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David Horn

Publications and source records attributed to David Horn.

At least 37 records · Page 2Linked to original sources
PubMed2005

A doubly inducible system for RNA interference and rapid RNAi plasmid construction in Trypanosoma brucei.

The most rapid method for the generation of conditional mutants in Trypanosoma brucei is the use of RNA interference. A single copy of the target sequence is cloned between two opposing T7 promoters bearing tet operators, and the resulting plasmid is integrated into the genome of cells expressing both the tet repressor and T7 RNA polymerase. Upon addition of tetracycline, double-stranded RNA is synthesised from the two T7 promoters. Unfortunately, repression of T7 promoter activity may sometimes be insufficient to prevent expression of toxic amounts of double-stranded RNA. We describe here cell lines in which the expression of T7 polymerase is under tetracycline control, and show that regulation of polymerase expression can modulate transcription from a constitutive T7 promoter. In addition we describe a construct containing two copies of the tn10 Tet repressor for easy creation of repressor-expressing trypanosomes, and an RNA interference vector which allows "TA" cloning of unmodified PCR products and blue/white selection.

Animals↗
PubMed2005

Motif extraction and protein classification.

We present a novel unsupervised method for extracting meaningful motifs from biological sequence data. This de novo motif extraction (MEX) algorithm is data driven, finding motifs that are not necessarily over-represented in the data. Applying MEX to the oxidoreductases class of enzymes, containing approximately 7000 enzyme sequences, a relatively small set of motifs is obtained. This set spans a motif-space that is used for functional classification of the enzymes by an SVM classifier. The classification based on MEX motifs surpasses that of two other SVM based methods: SVMProt, a method based on the analysis of physical-chemical properties of a protein generated from its sequence of amino acids, and SVM applied to a Smith-Waterman distances matrix. Our findings demonstrate that the MEX algorithm extracts relevant motifs, supporting a successful sequence-to-function classification.

Algorithms↗
PubMed2005

Memory capacity of balanced networks.

We study the problem of memory capacity in balanced networks of spiking neurons. Associative memories are represented by either synfire chains (SFC) or Hebbian cell assemblies (HCA). Both can be embedded in these balanced networks by a proper choice of the architecture of the network. The size w(E) of a pool in an SFC or of an HCA is limited from below and from above by dynamical considerations. Proper scaling of w(E) by radicalK, where K is the total excitatory synaptic connectivity, allows us to obtain a uniform description of our system for any given K. Using combinatorial arguments, we derive an upper limit on memory capacity. The capacity allowed by the dynamics of the system, alpha(c), is measured by simulations. For HCA, we obtain alpha(c) of order 0.1, and for SFC, we find values of order 0.065. The capacity can be improved by introducing shadow patterns, inhibitory cell assemblies that are fed by the excitatory assemblies in both memory models. This leads to a doubly balanced network, where, in addition to the usual global balancing of excitation and inhibition, there exists specific balance between the effects of both types of assemblies on the background activity of the network. For each of the memory models and for each network architecture, we obtain an allowed region (phase space) for w(E)/ radicalK in which the model is viable.

Action Potentials↗
PubMed2005

Traumatic atlanto-occipital dislocation in children.

BACKGROUND: Traumatic atlanto-occipital dislocation in children and adolescents is a rare and often fatal injury. Although historically most reported cases have been fatal, the advent of modern prehospital care has led to an increase in survival following this injury. As a consequence, some patients may achieve or maintain satisfactory neurologic function following early intervention, stabilization, and definitive management. We analyzed the data on children and adolescents in whom traumatic atlanto-occipital dislocation had been treated with modern resuscitation techniques at our institution. METHODS: Atlanto-occipital dislocation is defined as disruption of the ligaments and other supporting soft tissues as indicated by displacement in either a transverse or vertical direction. With use of the Trauma Registry database at our institution, we identified sixteen such injuries that had occurred between 1986 and 2003. The hospital charts, clinic notes, and radiographs were reviewed. A careful neurological evaluation was performed for all of the survivors at the time of the latest follow-up. RESULTS: The mean age of the sixteen patients at the time of the injury was 7.6 years. The mechanisms of injury were diverse. The mean Glasgow Coma Scale score was 7.4 points. Eleven of the sixteen patients underwent intubation in the field, two were intubated in the emergency department, and three were not intubated. Eight of the sixteen patients were declared dead on arrival in the emergency department. The eight surviving patients initially were immobilized with either a halo vest or another orthosis. All patients except one received intravenous steroids in the emergency department. Three of the patients who survived the initial injury subsequently died while undergoing neurosurgical procedures for the treatment of extensive intracranial injuries. Four of the remaining five survivors underwent occiput-C2 fusion, and one was managed with a Minerva cast. At the time of the final follow-up, at a mean of 4.2 years after the injury, one patient was neurologically normal, three had mild spastic hemiparesis and were very functional, and one had spastic quadriplegia and was ventilator-dependent. CONCLUSIONS: Prompt recognition and treatment of traumatic atlanto-occipital dislocation in children and adolescents can result in improved survival. Early diagnosis, prompt intubation, early and adequate immobilization of the head and neck, and the use of intravenous steroids appear to facilitate survival. We recommend arthrodesis from the occiput to C2 (or the nearest adjacent intact and stable vertebra caudad to C2) for all children who survive a traumatic atlanto-occipital dislocation, particularly those with an incomplete spinal cord injury.

