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At least 127 records · Page 7Linked to original sources
PubMed2006

Intersensory redundancy educates selective attention in bobwhite quail embryos.

We assessed whether exposure to amodal properties in bimodal stimulation (e.g. rhythm, rate, duration) could educate attention to amodal properties in subsequent unimodal stimulation during prenatal development. Bobwhite quail embryos were exposed to an individual bobwhite maternal call under several experimental and control conditions during the day prior to hatching. Experimental groups received redundant auditory and visual exposure to the temporal features of an individual maternal call followed by unimodal auditory exposure to the same call immediately or after a 2-hr or 4-hr delay. Control groups received (1) the same exposure but in the reverse sequence (unimodal --> redundant bimodal), (2) asynchronous bimodal --> unimodal, (3) only unimodal exposure, or (4) only bimodal exposure. All experimental groups showed a significant preference for the familiar maternal call over a novel maternal call when tested 2 days after hatching, whereas none of the control groups showed a significant preference for the familiar call. These results indicate that intersensory redundancy can direct attention to amodal properties in bimodal stimulation and educate attention to the same amodal properties in subsequent unimodal stimulation where no intersensory redundancy is available.

Acoustic Stimulation↗
PubMed2006

Redundancy in designs.

The author contends that a previous Risk Analysis article overemphasized the pitfalls of incorporating redundancy into designs. Relevant aspects of that article are reviewed and commented upon, then the potentials and pitfalls of redundancy in systems and procedures are more broadly discussed. To provide a solid foundation for that discussion, some definitions for systems risk analysis terminology are presented. It is shown that pairs and larger sets of related failures (the physical causes of shortfalls in redundancy effectiveness) can be divided into two types: (1) cascading/induced failures and (2) common-external-cause failures. Each type has its own physical characteristics and implications for mathematical modeling. Service experience with large-commercial-airplane jet-engine propulsion systems is used to illustrate the two types of related failures. Finally, an overview is provided of event-sequence analysis, an alternative approach to systems risk analysis. When the possibility of related failures of mutually-redundant system elements must be accounted for, event-sequence analysis can usually do that better than fault-tree analysis.

Journal Article↗
PubMed2000

Bacterial functional redundancy along a soil reclamation gradient.

A strategy to measure bacterial functional redundancy was developed and tested with soils collected along a soil reclamation gradient by determining the richness and diversity of bacterial groups capable of in situ growth on selected carbon substrates. Soil cores were collected from four sites along a transect from the Jamari tin mine site in the Jamari National Forest, Rondonia, RO, Brazil: denuded mine spoil, soil from below the canopy of invading pioneer trees, revegetated soil under new growth on the forest edge, and the forest floor of an adjacent preserved forest. Bacterial population responses were analyzed by amending these soil samples with individual carbon substrates in the presence of bromodeoxyuridine (BrdU). BrdU-labeled DNA was then subjected to a 16S-23S rRNA intergenic analysis to depict the actively growing bacteria from each site. The number and diversity of bacterial groups responding to four carbon substrates (L-serine, L-threonine, sodium citrate, and alpha-lactose hydrate) increased along the reclamation-vegetation gradient such that the preserved forest soil samples contained the highest functional redundancy for each substrate. These data suggest that bacterial functional redundancy increases in relation to the regrowth of plant communities and may therefore represent an important aspect of the restoration of soil biological functionality to reclaimed mine spoils. They also suggest that bacterial functional redundancy may be a useful indicator of soil quality and ecosystem functioning.

Bacteria↗
PubMed2001

Role of ADP-ribosyltransferase activity of pertussis toxin in toxin-adhesin redundancy with filamentous hemagglutinin during Bordetella pertussis infection.

Pertussis toxin (PT) and filamentous hemagglutinin (FHA) are two major virulence factors of Bordetella pertussis. FHA is the main adhesin, whereas PT is a toxin with an A-B structure, in which the A protomer expresses ADP-ribosyltransferase activity and the B moiety is responsible for binding to the target cells. Here, we show redundancy of FHA and PT during infection. Whereas PT-deficient and FHA-deficient mutants colonized the mouse respiratory tract nearly as efficiently as did the isogenic parent strain, a mutant deficient for both factors colonized substantially less well. This was not due to redundant functions of PT and FHA as adhesins, since in vitro studies of epithelial cells and macrophages indicated that FHA, but not PT, acts as an adhesin. An FHA-deficient B. pertussis strain producing enzymatically inactive PT colonized as poorly as did the FHA-deficient, PT-deficient strain, indicating that the ADP-ribosyltransferase activity of PT is required for redundancy with FHA. Only strains producing active PT induced a local transient release of tumor necrosis factor alpha (TNF-alpha), suggesting that the pharmacological effects of PT are the basis of the redundancy with FHA, through the release of TNF-alpha. This may lead to damage of the pulmonary epithelium, allowing the bacteria to colonize even in the absence of FHA.

