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PubMed2006

Robustness of coalescent estimators to between-lineage mutation rate variation.

Data from HIV and from human neoplastic cells can show substantial between-lineage mutation rate variation even within a single population. Such variation may affect estimators of population quantities such as Theta = 4N(e)mu. Using simulated DNA data, I measured the effect of rate variation on recovery of Theta by the summary-statistic estimator of Watterson (Watterson GA. 1975. On the number of segregating sites in genetical systems without recombination. Theor Popul Biol. 7:256-276) and the coalescent maximum likelihood algorithm LAMARC (Kuhner MK. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics. Advance Access doi: 10.1093/bioinformatics/btk051). Watterson's estimator showed a downward bias, as expected, with high values of Theta. LAMARC's mean estimate was accurate for all tested values of Theta and rate variation except for a downward bias when rate variation was maximal (i.e., the slow rate was zero). LAMARC had consistently narrower confidence intervals (CIs) than Watterson's estimator. Both methods tended to reject the truth too often when rate variation was 8x or greater and independent among branches, as well as when variation was 4x or greater and correlated among branches. In the case of Watterson's estimate, this excess rejection was fully attributable to variation among genealogies in the amount of total branch length associated with the fast and slow rates. However, in the case of LAMARC, some excess rejection was still observed even when between-genealogy variation was taken into account. Both estimators are robust to modest rate variation; however, their use should be coupled with a statistical test to rule out extreme rate variation as the resulting CIs may not be reliable.

Algorithms↗
PubMed2006

Robust analysis of 5'-transcript ends (5'-RATE): a novel technique for transcriptome analysis and genome annotation.

Complicated cloning procedures and the high cost of sequencing have inhibited the wide application of serial analysis of gene expression and massively parallel signature sequencing for genome-wide transcriptome profiling of complex genomes. Here we describe a new method called robust analysis of 5'-transcript ends (5'-RATE) for rapid and cost-effective isolation of long 5' transcript ends (approximately 80 bp). It consists of three major steps including 5'-oligocapping of mRNA, NlaIII tag and ditag generation, and pyrosequencing of NlaIII tags. Complicated steps, such as purification and cloning of concatemers, colony picking and plasmid DNA purification, are eliminated and the conventional Sanger sequencing method is replaced with the newly developed pyrosequencing method. Sequence analysis of a maize 5'-RATE library revealed complex alternative transcription start sites and a 5' poly(A) tail in maize transcripts. Our results demonstrate that 5'-RATE is a simple, fast and cost-effective method for transcriptome analysis and genome annotation of complex genomes.

5' Untranslated Regions↗
PubMed2005

Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum.

Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1x coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40-70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP-dROX, we assembled a physical map for P.chrysogenum, with 2-3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes.

Chromosomes, Artificial, Bacterial↗
PubMed1994

Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia.

A partial nucleotide sequence of the mRNA encoding a major part of elongation factor 1 alpha (EF1 alpha) from a mitochondria-lacking protozoan, Giardia lamblia, was reported, and the phylogenetic relationship among lower eukaryotes was inferred by the maximum-likelihood and maximum-parsimony methods of protein phylogeny. Both the methods consistently demonstrated that, G. lamblia among the four protozoan species being analyzed, is the earliest offshoot of the eukaryotic tree. Although the Giardia EF1 alpha gene showed an extremely high G+C content as compared with those of other protozoa, it was concentrated only at the third codon positions, resulting in no remarkable differences of amino acid frequencies vis-à-vis those of other species. This clearly suggests (a) that the amino acid frequencies of conservative proteins are free from the drastic bias of genome G+C content, which is a serious problem in the widely used tree of ribosomal RNA, and (b) that protein phylogeny gives a robust estimation for the early divergences in the evolution of eukaryotes.

Amino Acid Sequence↗
PubMed1995

The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining.

The robustness (sensitivity to violation of assumptions) of the maximum-likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes-Cantor, Kimura, and gamma models of DNA substitution. Simulations were performed in which the assumptions of the methods were violated to varying degrees on three model four-taxon trees. The performance of the methods was evaluated with respect to ability to correctly estimate the unrooted four-taxon tree. Maximum likelihood outperformed neighbor joining in 29 of the 36 cases in which the assumptions of both methods were satisfied. In 133 of 180 of the simulations in which the assumptions of the maximum-likelihood and neighbor-joining methods were violated, maximum likelihood outperformed neighbor joining. These results are consistent with a general superiority of maximum likelihood over neighbor joining under comparable conditions. They extend and clarify an earlier study that found an advantage for neighbor joining over maximum likelihood for gamma-distributed mutation rates.

