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Assessing different classification methods for virtual screening.

How well do different classification methods perform in selecting the ligands of a protein target out of large compound collections not used to train the model? Support vector machines, random forest, artificial neural networks, k-nearest-neighbor classification with genetic-algorithm-optimized feature selection, trend vectors, naïve Bayesian classification, and decision tree were used to divide databases into molecules predicted to be active and those predicted to be inactive. Training and predicted activities were treated as binary. The database was generated for the ligands of five different biological targets which have been the object of intense drug discovery efforts: HIV-reverse transcriptase, COX2, dihydrofolate reductase, estrogen receptor, and thrombin. We report significant differences in the performance of the methods independent of the biological target and compound class. Different methods can have different applications; some provide particularly high enrichment, others are strong in retrieving the maximum number of actives. We also show that these methods do surprisingly well in predicting recently published ligands of a target on the basis of initial leads and that a combination of the results of different methods in certain cases can improve results compared to the most consistent method.

Algorithms↗

PubMed1984

Clinical classification of regional cerebral blood flow (RCBF) by partitioning.

An algorithm is proposed to classify the regional cerebral blood flow (RCBF) of two groups of subjects. A 32-tuple training vector is defined corresponding to 32 detectors used to measure 133Xe washout following inhalation. For any index of 133Xe washout, each detector is associated with two cumulative distributions (cds) each corresponding to a population. The 32 index values at which the differences between cds are maximum are defined as partition values. All index values are then compared to their partitions and are designated binary values of 1 or 0 for being above or below the partitions. A representative sum of the binary numbers (0 to 16) indicates the number of detectors in each hemisphere which exceed their respective threshold. In the example, a normal group of subjects (n = 40) is compared to an abnormal group (n = 82). The abnormal group was identified independently of RCBF by clinical testing as having Alzheimer's disease, a subcategory of dementing diseases. The classification algorithm defined a training vector to which the two populations were compared. The normal subjects had higher representative scores than the abnormals with a tight clustering of these scores. Although some abnormals scored well, the great majority had representative scores well below 12 for each cerebral hemisphere. The training vector can be used to classify new studies or can be updated by new studies until no significant changes result. At this point, the new tracing vector is used as a reference set of partition values.

Alzheimer Disease↗

PubMed2004

Multistage classification and recognition that employs vector quantization coding and criteria extracted from nonorthogonal and preprocessed signal representations.

Classification decision tree algorithms have recently been used in pattern-recognition problems. In this paper, we propose a self-designing system that uses the classification tree algorithms and that is capable of recognizing a large number of signals. Preprocessing techniques are used to make the recognition process more effective. A combination of the original, as well as the preprocessed, signals is projected into different transform domains. Enormous sets of criteria that characterize the signals can be developed from the signal representations in these domains. At each node of the classification tree, an appropriately selected criterion is optimized with respect to desirable performance features such as complexity and noise immunity. The criterion is then employed in conjunction with a vector quantizer to divide the signals presented at a particular node in that stage into two approximately equal groups. When the process is complete, each signal is represented by a unique composite binary word index, which corresponds to the signal path through the tree, from the input to one of the terminal nodes of the tree. Experimental results verify the excellent classification accuracy of this system. High performance is maintained for both noisy and corrupt data.

Journal Article↗

PubMed2004

Intervention in context-sensitive probabilistic Boolean networks.

MOTIVATION: Intervention in a gene regulatory network is used to help it avoid undesirable states, such as those associated with a disease. Several types of intervention have been studied in the framework of a probabilistic Boolean network (PBN), which is essentially a finite collection of Boolean networks in which at any discrete time point the gene state vector transitions according to the rules of one of the constituent networks. For an instantaneously random PBN, the governing Boolean network is randomly chosen at each time point. For a context-sensitive PBN, the governing Boolean network remains fixed for an interval of time until a binary random variable determines a switch. The theory of automatic control has been previously applied to find optimal strategies for manipulating external (control) variables that affect the transition probabilities of an instantaneously random PBN to desirably affect its dynamic evolution over a finite time horizon. This paper extends the methods of external control to context-sensitive PBNs. RESULTS: This paper treats intervention via external control variables in context-sensitive PBNs by extending the results for instantaneously random PBNs in several directions. First, and most importantly, whereas an instantaneously random PBN yields a Markov chain whose state space is composed of gene vectors, each state of the Markov chain corresponding to a context-sensitive PBN is composed of a pair, the current gene vector occupied by the network and the current constituent Boolean network. Second, the analysis is applied to PBNs with perturbation, meaning that random gene perturbation is permitted at each instant with some probability. Third, the (mathematical) influence of genes within the network is used to choose the particular gene with which to intervene. Lastly, PBNs are designed from data using a recently proposed inference procedure that takes steady-state considerations into account. The results are applied to a context-sensitive PBN derived from gene-expression data collected in a study of metastatic melanoma, the intent being to devise a control strategy that reduces the WNT5A gene's action in affecting biological regulation, since the available data suggest that disruption of this influence could reduce the chance of a melanoma metastasizing.

