Microarray profiling analysis of long non‐coding RNAs expression in tendinopathy: identification for potential biomarkers and mechanisms

The role of lncRNAs in pathologies of tendinopathy has not been researched so far, this study aims to identify the role and potent mechanism of lncRNAs in tendinopathy with a bioinformatic analysis. The gene profile of GSE26051 based on the platform of Affymetrix Human Genome U133B Array condensed was downloaded from Gene Expression Omnibus. A total of 46 specimens (including 23 normal samples and 23 tendinopathy specimens) were available. Compared with the control samples, differentially expressed genes (DEGs) of tendinopathy was identified the by packages in R. The selected DEGs were further analysed using bioinformatics methods including co‐expression and enrichment analysis to detect the potential role of lncRNAs. A total of 40 different expressed lncRNAs were identified. However, most of the identified lncRNAs have not been researched before. And this study only annotate one of the identified lncRNAs successfully, the LOC100507027 (myoregulin), with the potential role in regulating skeletal muscle tissue development and skeletal muscle organ development.     

GABAergic inhibition upon auditory response properties of neurons in the dorsal cochlear nucleus of the rat

Summary It is well known that the superficial layers of the dorsal cochlear nucleus (DCN) are rich in GABAergic neurons. We investigated the effects of topical application of GABA receptor agonists and/or antagonists upon the auditory response properties of DCN neurons in rats anesthetized with alpha chloralose-urethane. Auditory stimuli consisted of 20 ms tone bursts presented in a free field. Response properties of DCN neurons were studied before and during iontophoretic application of GABA, bicuculline methiodide (BIC) and muscimol (MUS) alone and GABA with MUS or BIC through triple barrel electrodes glued to the recording microelectrode. Of 68 DCN neurons studied, 27 were sensitive to topical application of the GABA agonists or antagonist. In these neurons, BIC enhanced spontaneous activity as well as auditory responses and decreased the Q-30 quality factor values. MUS reduced auditory responses. BIC often increased the width of the tuning curve but GABA and/or MUS reduced it. Without drug application, GABA sensitive neurons tended to have longer response latencies and larger tuning widths at 30 dB above threshold as well as larger Q-30 values as compared with neurons that were insensitive to GABA. These findings suggest that: 1) GABAergic neurons determine the width of the tuning curve in neurons with GABA receptors by curtailing the excitatory response area, and 2) such neurons receive tonic inhibition from intrinsic GABAergic neurons.     

中脑神经干细胞分化的神经元体外表达突触素的动态分析

目的：观察中脑神经干细胞(NSCs)分化的神经元在不同条件下及不同时间内表达突触素的动态变化。方法：使用骨髓基质细胞(BMSCs)的条件液培养中脑NSCs,免疫细胞化学染色方法观察NSCs分化的神经元表达突触素的状态。结果：在NSCs分化后的12d,可观察到神经元能够表达突触素,但水平较低;18d,NSCs分化的神经元表达突触素的水平接近体外培养3d的海马神经元,并且也呈现典型的串珠样分布。结论：中脑NSCs分化而来的神经元在体外能够表达突触素,但与原代海马神经元相比,则需要更长的体外培养时间,提示NSCs分化的神经元发育成熟可能需要一定时间。     

A computational method to geometric measure of biological particles and application to DNA microarray spot size estimation

Geometric measures (volume, area and length) of biological particles are of fundamental interest for biological studies. Many times, the measures are at micro-/nano-scale, and based on images of the biological particles. This paper proposes a computational method to geometric measure of biological particles. The method has been applied to DNA microarray spot size estimation. Compared with existing algorithms for microarray spot size estimation, the proposed method is computational efficient and also provides confidence probability on the measure. The contributions of this paper include a generic computational method to geometric measure of biological particles and application to DNA microarray spot size estimation.     

