task, the unit of processing can be the letter string or the single letter. In reading, the letter string is treated as a whole while in copying it is processed element-by-element. Left neglect differentially affects the processing of single words: in reading errors involve the left, initial letters, while in copying they involve the single letters, or the left part of the letters, independently of their position within the stimulus.

Aged↗

PubMed1994

Comparison of expression of a humanized monoclonal antibody in mouse NSO myeloma cells and Chinese hamster ovary cells.

We report a detailed comparison of two commonly used stable, amplifiable mammalian expression systems (Chinese Hamster Ovary cells/dihydrofolate reductase and Mouse NSO myeloma/glutamine synthetase) used to express a humanized IgG1 monoclonal antibody. We compare copy number and steady state mRNA levels of both the selectable marker and heavy chain of the antibody throughout the selection and amplification process. In both cell lines, copy number and steady state levels of heavy chain and selectable marker increased during selection and were further increased during amplification. As expected, an increase in steady state mRNA levels of heavy chain correlated with an increase in expression of antibody whilst an increase in the steady state levels of mRNA of the selectable marker correlated with increased resistance to the selective agent. In NSO and CHO cells producing equivalent amounts of antibody, the copy number of the antibody genes and selectable marker was significantly higher in the CHO cells than in the NSO cells. However, the steady state mRNA levels of the heavy chain of the antibody were virtually identical. Rates of protein secretion in the two cell lines were also compared and found to be very similar. When the antibody purified from both systems was compared in a number of functional assays they behaved identically.

Animals↗

PubMed1988

DNA sequence duplications trigger gene inactivation in Neurospora crassa.

Transforming sequences are faithfully replicated in vegetative cells of Neurospora but are typically subject at high frequency to sequence alterations and methylation in the period between fertilization and nuclear fusion. Previous work showed a correlation between the occurrence of these radical changes, referred to by the acronym RIP, and the presence of sequence duplications resulting from the introduced DNA. Various possible causes for the RIP process were investigated. Introduction of a single copy of a DNA fragment containing the Neurospora am gene into a strain having a deletion of this DNA did not lead to RIP, whereas introduction of two or more copies of the same fragment did. A conventional cross of strains having single copies of am at unlinked chromosomal locations was used to build a strain duplicated for am. Both copies of the duplicated gene were subject to the RIP process in crosses of this strain. We conclude that sequence duplications, per se, trigger RIP.

Base Sequence↗

PubMed2006

Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion.

Several large-scale studies of human genetic variation have provided insights into processes such as recombination that have shaped human diversity. However, regions such as low-copy repeats (LCRs) have proven difficult to characterize, hindering efforts to understand the processes operating in these regions. We present a detailed study of genetic variation and underlying recombination processes in two copies of an LCR (NF1REPa and NF1REPc) on chromosome 17 involved in the generation of NF1 microdeletions and in a third copy (REP19) on chromosome 19 from which the others originated over 6.7 million years ago. We find evidence for shared hotspots of recombination among the LCRs. REP19 seems to contain hotspots in the same place as the nonallelic recombination hotspots in NF1REPa and NF1REPc. This apparent conservation of patterns of recombination hotspots in moderately diverged paralogous regions contrasts with recent evidence that these patterns are not conserved in less-diverged orthologous regions of chimpanzees.

Animals↗

PubMed2006

Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes.

Despite the wide distribution of processed pseudogenes in mammalian genomes, such as those of human and mouse, relatively little is known about their roles in genomic evolution. While gene duplications are recognized as one of the major driving forces in genome evolution, processed pseudogenes, which are retrotransposed copies of mRNAs, have been regarded as junk or selfish DNA for a long time. In order to elucidate the quantitative and qualitative contribution of processed pseudogenes to the mammalian genome evolution, we attempted to detect processed pseudogenes by extensively mapping the mRNAs to both the human and mouse genomes, and then we estimated the rate of their emergence. As a result, we revealed that the rate of pseudogene emergence was about 1-2% per gene per million years, which was as high as the rate (0.9%) of gene duplication in the human genome, although the rate of pseudogene emergence was found to drastically decrease in the hominid lineage. Furthermore, 1% of the processed pseudogenes seemed to be reinvigorated by post-retrotransposition transcription, many of them preserving the intact coding regions. Since the expression patterns of transcribed pseudogenes in various tissues were quite different between human and mouse, their emergence might have led to species-specific evolution. Our results indicate that the generation of processed pseudogenes was not wholly futile but instead has been an indispensable resource, driving dynamic evolution of the mammalian genomes.

