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PubMed2005

Robustness of gene expression profiling in glioma specimen samplings and derived cell lines.

One of the most promising applications of microarrays is class distinction through gene expression profiling as a diagnostic tool. However, as there is apparent spatial heterogeneity in the morphology of cancer cells within a tumor, it is unclear if tumor sampling can be applied and yield consistent signals. In this report, we examined six brain tumors, four glioblastoma, and two oligodendroglioma biopsies. The six brain tumor tissues from two distinct different classes were dissected in four distinct areas and gene expression was profiled using microarrays. We used hierarchical clustering to compare the variability of gene expression profiles between spatially distinct biopsies of the same tumor as compared to the variability between tumors of the same histologic group. We conclude that, in general, repeat spatially distinct samples are not needed for microarray experiments and the gene expression signatures are robust across the tumor. Predominantly, variation was much greater between samples from different patients than from the multiple samplings of given tumor. Further, we compared biopsy expression profiles to the cell lines derived from those tissues. In general, the tumor cell lines vary greatly from the parental tissues and cluster more strongly with each other than the parental tissue. We select and examine the set of genes altered in expression to allow adaptation to cell culture.

Brain Neoplasms↗

PubMed2004

A robust toolkit for functional profiling of the yeast genome.

Study of mutant phenotypes is a fundamental method for understanding gene function. The construction of a near-complete collection of yeast knockouts (YKO) and the unique molecular barcodes (or TAGs) that identify each strain has enabled quantitative functional profiling of Saccharomyces cerevisiae. By using these TAGs and the SGA reporter, MFA1pr-HIS3, which facilitates conversion of heterozygous diploid YKO strains into haploid mutants, we have developed a set of highly efficient microarray-based techniques, collectively referred as dSLAM (diploid-based synthetic lethality analysis on microarrays), to probe genome-wide gene-chemical and gene-gene interactions. Direct comparison revealed that these techniques are more robust than existing methods in functional profiling of the yeast genome. Widespread application of these tools will elucidate a comprehensive yeast genetic network.

Gene Expression Profiling↗

PubMed2005

Robust dysregulation of gene expression in substantia nigra and striatum in Parkinson's disease.

Large-scale genomics approaches are now widely utilized to study a myriad of human diseases. These powerful techniques, when combined with data analysis tools, detect changes in transcript abundance in diseased tissue relative to control. We hypothesize that specific differential gene expression underlies important pathogenic processes in Parkinson's disease, which is characterized by the gradual loss of dopaminergic neurons in the substantia nigra and consequent loss of dopamine in the striatum. We have therefore examined gene expression levels in the human parkinsonian nigrostriatal pathway, and compared them with those of neurologically normal controls. Using unsupervised clustering methods, we demonstrate that relatively few genes' expression levels can effectively distinguish between disease and control brains. Further, we identify several interesting patterns of gene expression that illuminate pathogenic cascades in Parkinson's disease. In particular is the robust loss of synaptic gene expression in diseased substantia nigra and striatum.

Aged↗

PubMed2004

A robust method for distinguishing between learned and spurious attractors.

Hopfield/constraint satisfaction type networks can be used to learn (autoassociate) patterns. Random inputs to the network will sometimes converge on states which are learned patterns, and sometimes converge on states which are unlearned/spurious. It would be useful for many reasons to be able to tell whether or not a given state was learned or spurious. In this paper we present a robust and general method, based on 'energy profiles', which allows us to make this distinction. We briefly describe related research, and note links with the study of recall, recognition and familiarity in the psychological literature.

Algorithms↗

PubMedDate not supplied

A simple cell model with dominating opponent inhibition for robust image processing.