Development of a microarray platform for FFPET profiling: application to the classification of human tumors

Background

mRNA profiling has become an important tool for developing and validating prognostic assays predictive of disease treatment response and outcome. Archives of annotated formalin-fixed paraffin-embedded tissues (FFPET) are available as a potential source for retrospective studies. Methods are needed to profile these FFPET samples that are linked to clinical outcomes to generate hypotheses that could lead to classifiers for clinical applications.

Methods

We developed a two-color microarray-based profiling platform by optimizing target amplification, experimental design, quality control, and microarray content and applied it to the profiling of FFPET samples. We profiled a set of 50 fresh frozen (FF) breast cancer samples and assigned class labels according to the signature and method by van 't Veer et al [1] and then profiled 50 matched FFPET samples to test how well the FFPET data predicted the class labels. We also compared the sorting power of classifiers derived from FFPET sample data with classifiers derived from data from matched FF samples.

Results

When a classifier developed with matched FF samples was applied to FFPET data to assign samples to either "good" or "poor" outcome class labels, the classifier was able to assign the FFPET samples to the correct class label with an average error rate = 12% to 16%, respectively, with an Odds Ratio = 36.4 to 60.4, respectively. A classifier derived from FFPET data was able to predict the class label in FFPET samples (leave-one-out cross validation) with an error rate of ~14% (p-value = 3.7 × 10^-7). When applied to the matched FF samples, the FFPET-derived classifier was able to assign FF samples to the correct class labels with 96% accuracy. The single misclassification was attributed to poor sample quality, as measured by qPCR on total RNA, which emphasizes the need for sample quality control before profiling.

Conclusion

We have optimized a platform for expression analyses and have shown that our profiling platform is able to accurately sort FFPET samples into class labels derived from FF classifiers. Furthermore, using this platform, a classifier derived from FFPET samples can reliably provide the same sorting power as a classifier derived from matched FF samples. We anticipate that these techniques could be used to generate hypotheses from archives of FFPET samples, and thus may lead to prognostic and predictive classifiers that could be used, for example, to segregate patients for clinical trial enrollment or to guide patient treatment.     

Development and validation of a microarray for the confirmation and typing of norovirus RT-PCR products

Noroviruses are implicated in many worldwide institutional, food and waterborne outbreaks each year. Genetic typing of isolates is valuable for monitoring outbreak spread as well as variation in circulating strains. Microarrays have the potential to provide rapid genotype information for norovirus samples. The NoroChip v3.0 provides an oligonucleotide hybridization platform to screen for over 600 potential interactions in each experiment. The NoroChip v3.0 was developed at Health Canada and validated in seven international partner laboratories. Each laboratory validated the NoroChip v3.0 using norovirus amplicons routinely characterized in their testing protocols. Fragments from the capsid region (region C) and a 2.4 kb amplicon spanning polymerase and capsid sequences (region AD) were validated in six of the partner laboratories and provided correct genogroup typing information (GI or GII) when hybridized to the NoroChip v3.0. Results indicate that the current limiting factor for implementing the NoroChip v3.0 as a strain typing tool is the difficulty obtaining a long, specific amplicon from all circulating norovirus strains. Data obtained with the longer region AD amplicon provided the best discrimination between norovirus strains.     

Genomic expression profiling of NK cells in health and disease

NK cells are important components of innate and adaptive immunity. Functionally, they play key roles in host defense against tumors and infectious pathogens. Within the past few years, genomic‐scale experiments have provided us with a plethora of gene expression data that reveal an extensive molecular and biological map underlying gene expression programs. In order to better explore and take advantage of existing datasets, we review here the genomic expression profiles of NK cells and their subpopulations in resting or stimulated states, in diseases, and in different organs; moreover, we contrast these expression data to those of other lymphocytes. We have also compiled a comprehensive list of genomic profiling studies of both human and murine NK cells in this review.     