Amino Acid Sequence↗

PubMed1983

A process approach to the Bender-Gestalt test and its use in differentiating schizophrenic, brain-damaged, and medical patients.

Developed a processing model that would account for the shifting of attention that occurs as individuals copy Bender-Gestalt designs. Process-oriented variations of the Bender-Gestalt test were designed that emphasized each of the three processes hypothesized to contribute to Bender-Gestalt performance: Perceptual-motor integration, attentional factors, and short-term memory. A standard Bender-Gestalt and the three variations were administered to 24 schizophrenics, 24 brain-damaged patients, and 24 medical patients, matched for intelligence and sex. Protocols were scored blindly by the Pascal-Suttell and Hain methods. Discriminant function analysis based upon the four versions of the Bender-Gestalt test classified patients as schizophrenic or brain-damaged at a significantly higher rate than the standard Bender-Gestalt scored by either the Pascal-Suttell or Hain system.

Attention↗

PubMed1996

Positive association between copia transposition rate and copy number in Drosophila melanogaster.

Rates of copia transposition were determined directly, by cytological in situ hybridization analysis of sites of copia insertion in progeny of males from sublines of an inbred strain with different genomic copia copy numbers. Copia transposition rate was positively and nonlinearly associated with copia copy number. This relation cannot be simply explained by mutations in a single host factor that normally suppresses transposition, or by mutations in copia elements themselves. We postulate that the number of copia virus-like particles, necessary for copia transposition, could depend nonlinearly on copia copy number. Deleterious side-effects of the transposition process may be an important force controlling copia copy number in natural populations.

Analysis of Variance↗

PubMed2001

Liquid crystalline spinning of spider silk.

Spider silk has outstanding mechanical properties despite being spun at close to ambient temperatures and pressures using water as the solvent. The spider achieves this feat of benign fibre processing by judiciously controlling the folding and crystallization of the main protein constituents, and by adding auxiliary compounds, to create a composite material of defined hierarchical structure. Because the 'spinning dope' (the material from which silk is spun) is liquid crystalline, spiders can draw it during extrusion into a hardened fibre using minimal forces. This process involves an unusual internal drawdown within the spider's spinneret that is not seen in industrial fibre processing, followed by a conventional external drawdown after the dope has left the spinneret. Successful copying of the spider's internal processing and precise control over protein folding, combined with knowledge of the gene sequences of its spinning dopes, could permit industrial production of silk-based fibres with unique properties under benign conditions.

Animals↗

PubMed1986

Sequence of preprocaerulein cDNAs cloned from skin of Xenopus laevis. A small family of precursors containing one, three, or four copies of the final product.

From skin of Xenopus laevis, cDNA libraries were constructed and clones coding for the precursors of caerulein were isolated and sequenced. Using restriction endonuclease digestions, three different types of preprocaerulein cDNAs could be discerned. These were termed types I, III, and IV in accordance with the number of caerulein copies present in the sequence, the type III being the most abundant one. An incomplete copy of a fourth variant, termed type I', was also found. Besides deletions/insertions encompassing one or two caerulein sequences, these types also differ from each other by several point mutations. In the homologous precursor polypeptides deduced from the nucleotide sequence of these cloned cDNAs, the caerulein copies are flanked by complex processing sequences. These are Arg-Arg-Phe-Ala-Asp-Gly or Arg-Arg-Asp-Gly at the amino-terminal side and Gly-Arg-Arg at the carboxyl end. Between caerulein copies, highly homologous segments are present both at the polypeptide and cDNA level. This homology is evident both within a given precursor, where up to three such segments are present, and between the different types of precursors. We conclude that preprocaerulein cDNAs in the skin of X. laevis represent a small family, at least part of which is derived from different genes rather than being formed by alternative splicing of pre-mRNAs.

Amino Acid Sequence↗

PubMed2005

The first cell.