The extraction of oriented contrast information by cortical simple cells is a fundamental step in early visual processing. The orientation selectivity originates at least partly from the input of lateral geniculate nuclei neurons with properly aligned receptive fields. In the present article, we investigate the feedforward interactions between on- and off-pathways. Based on physiological evidence we propose a push-pull model with dominating opponent inhibition (DOI). We show that the model can account for empirical data on simple cells, such as contrast-invariant orientation tuning, sharpening of orientation tuning with increasing inhibition, and strong response decrements to stimuli with luminance gradient reversal. With identical parameter settings, we apply the model for the processing of synthetic and real world images. We show that the model with DOI can robustly extract oriented contrast information from noisy input. More important, noise is adaptively suppressed, i.e. the model simple cells do not respond to homogeneous regions of different noise levels, while remaining sensitive to small contrast changes. The image processing results reveal a possible functional role of the strong inhibition as observed empirically, namely to adaptively suppress responses to noisy input.

Animals↗

PubMed2005

A robust classifier combined with an auto-associative network for completing partly occluded images.

This paper describes an approach for constructing a classifier which is unaffected by occlusions in images. We propose a method for integrating an auto-associative network into a simple classifier. As the auto-associative network can recall the original image from a partly occluded input image, we can employ it to detect occluded regions and complete the input image by replacing those regions with recalled pixels. By iterating this reconstruction process, the integrated network is able to classify target objects with occlusions robustly. To confirm the effectiveness of this method, we performed experiments involving face image classification. It is shown that the classification performance is not decreased, even if about 30% of the face image is occluded.

Artificial Intelligence↗

PubMed2005

Chronic stress, as well as acute stress, reduces BDNF mRNA expression in the rat hippocampus but less robustly.

Daily restraint for 3 weeks was shown to atrophy dendrites of hippocampal pyramidal neurons in rats. Brain-derived neurotrophic factor (BDNF), which maintains neuronal survival and morphology, has been shown to decrease in response to acute stress. Plasma glucocorticoid (GC) and serotonergic projections from the raphe nuclei play major roles in reducing BDNF synthesis in the hippocampus. We investigated BDNF mRNA levels there, together with plasma GC levels, GC receptors in the hippocampus/hypothalamus and 5-HT synthesizing enzyme, tryptophan hydroxylase in the raphe nuclei, in animals chronically stressed for 1-3 weeks, using in situ hybridization and immunohistochemistry. In these animals, BDNF mRNA levels were significantly decreased in the hippocampus after 6 h of restraint, but the ability of restraint to reduce BDNF synthesis seemed less robust than that seen in acute stress models. HPA axis response to stress in these animals assessed by plasma GC levels was delayed and sustained, and the GC receptor in the paraventricular hypothalamic nucleus was increased at 1 week. Tryptophan hydroxylase immunoreactivity was increased in the median raphe nucleus at 2-3 weeks. Repetitive stress-induced reduction of BDNF may partly contribute to the neuronal atrophy/death and reduction of hippocampal volume observed both in animals and humans suffering chronic stress and/or depression.

Animals↗

PubMedDate not supplied

Aged-obese rats exhibit robust responses to a melanocortin agonist and antagonist despite leptin resistance.

To address whether defective melanocortin activation is one element of leptin resistance with age, we infused centrally the melanocortin agonist, MTII and antagonist, SHU9119 in young and old rats. Food intake, energy expenditure, adiposity, BAT UCP1, and leptin expression in white fat as well as hypothalamic expressions of MC3R, MC4R, POMC, AgRP and NPY were assessed. The MTII-evoked anorexia was transient whereas the SHU9119-induced hyperphagia was sustained in young and old. MTII elevated oxygen consumption in both ages. The oxygen consumption waned gradually in young but increased continuously in aged following MTII infusion. The MTII-mediated induction in BAT UCP1 was similarly robust in both ages as was the SHU9119-mediated suppression in UCP1. POMC and MC3/4 receptor expressions were unaltered with age. These findings demonstrate the effectiveness of MTII to bypass leptin resistance in aged-obese rats. The equally strong orexigenic response to SHU9119 coupled with unaltered POMC expression and food intake in the young versus old suggest that melanocortin tone is unchanged with age despite impaired melanocortin activation by leptin.

Age of Onset↗

PubMed2005

Neocortical synaptic bouton number is maintained despite robust amyloid deposition in APP23 transgenic mice.

