Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Copying Processes”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources
PubMed1985

Aplysia neurons express a gene encoding multiple FMRFamide neuropeptides.

The neuroactive peptide Phe-Met-Arg-Phe-NH2 (FMRF-amide) has a variety of effects on both mammalian and invertebrate tissues; moreover, FMRFamide-like immunoreactivity is found throughout the animal kingdom. Here we describe the isolation and characterization of a cDNA clone from an Aplysia abdominal ganglion cDNA library that encodes a precursor protein that may give rise to as many as 19 individual FMRFamide peptides. Nearly all of the FMRF sequences are flanked on the amino terminus by Lys-Arg residues and on the carboxy terminus by Gly-Lys residues, suggesting that the single lysine residues function to signal cleavage by processing enzymes. The gene is present in a single copy per haploid genome and gives rise to multiple transcripts, at least some of which appear to arise through alternate RNA splicing. Immunohistochemical analysis suggests that the peptide is present in many neurons throughout the Aplysia nervous system and that these neurons send processes to a variety of different tissues.

Amino Acid Sequence↗
PubMed1993

PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids.

The replication of ColE1-related plasmids is controlled by an unstable antisense RNA, RNAI, which can interfere with the successful processing of the RNAII primer of replication. We show here that a host protein, PcnB, supports replication by promoting the decay of RNAI. In bacterial strains deleted for PcnB a stable, active form of RNAI, RNAI*, which appears to be identical to the product of 5'-end processing by RNAase E, accumulates. This leads to a reduction in plasmid copy number. We show, using a GST-PcnB fusion protein, that PcnB does not interfere with RNAI/RNAII binding in vitro. The fusion protein, like PcnB, has polyadenylating activity and is able to polyadenylate RNAI (and also another antisense RNA, CopA) in vitro.

Ampicillin Resistance↗
PubMed1994

The use of shuttle vectors for mutation analysis in transgenic mice and rats.

The establishment in recent years of transgenic shuttle vector-based mutagenicity assays has provided improved systems for analysis of mutagenic and carcinogenic processes. Results in the mouse have stimulated the development of an alternate species suitable for mutation analysis and have increased our understanding of the existing models. A previously described shuttle vector (lambda LIZ), based on a lacI target gene, was constructed in this laboratory for the study of mutagenesis in transgenic mice and in cultured cell lines. The shuttle vector allows for several options in its recovery from the host genome and in mutant identification. Of the 9 transgenic lineages that were generated with the lambda LIZ vector, one was chosen for use in a standardized mutagenicity assay (Big Blue, mouse lineage A1). Characterization of this lineage included copy-number determination, chromosomal localization of transgene integration and analysis of copy-number stability. As part of the validation process, the standardized color-screening assay has been tested in the mouse, both for spontaneous mutant frequencies and with a variety of model mutagenic compounds, and has been shown to identify most major classes of mutations as evidenced by mutant spectra data. A discussion of the relative sensitivity of the shuttle vector to each of these classes of mutations is included. These studies have now been extended to the generation of transgenic rats containing the same shuttle vector for cross-species analysis. Spontaneous mutant frequencies in two transgenic rat lineages were measured in liver and in germ cells. Preliminary data suggest that spontaneous mutant frequencies in somatic tissue are lower in rats than in mice, a result consistent with historical observations of DNA damage and repair in these two species. Also under evaluation are alternative selectable systems for mutant identification, and hybrid animals obtained from mating lambda LIZ transgenics with genetically engineered mice possessing an inactivated tumor suppressor gene. It is expected that each of these widely varying endeavors will contribute, not only in furthering our understanding of the role transgenic systems should play in human risk assessment, but in illuminating the mechanisms of mutation in general.

Animals↗
PubMed1993

Characterization of seven processed pseudogenes of nucleophosmin/B23 in the human genome.