Algorithms↗

PubMed2000

Expression of wild-type and noncleavable Fas ligand by tetracycline-regulated adenoviral vectors to limit intimal hyperplasia in vascular lesions.

Proliferation of vascular smooth muscle cells (VSMCs) and the infiltration of T cells and macrophages into vessel wall are considered to be important for intimal lesion formation after balloon angioplasty. Previous studies have shown that Fas ligand (FasL) gene transfer to balloon-injured vessels inhibits lesion formation by killing both proliferating VSMCs and infiltrating inflammatory cells. Here, we describe the construction and utility of a binary, tetracycline-regulated adenovirus system that provides controlled transgene expression in vitro and in vivo. In this system, optimal transgene expression required cotransfection with an adenovirus encoding the tetracycline-dependent trans-activator (rtTA) and induction with doxycycline hydrochloride (DOX), an analog of tetracycline. Using this system, adenovirus constructs were designed that allow regulated expression of wild-type FasL and a noncleavable mutant of FasL (FasL-NC). Transduction of FasL and FasL-NC induced similar extents of apoptosis in proliferating VSMCs in vitro in a manner that was dependent on the doses of the rtTA adenovirus and the presence of DOX in the medium. Furthermore, inhibition of intimal hyperplasia in injured carotid arteries by FasL or FasL-NC transduction was also dependent on cotransfection with the rtTA adenovirus and administration of DOX by subcutaneous injection. In contrast to wild-type FasL, transduction of FasL-NC did not result in the production of soluble (cleaved) FasL in the medium of infected cells in vitro, or in the serum of rats after local gene transfer to carotid arteries. In conclusion, this binary tetracycline-inducible adenovirus system may allow for safer delivery of cytotoxic genes for therapeutic purposes.

Adenoviridae↗

PubMed1997

The bacteriophage T7 binary system activates transient transgene expression in zebrafish (Danio rerio) embryos.

The bacteriophage T7 binary expression system is widely used in vitro for high level selective expression of cloned genes but its application to in vivo models has not yet been investigated. In the present work, we show that coinjection into fertilized zebrafish eggs of pE1T7R, an expression plasmid bearing the T7 RNA polymerase gene driven by the cytomegalovirus (CMV) promoter, together with reporter vectors containing the Escherichia coli lacZ gene driven by the T7 promoter, resulted in the efficient expression of the reporter gene in 24-h mosaic transgenic embryos. Conversely, embryos receiving an unrelated CMV-expression plasmid, instead of pE1T7R, lacked significant reporter gene activity, indicating the strict requirement of T7 polymerase to activate the T7 promoter in these embryos. The present study demonstrates the possibility of applying efficiently the bacteriophage T7 binary system in vivo to a vertebrate model.

Animals↗

PubMed2003

Recombinant bacteria for mosquito control.

Bacterial insecticides have been used for the control of nuisance and vector mosquitoes for more than two decades. Nevertheless, due primarily to their high cost and often only moderate efficacy, these insecticides remain of limited use in tropical countries where mosquito-borne diseases are prevalent. Recently, however, recombinant DNA techniques have been used to improve bacterial insecticide efficacy by markedly increasing the synthesis of mosquitocidal proteins and by enabling new endotoxin combinations from different bacteria to be produced within single strains. These new strains combine mosquitocidal Cry and Cyt proteins of Bacillus thuringiensis with the binary toxin of Bacillus sphaericus, improving efficacy against Culex species by 10-fold and greatly reducing the potential for resistance through the presence of Cyt1A. Moreover, although intensive use of B. sphaericus against Culex populations in the field can result in high levels of resistance, most of this can be suppressed by combining this bacterial species with Cyt1A; the latter enables the binary toxin of this species to enter midgut epithelial cells via the microvillar membrane in the absence of a midgut receptor. The availability of these novel strains and newly discovered mosquitocidal proteins, such as the Mtx toxins of B. sphaericus, offers the potential for constructing a range of recombinant bacterial insecticides for more effective control of the mosquito vectors of filariasis, Dengue fever and malaria.

Animals↗

PubMed2005

Cell-based models of sustained, interferon-sensitive hepatitis C virus genotype 1 replication.

