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At least 253 records · Page 14Linked to original sources
PubMed2002

Genome plasticity in Festuca arundinacea: direct response to temperature changes by redundancy modulation of interspersed DNA repeats.

The response of the genome of Festuca arundinacea seedlings to changes in the temperature at which they were grown was investigated. Fifteen repeated sequences in the nuclear DNA were isolated and hybridized to the genomic DNA of seedlings grown at 10 degrees C or 30 degrees C. The redundancies of sequences recognized by four probes ( FaA5, FaH8, FaH13 and FaH14), were found to differ significantly in the two DNAs. DNA sequences recognized by FaH8, FaH13 and FaH14 were more represented in the genome of the 30 degrees C-raised seedlings than in the genome of the 10 degrees C-raised seedlings (76.5 x 10(3), 1.9 x 10(3), and 111.8 x 10(3) copies per haploid, 1C genome vs 62.7 x 10(3), 1.3 x 10(3), and 80.8 x 10(3) copies, respectively). In contrast, FaA5-related sequences were more represented in the genome of seedlings grown at the lower temperature (15.5 x 10(3) vs 10.2 x 10(3) copies, respectively). Southern-blot hybridization of these repeats to digested genomic DNA produced patterns which indicated that the probe sequences were part of longer repeated sequences having a limited degree of structural heterogeneity. These patterns were partly different when the probes were hybridized to the DNA from seedlings grown at 10 degrees C or 30 degrees C. In situ hybridization showed that the DNA sequences recognized by each probe were scattered along the length of all the chromosomes, with preferential location of FaA5- and FaH13-related sequences at given, mainly centromeric, regions of certain chromosomes. These findings suggest that redundancy modulations of interspersed repeated sequences allow direct responses of the genome of F. arundinacea to changes in environmental temperature.

Journal Article↗
PubMed2001

Structure of motor variability in marginally redundant multifinger force production tasks.

The framework of the uncontrolled manifold hypothesis (UCM hypothesis) was applied to the analysis of the structure of finger force variability during oscillatory force production tasks. Subjects produced cycles of force with one, two (index and middle), or three (index, middle, and ring) fingers acting in parallel against force sensors mounted inside a small frame. The frame could be placed on the top of a table (stable conditions) or on a 4-mm-wide supporting surface (unstable conditions). Subjects were less variable when they used two fingers than when using one finger; adding the third finger did not change indices of variability of the performance. Components of finger force variance that did (VUN) or did not (VCOMP) change the value of a particular functional variable were computed for two control hypotheses: (1) at each time, the subjects tried to stabilize the total value of force (force-control); and (2), at each time, the subjects tried to stabilize the total moment produced with respect to an axis parallel to the hand/forearm (moment-control). Most subjects showed selective stabilization of moment and destabilization of force throughout most of the force cycle, in both stable and unstable conditions. The shapes of VUN and VCOMP suggested a possibility of selective compensation of timing errors across fingers within force cycles. One subject showed different relations between VUN and VCOMP, suggesting that these relations did in fact reflect particular central strategies of solving the tasks. The UCM method is applicable to force production tasks. It allows the comparison of control hypotheses in a quantitative way and unveils central strategies of control of redundant motor systems. Within this approach, redundancy (rather, abundance) is not a problem but an inherent part of a solution for natural motor tasks.

Adult↗
PubMedDate not supplied

On the evolution of redundancy in genetic codes.

We simulate a deterministic population genetic model for the coevolution of genetic codes and protein-coding genes. We use very simple assumptions about translation, mutation, and protein fitness to calculate mutation-selection equilibria of codon frequencies and fitness in a large asexual population with a given genetic code. We then compute the fitnesses of altered genetic codes that compete to invade the population by translating its genes with higher fitness. Codes and genes coevolve in a succession of stages, alternating between genetic equilibration and code invasion, from an initial wholly ambiguous coding state to a diversified frozen coding state. Our simulations almost always resulted in partially redundant frozen genetic codes. Also, the range of simulated physicochemical properties among encoded amino acids in frozen codes was always less than maximal. These results did not require the assumption of historical constraints on the number and type of amino acids available to codes nor on the complexity of proteins, stereochemical constraints on the translational apparatus, nor mechanistic constraints on genetic code change. Both the extent and timing of amino-acid diversification in genetic codes were strongly affected by the message mutation rate and strength of missense selection. Our results suggest that various omnipresent phenomena that distribute codons over sites with different selective requirements--such as the persistence of nonsynonymous mutations at equilibrium, the positive selection of the same codon in different types of sites, and translational ambiguity--predispose the evolution of redundancy and of reduced amino acid diversity in genetic codes.

