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PubMed1998

Distributed torsion angle grid search in high dimensions: a systematic approach to NMR structure determination.

Two complementary approaches for systematic search in torsion angle space are described for the generation of all conformations of polypeptides which satisfy experimental NMR restraints, hard-sphere van der Waals radii, and rigid covalent geometry. The first procedure is based on a recursive, tree search algorithm for the examination of linear chains of torsion angles, and uses a novel treatment to propagate the search results to neighboring regions so that the structural consequences of the restraints are fully realized. The second procedure is based on a binary combination of torsion vector spaces for connected submolecules, and produces intermediate results in Cartesian space for a more robust restraint analysis. Restraints for NMR applications include bounds on torsion angles and internuclear distances, including relational and degenerate restraints involving equivalent and nonstereoassigned protons. To illustrate these methods, conformation search results are given for the tetrapeptide APGA restrained to an idealized beta-turn conformation, an alanine octapeptide restrained to a right-handled helical conformation, and the structured region of the peptide SYPFDV.

Algorithms↗

PubMed2004

Superoxide dismutase transgenes in sugarbeets confer resistance to oxidative agents and the fungus C. beticola.

Sugarbeets carrying superoxide dismutase transgenes were developed in order to investigate the possibility of enhancing their resistance to oxidative stress. Binary T-DNA vectors carrying the chloroplastic and cytosolic superoxide dismutase genes from tomato, were used for Agrobacterium-mediated transformation of sugarbeet petioles. The transgenic plants were subjected to treatments known to cause oxidative stress, such as the herbicide methyl viologen and a natural photosensitizer toxin produced by the fungus Cercospora beticola, namely cercosporin. The transgenic plants exhibited increased tolerance to methyl viologen, to pure cercosporin, as well as to leaf infection with the fungus C. beticola.

Ascomycota↗

PubMed1998

Graded transcriptional response to different concentrations of a single transactivator.

Threshold mechanisms of transcriptional activation are thought to be critical for translating continuous gradients of extracellular signals into discrete all-or-none cellular responses, such as mitogenesis and differentiation. Indeed, unequivocal evidence for a graded transcriptional response in which the concentration of inducer directly correlates with the level of gene expression in individual eukaryotic cells is lacking. By using a novel binary tetracycline regulatable retroviral vector system, we observed a graded rather than a threshold mechanism of transcriptional activation in two different model systems. When polyclonal populations of cells were analyzed at the single cell level, a dose-dependent, stepwise increase in expression of the reporter gene, green fluorescent protein (GFP), was observed by fluorescence-activated cell sorting. These data provide evidence that, in addition to the generally observed all-or-none switch, the basal transcription machinery also can respond proportionally to changes in concentration of extracellular inducers and trancriptional activators.

Animals↗

PubMed2006

Synergistic interactions of the plant cell death pathways induced by Phytophthora infestans Nepl-like protein PiNPP1.1 and INF1 elicitin.

Cell death plays a ubiquitous role in plant-microbe interactions, given that it is associated with both susceptible and resistance interactions. A class of cell death-inducing proteins, termed Nepl-like proteins (NLPs), has been reported in bacteria, fungi, and oomycetes. These proteins induce nonspecific necrosis in a variety of dicotyledonous plants. Here, we describe three members of the NLP family from the oomycete Phytophthora infestans (PiNPP1.1, PiNPP1.2, and PiNPP1.3). Using agroinfection with a binary Potato virus X vector, we showed that PiNPP1.1 induces cell death in Nicotiana benthamiana and the host plant tomato. Expression analyses indicated that PiNPP1.1 is up-regulated during late stages of infection of tomato by P. infestans. We compared PiNPP1.1 necrosis-inducing activity to INF1 elicitin, a well-studied protein that triggers the hypersensitive response in Nicotiana spp. Using virus-induced gene silencing, we showed that the cell death induced by PiNPP1.1 is dependent on the ubiquitin ligase-associated protein SGT1 and the heat-shock protein HSP90. In addition, cell death triggered by PiNPP1.1 but not that by INF1 was dependent on the defense-signaling proteins COI1, MEK2, NPR1, and TGA2.2, suggesting distinct signaling requirements. Combined expression of PiNPP1.1 and INF1 in N. benthamiana resulted in enhanced cell death, suggesting synergistic interplay between the two cell-death responses. Altogether, these results point to potentially distinct but interacting cell-death pathways induced by PiNPP1.1 and INF1 in plants.

Algal Proteins↗

PubMed1985

High efficiency transformation of cultured tobacco cells.