We have previously reported hepatitis C virus (HCV) replication using a novel binary expression system in which mammalian cells were transfected with a T7 polymerase-driven full-length genotype 1a HCV cDNA plasmid (pT7-flHCV-Rz) and infected with vaccinia-T7 polymerase. We hypothesized that the use of replication-defective adenoviral vectors expressing T7 (Ad-T7pol) or cell lines stably transfected with T7 (Huh-T7) would alleviate cell toxicity and allow for more sustained HCV replication. CV-1, Huh7, and Huh-T7 cells were transfected with pT7-flHCV-Rz and treated with Ad-T7pol (CV-1 and Huh7 only). Protein and RNA were harvested from cells on days 1, 2, 3, 5, 7, and 9 post-infection. No cytotoxicity was observed at 9 days post-infection in any cell type. HCV positive- and negative-strand RNA expression were strongest during days 1-3 post-infection; however, HCV RNA remained detectable throughout the 9-day observation period. Furthermore, transfection with a replication-incompetent plasmid suggested that efficient HCV replication is dependent upon NS5B gene expression. Finally, after 1-2 days of IFN treatment, HCV positive-strand levels decreased significantly compared to HCV-infected but untreated samples (p<0.05). In conclusion, these refined binary systems offer more durable and authentic models for identification of host cellular processes critical to HCV replication and will permit longer-term analysis of virus-host interactions critical to HCV pathogenesis and the treatment of genotype 1 infections.

Antiviral Agents↗

PubMed2004

Long-term transgene expression in proliferating cells mediated by episomally maintained high-capacity adenovirus vectors.

High-capacity "gutless" adenovirus vectors (HC-AdV) mediate long-term transgene expression in resting cells in vitro and in vivo because of low toxicity and immunogenicity. However, in proliferating cells, expression is transient since HC-AdV genomes do not possess elements that allow for replication and segregation of the replicated genomes to daughter cells. We developed a binary HC-AdV system that, under certain conditions, allows for significantly prolonged episomal maintenance of HC-AdV genomes in proliferating tissue culture cells, resulting in sustained transgene expression. After transduction of target cells the linear HC-AdV genomes were circularized by the DNA recombinase FLPe, which was expressed from the second HC-AdV. The oriP/EBNA-1 replication system derived from Epstein-Barr virus, as well as the human replication origin from the lamin B2 locus, were used as cis elements to test for replication of the 28-kb circular vector genomes with or without selective pressure. Depending on the system, up to 98% of the circularized genomes were replicated and segregated to daughter cells, as demonstrated by Southern assays and as confirmed by monitoring EGFP transgene expression. Surprisingly, in the absence of FLPe recombinase, a small but significant number of HC-AdV genomes spontaneously circularized after transduction of target cells. These circles, found to contain end-to-end joined adenovirus termini, replicated with increased efficiency compared to vectors circularized by FLPe. After further improvements, this HC-AdV system might be suitable for gene therapy applications requiring long-term transgene expression.

Adenoviruses, Human↗

PubMed2003

Surface charge density determines the efficiency of cationic gemini surfactant based lipofection.

The efficiencies of the binary liposomes composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and cationic gemini surfactant, (2S,3R)-2,3-dimethoxy-1,4-bis(N-hexadecyl-N,N-dimethylammonium)butane dibromide as transfection vectors, were measured using the enhanced green fluorescent protein coding plasmid and COS-1 cells. Strong correlation between the transfection efficiency and lipid stoichiometry was observed. Accordingly, liposomes with X(SR-1) > or = 0.50 conveyed the enhanced green fluorescent protein coding plasmid effectively into cells. The condensation of DNA by liposomes with X(SR-1) > 0.50 was indicated by static light scattering and ethidium bromide intercalation assay, whereas differential scanning calorimetry and fluorescence anisotropy of diphenylhexatriene revealed stoichiometry dependent reorganization in the headgroup region of the liposome bilayer, in alignment with our previous Langmuir-balance study. Surface charge density and the organization of positive charges appear to determine the mode of interaction of DNA with (2S,3R)-2,3-dimethoxy-1,4-bis(N-hexadecyl-N,N-dimethylammonium)butane dibromide/1,2-dimyristoyl-sn-glycero-3-phosphocholine liposomes, only resulting in DNA condensation when X(SR-1) > 0.50. Condensation of DNA in turn seems to be required for efficient transfection.

Animals↗

PubMed2000

Antitumor effect of adenovirus-mediated Bax gene transfer on p53-sensitive and p53-resistant cancer lines.