Codon↗
PubMed1999

A family of dispersed repeats in the genome of Vicia faba: structure, chromosomal organization, redundancy modulation, and evolution.

A family of repeated DNA sequences of about 1200 bp in length and bordered by well-conserved, 18 bp inverted repeats (VfB family) was found in the nuclear genome of Vicia faba. The structure, chromosomal organization, redundancy modulation and evolution of these sequences were investigated. They are enriched in A+T base pairs (about 40% G+C) and lack any obvious internally repeated motif. A 64%-73% nucleotide sequence identity was found when pairwise comparisons between VfB sequences were carried out (average 69%). Direct repeats were not found to flank the inverted repeats that border these DNA sequences. The results obtained by hybridizing VfB repeats to Southern blots of V. faba genomic DNA digested with EcoRI indicated that these DNA elements are interspersed in the genome. The appearance of bands in these Southern blots and comparison of the structure of the sequences that flank different VfB elements showed that these repeats might be part of other, longer repeated DNA sequences. A high degree of dispersion throughout the genome was confirmed by cytological hybridization, which showed VfB sequences to be scattered along the length of all chromosomes and to be absent or rare only at heterochromatic chromosomal regions. These sequences contribute to intraspecific alterations of genomic size. Indeed, dot-blot hybridizations proved that their redundancy, which is positively correlated with the overall amount of nuclear DNA in each accession, varies between V. faba land races (27x10(3)-230x10(3) copies per 1C DNA). Southern blot hybridization of VfB repeats to restriction endonuclease-digested genomic DNAs of V. faba, V. narbonensis, V. sativa, Phaseolus coccineus, Populus deltoides, and Triticum durum revealed nucleotide sequence homology of these DNA elements, whatever the stringency conditions, only to the DNAs of Vicia species, and to a reduced extent to the DNAs of V. narbonensis and V. sativa compared with that of V. faba. It is concluded that VfB repeats might be descended from mobile DNA elements and contribute to change genomic size and organization during evolution.

Base Composition↗
PubMed2005

The maize heat shock factor-binding protein paralogs EMP2 and HSBP2 interact non-redundantly with specific heat shock factors.

The heat shock response (HSR) is a conserved mechanism by which transcripts of heat shock protein (hsp) genes accumulate following mobilization of heat shock transcription factors (HSFs) in response to thermal stress. Studies in animals identified the heat shock factor-binding protein1 (HSBP1) that interacts with heat shock transcription factor1 (HSF1) during heat shock attenuation; overexpression analyses revealed that the coiled-coil protein HSBP1 functions as a negative regulator of the HSR. Zea mays contains two HSBP paralogs, EMP2 and HSBP2, which exhibit differential accumulation during the HSR and plant development. Embryo-lethal recessive emp2 mutations revealed that EMP2 is required for the down-regulation of hsp transcription during embryogenesis, whereas accumulation of HSBP2 is induced in seedlings following heat shock. Notwithstanding, no interaction has yet been demonstrated between a plant HSBP and a plant HSF. In this report 22 maize HSF isoforms are identified comprising three structural classes: HSF-A, HSF-B and HSF-C. Phylogenetic analysis of Arabidopsis, maize and rice HSFs reveals that at least nine ancestral HSF isoforms were present prior to the separation of monocot and eudicots, followed by differential amplification of HSF members in these lineages. Yeast two-hybrid analyses show that EMP2 and HSBP2 interact non-redundantly with specific HSF-A isoforms. Site-specific mutagenesis of HSBP2 reveals that interactions between hydrophobic residues within the coiled coil are required for HSF::HSBP2 binding; domain swapping demonstrate that the isoform specificity of HSF::HSBP interaction is conferred by residues outside of the coiled coil. These data suggest that the non-redundant functions of the maize HSBPs may be explained, at least in part, by the specificity of HSBP::HSF interactions during plant development.

Amino Acid Motifs↗
PubMed2004

ENHANCER of TRY and CPC 2 (ETC2) reveals redundancy in the region-specific control of trichome development of Arabidopsis.