Adolescent↗
PubMed2004

Dynamic proximity of spatio-temporal sequences.

Recurrent networks can generate spatio-temporal neural sequences of very large cycles, having an apparent random behavior. Nonetheless a proximity measure between these sequences may be defined through comparison of the synaptic weight matrices that generate them. Following the dynamic neural filter (DNF) formalism we demonstrate this concept by comparing teacher and student recurrent networks of binary neurons. We show that large sequences, providing a training set well exceeding the Cover limit, allow for good determination of the synaptic matrices. Alternatively, assuming the matrices to be known, very fast determination of the biases can be achieved. Thus, a spatio-temporal sequence may be regarded as spatio-temporal encoding of the bias vector. We introduce a linear support vector machine (SVM) variant of the DNF in order to specify an optimal weight matrix. This approach allows us to deal with noise. Spatio-temporal sequences generated by different DNFs with the same number of neurons may be compared by calculating correlations of the synaptic matrices of the reconstructed DNFs. Other types of spatio-temporal sequences need the introduction of hidden neurons, and/or the use of a kernel variant of the SVM approach. The latter is being defined as a recurrent support vector network (RSVN).

Action Potentials↗
PubMed2004

Trypanosomatid histones.

The histones are responsible for packaging and regulating access to eukaryotic genomes. Trypanosomatids are flagellated protists that diverged early from the eukaryotic lineage and include parasites that cause disease in humans and other mammals. Here, we review the properties of histones in parasitic trypanosomatids, from gene organization and sequence to expression, post-translational modification and function within chromatin. Phylogenetic and experimental analysis indicates that certain specifically conserved histone sequence motifs, particularly within the N-terminal 'tail' domains, possibly represent functionally important modification substrates conserved throughout the eukaryotic lineage. For example, histone H3 contains a highly conserved methylation substrate. Trypanosomatids also possess at least three variant histones. Among these is an orthologue of H2A.Z, a histone involved in protecting 'active' chromatin from silencing in yeast. Histones provide docking platforms for a variety of regulatory factors. The presence of histone modification and variant histones in trypanosomatids therefore represents evidence for a network that provides the discrimination required to regulate transcription, recombination, repair and chromosome replication and segregation.

Animals↗
PubMed2004

Modeling of synchronized bursting events: the importance on inhomogeneity.

Cultured in vitro neuronal networks are known to exhibit synchronized bursting events (SBE), during which most of the neurons in the system spike within a time window of approximately 100 msec. Such phenomena can be obtained in model networks based on Markram-Tsodyks frequency-dependent synapses. In order to account correctly for the detailed behavior of SBEs, several modifications have to be implemented in such models. Random input currents have to be introduced to account for the rising profile of SBEs. Dynamic thresholds and inhomogeneity in the distribution of neuronal resistances enable us to describe the profile of activity within the SBE and the heavy-tailed distributions of interspike intervals and interevent intervals. Thus, we can account for the interesting appearance of Levy distributions in the data.

Algorithms↗
PubMed2004

The molecular control of antigenic variation in Trypanosoma brucei.

The African trypanosome, Trypanosoma brucei, is a protozoan that causes sleeping sickness in humans and N'gana in livestock. These flagellated parasites are directly exposed to immune defences as they circulate in the mammalian host bloodstream but they maintain persistent infections by undergoing antigenic variation. Central to this process is mono-allelic transcription and switching of the expressed variant-surface glycoprotein (VSG) gene which encodes the vast majority of their dense surface coat. The active telomeric VSG is transcribed by RNA polymerase I in an 'expression site body' (ESB) while transcription attenuation occurs at 'inactive' telomeres. Here, I review what is known about the molecular mechanisms involved in achieving antigenic variation and outline how we intend to exploit genome sequence and new tools, particularly RNA interference, to identify and characterise factors required for VSG regulation.