Antitumor effects of the proapoptotic Bax gene have been evaluated in vitro and in vivo by a binary adenovirus system expressing the human Bax gene. Overexpression of the Bax gene in cultured cell lines from human lung carcinoma results in caspase activation, apoptosis induction, and cell growth suppression. Intratumoral injection of adenovirus vector expressing the Bar gene suppressed growth of human lung cancer xenografts established in nude mice. Histological examination of tumors from mice treated with the Bax gene demonstrated high levels of Bax expression and extensive apoptosis in tumors. In comparison with the treatment by an adenoviral vector expressing human p53, the Bax gene can effectively suppress tumor growth in both p53-sensitive and p53-resistant human lung carcinoma cell lines. Toxicity was not detected in liver and other systems in animals treated intralesionally with the Bax gene. Therefore, our results suggest that the Bar gene may be useful in cancer treatment.

Adenoviridae↗

PubMed1997

Trypanosoma Mukasai (HOARE, 1932) in its biological vector Batracobdelloides tricarinata (BLANCHARD, 1897) and their life cycles.

Trypanosoma mukasai from the blood of the fish Clarias lazera underwent a multiplicative development in the gut of the fresh water leech B. tricarinata. The blood stream forms transformed into short flagellates and 2 days post-infection, they divided by binary fission to produce numerous stumpy epimastigotes which later transformed into sphaeromastigotes, amastigotes, promastigotes and more numerous into long slender epimastigotes and metacyclic trypomastigotes. The epimastigotes and the metacyclic forms persisted in the leech for more than 21 days. The metacyclic forms developed into typical small slender trypomastigotes only in uninfected blood of Clarias lazera when the leech fed again. As time proceeded, the slender trypomastigotes developed into intermediate and finally into large broad form. The behaviour and the life history of the leech B tricarinata were studied in detail with special relevance to its activity and the development of eggs, embryos and immature leeches.

Animals↗

PubMed2000

Tumor-specific transgene expression from the human telomerase reverse transcriptase promoter enables targeting of the therapeutic effects of the Bax gene to cancers.

Human telomerase reverse transcriptase (hTERT) is the catalytic subunit of telomerase, which is highly active in immortalized cells and >85% of human cancers but is quiescent in most normal somatic cells. To test the feasibility of using the hTERT promoter to induce tumor-specific transgene expression in cancer gene therapy, we constructed an adenoviral vector expressing a LacZ reporter gene driven by the hTERT core promoter and evaluated its activity in vitro and in vivo. The hTERT promoter could drive high-level expression of LacZ in tumor cells but not in normal cells and normal mouse tissues. Using a binary adenoviral system that can induce Bax gene expression, we showed that induction of the Bax gene expression via the hTERT promoter elicited tumor-specific apoptosis in vitro, suppressed tumor growth in nude mice, and prevented the toxicity of the Bax gene in vitro and in vivo. Thus, the hTERT promoter is apparently a strong and tumor-selective promoter with potential application in targeted cancer gene therapy.

Adenoviridae↗

PubMed1997

Sparsely Connected, Hebbian Networks with Strikingly Large Storage Capacities.

Conspicuous problems confront the use of fully-connected networks (F-nets) in the construction of realistic partial models of biological memory. These problems include the high synaptic densities of F-nets, and the low information storage capacities of F-nets with simple, biologically realistic learning rules. Most auto-associative networks constructed with low connectivities have employed random projections of path length 1. Projective networks (P-nets) are nonrandom, multilayer networks which achieve extremely low connectivities by linking all neurons in the same layer through paths of length 2. In this paper we derive a lower bound on the storage capacities of a class of simple, two-layer P-nets with binary Hebbian synapses. Given a 1% tolerance for spurious neurons, we find that the P-net with 1000 synapses per neuron (2 x 10(6) neurons) will store more than 1.5 x 10(6) training vectors with 20 active neurons per vector (0.25 bits per synapse). Copyright 1997 Elsevier Science Ltd.

Journal Article↗

PubMed1995

Classifying and counting linear phylogenetic invariants for the Jukes-Cantor model.

Linear invariants are useful tools for testing phylogenetic hypotheses from aligned DNA/RNA sequences, particularly when the sites evolve at different rates. Here we give a simple, graph theoretic classification for each phylogenetic tree T, of its associated vector space I(T) of linear invariants under the Jukes-Cantor one-parameter model of nucleotide substitution. We also provide an easily described basis for I(T), and show that if I is a binary (fully resolved) phylogenetic tree with n sequences at its leaves then: dim[I(T)] = 4n-F2n-2 where Fn is the nth Fibonacci number. Our method applies a recently developed Hadamard matrix-based technique to describe elements of I(T) in terms of edge-disjoint packings of subtrees in T, and thereby complements earlier more algebraic treatments.