An evolutionarily conserved set of proteins consisting of MYB and bHLH transcription factors and a WD40 domain protein is known to act in concert to control various developmental processes including trichome and root hair development. Their function is difficult to assess because most of them belong to multigene families and appear to act in a redundant fashion. In this study we identified an enhancer of the two root hair and trichome patterning mutants triptychon (try) and caprice (cpc), enhancer of try and cpc2 (etc2). The ETC2 gene shows high sequence similarity to the single-repeat MYB genes CPC and TRY. Overexpression results in the suppression of trichomes and overproduction of root hairs similarly as observed for TRY and CPC suggesting that ETC2 has similar biochemical properties. The etc2 single mutant shows an increase in trichome number on leaves and petioles. Double and triple mutant analysis indicates that the ETC2 gene acts redundant with TRY and CPC in trichome patterning.

Amino Acid Sequence↗
PubMed1996

Implicit redundant-targets effect in visual extinction.

Patients with left visual extinction as a result of unilateral right hemisphere damage were tested on a redundant-targets effect paradigm (RTE). LED-generated brief flashes were lateralized either to the left or to the right visual hemifield or presented bilaterally. Subjects were asked to press a key as fast as possible following either unilateral or bilateral stimuli and immediately afterwards to report on the number of stimuli presented. As previously found in normal subjects, bilateral stimuli were responded to faster than unilateral ones, and this was evidence of a RTE. The main thrust of this study was that extinction patients showed a RTE not only for correctly perceived bilateral stimuli but also in trials in which they extinguished the stimulus on the field contralateral to the lesion. This result is compatible with a preserved processing of the extinguished input at least up to the stage at which it may interact with the input from the normal side to yield a speeded motor response. Interestingly, the implicit redundancy gain of extinction patients was found to fit a coactivation (i.e. neural) rather than a probabilistic model.

Aged↗
PubMed1982

Differences between rats and undernourished preweaning, and controls in learning about a redundant stimulus during acquisition of a conditioned emotional response.

Male rats were undernourished during the first three weeks of life by restricting maternal food consumption. Following nutritional rehabilitation, previously undernourished (PU) and control (C) rats were trained to operate a lever to obtain food reward on a variable interval schedule. When rates of responding had stabilised, the rats were tested for suppression of lever-pressing during the illumination of a light which preceded footshock. There were not differences between PU and C groups in the acquisition of this conditioned emotional response, nor were there differences in suppression when a redundant, tone stimulus was presented contemporaneously with the light to predict shock. When the tone was subsequently tested alone for its ability to suppress lever-pressing it was found to have acquired this property in C, but not in PU animals. In a second experiment, PU and C rats were found not to differ in their response to the tone when it was presented as a novel stimulus, nor in suppression to the tone when it was made the sole predictor of footshock. It was concluded that PU and C rats differed in learning about a stimulus predicting footshock, only when that stimulus was redundant. Among the possible explanations for this behavioural difference between PU and control rats are differences in motivation, curiosity, or strength of conditioning. These possibilities are evaluated within the context of current formal theories of conditioning.

Animals↗
PubMedDate not supplied

Randomness, redundancy and repair: roles and relevance to biological aging.

In this paper, some of the key findings of the last decade will briefly be surveyed and, where possible, be related to two separate computer simulation models which have been designed to determine the validity of certain widely accepted dogmas and to define the limits and restrictions imposed by attrition of or ambiguity of information retrieval from information storage systems. It is known: (1) that the idealized rectangular survival curve in an "ideal" environment is an extrapolation that is inconsistent with reasonable primary assumptions; (2) that loss of redundant copies of functional "housekeeping" genes may well be a dominant contributor to human senescence; and (3) that redundancy, particularly of informational storage, not only confers greater stability on an organism in dealing with stochastic or programmed age changes, but that it also provides a means through which a more optimized use of informational storage space may be attained.

Aging↗
PubMed1981

Redundant nerve roots of the cauda equina.

Four cases of redundant nerve roots of the cauda equina are reported, and the pertinent literature is reviewed. This disorder mainly affects males. The clinical history ranges from months to decades. The illness often starts with low back pain or sciatica, or both. Motor and sensory impairment of the legs dominate the further course of the disease. Serpentine filling defects in the column of contrast are a characteristic (but inconstant) feature on myelograms. Abatement of signs and symptoms occurs following adequate decompression of the redundant roots.