Animals↗
PubMed2003

Novel clustering algorithm for microarray expression data in a truncated SVD space.

MOTIVATION: This paper introduces the application of a novel clustering method to microarray expression data. Its first stage involves compression of dimensions that can be achieved by applying SVD to the gene-sample matrix in microarray problems. Thus the data (samples or genes) can be represented by vectors in a truncated space of low dimensionality, 4 and 5 in the examples studied here. We find it preferable to project all vectors onto the unit sphere before applying a clustering algorithm. The clustering algorithm used here is the quantum clustering method that has one free scale parameter. Although the method is not hierarchical, it can be modified to allow hierarchy in terms of this scale parameter. RESULTS: We apply our method to three data sets. The results are very promising. On cancer cell data we obtain a dendrogram that reflects correct groupings of cells. In an AML/ALL data set we obtain very good clustering of samples into four classes of the data. Finally, in clustering of genes in yeast cell cycle data we obtain four groups in a problem that is estimated to contain five families. AVAILABILITY: Software is available as Matlab programs at http://neuron.tau.ac.il/~horn/QC.htm.

Algorithms↗
PubMed2003

RNA interference identifies two hydroperoxide metabolizing enzymes that are essential to the bloodstream form of the african trypanosome.

Detoxification of hydroperoxides in trypanosomes is mediated by a series of linked redox pathways that are dependent on the parasite-specific thiol trypanothione for reducing equivalents. These pathways are characterized by differences in subcellular location, electron transport molecules, and substrate specificity. To determine the functional significance of the enzymes involved, we have used a tetracycline-inducible RNA interference system to down-regulate expression of each of the corresponding transcripts in bloodstream form Trypanosoma brucei. We have identified two peroxidases, a cytosolic peroxiredoxin (TbCPX) and a member of the non-selenium glutathione-dependent peroxidase family (TbGPXI), that appear to be essential for the viability of this clinically relevant stage of the parasite life cycle. The addition of tetracycline to the cultures resulted in a major reduction in mRNA levels and enzyme activity, a dramatic fall in growth rate, and significant cell death. Furthermore, within 20 h of adding tetracycline, cells in which the cytosolic peroxiredoxin transcript was targeted were found to be 16-fold more susceptible to killing by exogenous hydrogen peroxide. We also observed that knockdown of the tryparedoxin TbT-PNI, a thioredoxin-like protein that facilitates electron transport to both TbCPX and TbGPXI, resulted in a reduction in growth rate. These experiments therefore identify redox pathways that are essential for oxidative defense in T. brucei and validate the corresponding peroxidases as targets for drug design.

Amino Acid Sequence↗
PubMed2003

Dynamic range enhancement for cochlear implants.

HYPOTHESIS: The addition of a continuous, unmodulated, high-rate pulse train to sinusoidal stimuli presented by the cochlear implant to implant recipients will result in increases in the psychophysical dynamic range. BACKGROUND: The hearing dynamic range of cochlear implant patients is markedly reduced compared with that of normal-hearing individuals. This has negative implications for both speech perception and sound quality in these patients. It has been suggested that the addition of an unmodulated high-rate pulse train to deafened auditory nerves could create spontaneous-like neural activity, similar to that recorded from normal ears, of which one significant benefit would be an increase in the dynamic range of cochlear implant users. METHODS: Twenty-nine patients who underwent implantation with the Clarion CII device participated in this single-blinded prospective study. The psychophysical dynamic range of 28 of these subjects was measured with sinusoidal stimuli in response to various levels of an additional unmodulated high-rate pulse train. RESULTS: All the tested subjects (n = 28) demonstrated an increase in dynamic range in response to an appropriate level of unmodulated high-rate pulse train. The largest increase in dynamic range for each subject had a mean value of 6.7 dB. CONCLUSION: The addition of an unmodulated high-rate pulse train to the electric signal presented to cochlear implant patients results in significant increases in dynamic range for sinusoidal stimuli.

Acoustic Stimulation↗
PubMed2003

The dynamic neural filter: a binary model of spatiotemporal coding.