Base Sequence↗

PubMed1998

Cr(III)-mediated crosslinks of glutathione or amino acids to the DNA phosphate backbone are mutagenic in human cells.

Carcinogenic Cr(VI) compounds were previously found to induce amino acid/glutathione-Cr(III)-DNA crosslinks with the site of adduction on the phosphate backbone. Utilizing the pSP189 shuttle vector plasmid we found that these ternary DNA adducts were mutagenic in human fibroblasts. The Cr(III)-glutathione adduct was the most potent in this assay, followed by Cr(III)-His and Cr(III)-Cys adducts. Binary Cr(III)-DNA complexes were only weakly mutagenic, inducing a significant response only at a 10 times higher number of adducts compared with Cr(III)-glutathione. Single base substitutions at the G:C base pairs were the predominant type of mutations for all Cr(III) adducts. Cr(III), Cr(III)-Cys and Cr(III)-His adducts induced G:C-->A:T transitions and G:C-->T:A transversions with almost equal frequency, whereas the Cr(III)-glutathione mutational spectrum was dominated by G:C-->T:A transversions. Adduct-induced mutations were targeted toward G:C base pairs with either A or G in the 3' position to the mutated G, while spontaneous mutations occurred mostly at G:C base pairs with a 3' A. No correlation was found between the sites of DNA adduction and positions of base substitution, as adducts were formed randomly on DNA with no base specificity. The observed mutagenicity of Cr(III)-induced phosphotriesters demonstrates the importance of a Cr(III)-dependent pathway in Cr(VI) carcinogenicity.

Adenine↗

PubMed2004

Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping.

Two plant-transformation-competent large-insert binary clone bacterial artificial chromosome (hereafter BIBAC) libraries were previously constructed for soybean cv. Forrest, using BamHI or HindIII. However, they are not well suited for clone-based genomic sequencing due to their larger ratio of vector to insert size (27.6 kbp:125 kbp). Therefore, we developed a larger-insert bacterial artificial chromosome (BAC) library for the genotype in a smaller vector (pECBAC1), using EcoRI. The BAC library contains 38,400 clones; about 99.1% of the clones have inserts; the average insert size is 157 kbp; and the ratio of vector to insert size is much smaller (7.5 kbp:157 kbp). Colony hybridization with probes derived from several chloroplast and mitochondrial genes showed that 0.89% and 0.45% of the clones were derived from the chloroplast and mitochondrial genomes, respectively. Considering these data, the library represents 5.4 haploid genomes of soybean. The library was hybridized with six RFLP marker probes, 5S rDNA and 18S-5.8S-25S rDNA, respectively. Each RFLP marker hybridized to about six clones, and the 5S and 18S-5.8S-25S rDNA probes collectively hybridized to 402 BACs--about 1.05% of the clones in the library. The BAC library complements the existing soybean Forrest BIBAC libraries by using different restriction enzymes and vector systems. Together, the BAC and BIBAC libraries encompass 13.2 haploid genomes, providing the most comprehensive clone resource for a single soybean genotype for public genome research. We show that the BAC library has enhanced the development of the soybean whole-genome physical map and use of three complementary BAC libraries improves genome physical mapping by fingerprint analysis of most of the clones of the library. The rDNA-containing clones were also fingerprinted to evaluate the feasibility of constructing contig maps of the rDNA regions. It was found that physical maps for the rDNA regions could not be readily constructed by fingerprint analysis, using one or two restriction enzymes. Additional data to fingerprints and/or different fingerprinting methods are needed to build contig maps for such highly tandem repetitive regions and thus, the physical map of the entire soybean genome.

Chromosomes, Artificial, Bacterial↗

PubMed2000

Image restoration with the Viterbi algorithm.

The Viterbi algorithm (VA) is known to given an optimal solution to the problem of estimating one-dimensional sequences of discrete-valued pixels corrupted by finite-support blur and memoryless noise. A row-by-row estimation along with decision feedback and vector quantization is used to reduce the computational complexity of the VA and allow the estimation of two-dimensional images. This reduced-complexity VA (RCVA) is shown to produce near-optimal estimation of random binary images. In addition, simulated restorations of gray-scale images show the RCVA estimates to be an improvement over the estimates obtained by the conventional Wiener filter (WF). Unlike the WF, the RCVA is capable of superresolution and is adaptable for use in restoring data from signal-dependent Poisson noise corruption. Experimental restorations of random binary data gathered from an optical imaging system support the simulations and show that the RCVA estimate has fewer than one third of the errors of the WF estimate.

Algorithms↗