Major pathological findings in Alzheimer's disease (AD) brain include the deposition of amyloid-beta and synapse loss. Synaptic loss has been shown to correlate with the cognitive decline in AD patients, but the relationship between cerebral amyloidosis and synapse loss is complicated by the presence of neurofibrillary tangles and other lesions in AD brain. With the use of the APP23 transgenic mouse model that overexpresses human amyloid precursor protein (APP) with the Swedish double mutation, we investigated whether the development of cortical amyloid deposition was accompanied by synaptic bouton loss. With stereological methods, we show that despite robust age-related cortical amyloid deposition with associated synaptic degeneration, the total number of cortical synaptophysin-positive presynaptic terminals is not changed in 24-month-old animals compared with 3-, 8-, and 15-month-old APP23 mice. Wild-type mice also do not show an age-related loss of presynaptic boutons in the neocortex and are not significantly different from APP23 mice. Synaptophysin Western blotting revealed no significant difference between APP23 mice and wild-type controls at 3 and 25 months of age. Our results suggest that cerebral amyloidosis is not sufficient to account for the global synapse loss in AD. Alternatively, a putative trophic effect of APP may prevent, compensate, or delay a loss of synapses in this mouse model.

Age Factors↗

PubMed2004

Measuring temporal morphological changes robustly in brain MR images via 4-dimensional template warping.

Robustly measuring subtle longitudinal brain changes is a major challenge in computational neuroanatomy. This paper describes a method for measuring temporal morphological brain changes, by means of a 4-dimensional image warping mechanism. Longitudinal stability is achieved by considering all temporal MR images of an individual simultaneously, rather than by individually warping a template to an individual, or by warping the images of one time-point to those of another time-point. Following earlier work in 3D, a local morphological signature is attached to each voxel of a sequence of images, and it includes a set of image attributes reflecting morphological characteristics of the spatiotemporal structure around the respective voxel at different scales. This attribute vector forms the basis for searching in the 4-dimensional space for a counterpart that has similar morphological signature, thereby leading to automated detection of anatomical correspondence. Ambiguities in this process are reduced by constructing attribute vectors that are highly distinctive of respective voxels, and by using a hierarchical matching procedure in which reliable and easily distinguishable voxels are used to guide the 4D deformation process. The resultant deformations are smooth both in the spatial and temporal dimensions, and are shown to significantly improve warping accuracy over a series of independent 3D warpings, in longitudinal measurements.

Algorithms↗

PubMed2005

A fully noninvasive and robust experimental protocol for longitudinal fMRI studies in the rat.

Functional magnetic resonance imaging (fMRI) is a unique tool to study brain activity and plasticity changes. Combination of blood-oxygen level-dependent (BOLD) fMRI and electrical forepaw stimulation has been used as a standard model to study the somatosensory pathway and brain rehabilitation in rats. The majority of fMRI studies have been performed in animals anesthetized with alpha-chloralose as functional-metabolic coupling is best preserved under this anesthesia. However, alpha-chloralose is not suitable for survival procedures due to side effects, limiting its use to single time point studies of the same animal. We therefore developed a new, totally noninvasive fMRI protocol, using sedation with the alpha2-adrenoreceptor agonist medetomidine in combination with transcutaneous monitoring of blood gases. The continuous subcutaneous administration of medetomidine resulted in stable physiological conditions over a long time and all animals tolerated the repetitive fMRI experiments well. A robust and reproducible, significant BOLD signal increase was observed upon forepaw stimulation in the contralateral primary somatosensory cortex in two consecutive medetomidine sessions in all rats, which was similar to the BOLD signal increase observed in the same animals under alpha-chloralose during a third independent session. Activation in the secondary somatosensory cortex was observed less frequently under both medetomidine and alpha-chloralose. No head motion artifacts or nonspecific brain activation was present. Sedation was quickly reversed by the administration of the antagonist atipamezole after the fMRI experiment. These results demonstrate that longitudinal fMRI studies can be performed safely under sedation with medetomidine to study functional recovery processes upon therapeutical treatment.