A second type of striatonigral neuron: a comparison between retrogradely labelled and Golgi-stained neurons at the light and electron microscopic levels

In a light and electron microscopic examination of the neostriata of rats that had received injections of horseradish peroxidase into the ipsilateral substantia nigra, two morphologically distinct types of horseradish peroxidase-labelled neurons were observed. In confirmation of previous findings, one type was of medium-size and was characterized by Golgi-staining and gold-toning as the densely spinous type. The second type of neuron was in contrast, larger, had an indented nucleus and numerous cytoplasmic organelles. The synaptic input to the perikarya of the latter neurons consisted of numerous boutons containing large round and oval vesicles. The boutons formed symmetrical synaptic contacts and were similar to those of the local axon collaterals of medium-size densely spiny striatonigral neurons.In an attempt to establish what type of Golgi-impregnated neuron the second type of horseradish peroxidase-labelled neuron was, seventeen Golgi-stained or gold-toned neurons were examined in the electron microscope. Three of them were very similar in their ultrastructural features and synaptic input to the horseradish peroxidase-labelled neurons. All three were of a similar morphological appearance in the light-microscope and characteristically had long (up to 700 μm), essentially smooth dendrites. Both the large horseradish peroxidase-labelled neurons and the Golgi-impregnated neurons with long dendrites have so far only been found in the most ventral regions of the neostriatum.It is concluded that there are at least two morphologically distinct types of striatonigral neurons.     

Quantitative analysis of the feline dorsal column nuclei and their GABAergic and non-GABAergic neurons

Summary The gracile and internal and external cuneate nuclei of four adult cats were studied, using recently developed stereological techniques. The length, volume and position of the nuclei in relation to the level of obex were calculated, as well as the number of neurones, the neuronal density and volume of the three nuclei and different regions in the gracile and internal cuneate nucleus. Material processed for GABA immunocytochemistry was used in order to compare GABAergic and non-GABAergic neurones. The results demonstrate variations in the same nucleus in different animals, and in the nucleus of the left and right sides of the same animal. The same nucleus can vary up to 4 mm in its rostrocaudal position in relation to the obex. The mean sizes of the gracile, internal and external cuneate nuclei are 4.2, 8.4 and 5.6 mm', respectively and their mean neuronal numbers are about 52000, 76 000 and 33000, respectively. The neuronal density was highest (12907 cells/mm³) in the gracile, and lowest in the external cuneate nucleus (5987 cells/mm³). The external cuneate nucleus had a larger relative volume (7.9%) occupied by nerve cell bodies compared with the two medial nuclei (5.1% and 5.8%). In the gracile and internal cuneate nuclei, the GABAergic neurones constituted 28% and 25% of the whole population, respectively, while the external cuneate nucleus was devoid of such cells. All the nuclei contained GABA-positive boutons, however. The mean volume of the GABA-stained neurones in the gracile nucleus was 2319, and internal cuneate 3065 m³, while the corresponding volume of unlabelled neurones in the gracile, internal and external cuneate nuclei was 3745, 8147 and 13 318 m³, respectively. When cyto-fibro-architectonic characteristics were used to subdivide the gracile and cuneate nuclei into rostral, middle and caudal regions, and the data of the three compartments compared, it was found that in both nuclei the middle region had the highest neuronal packing density, and the caudal region the largest mean nerve cell volume.This paper is dedicated to Professor Fred Walberg on the occasion of his 70th birthday.     

The role of GABAergic neuron on NMDA- and SP-induced phase delays in the suprachiasmatic nucleus neuronal activity rhythm in vitro

Gamma-aminobutyric acid (GABA), and its biosynthetic enzyme, glutamic decarboxylase, are widely distributed in the suprachiasmatic nucleus (SCN). In the present study, we examined the role of the GABA_A receptor on in vitro SCN responses to photic-like signals. We found that 100 μM GABA_A receptor antagonist bicuculline partially blocked field potentials evoked by optic nerve stimulation. NMDA- and SP-induced phase shifts of SCN neuronal activity rhythms, were blocked with 10 μM bicuculline. Application of 100 μM bicuculline alone induced phase advance of SCN neuronal activity rhythm. These results show that NMDA- and SP-induced phase shifts are blocked by bicuculline and suggest GABA has an important role as neurotransmitter in the neuronal network regulating phase shifts of the circadian clock.     