Tobacco calli were transformed at levels up to 50% by cocultivation of tobacco cultured cells with Agrobacterium tumefaciens harboring the binary transfer-DNA vector, pGA472, containing a kanamycin resistance marker. Transformation frequency was dependent on the physiological state of the tobacco cells, the nature of Agrobacterium strain and, less so, on the expression of the vir genes of the tumor-inducing plasmid. Maximum transformation frequency was obtained with exponentially growing plant cells, suggesting that rapid growth of plant cells is an essental factor for efficient transformation of higher plants.

Journal Article↗

PubMed2005

Molecular evidence of placental hypoxia in preeclampsia.

BACKGROUND: Oxygen plays a central role in human placental pathologies including preeclampsia, a leading cause of fetal and maternal death and morbidity. Insufficient uteroplacental oxygenation in preeclampsia is believed to be responsible for the molecular events leading to the clinical manifestations of this disease. DESIGN: Using high-throughput functional genomics, we determined the global gene expression profiles of placentae from high altitude pregnancies, a natural in vivo model of chronic hypoxia, as well as that of first-trimester explants under 3 and 20% oxygen, an in vitro organ culture model. We next compared the genomic profile from these two models with that obtained from pregnancies complicated by preeclampsia. Microarray data were analyzed using the binary tree-structured vector quantization algorithm, which generates global gene expression maps. RESULTS: Our results highlight a striking global gene expression similarity between 3% O(2)-treated explants, high-altitude placentae, and importantly placentae from preeclamptic pregnancies. We demonstrate herein the utility of explant culture and high-altitude placenta as biologically relevant and powerful models for studying the oxygen-mediated events in preeclampsia. CONCLUSION: Our results provide molecular evidence that aberrant global placental gene expression changes in preeclampsia may be due to reduced oxygenation and that these events can successfully be mimicked by in vivo and in vitro models of placental hypoxia.

Adult↗

PubMed2005

Molecular diagnosis. Classification, model selection and performance evaluation.

OBJECTIVES: We discuss supervised classification techniques applied to medical diagnosis based on gene expression profiles. Our focus lies on strategies of adaptive model selection to avoid overfitting in high-dimensional spaces. METHODS: We introduce likelihood-based methods, classification trees, support vector machines and regularized binary regression. For regularization by dimension reduction, we describe feature selection methods: feature filtering, feature shrinkage and wrapper approaches. In small sample-size situations efficient methods of data re-use are needed to assess the predictive power of a model. We discuss two issues in using cross-validation: the difference between in-loop and out-of-loop feature selection, and estimating model parameters in nested-loop cross-validation. RESULTS: Gene selection does not reduce the dimensionality of the model. Tuning parameters enable adaptive model selection. The feature selection bias is a common pitfall in performance evaluation. Model selection and performance evaluation can be combined by nested-loop cross-validation. CONCLUSIONS: Classification of microarrays is prone to overfitting. A rigorous and unbiased assessment of the predictive power of the model is a must.

Gene Expression Profiling↗

PubMed2003

Tumor necrosis factor-related apoptosis-inducing ligand gene on human colorectal cancer cell line HT29.

AIM: To evaluate the therapeutic efficiency of Tumor Necrosis Factor-related Apoptosis-inducing Ligand (TRAIL) gene on human colorectal cancer cell line HT29. METHODS: Human embryonal kidney cells transformed by introducing sheared fragments of Ad5 DNA (293 cell) were used for amplification of adenoviral vectors: Ad/GT-TRAIL,Ad/GT-Bax, Ad/GT-LacZ and Ad/PGK-GV16. Human colorectal cancer cell line HT29 was transfected with binary adenovirus-mediated TRAIL gene. Bax gene was used as positive control, LacZ gene was used as the vector control,and cells treated with PBS only were used as a mock control. The morphological changes, cell growth and apoptosis were measured by reversmicroscope, MTT method and flow cytometry. RESULTS: All adenoviral vectors titer determined by optical absorbency at A260nm were 1X10(10) viral particle/ml(vp/ml). Obviously morphological changes of HT29 cells were observed when infected with Ad/GT-TRAIL, and these changes were much more obviously when Ad/PGK-GV16 was coinfected. The cell suppression percentage and the percentage of apoptotic cells were 52.5 % and 16.5 % respectively when infected with Ad/GT-TRAIL alone, while combining with Ad/PGK-GV16, the growth of HT29 was suppressed by 85.2 % and the percentage of apoptotic cells was 35.9 %. It showed a significantly enhanced therapeutic efficiency with binary system (P<0.05). CONCLUSION: A binary adenoviral vector system provides an effective approach to amplify viral vectors that express potentially toxic gene, TRAIL. Ad/GT-TRAIL showed a significantly enhanced therapeutic efficiency for HT29 when coinfected with Ad/PGK-GV16. Ad/GT-TRAIL could induce apoptosis of HT29 and inhibit its growth.

Adenoviridae↗

PubMedDate not supplied

A hierarchical classifier using new support vector machines for automatic target recognition.