We describe and discuss the properties of a binary neural network that can serve as a dynamic neural filter (DNF), which maps regions of input space into spatiotemporal sequences of neuronal activity. Both deterministic and stochastic dynamics are studied, allowing the investigation of the stability of spatiotemporal sequences under noisy conditions. We define a measure of the coding capacity of a DNF and develop an algorithm for constructing a DNF that can serve as a source of given codes. On the basis of this algorithm, we suggest using a minimal DNF capable of generating observed sequences as a measure of complexity of spatiotemporal data. This measure is applied to experimental observations in the locust olfactory system, whose reverberating local field potential provides a natural temporal scale allowing the use of a binary DNF. For random synaptic matrices, a DNF can generate very large cycles, thus becoming an efficient tool for producing spatiotemporal codes. The latter can be stabilized by applying to the parameters of the DNF a learning algorithm with suitable margins.

Algorithms↗
PubMed2002

Characterization of anthracenediones and their photoaffinity analogs.

In an attempt to overcome the cardiotoxicity and cross-resistance problems caused by the anticancer drugs anthracyclines and anthracenediones during chemotherapy, we have developed a series of aza-anthracenedione compounds by modifying the chromophore and the side arms of anthracyclines and anthracenediones. One of these aza-anthracenediones, 6,9-bis[(2-aminoethyl)amino]benzo[g]isoquinoline-5,10-dione (BBR 2778), which is currently under phase II clinical trials, showed remarkable antitumor activity and appeared to lack a cardiotoxic effect in preclinical studies. However, it was still cross-resistant against multidrug resistance (MDR) cells expressing P-glycoprotein (P-gp). In contrast, another aza-anthracenedione, 6,9-bis[[2-(dimethylamino)ethyl]amino]benzo[g]isoquinoline-5,10-dione, which has side arm structures different from those of BBR 2778, was highly active against MDR cells. In this study, BBR 2778, BBR 2378, and an anthracenedione compound, 1,4-bis[(2-aminoethyl)amino]-5,8-dimethyl-9,10-anthracenedione, were used to assess the relationship between the chemical structures of these drugs and their interactions with DNA and P-gp. In addition, the biological and pharmacological influences of photoaffinity labeling were also studied for BBR 2778 and DEH. As the results indicate, the photolabeled analogs of BBR 2778 and DEH were less DNA-reactive and less cytotoxic. The more lipophilic compound, BBR 2378, and the photolabeled analogs of BBR 2778 and DEH inhibited P-gp labeling by azidopine better than did the more hydrophilic parental compounds. These studies suggested that the DNA binding affinity of BBR 2778 and DEH could be important in determining their cytotoxicity, and that the chemical structure of the side arms and the lipophilicity of these drugs are critical in determining their cross-resistance.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2002

Histone deacetylases in Trypanosoma brucei: two are essential and another is required for normal cell cycle progression.

Reversible protein acetylation is established as a modification of major regulatory significance. In particular, histone acetylation regulates access to genetic information in eukaryotes. For example, class I and class II histone deacetylases are regulatory components of corepressor complexes involved in cell cycle progression and differentiation. Here, we have investigated the function of such enzymes in Trypanosoma brucei, mono-flagellated parasitic protozoa that branched very early from the eukaryotic lineage. Four T. brucei genes encoding histone deacetylase orthologues have been identified, cloned and characterized. The predicted deacetylases, DAC1-4 are approximately 43, 61, 75 and 64 kDa respectively. They share significant similarity with mammalian and yeast class I (DAC1 and DAC2) and class II (DAC3 and DAC4) histone deacetylases, and all except DAC2 have the critical residues predicted to be required for deacetylase activity. In gene targeting experiments, DAC1 and DAC3 appear to be essential whereas DAC2 and DAC4 are not required for viability. Of the two mutant cell types, the dac4 mutant displays a delay in the G2/M phase of the cell cycle. Our results provide genetic validation of DAC1 and DAC3 as potential chemotherapy targets and demonstrate that T. brucei expresses at least three probable histone deacetylases with distinct function.

Acetylation↗
PubMed2001

Algorithm for data clustering in pattern recognition problems based on quantum mechanics.

We propose a novel clustering method that is based on physical intuition derived from quantum mechanics. Starting with given data points, we construct a scale-space probability function. Viewing the latter as the lowest eigenstate of a Schrödinger equation, we use simple analytic operations to derive a potential function whose minima determine cluster centers. The method has one parameter, determining the scale over which cluster structures are searched. We demonstrate it on data analyzed in two dimensions (chosen from the eigenvectors of the correlation matrix). The method is applicable in higher dimensions by limiting the evaluation of the Schrödinger potential to the locations of data points.

Journal Article↗