The First Cell arose in the previously pre-biotic world with the coming together of several entities that gave a single vesicle the unique chance to carry out three essential and quite different life processes. These were: (a) to copy informational macromolecules, (b) to carry out specific catalytic functions, and (c) to couple energy from the environment into usable chemical forms. These would foster subsequent cellular evolution and metabolism. Each of these three essential processes probably originated and was lost many times prior to The First Cell, but only when these three occurred together was life jump-started and Darwinian evolution of organisms began. The replication of informational molecules that made only occasional mistakes allowed evolution to form all the basic components of cellular life. Ribozymes, the first informational molecules, were also catalytic. Energy coupling required the formation of a closed lipid surface to generate and maintain an ion-motive gradient. The closed vesicle partitioned components and avoided dilution within the primordial sea. Closed membranes were essential for the first self-reproducing cell to arise and for its descendants to disperse. Subsequent cellular development after the origin of The First Cell led to the beginnings of intermediary metabolism and membrane transport processes. This long process, subject to strong evolutionary selection, developed the cellular biology that is now shared by all extant organisms.

Animals↗

PubMed1994

Chemical self-replication of palindromic duplex DNA.

Molecular replication, a fundamental process of life, has in recent years been the subject of laboratory investigations using simple chemical systems. Whereas the work of Rebek's group has focused on molecular architectures not known in living systems, self-replicating and template-based self-assembling systems based on nucleotides are regarded as potential models for exploring the evolution of replicating systems on the early Earth. Previous replicating oligonucleotides have been of the single-stranded, self-complementary type: small oligonucleotide fragments are assembled on a pre-existing template and linked to form an exact copy of the template. This process cannot easily be reiterated, however, because of the strong binding of the newly formed strand to the original template. Furthermore, DNA replication in living systems operates by complementarity rather than self-complementarity--each newly assembled strand is complementary to, rather than identical to, its template--and the replication process starts and finishes with double helices. Here we report the self-replication of palindromic (symmetrical) duplex DNA-like oligonucleotides, 24 monomers long, in the absence of enzymes by means of a cycle that transfers information from template to copy and is potentially capable of extension to include non-symmetrical sequences, selection and mutation. Replication proceeds by a chemical process involving the formation of an intermediate triplex structure, and is sequence-selective in the sense that mismatches impair its efficiency. These results indicate that DNA-like double-helical molecules can replicate without assistance from proteins, a finding that may be relevant both to the appearance of replicating systems on the early Earth and to the development of new approaches to DNA amplification.

Base Sequence↗

PubMed1998

Glucocorticoids modulate the biosynthesis and processing of prothyrotropin releasing-hormone (proTRH).

The thyrotropin- (TRH) releasing hormone precursor (26 kDa) undergoes proteolytic cleavage at either of two sites, generating N-terminal 15 kDa/9.5 kDa or C-terminal 16.5/10 kDa intermediate forms that are processed further to yield five copies of TRH-Gly and seven non-TRH peptides. Glucocorticoids (Gcc) have been shown to enhance TRH gene expression in three different cell systems in vitro, an effect that occurs, at least in part, through transcriptional activation. Although this implies that an increase of TRH prohormone biosynthesis would take place, this had not been demonstrated as yet. We report here that the synthetic glucocorticoid dexamethasone (Dex) substantially elevated the de novo biosynthesis of the intact 26-kDa TRH prohormone and its intermediate products of processing in cultured anterior pituitary cells, an observation that is consistent with an overall upregulation of both the biosynthesis and degradation of the TRH precursor. We reasoned that Gcc may act not only at the transcriptional, but also at the translational/posttranslational level. To address this question we chose a different cell system, AtT20 cells transfected with a cDNA encoding preproTRH. Since TRH gene expression in these cells is driven by the CMV-IE promoter and not by an endogenous "physiological" promoter, these cells provide an ideal model to study selectively the effects of Gcc on the translation and posttranslational processing of proTRH without interference from a direct transcriptional activation of the TRH gene. Dex caused a significant 75.7% increase in newly synthesized 26-kDa TRH prohormone, suggesting that the glucocorticoid raised the translation rate. We then demonstrated that Dex treatment accelerated TRH precursor processing. Of interest, processing of the N- vs the C-terminal intermediate was influenced differentially by the glucocorticoid. Although the N-terminal intermediate product of processing accumulated, the C-terminal intermediate was degraded more rapidly. Consistent with these observations was the finding that the intracellular accumulation of the N-terminally derived peptide preproTRH 25-50 was enhanced, but levels of the C-terminally derived peptide preproTRH208-255 were reduced. Accumulation of TRH itself, whose five copies are N- and C-terminally derived, was also enhanced. We conclude that Gcc induce changes in the biosynthesis and processing of proTRH by increasing the translation rate and by differentially influencing the processing of N- vs C-terminal intermediates of the precursor molecule. These effects of Gcc at the translational and posttranslational levels result in an increase in TRH production accompanied by differential effects on the accumulation of N- and C-terminal non-TRH peptides.