Adult↗
PubMed1991

Relationship between the Brief Psychiatric Rating Scale and the Scale for the Assessment of Negative Symptoms: a study of their correlation and redundancy.

Because overlapping psychometric scales are used frequently in psychiatric research, examination of the relationship between scales has become increasingly important. The concept of relationship is the focus of this article. By way of illustration, the Brief Psychiatric Rating Scale (BPRS) and the Scale for the Assessment of Negative Symptoms (SANS) were compared for correlation and redundancy. Since these scales are frequently represented by derived summary variables (e.g., factors, total scores), it is also important to assess the effect of such representation on measures of relationship. The SANS and the BPRS were found to be highly intercorrelated. Nevertheless, the individual items and the subscale scores of the SANS contain information independent from the BPRS: the best BPRS predictor variates can explain only approximately half of the total variance of the SANS. When the SANS, however, is represented by a single variable (composite score), it becomes highly redundant with the anergia factor of the BPRS.

Adult↗
PubMed1981

Congenital stridor caused by redundant arytenoid mucosa.

Two cases of congenital stridor caused by merely unusual redundancy of the mucosa covering the arytenoids are reported in this paper. The stridor was noted only when the patients were awake, and was not affected by postural changes of patients. The patients who did not reach their full mental and physical development had congenital abnormalities: cleft palate in one case, and hypertrichiosis, short palpebral fissures of camptodactyly in the other. No abnormalities were revealed in the patients on examinations of chromosomes, thyroid hormones and brains using the techniques of computerized axial tomographic scanning and electroencephalography. The diagnosis of these cases should be confirmed by a direct laryngoscopy or a laryngofiberscopy. Although the etiology of redundant arytenoid mucosa is not known, it may be suggested that this condition is incidental to other congenital abnormalities.

Abnormalities, Multiple↗
PubMedDate not supplied

Drosophila abl and genetic redundancy in signal transduction.

Genetic studies on Drosophila Abl and, more recently, on mouse c-Abl and c-Src indicate that the functions of these non-receptor tyrosine kinases may duplicate activities of other molecules within signal transduction pathways. In Drosophila, second-site mutations have been recovered that disrupt the redundant functions so that the Abl tyrosine kinase is essential to the formation of axonal connections in the embryonic central nervous system and for attachment of embryonic muscles to the body wall. Molecular isolation and analysis of the genes identified by these second-site mutations should define the molecular basis for the genetic redundancy.

Alleles↗
PubMed2005

Midkine regulates pleiotrophin organ-specific gene expression: evidence for transcriptional regulation and functional redundancy within the pleiotrophin/midkine developmental gene family.

Midkine (MK) and the highly related cytokine pleiotrophin (PTN) constitute the PTN/MK developmental gene family. The Mk and Ptn genes are essential for normal development of the catecholamine and renin-angiotensin pathways and the synthesis of different collagens. It is not known whether the Ptn and Mk genes regulate each other or whether PTN and MK are functionally redundant in development. We have now compared the levels of expression of Ptn and Mk in genetically deficient Mk -/- and Ptn -/- mice and found highly significant increases in Ptn gene expression in spinal cord, dorsal root ganglia, eye, heart, aorta, bladder, and urethra, but not in brain, bone marrow, testis, and lung of Mk -/- mice compared with wild type mice; a remarkable approximately 230-fold increase in Ptn expression levels was found in heart of Mk -/- mice and highly significant but lesser increases were found in six other organs. Differences in levels of Mk gene expression in Ptn -/- mice could not be detected in any of the organs tested. The data demonstrate that MK regulates Ptn gene expression with a high degree of organ specificity, suggesting that Ptn gene expression follows Mk gene expression in development, that the increase in Ptn gene expression is compensatory for the absence of MK in Mk -/- mice, that PTN and MK share a high degree of functional redundancy, and that MK may be very important in the development of heart in mouse.

Animals↗
PubMed2006

Duplicate publications: redundancy in plastic surgery literature.