A binary hierarchical classifier is proposed for automatic target recognition. We also require rejection of non-object (non-target) inputs, which are not seen during training or validation, thus producing a very difficult problem. The SVRDM (support vector representation and discrimination machine) classifier is used at each node in the hierarchy, since it offers good generalization and rejection ability. Using this hierarchical SVRDM classifier with magnitude Fourier transform (|FT|) features, which provide shift-invariance, initial test results on infra-red (IR) data are excellent.

Algorithms↗

PubMed2004

New results on error correcting output codes of kernel machines.

We study the problem of multiclass classification within the framework of error correcting output codes (ECOC) using margin-based binary classifiers. Specifically, we address two important open problems in this context: decoding and model selection. The decoding problem concerns how to map the outputs of the classifiers into class codewords. In this paper we introduce a new decoding function that combines the margins through an estimate of their class conditional probabilities. Concerning model selection, we present new theoretical results bounding the leave-one-out (LOO) error of ECOC of kernel machines, which can be used to tune kernel hyperparameters. We report experiments using support vector machines as the base binary classifiers, showing the advantage of the proposed decoding function over other functions of the margin commonly used in practice. Moreover, our empirical evaluations on model selection indicate that the bound leads to good estimates of kernel parameters.

Neural Networks, Computer↗

PubMed2003

Slow dynamics of a confined supercooled binary mixture. II. Q space analysis.

We report the analysis in the wave vector space of the density correlator of a Lennard-Jones binary mixture confined in a disordered matrix of soft spheres upon supercooling. In spite of the strong confining medium the behavior of the mixture is consistent with the mode-coupling theory predictions for bulk supercooled liquids. The relaxation times extracted from the fit of the density correlator to the stretched exponential function follow a unique power law behavior as a function of wave vector and temperature. The von Schweidler scaling properties are valid for an extended wave vector range around the peak of the structure factor. The parameters extracted in the present work are compared with the bulk values obtained in literature.

Journal Article↗

PubMed1997

Identification and classification of autoantibody repertoires (Western blots) with a pattern recognition algorithm by an artificial neural network.

The screening of sera for autoantibodies with Western blots reveals complex repertoires. the compostion of such repertoires depends on genetic control of autoantibody-producing cells, the individual's history of exposure to its own and to foreign antigens, and also on the presence of autoimmune diseases. Our method shows how staining patterns of Western blots can be recoded as binary or grey-value vectors. Vectors are transferred to artificial neural networks for learning. Artificial neural networks are able to recognize group-specific antibody binding patterns. Staining patterns can be attributed to diagnostic groups. This may support diagnostic procedures.

Algorithms↗

PubMed2006

Reducing multiclass cancer classification to binary by output coding and SVM.

Multiclass cancer classification based on microarray data is presented. The binary classifiers used combine support vector machines with a generalized output-coding scheme. Different coding strategies, decoding functions and feature selection methods are incorporated and validated on two cancer datasets: GCM and ALL. Using random coding strategy and recursive feature elimination, the testing accuracy achieved is as high as 83% on GCM data with 14 classes. Comparing with other classification methods, our method is superior in classificatory performance.

Artificial Intelligence↗

PubMed2001

Efficiency and stability of high molecular weight DNA transformation: an analysis in tomato.

The efficiency of the binary bacterial artificial chromosome (BIBAC) vector for Agrobacterium-mediated stable transfer of high molecular weight DNA into plants was tested in tomato. Several variables affecting transformation efficiency were examined including insert size, Agrobacterium genetic background, and the presence of additional copies of the virG, virE1 and virE2 genes. It was found that a helper plasmid containing extra copies of virG was an absolute requirement for obtaining tomato transformants with the BIBAC. MOG101 with the virG helper plasmid was found to be the most efficient strain for transfer of high molecular weight DNA (150 kb). Selected high molecular weight DNA transformants were advanced several generations (up to the R4) to assess T-DNA stability. This analysis showed that the T-DNA was stably maintained and inherited through several meioses regardless of whether it was in the hemizygous or homozygous state. Expression of a selectable marker gene within the T-DNA was also examined through several generations and no gene silencing was observed. Thus, the BIBAC is a useful system for transfer of large DNA fragments into the plant genome.

Base Sequence↗

PubMed2002

Expression of a Phytophthora sojae necrosis-inducing protein occurs during transition from biotrophy to necrotrophy.