Genomic blot analysis revealed that the nucleophosmin/B23 gene belongs to a multigene family that has about 10 copies per haploid human genome. In searching for human nucleophosmin/B23 functional genes, seven processed pseudogenes (NG1-1.6, NG2-6, NG3-3, NG4-5, NG5-4, NG6-4, and NG7-6) were isolated and characterized. Four of them, NG2-6, NG3-3, NG4-5, and NG7-6, contain the sequences corresponding to the full-length cDNA. NG1-1.6 is 5'-truncated, whereas NG5-4 and NG6-5 are 3'-truncated pseudogenes. Of the seven pseudogenes, NG3-3 clone has the longest 5' untranslated sequence, which contains 104 nucleotides upstream of the translation initiation codon (AUG). Two processed pseudogenes (NG2-6 and NG3-3) have different polyadenylation sites from the mRNA, indicating the usage of alternative polyadenylation signals at the 3' sequence.

Base Sequence↗
PubMed1984

Biosynthesis of thyrotropin releasing hormone in the skin of Xenopus laevis: partial sequence of the precursor deduced from cloned cDNA.

Skin of Xenopus laevis contains relatively large quantities of thyrotropin releasing hormone (TRH). Total mRNA isolated from skin was cloned in the plasmid pUC8. Among 1400 cDNA clones, one was found with an insert of 478 nucleotides coding for the amino-terminal part of prepro-TRH. This clone was detected using a mixture of two synthetic undecanucleotides for colony hybridization. The single open reading frame starts with a methionine residue and a stretch of hydrophobic amino acids, as is typical for signal peptides, and terminates at the poly(C) tail without a stop codon. The deduced polypeptide of 123 amino acids contains three copies of the sequences Lys-Arg-Gln-His-Pro-Gly-Lys Arg-Arg and a fourth incomplete copy at the carboxyl end. Typical pro-hormone processing at this sequence would yield pGlu-His-Pro.NH2,i.e. TRH. It is concluded that the cloned part of the mRNA codes for prepro-TRH and that the TRH precursor from skin of X. laevis is a polyprotein containing at least four copies of the end product in its amino acid sequence.

Amino Acid Sequence↗
PubMed2002

Conservative treatment of primary gastric low-grade B-cell lymphoma of mucosa-associated lymphoid tissue: predictive factors of response and outcome.

OBJECTIVES: Primary gastric low-grade B-cell lymphoma of mucosa-associated lymphoid tissue may regress with conservative treatment such as anti-Helicobacterpylori therapy or monochemotherapy. The aims of the present study were to analyze the predictive factors of response to anti-H. pylori treatment, to assess the effects of an adjuvant therapy in responding patients, and to evaluate an alternative therapy in nonresponding patients. METHODS: From 1995 to 2000, 48 H. pylori-infected patients with localized primary gastric low-grade B-cell lymphoma of mucosa-associated lymphoid tissue were treated with anti-H. pylori therapy. Endoscopic and endoscopic ultrasonography features and histological grading of large cells' proportion were analyzed. Eradication of H. pylori and tumoral response were assessed at 2 and 6 months, respectively. From 1996, patients in remission at 6 months were randomized to receive either chlorambucil p.o. for 6 months or no treatment. Patients who did not respond to H. pylori eradication received chlorambucil p.o. for 1 yr. RESULTS: Among the 48 treated patients, 33 (69%) were in complete (n = 28) or in partial (n = 5) remission, and 15 (31%) were in treatment failure at 6 months. H. pylori was eradicated in 47 patients. The response was not correlated with the endoscopic features or with the histological grade. In contrast, it was related to ultrasonographic features: remission was achieved in 76% of patients when no perigastric lymph node was detected versus only 33% when endoscopic ultrasonography showed presence of lymph nodes (p = 0.025). All responding patients remained in remission (median 34 months) whatever the treatment they received (no treatment or chlorambucil). Remission could be achieved with chlorambucil in 58% of the nonresponding patients to anti-H. pylori treatment. CONCLUSIONS: The major negative predictive factor of the tumoral response to anti-H. pylori treatment in patients with primary gastric low-grade B-cell lymphoma of mucosaassociated lymphoid tissue was the presence of perigastric lymph nodes on endoscopic ultrasonography. In responding patients, remission remained stable, suggesting that adjuvant chemotherapy was not useful. In patients who failed to respond to H. pylori eradication, monochemotherapy with chlorambucil proved to be efficient, but new therapeutic modalities should be evaluated to improve the control of the tumoral process.