DNA↗
PubMed1995

Developmental changes in carbachol-stimulated phosphoinositide turnover in synaptoneurosomes of the robust nucleus of the archistriatum in the zebra finch.

The effects of acetylcholine (ACh) on synaptoneurosomes of the robust nucleus of the archistriatum (RA), one of the song control nuclei, were investigated during the sensitive period of song learning in the zebra finch. Carbachol (an ACh agonist) stimulated phosphoinositide (PI) turnover at three different ages. Corresponding to a marked increase in ACh levels in the RA, carbachol-stimulated PI turnover peaked during the most sensitive learning period in the life of the zebra finch. These findings suggest that ACh contributes to the regulation of synaptic plasticity in RA neurones involved with song learning in the zebra finch.

Analysis of Variance↗
PubMed1997

A 100 amino acid region in the GABA rho 1 subunit confers robust homo-oligomeric expression.

Retinal gamma-aminobutyric acid type C (GABAC) receptors are believed to be composed of rho subunits. Although rho 1 and rho 2 are over 80% similar, the whole-cell currents generated by rho 1 receptors in Xenopus oocytes are significantly greater than those generated by rho 2 receptors. In this study, chimeric subunits containing different portions of human rho 1 and human rho 2 were created to localize sequences facilitating robust rho 1 expression. Our results indicate that these sequences reside in a 100 amino acid domain in the N-terminus of rho 1, and may involve N-linked glycosylation. Since the N-terminus also contains subunit assembly signals, rho 1 receptors may be formed more efficiently than rho 2 receptors. Therefore, this study furthers our understanding of the molecular basis of GABA-mediated inhibition in the retina.

Amino Acid Sequence↗
PubMed1999

Robustness of anatomically guided pixel-by-pixel algorithms for partial volume effect correction in positron emission tomography.

Several algorithms have been proposed to improve positron emission tomography quantification by combining anatomical and functional information in a pixel-by-pixel correction scheme. The precision of these methods when applied to real data depends on the precision of the manifold correction steps, such as full-width half-maximum modeling, magnetic resonance imaging-positron emission tomography registration, tissue segmentation, or background activity estimation. A good understanding of the influence of these parameters thus is critical to the effective use of the algorithms. In the current article, the authors present a monodimensional model that allows a simple theoretical and experimental evaluation of correction imprecision. The authors then assess correction robustness in three dimensions with computer simulations, and evaluate the validity of regional SD as a correction performance criterion.

Algorithms↗
PubMed2002

Effect of the deficits of fragile X mental retardation protein on cognitive status of fragile x males and females assessed by robust pedigree analysis.

The effect of the fragile X mental retardation 1 (FMR1) gene product (fragile X mental retardation protein [FMRP]) deficits on Full-Scale IQ (FSIQ) and FSIQ-adjusted Wechsler subtests and index scores in fragile X disorder were assessed using a robust modification of the maximum likelihood estimators for pedigree data. The results from 144 extended families have demonstrated a linear effect of progressively reduced levels of FMRP on the FSIQ and all subtest and summary scores in either gender. The effect of FMRP in decreasing FSIQ-adjusted subtest scores was highly significant for Digit Span, Symbol Search, Object Assembly, and Picture Arrangement, with a consistent trend in both genders. Heritability for FSIQ and unadjusted subtest scores estimated from the covariance model did not exceed 50% and varied widely from the highest for Verbal score to the lowest for Picture Completion score. Possible mechanisms by which FMRP deficit impacts on specific weaknesses in fragile X are considered on the basis of present data.

Adolescent↗
PubMed2002

Analysis of robust innate immune response after transplantation in the absence of adaptive immunity.

BACKGROUND: Both animal models and clinical outcomes studies of transplantation suggest that antigen-independent mechanisms can alter graft survival and function. It has been suggested that antigen-independent processes interact with alloantigen-specific responses to augment the rejection reaction. A major link between antigen-specific adaptive immunity and pro-inflammatory stimuli is innate immunity. During transplantation, innate immunity may be stimulated by multiple factors, including ischemia, reperfusion, sterile injury, systemic stress, and cell death. METHODS: We investigated the hypothesis that transplantation induces a potent innate immune response in a murine model of vascularized solid organ transplantation. In our studies, we analyzed three experimental groups: (a) alymphoid group in which both the donor and recipients strains lacked an adaptive immune response due to deletion of the recombinase activating gene, thus blocking production of both T cell and B cell antigen receptors; (b) syngeneic group in which the donors and recipients were genetically identical; and (c) allogeneic group in which the donors and recipients had a complete MHC mismatch. To analyze a large number of parameters we determined the level of expression of a panel of cytokines, chemokines, receptors, and cell surface markers by RNase protection assays. In addition, serum cytokines were determined by ELISA and the infiltration of inflammatory cells was assessed by histology. RESULTS: Our results showed macrophage infiltration and up-regulation of multiple cytokines, chemokines, and chemokine receptors within the first day after transplantation in all groups, including the syngeneic and alymphoid recipients. CONCLUSIONS: Our study demonstrated a robust innate immune response that is independent of adaptive immunity and natural killer cell responses.