Phytophthora sojae is an oomycete that causes stem and root rot on soybean plants. To discover pathogen factors that produce disease symptoms or activate plant defense responses, we identified putative secretory proteins from expressed sequence tags (ESTs) and tested selected candidates using a heterologous expression assay. From an analysis of 3035 ESTs originating from mycelium, zoospore, and infected soybean tissues, we identified 176 putative secreted proteins. A total of 16 different cDNAs predicted to encode secreted proteins ranging in size from 6 to 26 kDa were selected for expression analysis in Nicotiana benthamiana using an Agrobacterium tumefaciens binary potato virus X (PVX) vector. This resulted in the identification of a 25.6-kDa necrosis-inducing protein that is similar in sequence to other proteins from eukaryotic and prokaryotic species. The genomic region encoding the P. sojae necrosis-inducing protein was isolated and the expression pattern of the corresponding gene determined by RNA blot hybridization and by RT-PCR. The activity of this P. sojae protein was compared to proteins of similar sequence from Fusarium oxysporum, Bacillus halodurans, and Streptomyces coelicolor by PVX-based expression in N. benthamiana and by transient expression via particle bombardment in soybean tissues. The P. sojae protein was a powerful inducer of necrosis and cell death in both assays, whereas related proteins from other species varied in their activity. This study suggests that the P. sojae necrosis-inducing protein facilitates the colonization of host tissues during the necrotrophic phase of growth.

Agrobacterium tumefaciens↗

PubMed1996

Stable transfer of intact high molecular weight DNA into plant chromosomes.

In conjunction with an enhanced system for Agrobacterium-mediated plant transformation, a new binary bacterial artificial chromosome (BIBAC) vector has been developed that is capable of transferring at least 150 kb of foreign DNA into a plant nuclear genome. The transferred DNA appears to be intact in the majority of transformed tobacco plants analyzed and is faithfully inherited in the progeny. The ability to introduce high molecular weight DNA into plant chromosomes should accelerate gene identification and genetic engineering of plants and may lead to new approaches in studies of genome organization.

Base Sequence↗

PubMed2005

Differences in intensity and specificity of hypersensitive response induction in Nicotiana spp. by INF1, INF2A, and INF2B of Phytophthora infestans.

Elicitins form a family of structurally related proteins that induce the hypersensitive response (HR) in plants, particularly Nicotiana spp. The elicitin family is composed of several classes. Most species of the plant-pathogenic oomycete genus Phytophthora produce the well-characterized 10-kDa canonical elicitins (class I), such as INF1 of the potato and tomato pathogen Phytophthora infestans. Two genes, inf2A and inf2B, encoding a distinct class (class III) of elicitin-like proteins, also occur in P. infestans. Unlike secreted class I elicitins, class III elicitins are thought to be cell-surface-anchored polypeptides. Molecular characterization of the inf2 genes indicated that they are widespread in Phytophthora spp. and occur as a small gene family. In addition, Southern blot and Northern blot hybridizations using gene-specific probes showed that inf2A and inf2B genes and transcripts can be detected in 17 different P. infestans isolates. Functional secreted expression in plant cells of the elicitin domain of the infl and inf2 genes was conducted using a binary Potato virus X (PVX) vector (agroinfection) and Agrobacterium tumefaciens transient transformation assays (agroinfiltration), and resulted in HR-like necrotic symptoms and induction of defense response genes in tobacco. However, comparative analyses of elicitor activity of INF1, INF2A, and INF2B revealed significant differences in intensity, specificity, and consistency of HR induction. Whereas INF1 induced the HR in Nicotiana benthamiana, INF2A induced weak symptoms and INF2B induced no symptoms on this plant. Nonetheless, similar to INF1, HR induction by INF2A in N. benthamiana required the ubiquitin ligase-associated protein SGT1. Overall, these results suggest that variation in the resistance of Nicotiana spp. to P. infestans is shadowed by variation in the response to INF elicitins. The ability of tobacco, but not N. benthamiana, to respond to INF2B could explain differences in resistance to P. infestans observed for these two species.

Algal Proteins↗

PubMed2005

Euler vector for search and retrieval of gray-tone images.

A new combinatorial characterization of a gray-tone image called Euler Vector is proposed. The Euler number of a binary image is a well-known topological feature, which remains invariant under translation, rotation, scaling, and rubber-sheet transformation of the image. The Euler vector comprises a 4-tuple, where each element is an integer representing the Euler number of the partial binary image formed by the gray-code representation of the four most significant bit planes of the gray-tone image. Computation of Euler vector requires only integer and Boolean operations. The Euler vector is experimentally observed to be robust against noise and compression. For efficient image indexing, storage and retrieval from an image database using this vector, a bucket searching technique based on a simple modification of Kd-tree, is employed successfully. The Euler vector can also be used to perform an efficient four-dimensional range query. The set of retrieved images are finally ranked on the basis of Mahalanobis distance measure. Experiments are performed on the COIL database and results are reported. The retrieval success can be improved significantly by augmentiong the Euler vector by a few additional simple shape features. Since Euler vector can be computed very fast, the proposed technique is likely to find many applications to content-based image retrieval.

Algorithms↗