Adrenergic alpha-Agonists↗

PubMed2006

Cerebral perfusion mapping using a robust and efficient method for deconvolution analysis of dynamic contrast-enhanced images.

Dynamic contrast-enhanced (DCE) imaging using MRI or CT is emerging as a promising tool for diagnostic imaging of cerebral disorders and the monitoring of tumor response to treatment. In this study, we present a robust and efficient deconvolution method based on a linearized model of the impulse residue function, which allows for the mapping of functional cerebral parameters such as cerebral blood flow, volume, mean transit time, and permeability. Monte Carlo simulation studies were performed to study the accuracy and stability of the proposed method, before applying it to clinical study cases of patients with cerebral tumors imaged using DCE CT. Functional parameter maps generated using the proposed method revealed the locations of the cerebral tumors and were found to be of sufficiently good clarity for marked regional differences in tissue vascularity and permeability to be assessed. In particular, tumor visualization and delineation were found to be better on the parameter maps that were indicative of the breakdown of the blood-brain barrier.

Adenoma↗

PubMed2006

A robust automated method to analyze rodent motion during fear conditioning.

A central question in the study of LTP has been to determine what role it plays in memory formation and storage. One valuable form of learning for addressing this issue is associative fear conditioning. In this paradigm an animal learns to associate a tone and shock, such that subsequent presentation of a tone evokes a fear response (freezing behavior). Recent studies indicate that overlapping cellular processes underlie fear conditioning and LTP. The fear response has generally been scored manually which is both labor-intensive and subject to potential artifacts such as inconsistent or biased results. Here we describe a simple automated method that provides unbiased and rapid analysis of animal motion. We show that measured motion, in units termed significant motion pixels (SMPs), is both linear and robust over a wide range of animal speeds and detection thresholds and scores freezing in a quantitatively similar manner to trained human observers. By comparing the frequency distribution of motion during baseline periods and to the response to fox urine (which causes unconditioned fear), we suggest that freezing and non-freezing are distinct behaviors. Finally, we show how this algorithm can be applied to a fear conditioning paradigm yielding information on long and short-term associative memory as well as habituation. This automated analysis of fear conditioning will permit a more rapid and accurate assessment of the role of LTP in memory.

Algorithms↗

PubMed2006

Robust increase of cutaneous sensitivity, cytokine production and sympathetic sprouting in rats with localized inflammatory irritation of the spinal ganglia.

We investigated the role and mechanisms of inflammatory responses within the dorsal root ganglion (DRG) in the development of chemogenic pathological pain. DRG inflammation was induced by a single deposit of the immune activator zymosan in incomplete Freund's adjuvant in the epidural space near the L5 DRG via a small hole drilled through the transverse process. After a single zymosan injection, rats developed bilateral mechanical hyperalgesia and allodynia which began by day 1 after surgery, peaked at days 3-7, and lasted up to 28 days. The number of macrophages in ipsilateral and contralateral DRGs increased significantly, lasting over 14 days. Robust glial activation was observed in inflamed ganglia. Cytokine profile analysis using a multiplexing protein array system showed that, in normal DRG, all but interleukin (IL)-5, IL-10 and granulocyte-macrophage colony stimulating factor (GM-CSF) were detectable with concentrations of up to 180 pg/mg protein. Local inflammatory irritation selectively increased IL-1beta, IL-6, IL-18, monocyte chemoattractant protein-1 (MCP-1), and growth-related oncogene (GRO/KC) up to 17-fold, and decreased IL-2 and IL-12 (p70) up to threefold. Inflaming the DRG also remarkably increased the incidence of spontaneous activity of A- and C-fibers recorded in the dorsal root. Many of the spontaneously active A-fibers exhibited a short-bursting discharge pattern. Changes in cytokines and spontaneous activity correlated with the time course of pain behaviors, especially light stroke-evoked tactile allodynia. Finally, local inflammation induced extensive sprouting of sympathetic fibers, extending from vascular processes within the inflamed DRG. These results demonstrate the feasibility of inducing chronic localized inflammatory responses in the DRG in the absence of traumatic nerve damage, and highlight the possible contribution of several inflammatory cytokines/chemokines to the generation of spontaneous activity and development and persistence of chemogenic pathologic pain.