Animals↗
PubMed2006

Percent change in wound area of diabetic foot ulcers over a 4-week period is a robust predictor of complete healing in a 12-week prospective trial.

OBJECTIVE: To assess the ability of the 4-week healing rate to predict complete healing over a 12-week period in a large prospective multicenter trial of diabetic patients with foot ulceration. RESEARCH DESIGN AND METHODS: We examined the change in ulcer area over a 4-week period as a predictor of wound healing within 12 weeks in patients who were seen weekly in a prospective, randomized controlled trial. RESULTS: Wound area measurements at baseline and after 4 weeks were performed in 203 patients. The midpoint between the percentage area reduction from baseline at 4 weeks in patients healed versus those not healed at 12 weeks was found to be 53%. Subjects with a reduction in ulcer area greater than the 4-week median had a 12-week healing rate of 58%, whereas those with reduction in ulcer area less than the 4-week median had a healing rate of only 9% (P < 0.01). The absolute change in ulcer area at 4 weeks was significantly greater in healers versus nonhealers (1.5 versus 0.8 cm2, P < 0.02). The percent change in wound area at 4 weeks in those who healed was 82% (95% CI 70-94), whereas in those who failed to heal, the percent change in wound area was 25% (15-35; P < 0.001). CONCLUSIONS: The percent change in foot ulcer area after 4 weeks of observation is a robust predictor of healing at 12 weeks. This simple tool may serve as a pivotal clinical decision point in the care of diabetic foot ulcers for early identification of patients who may not respond to standard care and may need additional treatment.

Journal Article↗
PubMed2005

Robust tolerance to fully allogeneic islet transplants achieved by chimerism with minimal conditioning.

BACKGROUND: Whether mixed chimeras induced by nonmyeloablative conditioning are tolerant to challenge with donor allogeneic islet grafts is unknown. Here we investigate whether our nonmyeloablative, costimulation blockade-free and sirolimus (SRL)-based protocol could facilitate mixed chimerism via bone marrow transplantation (BMT) and induce islet allograft tolerance. METHODS: After low dose (1-3 Gy) total body irradiation (TBI, day -1), with or without prior lymphocyte depletion, C57BL/6 mice were transfused with 40 x 10(6) BALB/c bone marrow cells (day 0) and received SRL (3 mg/kg/day) for 4 weeks. Chimerism was monitored by flow cytometry and the recipients were rendered diabetic chemically and challenged with donor islets. RESULTS: Mixed chimerism was achieved in mice treated with TBI 3 Gy/SRL but it declined over time in 60% (9/15) of them. Long-term stable chimerism was established in 100% of recipients over 50 weeks with either antilymphocyte serum (ALS, 9/9), anti-CD4 (4/4), or anti-CD4 plus anti-CD8 (5/5) prior to BMT. TBI conditioning could be reduced to 1 Gy, with 90% (9/10) maintaining chimerism in the long-term. When TBI was substituted with cyclophosphamide (CTX) or busulfan (BUS), all mice remained chimeric in the long-term. The chimeras showed no proliferative response to donor antigen and accepted both first and second donor-specific islet grafts indefinitely while rejecting third-party grafts. CONCLUSIONS: This data provides the first evidence that stable fully allogeneic chimeras induced with BMT after nonmyeloablative conditioning with SRL and lymphocyte-depleting antibodies exhibit robust donor-specific tolerance to islet grafts.

Animals↗
PubMed2000

Robustness of reserve selection procedures under temporal species turnover.

Complementarity-based algorithms for the selection of reserve networks emphasize the need to represent biodiversity features efficiently, but this may not be sufficient to maintain those features in the long term. Here, we use data from the Common Birds Census in Britain as an exemplar data set to determine guidelines for the selection of reserve networks which are more robust to temporal turnover in features. The extinction patterns found over the 1981-1991 interval suggest that two such guidelines are to represent species in the best sites where they occur (higher local abundance) and to give priority to the rarer species. We tested five reserve selection strategies, one which finds the minimum representation set and others which incorporate the first or both guidelines proposed. Strategies were tested in terms of their efficiency (inversely related to the total area selected) and effectiveness (inversely related to the percentage of species lost) using data on eight pairs of ten-year intervals. The minimum set strategy was always the most efficient, but suffered higher species loss than the others, suggesting that there is a trade-off between efficiency and effectiveness. A desirable compromise can be achieved by embedding the concerns about the long-term maintenance of the biodiversity features of interest in the complementarity-based algorithms.