Adult↗
PubMed1992

Induction of DNA amplification in the Bacillus subtilis chromosome.

A system allowing the induction of DNA amplification in Bacillus subtilis was developed, based on a thermosensitive plasmid, pE194, stably integrated in the bacterial chromosome. An amplification unit, comprising an antibiotic resistance marker flanked by directly repeated sequences, was placed next to the integrated plasmid. Activation of pE194 replication led to DNA amplification. Two different amplification processes appeared to take place: one increased the copy number of all sequences in the vicinity of the integrated plasmid and was possibly of the onion skin type, while the other increased the copy number of the amplification unit only and generated long arrays of amplification units. These arrays were purified and shown to consist mainly of directly repeated amplification units but to also contain non-linear regions, such as replication forks and recombination intermediates. They were attached to the chromosome at one end only, and were, in general, not stably inherited, which suggests that they are early amplification intermediates. Longer arrays were detected before the shorter ones during amplification. When the parental amplification unit contained repeats which differed by a restriction site the arrays which derived thereof contained in a majority of cases only a single type of repeat. We propose that the amplified DNA is generated by rolling circle replication, and that such a process might underlie a number of amplification events.

Bacillus subtilis↗
PubMed1996

Peptides in the nervous systems of cnidarians: structure, function, and biosynthesis.

Cnidarians are the lowest animal group having a nervous system and it was probably within this phylum or in a related ancestor group that nervous systems first evolved. The primitive nervous systems of cnidarians are strongly peptidergic. From a single sea anemone species, Anthopleura elegantissima, 17 different neuropeptides have been isolated so far, and we expect that many more neuropeptides (more than 30) must be present. All peptides are localized in neurons of cnidarians and we have demonstrated the presence of some of the peptides in neurosecretory dense-cored vesicles. Most neuropeptides have an excitatory or inhibitory action on whole cnidarians, muscle preparations, and isolated muscle cells, suggesting that these peptides are neurotransmitters or neuromodulators. One neuropeptide induces metamorphosis in planula larvae to become a polyp. This shows that cnidarian neuropeptides also are involved in developmental processes, such as cell differentiation and pattern formation. We have cloned the preprohormones for most of the cnidarian neuropeptides. These preprohormones have a high copy number of the immature neuropeptide sequence, which can be up to 37 neuropeptide copies per precursor molecule. In addition to well-known, "classical" processing enzymes, novel prohormone processing enzymes must be present in cnidarian neurons. These include a processing enzyme hydrolyzing at the C-terminal sides of acidic (Asp and Glu) residues and a dipeptidyl aminopeptidase digesting at the C-terminal sides of N-terminally located X-Pro and X-Ala sequences. All this shows that the primitive nervous systems of cnidarians are already quite complex, and that neuropeptides play a central role in the physiology of these animals.

Amino Acid Sequence↗
PubMed2006

The Hill-Robertson effect and the evolution of recombination.

In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This "Hill-Robertson effect" generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.

Alleles↗
PubMed1990

Electrosensory systems in fish.