Adhesins, Bacterial↗
PubMed1976

Sequence arrangement in herpes simplex virus type 1 DNA: identification of terminal fragments in restriction endonuclease digests and evidence for inversions in redundant and unique sequences.

It has been proposed by Sheldrick and Berthelot (1974) that the terminal sequences of herpes simplex virus type 1 (HSV-1) DNA are repeated in an internal inverted form and that the inverted redundant sequences delimit and separate two unique sequences, S and L. In this study the sequence arrangement in HSV-1 DNA has been investigated with restriction endonuclease cleavage, end-labeling studies, and molecular hybridization experiments. The terminal fragments in digests with restriction endonucleases Hind III, Hpa-1, EcoRI and Bum were identified and shown to be consistent with the Sheldrick and Berthelot model. Inverted fragments which contain unique sequences as well as redundant sequences, and which the model predicts, were identified by DNA-DNA hybridization studies. Further cleavage of Bum fragments with Hpa-1 also revealed inversions of the terminal sequences that contained unique sequences. The results obtained showed that the unique sequences S and L are relatively inverted in different DNA molecules in the population, resulting in the presence of four related genomes with rearranged sequences in apparently equal amounts. The redundant sequences bounding S do not share complete sequence homology with those bounding L, but hybridization studies are presented which show that the terminal 0.3% of the genome is repeated in every redundant sequence.

Base Sequence↗
PubMed1981

Regulatory and coding potential of the mouse mammary tumor virus long terminal redundancy.

Molecular clones containing the 3' half of newly integrated mouse mammary tumor virus (MMTV) DNA with adjacent mouse cellular sequences were characterized. In addition, we cloned the long terminal redundancy joint from the unintegrated circular form of MMTV DNA. The entire nucleotide sequence of the integrated and part of the unintegrated terminal redundancy was determined; this allowed us to delineate the boundaries of the MMTV long terminal redundancy, which comprises 1,327 base pairs. The position of possible RNA polymerase II initiation and termination signals corresponded closely to the expected regions of viral RNA initiation and termination specified by current models. The MMTV long terminal redundancy also contained a large open reading frame with sufficient information for a protein of 198 amino acids. Initial comparison of flanking 3' cellular sequences from three independent integrated clones suggested there was no host sequence specificity in the MMTV integration event. However, specificity of integration with respect to viral sequences was precise.

Bacteriophage lambda↗
PubMed2003

Template switches during plus-strand DNA synthesis of duck hepatitis B virus are influenced by the base composition of the minus-strand terminal redundancy.

Two template switches are necessary during plus-strand DNA synthesis of the relaxed circular (RC) form of the hepadnavirus genome. The 3' end of the minus-strand DNA makes important contributions to both of these template switches. It acts as the donor site for the first template switch, called primer translocation, and subsequently acts as the acceptor site for the second template switch, termed circularization. Circularization involves transfer of the nascent 3' end of the plus strand from the 5' end of the minus-strand DNA to the 3' end, where further elongation can lead to production of RC DNA. In duck hepatitis B virus (DHBV), a small terminal redundancy (5'r and 3'r) on the ends of the minus-strand DNA has been shown to be important, but not sufficient, for circularization. We investigated what contribution, if any, the base composition of the terminal redundancy made to the circularization process. Using a genetic approach, we found a strong positive correlation between the fraction of A and T residues within the terminal redundancy and the efficiency of the circularization process in those variants. Additionally, we found that the level of in situ priming increases, at the expense of primer translocation, as the fraction of A and T residues in the 3'r decreases. Thus, a terminal redundancy rich in A and T residues is important for both plus-strand template switches in DHBV.

Animals↗
PubMed1997

Implicit representation in genetic algorithms using redundancy.