The practice of duplicate publication has been condemned widely in the scientific community and several studies have been conducted to establish the level of the problem in various surgical fields. A retrospective review of original articles from the British Journal of Plastic Surgery and Plastic and Reconstructive Surgery during 2000 was conducted, using Medline (PubMed). A total of 431 abstracts were screened, from which 27 index articles related to 33 'suspected redundant' publications. Further evaluation was carried out by comparing the full text versions of these articles and assigning a grade of non-dual, dual, potentially dual and 'salami-slicing'. Only four suspect articles were confirmed as having some degree of redundancy, and these related to three index articles (3/431, <1%). The incidence of duplication in plastic surgery literature seems to be much lower compared to other surgical specialties, providing reassurance for reviewers, editors and readers of these journals.

Bibliometrics↗
PubMed2003

Cytokines and autoimmunity: redundancy defines their complex nature.

Cytokines are critical mediators in autoimmunity and a better understanding of their mode of action should contribute to the development of strategies for controlling harmful autoimmune reactions. Their complicated nature makes it difficult to classify them as pro- or anti-inflammatory mediators; redundancy in their mode of action has been widely reported. Their complexity is further exemplified by the fact that several cytokines display redundancy in their receptor usage, with the recently identified IL-12 and IL-10 families being prototypical examples. Several aspects--including kinetics of expression, mode of induction, regulation of receptor expression and competition for occupancy, and the stage (acute vs chronic) of the disease--are critical to the net effect, and all these aspects need to be understood if we are to define a cytokine's whole nature.

Animals↗
PubMed2006

SynMuv genes redundantly inhibit lin-3/EGF expression to prevent inappropriate vulval induction in C. elegans.

Activation of EGFR-Ras-MAPK signaling in vulval precursor cells (VPCs) by LIN-3/EGF from the gonad induces vulval development in C. elegans. The prevailing view is that LIN-3 overcomes an "inhibitory signal" from the adjacent hyp7 hypodermal syncytium. This view originated from observations indicating that inactivation of functionally redundant Synthetic Multivulva (SynMuv) genes in hyp7 can activate EGFR-Ras-MAPK signaling in the VPCs. Many SynMuv genes encode transcription and chromatin-associated factors, including the Rb ortholog. Here, we show that the SynMuv A and SynMuv B gene classes are functionally redundant for transcriptional repression of the key target gene, lin-3/EGF, in the hypodermis. These observations necessitate a revision of the concept of "inhibitory signaling." They also underscore the importance of preventing inappropriate cell signaling during development and suggest that derepression of growth factors may be the mechanism by which tumor suppressor genes such as Rb can have cell nonautonomous effects.

Animals↗
PubMed2005

MURF-1 and MURF-2 target a specific subset of myofibrillar proteins redundantly: towards understanding MURF-dependent muscle ubiquitination.

MURF-1, MURF-2 and MURF-3 are a specific class of RING finger proteins that are expressed in striated muscle tissues. MURF-1 has been suggested to act as an ubiquitin ligase, thereby controlling proteasome-dependent degradation of muscle proteins. Here, we performed yeast two-hybrid (YTH) screens of skeletal muscle cDNA libraries with MURF-1 baits to identify potential myocellular targets of MURF-1-dependent ubiquitination. This identified eight myofibrillar proteins as binding partners of MURF-1: titin, nebulin, the nebulin-related protein NRAP, troponin-I (TnI), troponin-T (TnT), myosin light chain 2 (MLC-2), myotilin and T-cap. YTH mating studies with MURF-1,2,3 baits indicated that these eight myofibrillar proteins are all targeted redundantly by both MURF-1 and MURF-2. Western blot studies on cardiac tissues from wild-type and MURF-1-deficient mice suggested that titin and nebulin were ubiquitinated at similar levels, and MLC-2 and TnI at reduced levels in MURF-1 KO mice. Mapping of the TnI and titin binding sites on MURF-1 peptide scans demonstrated their binding to motifs highly conserved between MURF-1 and MURF-2. Our data are consistent with a model in which MURF-1 and MURF-2 together target a specific set of myofibrillar proteins redundantly, most likely to control their ubiquitination-dependent degradation. Finally, our YTH screens identified the interaction of MURF-1 with 11 enzymes required for ATP/energy production in muscle including the mitochondrial ATP synthase and cytoplasmic creatine kinase. These data raise the possibility that MURF-1 may coordinately regulate the energy metabolism of mitochondrial and cytoplasmic compartments.

Amino Acid Sequence↗