A close integration of behavioral, neurophysiological, and neuroanatomical approaches has guided research on the neural basis of electrosensation and the generation of behaviors associated with this modality. By postulating neuronal implementations of specific computations in sensory information processing, behavioral studies have been crucial in focusing studies at the neuronal level onto behaviorally relevant structural and functional aspects. Physiological and anatomical studies have analyzed a) neural networks underlying the distributed processing of sensory information, b) the role of descending recurrent pathways and efference copy mechanisms for the filtering of incoming information, c) the significance of multiple topographic representations for sensory information processing, and d) the modulation of sensory and motor structures through various transmitters and receptor subtypes. Developmental studies have explored the significance of steroid hormones for the tuning of electroreceptors to the frequency of an endogenous neuronal oscillator which drives the electric current pulses necessary for their stimulation. Embryological studies have revealed that the development of mechanoreceptors and electroreceptors in the fish's skin is induced by the innervation of primary afferent nerve fibers which are specific with regard to their central connections as well as with regard to the type of receptor induced in the periphery.

Animals↗
PubMedDate not supplied

[Supercopy plasmid based on the replicon from the temperate N15 bacteriophage].

Mini-plasmids, based on the N15 temperate bacteriophage replicon, are described. One of these, N15-203 linear 13.8 kb plasmid, has anomalously high copy number--more than 250 per one bacterial chromosome and the amount of plasmid DNA comprises about half of the total DNA of a cell. This property of N15-203 plasmid is realized only in the strain lysogenic for a N15 phage and is lost for the circular deletion versions of N15-203. The efficiency of transformation of E. coli C (N15) strain is essentially the same for N15-203 and pUC4K plasmids. Insertion of foreign DNA with a size up to 20 kb into BgIII cloning site of N15-203 plasmid does not decrease significantly efficiency of transformation calculated per number of DNA molecules and the total amount of plasmid DNA in a cell. N15-203 plasmid may be used as a vector for molecular cloning of relatively large DNA fragments, and in those biotechnology processes when productivity depends on a vector's copy number.

Bacteriophages↗
PubMed1993

Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies.

The synthesis of ribosomal RNA is a complex and highly regulated process. To study this process, we have used deletion-insertions to disrupt sequentially from one to four of the seven rRNA (rrn) operons on the Escherichia coli genome. Inactivation of four rrn operons caused a 2.3-fold increase in the expression of a chloramphenicol acetyl transferase reporter gene fused to the tandem promoters of rrnA and a similar increase in the expression of the trp tRNA gene at the end of rrnC. This reflected enhanced expression of the remaining operons to compensate for having only three intact copies. The elevated expression was caused by an increase in both transcription initiation and RNA polymerase elongation rates specifically on rrn operons and occurred in the absence of changes in the intracellular concentration of ppGpp, suggesting that ppGpp is not involved in the regulation of this phenomenon. We discuss these results in relation to the ribosome feedback inhibition model described by Nomura and coworkers.

Base Sequence↗
PubMed1983

Presence in brain of synenkephalin, a proenkephalin-immunoreactive protein which does not contain enkephalin.

The primary sequence of adrenal proenkephalin has recently been reported by three groups who have isolated and sequenced the cDNA for this prohormone. Several intermediates in the processing of proenkephalin, containing from one to four copies of [Met] enkephalin, have been purified from the adrenal medulla. Although there is evidence that the proenkephalin is identical in the brain and the adrenal medulla, similar intermediates have not been isolated from brain. We report here the production of an antiserum directed against a purified enkephalin precursor derived from the amino terminus of adrenal proenkephalin which cross-reacts with an antigen in brain. The immunoreactive protein in brain does not contain the sequence of enkephalin, but shows a pattern of distribution in immunohistochemical studies parallel to that of the enkephalins. In extracts of bovine caudate-putamen, this antigen is present in a molar concentration approximately one-fifth of that of [Met] enkephalin. The results demonstrate that the antiserum recognizes antigenic determinants within the N-terminal 72 amino acid residues of adrenal proenkephalin and that the enkephalin precursor in brain is similar to that found in the adrenal medulla. Furthermore, the absence of the enkephalin sequence in the brain protein indicates that concentrations of the larger intermediates in the processing of proenkephalin are much lower in the brain than in the adrenal medulla.