A new representation combining redundancy and implicit fitness constraints is introduced that performs better than a simple genetic algorithm (GA) and a structured GA in experiments. The implicit redundant representation (IRR) consists of a string that is over-specified, allowing for sections of the string to remain inactive during function evaluation. The representation does not require the user to prespecify the number of parameters to evaluate or the location of these parameters within the string. This information is obtained implicitly by the fitness function during the GA operations. The good performance of the IRR can be attributed to several factors: less disruption of existing fit members due to the increased probability of crossovers and mutation affecting only redundant material; discovery of fit members through the conversion of redundant material into essential information; and the ability to enlarge or reduce the search space dynamically by varying the number of variables evaluated by the fitness function. The IRR GA provides a more biologically parallel representation that maintains a diverse population throughout the evolution process. In addition, the IRR provides the necessary flexibility to represent unstructured problem domains that do not have the explicit constraints required by fixed representations.

Algorithms↗
PubMed2006

A Zn-finger/FH2-domain containing protein, FOZI-1, acts redundantly with CeMyoD to specify striated body wall muscle fates in the Caenorhabditis elegans postembryonic mesoderm.

Striated muscle development in vertebrates requires the redundant functions of multiple members of the MyoD family. Invertebrates such as Drosophila and Caenorhabditis elegans contain only one MyoD homolog in each organism. Earlier observations suggest that factors outside of the MyoD family might function redundantly with MyoD in striated muscle fate specification in these organisms. However, the identity of these factors has remained elusive. Here, we describe the identification and characterization of FOZI-1, a putative transcription factor that functions redundantly with CeMyoD (HLH-1) in striated body wall muscle (BWM) fate specification in the C. elegans postembryonic mesoderm. fozi-1 encodes a novel nuclear-localized protein with motifs characteristic of both transcription factors and actin-binding proteins. We show that FOZI-1 shares the same expression pattern as CeMyoD in the postembryonic mesodermal lineage, the M lineage, and that fozi-1-null mutants exhibit similar M lineage-null defects to those found in animals lacking CeMyoD in the M lineage (e.g. loss of a fraction of M lineage-derived BWMs). Interestingly, fozi-1-null mutants with a reduced level of CeMyoD lack most, if not all, M lineage-derived BWMs. Our results indicate that FOZI-1 and the Hox factor MAB-5 function redundantly with CeMyoD in the specification of the striated BWM fate in the C. elegans postembryonic mesoderm, implicating a remarkable level of complexity for the production of a simple striated musculature in C. elegans.

Alleles↗
PubMed1998

Vertebrate tinman homologues XNkx2-3 and XNkx2-5 are required for heart formation in a functionally redundant manner.

Tinman is a Drosophila homeodomain protein that is required for formation of both visceral and cardiac mesoderm, including formation of the dorsal vessel, a heart-like organ. Although several vertebrate tinman homologues have been characterized, their requirement in earliest stages of heart formation has been an open question, perhaps complicated by potential functional redundancy of tinman homologues. We have utilized a novel approach to investigate functional redundancy within a gene family, by coinjecting DNA encoding dominantly acting repressor derivatives specific for each family member into developing Xenopus embryos. Our results provide the first evidence that vertebrate tinman homologues are required for earliest stages of heart formation, and that they are required in a functionally redundant manner. Coinjection of dominant repressor constructs for both XNkx2-3 and XNkx2-5 is synergistic, resulting in a much higher frequency of mutant phenotypes than that obtained with injection of either dominant repressor construct alone. Rescue of mutant phenotypes can be effected by coinjection of either wild-type tinman homologue. The most extreme mutant phenotype is a complete absence of expression of XNkx2-5 in cardiogenic mesoderm, an absence of markers of differentiated myocardium, and absence of morphologically distinguishable heart on the EnNkxHD-injected side of the embryo. This phenotype represents the most severe cardiac phenotype of any vertebrate mutant yet described, and underscores the importance of the tinman family for heart development. These results provide the first in vivo evidence that XNkx2-3 and XNkx2-5 are required as transcriptional activators for the earliest stages of heart formation. Furthermore, our results suggest an intriguing mechanism by which functional redundancy operates within a gene family during development. Our experiments have been performed utilizing a recently developed transgenic strategy, and attest to the efficacy of this strategy for enabling transgene expression in limited cell populations within the developing Xenopus embryo.

Amino Acid Sequence↗
PubMed2000

Evolutionary conservation of redundancy between a diverged pair of forkhead transcription factor homologues.