Algorithms↗
PubMed2000

Using presence-absence data to establish reserve selection procedures that are robust to temporal species turnover.

Previous studies suggest that a network of nature reserves with maximum efficiency (obtained by selecting the minimum area such that each species is represented once) is likely to be insufficient to maintain species in the network over time. Here, we test the performance of three selection strategies which require presence-absence data, two of them previously proposed (multiple representations and selecting an increasing percentage of each species' range) and a novel one based on selecting the site where each species has exhibited a higher permanence rate in the past. Multiple representations appear to be a safer strategy than selecting a percentage of range because the former gives priority to rarer species while the latter favours the most widespread. The most effective strategy was the one based on the permanence rate, indicating that the robustness of reserve networks can be improved by adopting reserve selection procedures that integrate information about the relative value of sites. This strategy was also very efficient, suggesting that the investment made in the monitoring schemes may be compensated for by a lower cost in reserve acquisition.

Animals↗
PubMed2000

Robustness as an evolutionary principle.

We suggest simulating evolution of complex organisms using a model constrained solely by the requirement of robustness in its expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence for dynamical features in the evolved networks is found that can be related to biological observables.

Animals↗
PubMed2003

Robust quantum information processing with techniques from liquid-state NMR.

While nuclear-magnetic-resonance (NMR) techniques are unlikely to lead to a large-scale quantum computer, they are well suited to investigating basic phenomena and developing new techniques. Indeed, it is likely that many existing NMR techniques will find uses in quantum information processing. Here I describe how the composite-rotation (composite-pulse) method can be used to develop quantum logic gates which are robust against systematic errors.

Journal Article↗
PubMed2006

Broad cellular immunity with robust memory responses to simian immunodeficiency virus following serial vaccination with adenovirus 5- and 35-based vectors.

Adenovirus serotype 35 (Ad35) is a promising vaccine platform for human immunodeficiency virus (HIV) infection and emerging infectious diseases as it is uncommon in humans worldwide and is distinct from Ad5, the major vaccine serotype for which many individuals have pre-existing immunity. The immunogenicity of a first-generation, replication-competent Ad35-based vaccine was tested in the simian immunodeficiency virus (SIV) rhesus macaque model by evaluating its capacity to boost immunity generated by Ad5-based vectors. A series of four immunizations with replication-defective Ad5 vectors expressing SIVmac239 gag induced high-frequency responses mediated by both CD8(+) and CD4(+) T cells directed against several epitopes. Ad5-specific neutralizing antibody responses that did not neutralize Ad35 were rapidly induced but waned over time. Subsequent immunization with Ad5-based vectors was minimally effective, whereas immunization with Ad35-based vectors generated a strong increase in the frequency of Gag-specific T cells with specificities that were unchanged. While this boosting response was relatively transient, challenge with the distinct pathogenic isolate SIV/DeltaB670 generated robust and selective recall responses to Gag with similar specificities as induced by vaccination that were elevated for 25 weeks relative to controls. Vaccination had measurable albeit minor effects on virus load. Unexpectedly, regional hypervariability within the Gag sequence of SIV/DeltaB670 was associated with mutation of the conserved CD8(+) T-cell epitope CM9 without concurrent flanking mutations and in the absence of immune pressure. These findings support the further development of Ad35 as a vaccine vector, and promote vaccine regimens that utilize serial administration of heterologous adenoviruses.

Adenoviruses, Human↗
PubMed2006

Electrochemical study of biotin-modified self-assembled monolayers: recommendations for robust preparation.

The development of the underpinning methodology for the production of robust, well-formed, and densely packed biotin-HPDP functionalised gold surfaces, the crucial first step in immobilising bimolecules on surfaces, is described. Self-assembled monolayers (SAMs) with biotin end-groups were prepared on polycrystalline gold surfaces according to a published method. The layers formed were studied using cyclic voltammetry to determine the composition of the layer and its quality. Crystal impedance spectroscopy was also applied as a complimentary indicator of the composition of the layer. For the first time, the effect of assembly time on the properties of the layer was studied along with the composition of the layer and the ability of the precursor molecule to self-assemble by oxidative addition.

Adsorption↗