Animals↗

PubMed1999

Deafferentation and pointing with visual double-step perturbations.

The capability of reprogramming movement responses following changes in the visual goal has been studied through the double-step paradigm. These studies have shown that: (a) continuous internal feedback-loops correct unconsciously the dynamic errors throughout the movement; (b) proprioceptive information and/or the efference copy have a privileged status among central processes, insuring on-line regulation of the initial motor commands; and (c) generation of the motor program starts after target presentation, and is continuously updated in the direction of the current internal representation of the target, at least until the onset of hand movement. This main corrective process of the initial program appears to be basically independent of visual reafference from the moving hand. However, the agreement with the possibility of a visuomotor loop, based on the comparison of the new updated representation of the target position and on the information from the moving hand, has not determined whether the correcting process is proprioceptive feedback dependent, or whether internal feedback-loops (efferent copies) are responsible for quick corrections of unfolding motor responses. To answer this question, the present experiment investigated the pointing behavior of a deafferented subject, using a double-step paradigm under various conditions of visual feedback and movement initiation. Overall, the present study (a) clearly showed the capacity of the motor system to modify and correct erroneous trajectories on the mere basis of internal feedback-loops and (b) emphasized the crucial role played by the target jump/arm triggering delay and the importance of the eye efferent copy for providing information about the spatial goal of the movement.

Afferent Pathways↗

PubMed1995

Molecular cloning of a preprohormone from sea anemones containing numerous copies of a metamorphosis-inducing neuropeptide: a likely role for dipeptidyl aminopeptidase in neuropeptide precursor processing.

Neuropeptides are an important group of hormones mediating or modulating neuronal communication. Neuropeptides are especially abundant in evolutionarily "old" nervous systems, such as those of cnidarians, the lowest animal group having a nervous system. Cnidarians often have a life cycle including a polyp, a medusa, and a planula larva stage. Recently, a neuropeptide, < Glu-Gln-Pro-Gly-Leu-Trp-NH2, has been isolated from sea anemones that induces metamorphosis in a hydroid planula larva to become a hydropolyp [Leitz, T., Morand, K. & Mann, M. (1994) Dev. Biol. 163, 440-446]. Here, we have cloned the precursor protein for this metamorphosis-inducing neuropeptide from sea anemones. The precursor protein is 514-amino acid residues long and contains 10 copies of the immature, authentic neuropeptide (Gln-Gln-Pro-Gly-Leu-Trp-Gly). All neuropeptide copies are preceded by Xaa-Pro or Xaa-Ala sequences, suggesting a role for dipeptidyl aminopeptidase in neuropeptide precursor processing. In addition to these neuropeptide copies, there are 14 copies of another, closely related neuropeptide sequence (Gln-Asn-Pro-Gly-Leu-Trp-Gly). These copies are flanked by basic cleavage sites and, therefore, are likely to be released from the precursor protein. Furthermore, there are 13 other, related neuropeptide sequences having only small sequence variations (the most frequent sequence: Gln-Pro-Gly-Leu-Trp-Gly, eight copies). These variants are preceded by Lys-Arg, Xaa-Ala, or Xaa-Pro sequences, and are followed by basic cleavage sites, and therefore, are also likely to be produced from the precursor. Thus, there are at least 37 closely related neuropeptides localized on the precursor protein, making this precursor one of the most productive preprohormones known so far. This report also shows that unusual processing sites are common in cnidarian preprohormones.

Amino Acid Sequence↗