The Caenorhabditis elegans gene pes-1 encodes a transcription factor of the forkhead family and is expressed in specific cells of the early embryo. Despite these observations suggesting pes-1 to have an important regulatory role in embryogenesis, inactivation of pes-1 caused no apparent phenotype. This lack of phenotype is a consequence of genetic redundancy. Whereas a weak, transitory effect was observed upon disruption of just T14G12.4 (renamed fkh-2) gene function, simultaneous disruption of the activity of both fkh-2 and pes-1 resulted in a penetrant lethal phenotype. Sequence comparison suggests these two forkhead genes are not closely related and the functional association of fkh-2 and pes-1 was only explored because of the similarity of their expression patterns. Conservation of the fkh-2/pes-1 genetic redundancy between C. elegans and the related species C. briggsae was demonstrated. Interestingly the redundancy in C. briggsae is not as complete as in C. elegans and this could be explained by alterations of pes-1 specific to the C. briggsae ancestry. With overlapping function retained on an evolutionary time-scale, genetic redundancy may be extensive and expression pattern data could, as here, have a crucial role in characterization of developmental processes.

Amino Acid Sequence↗
PubMed2001

The homeobox genes vox and vent are redundant repressors of dorsal fates in zebrafish.

Ventralizing transcriptional repressors in the Vox/Vent family have been proposed to be important regulators of dorsoventral patterning in the early embryo. While the zebrafish genes vox (vega1) and vent (vega2) both have ventralizing activity in overexpression assays, loss-of-function studies are needed to determine whether these genes have distinct or redundant functions in dorsoventral patterning and to provide critical tests of the proposed regulatory interactions among vox, vent and other genes that act to establish the dorsoventral axis. We show that vox and vent are redundant repressors of dorsal fates in zebrafish. Mutants that lack vox function have little or no dorsoventral patterning defect, and inactivation of either vox or vent by injection of antisense morpholino oligonucleotides has little or no effect on the embryo. In contrast, embryos that lack both vox and vent function have a dorsalized phenotype. Expression of dorsal mesodermal genes, including chordin, goosecoid and bozozok, is strongly expanded in embryos that lack vox and vent function, indicating that the redundant action of vox and vent is required to restrict dorsal genes to their appropriate territories. Our genetic analysis indicates that the dorsalizing transcription factor Bozozok promotes dorsal fates indirectly, by antagonizing the expression of vox and vent. In turn, vox and vent repress chordin expression, restricting its function as an antagonist of ventral fates to the dorsal side of the embryo. Our results support a model in which BMP signaling induces the expression of ventral genes, while vox and vent act redundantly to prevent the expression of chordin, goosecoid and other dorsal genes in the lateral and ventral mesendoderm.

Animals↗
PubMed2005

Flux analysis uncovers key role of functional redundancy in formaldehyde metabolism.

Genome-scale analysis of predicted metabolic pathways has revealed the common occurrence of apparent redundancy for specific functional units, or metabolic modules. In many cases, mutation analysis does not resolve function, and instead, direct experimental analysis of metabolic flux under changing conditions is necessary. In order to use genome sequences to build models of cellular function, it is important to define function for such apparently redundant systems. Here we describe direct flux measurements to determine the role of redundancy in three modules involved in formaldehyde assimilation and dissimilation in a bacterium growing on methanol. A combination of deuterium and (14)C labeling was used to measure the flux through each of the branches of metabolism for growth on methanol during transitions into and out of methylotrophy. The cells were found to differentially partition formaldehyde among the three modules depending on the flux of methanol into the cell. A dynamic mathematical model demonstrated that the kinetic constants of the enzymes involved are sufficient to account for this phenomenon. We demonstrate the role of redundancy in formaldehyde metabolism and have uncovered a new paradigm for coping with toxic, high-flux metabolic intermediates: a dynamic, interconnected metabolic loop.

Deuterium↗
PubMed2003

All parts of an item are not equal: effects of phonological redundancy on immediate recall.

The process of redintegration is thought to use top-down knowledge to repair partly damaged memory traces. We explored redintegration in the immediate recall of lists from a limited pool of partly phonologically redundant pseudowords. In Experiment 1, four kinds of stimuli were created by adding the syllable /ne/ to two-syllable pseudowords, either to the middle (/tepa/ vs. /tenepa/) or to the end (/tepane/), or adding a different syllable to each item (/tepalo/, /vuropi/). The repeated syllable was thought to be available for redintegration. Lists of two-syllable pseudowords were recalled best, items with a redundant end were intermediate, and items with a redundant middle-syllable were as hard as nonredundant three-syllable items. In Experiment 2, the last syllable was predictable from context but not shared between all stimuli, reducing phonological similarity between items. Performance did not differ from the situation with identicallast syllables. In Experiment 3, a shared first syllable had a detrimental effecton memory. An error analysis showed that beneficial redundancy effects were accompanied by harmful similarity effects, impairing memory for nonredundant syllables. The balance between the two effects depended on syllable position.