Adrenal Medulla↗
PubMed1990

Distribution of thyrotropin-releasing hormone (TRH) and precursor peptide (TRH-Gly) in adult rat tissues.

TRH (pGlu-His-Pro-NH2) arises from the post-translational processing of a larger precursor peptide containing multiple copies of the TRH progenitor sequence, Gln-His-Pro-Gly. Concentrations of TRH and its precursor peptide (TRH-Gly) were determined in serum and a variety of tissues of the rat using specific RIA systems. TRH and TRH-Gly immunoreactivities were detectable in almost all tissues studied. TRH was distributed mainly in neural tissues, with the highest mean concentration (126 pg/mg tissue) in hypothalamus. In extra-neural tissues, mean TRH levels ranged from 0.6-4.8 pg/mg tissue; the mean serum concentration was 12.4 pg/ml. In contrast to the distribution of TRH, relatively higher mean TRH-Gly concentrations were observed in serum (76.5 pg/ml) and in extraneural tissues, including prostate (83.3 pg/mg tissue), spleen (19.0 pg/mg), adrenal (16.2 pg/mg), kidney (13.3 pg/mg), and gastrointestinal tract (6.3-19.8 pg/mg). Among brain tissues, the TRH-Gly concentration was highest in pituitary gland (13.1 pg/mg). The mean ratio of TRH-Gly/TRH concentrations was less than 1 in neural tissues and pancreas. The lowest ratio (0.04) was observed in hypothalamus, and the highest ratio (66) in prostate gland. Assuming that tissue TRH-Gly levels reflect TRH synthesis, these results suggest that 1) the processing of TRH-Gly to TRH varies among tissues, 2) TRH-Gly to TRH conversion occurs most efficiently in neural tissues, and 3) TRH-Gly to TRH conversion may be a rate-limiting step in TRH biosynthesis.

Animals↗
PubMed2005

DNA copy number changes at 8q11-24 in metastasized colorectal cancer.

BACKGROUND: C-Myc, a well-known oncogene located on 8q24.12-q24.23, is often amplified and over-expressed in both primary and metastasizing colorectal cancer. In addition, PRL-3 (also known as PTP4A3), a tyrosine phosphatase located on 8q24.3, is amplified in colorectal cancer metastasis. Beside PRL-3 and c-myc, other oncogenes located on the 8q23-24 region might be involved in this process. Therefore, the present study aims to correlate DNA copy number status of a series of genes at 8q23-24 in colorectal cancer at high resolution in correlation to metastatic disease. MATERIALS AND METHODS: Thirty-two cases of colorectal cancer, 10 stage B1, 10 B2 and 12 D (Astler-Coller) with their corresponding liver metastasis and one colorectal cell line (colo205, previously analyzed by array-CGH), were included in this study. A chromosome 8 specific MLPA probe mixture was used to analyze the presence of DNA copy number changes. The probe mixture contained 29 probes covering 25 genes on chromosome 8, as well as 6 control probes on other chromosomes. RESULTS AND DISCUSSION: MLPA results obtained of the colo205 colorectal cell line were comparable with previous array-CGH results, thus validating the MLPA probe mixture. Astler-Coller B1 and B2 colorectal cancers differed significantly in DNA copy number of the genes, MOS (p=0.04), MYC (p=0.007), DDEF1 (p=0.004), PTK2 (p=0.02) and PTP4A3 (p=0.04). When comparing these with Astler-Coller D primary tumors, significant differences were seen for several genes as well (MYC (p<0.000), DDEF1 (p<0.000), SLA (p<0.000), PTK2 (p<0.000), PTP4A3 (p=0.002), and RECQL4 (p=0.01)). When comparing primary Astler-Coller D tumors and their corresponding liver metastases, a similar pattern of gains and losses was observed. Most of the liver metastases showed higher DNA copy number ratios than the corresponding primary tumors, but this difference was only significant for TPD52 (p=0.02) and EIF3S6 (p=0.007). CONCLUSION: In addition to c-myc, multiple genes on chromosome 8 differed significantly between primary colorectal cancers with and without liver metastases. This observation is consistent with the concept that clinical behaviour, like risk of liver metastasis, is determined by the genomic profile that is already present in the primary tumor.