Action Potentials↗

PubMed2006

Robustness of central carbohydrate metabolism in developing maize kernels.

The central carbohydrate metabolism provides the precursors for the syntheses of various storage products in seeds. While the underlying biochemical map is well established, little is known about the organization and flexibility of carbohydrate metabolic fluxes in the face of changing biosynthetic demands or other perturbations. This question was addressed in developing kernels of maize (Zea mays L.), a model system for the study of starch and sugar metabolism. (13)C-labeling experiments were carried out with inbred lines, heterotic hybrids, and starch-deficient mutants that were selected to cover a wide range of performances and kernel phenotypes. In total, 46 labeling experiments were carried out using either [U-(13)C(6)]glucose or [U-(13)C(12)]sucrose and up to three stages of kernel development. Carbohydrate flux distributions were estimated based on glucose isotopologue abundances, which were determined in hydrolysates of starch by using quantitative (13)C-NMR and GC-MS. Similar labeling patterns in all samples indicated robustness of carbohydrate fluxes in maize endosperm, and fluxes were rather stable in response to glucose or sucrose feeding and during development. A lack of ADP-glucose pyrophosphorylase in the bt2 and sh2 mutants triggered significantly increased hexose cycling. In contrast, other mutations with similar kernel phenotypes had no effect. Thus, the distribution of carbohydrate fluxes is stable and not determined by sink strength in maize kernels.

Carbohydrate Metabolism↗

PubMed2005

Assessment of the robustness of a serendipitous zinc binding fold: mutagenesis and protein grafting.

Zinc binding motifs have received much attention in the area of protein design. Here, we have tested the suitability of a recently discovered nonnative zinc binding structure as a protein design scaffold. A series of multiple alanine mutants was created to investigate the minimal requirements for folding, and solution structures of these mutants showed that the original fold was maintained, despite changes in approximately 50% of the sequence. We next attempted to transplant binding faces from chosen bimolecular interactions onto one of these mutants, and many of the resulting "chimeras" were shown to adopt a native-like fold. These results both highlight the robust nature of small zinc binding domains and underscore the complexity of designing functional proteins, even using such small, highly ordered scaffolds as templates.

Alanine↗

PubMed2004

Merging the senses into a robust percept.

To perceive the external environment our brain uses multiple sources of sensory information derived from several different modalities, including vision, touch and audition. All these different sources of information have to be efficiently merged to form a coherent and robust percept. Here we highlight some of the mechanisms that underlie this merging of the senses in the brain. We show that, depending on the type of information, different combination and integration strategies are used and that prior knowledge is often required for interpreting the sensory signals.

Brain↗

PubMed2005

The nonreplicating smallpox candidate vaccines defective vaccinia Lister (dVV-L) and modified vaccinia Ankara (MVA) elicit robust long-term protection.

Current smallpox vaccines are live vaccinia viruses that replicate in the vaccinee inducing immunity against the deadly disease smallpox. Replication resulting in virus spread within the host, however, is the major cause of severe postvaccinal adverse events. Therefore, attenuated strains such as modified vaccinia Ankara (MVA) or LC16m8 are candidates as next generation vaccines. These strains are usually grown in primary cells in which mass production is difficult and have an unknown protective potential in humans. Proven vaccine strains of defined origin and modern production techniques are therefore desirable. In this study, defective vaccinia virus (dVV) lacking a gene essential for replication (derived from the Lister vaccine in a complementing cell line) was compared with the Wyeth smallpox vaccine strain and with MVA in mouse animal models using cowpox and ectromelia virus challenge. Similar to MVA, prime-boost immunizations with defective vaccinia induced robust long-term immunity, suggesting it as a promising next generation smallpox vaccine.

Animals↗