Adult↗
PubMed1993

Redundancy gains and coactivation with two different targets: the problem of target preferences and the effects of display frequency.

When a visual display contains two targets, both of which require the same response, reaction times (RTs) are faster than when only one target appears. This effect has previously been obtained regardless of whether the redundant targets are the same or different in shape, and in at least one set of two-target experiments, the redundancy gains have been larger for different targets (Grice & Reed, 1992). Experiments with two different targets have also revealed violations of the race-model inequality, suggesting that redundant targets coactivate the response (Miller, 1982). The present paper reexamines both of these findings, because both appear to be inconsistent with the interactive race model (Mordkoff & Yantis, 1991). Experiment 1 shows that the race-model inequality is not violated when the experimental design is free of biased contingencies; Experiment 1 also provides evidence that target preferences may artifactually produce the RT advantage for different- over same-target trials. Experiment 2, however, shows that the race-model inequality is violated when the frequencies of single- and redundant-target displays are equated (without introducing any biased contingencies), implying that the interactive race model cannot account for the results of experiments involving more than one type of target. Alternative loci for coactivation are briefly discussed.

Adult↗
PubMed1991

On the locus of redundancy effects in a letter-detection task.

It takes longer to detect a target if it is the initial letter of a nonredundant letter string such as BNHTW than if it is the initial letter of a redundant letter string such as BBBBB (Johnson, 1986b; Johnson & Blum, 1988). The results of the present study reveal that the redundancy effect also occurs for mixed-case letters strings (e.g., BbbBb) and digit strings (e.g., 22222). In addition, these results suggest that the cause of the redundancy effect is not related to the visual properties of the noninitial letters per se but is instead related to the presence of the target in noninitial positions. Together, these results rule out a number of hypotheses about the cause of the redundancy effect and suggest that the locus of this effect is in processes involved in response selection and/or the read-out of information from the perceptual system.

Adult↗
PubMed2002

Visual search for dimensionally redundant pop-out targets: parallel-coactive processing of dimensions is location specific.

Three visual search experiments investigated redundancy gains for single and dual odd-one-out feature targets that differed from distractors in orientation, color, or both. In Experiment 1, redundant-target displays contained (a) a single target defined in 2 dimensions, (b) dual targets each defined in a different dimension, or (c) dual targets both defined in the same dimension. The redundancy gains, relative to single nonredundant targets, decreased from the first condition on, with violations of J. Miller's (1982) race model inequality (RMI) manifested only in the first 2 conditions. Experiment 2 systematically varied the spatial separation between dual targets each defined in a different dimension. Violations of the RMI were evident only when the 2 targets occupied nearby locations. Experiment 3 provided evidence of RMI violations by dimensionally redundant targets at both precued (likely) and noncued (unlikely) display locations. Taken together, these results suggest that there is coactivation of a common mechanism by target signals in different dimensions (not by signals in the same dimension), that the coactivation effects are spatially specific, and that the coactivated mechanisms are located at a preattentive, perceptual stage of processing.

Adult↗
PubMed2005

Effect of item redundancy on Rasch item and person estimates.

One of the assumptions of many latent trait models is local independence. This assumption specifies that, after controlling for the underlying trait, item responses are independent. Given the lack of studies of model robustness against such violations, it appears that this assumption is frequently taken for granted. Therefore, this study investigated the robustness of Rasch item and person estimates with simulated data under varying number of items, sample sizes, and levels of item redundancy. Item and person reliabilities, the standard deviations of the person and item estimates, the root mean squared differences and mean signed differences among person and item estimates, the correlations between person estimates, and the percentage of person estimates shifting by more than .50 logits were used to evaluate the impact of item redundancy. Both norm and criterion-reference interpretations may be influenced by the imputation of redundancy into the data. However, it appears that the amount of redundancy needs to be considerable before such interpretations would be adversely impacted. Suggestions for further simulation research are provided.

Humans↗