Base Sequence↗
PubMed1990

The mammalian genome contains a high proportion of processed pseudogenes corresponding to ribosomal protein L19.

The mammalian genome contains multiple copies of ribosomal protein (rp) L19-related sequences. Screening of mouse and rat genomic libraries with cloned rpL19 cDNA yielded seventeen independent lambda Charon 4A recombinant phages containing twelve and five genes for mouse and rat rpL19, respectively. Structural analysis indicated that all of these rpL19 genes contain the entire coding sequence (approx. 700 bp) but lack introns. The nucleotide sequence of a mouse gene (rpL19-17), exhibiting the highest homology with the mouse rpL19 cDNA, revealed genetic lesions which would preclude the translation of an intact protein, from a putative transcript. Based on these features we propose that these clones represent processed genes of which most, if not all, are pseudogenes.

Animals↗
PubMed2004

The amplification model for adaptive mutation: simulations and analysis.

It has been proposed that the lac revertants arising under selective conditions in the Cairns experiment do not arise by stress-induced mutagenesis of stationary phase cells as has been previously assumed. Instead, these revertants may arise within growing clones initiated by cells with a preexisting duplication of the weakly functional lac allele used in this experiment. It is proposed that spontaneous stepwise increases in lac copy number (amplification) allow a progressive improvement in growth. Reversion is made more likely primarily by the resultant increase in the number of mutational targets--more cells with more lac copies. The gene amplification model requires no stress-induced variation in the rate or target specificity of mutation and thus does not violate neo-Darwinian theory. However, it does require that a multistep process of amplification, reversion, and amplification segregation be completed within approximately 20 generations of growth. This work examines the proposed amplification model from a theoretical point of view, formalizing it into a mathematical framework and using this to determine what would be required for the process to occur within the specified period. The analysis assumes no stress-induced change in mutation rate and describes only the growth improvement occurring during the process of amplification and subsequent elimination of excess mutant lac copies. The dynamics of the system are described using Monte Carlo simulations and numerical integration of the deterministic equations governing the system. The results imply that the amplification model can account for the behavior of the system using biologically reasonable parameter values and thus can, in principle, explain Cairnsian adaptive mutation.

Adaptation, Biological↗
PubMed2004

Chromatin loops are selectively anchored using scaffold/matrix-attachment regions.

The biological significance of nuclear scaffold/matrix-attachment regions (S/MARs) remains a topic of long-standing interest. The key to understanding S/MAR behavior relies on determining the physical attributes of in vivo S/MARs and whether they serve as rigid or flexible chromatin loop anchors. To analyze S/MAR behavior, single and multiple copies of the S/MAR-containing constructs were introduced into various host genomes of transgenic mice and transfected cell lines. These in vivo integration events provided a system to study the association and integration patterns of each introduced S/MAR. By utilizing FISH to visualize directly the localization of S/MARs on the nuclear matrix or chromatin loop, we were able to assign specific attributes to the S/MAR. Surprisingly, when multiple-copy S/MARs were introduced they were selected and used as nuclear matrix anchors in a discriminatory manner, even though they all contained identical primary sequences. This selection process was probably mediated by S/MAR availability including binding strength and copy number, as reflected by the expression profiles and association of multi-copy tandem inserted constructs. Whereas S/MARs functioned as the mediators of loop attachment, they were used in a selective and dynamic fashion. Consequently, S/MAR anchors were necessary but not sufficient for chromatin loops to form. These observations reconcile many seemingly contradictory attributes previously associated with S/MARs.

Animals↗