Contributions of GABAergic and glutamatergic mechanisms to isoflurane-induced suppression of thalamic somatosensory information transfer

Indications for a pivotal role of the thalamocortical network in producing the state of anesthesia have come from in vivo animal studies as well as imaging studies in humans. We studied possible synaptic mechanisms of anesthesia-induced suppression of touch perception in the rat’s thalamus. Thalamocortical relay neurons (TCNs) receive ascending and descending glutamatergic excitatory inputs via NMDA and non-NMDA receptors (AMPAR) and are subjected to GABA_Aergic inhibitory input which shapes the sensory information conveyed to the cortex. The involvement of these synaptic receptors in the suppressive effects of the prototypic volatile anesthetic isoflurane was assessed by local iontophoretic administration of receptor agonists/antagonists during extracellular recordings of TCNs of the ventral posteromedial nucleus responding to whisker vibration in rats anesthetized with isoflurane concentrations of ∼0.9 vol.% (baseline) and ∼1.9 vol.% (ISO high). ISO high induced a profound suppression of response activity reflected by a conversion of the sustained vibratory responses to ON responses. Administration of NMDA, AMPA, or GABA_AR antagonists caused a reversal to sustained responses in 88, 94 and 88% of the neurons, respectively, with a recovery to baseline levels of response activity. The data show that the block of thalamocortical transfer of tactile information under ISO high may result from an enhancement of GABA_Aergic inhibition and/or a reduction of glutamatergic excitation. Furthermore, they show that the ascending vibratory signals still reach the thalamic neurons under the high isoflurane concentration, indicating that this input is resistant to isoflurane while the attenuation of excitation may be brought about at the corticothalamic glutamatergic facilitatory input.     

GABAergic regulation of auditory sensory gating in low- and high-anxiety rats submitted to a fear conditioning procedure

The inferior colliculus (IC) is primarily involved in the processing of acoustic stimuli, being in a position to send auditory information to motor centers that participate in behaviors such as prey catching and predators' avoidance. The role of the central nucleus of the IC (CIC) on fear and anxiety has been suggested on the basis that rats are able to engage in tasks to decrease the aversiveness of CIC stimulation, increased Fos immunolabeling during diverse aversive states and increased CIC auditory evoked potentials (AEP) induced by conditioned fear stimuli. Additionally, it was shown that brainstem AEP, represented by wave V, for which the main generator is the IC, is increased during experimentally-induced anxiety. Rats segregated according to their low or high emotional reactivity have been used as an important tool in the study of fear and anxiety. The IC contains a high density of GABA receptors. Since the efficacy of an anxiolytic compound is a function of the animal's anxiety level, it is possible that GABA-benzodiazepine (Bzp) agents affect LA and HA animals differently. In this study we investigated the GABA-Bzp influence on the modulation of AEP in rats with low- (LA) or high-anxiety (HA) levels, as assessed by the elevated plus-maze test (EPM). GABA-Bzp modulation on the unconditioned AEP response was analyzed by using intra-CIC injections (0.2 μl) of the GABA-Bzp agonists muscimol (121 ng) and diazepam (30 μg), or the GABA inhibitors bicuculline (10 ng) and semicarbazide (7 μg). In a second experiment, we evaluate the effects of contextual aversive conditioning on AEP using foot-shocks as unconditioned stimuli. On the unconditioned fear paradigm GABA inhibition increased AEP in LA rats and decreases this measure in HA counterparts. Muscimol was effective in reducing AEP in both LA and HA rats. Contextual fear stimuli increased the magnitude of AEP. In spite of no effect obtained with diazepam in LA rats the drug inhibited AEP in HA animals. The specificity of the regulatory mechanisms mediated by GABA-Bzp for the ascending neurocircuits responsible for the acquisition of aversive information in LA and HA animals shed light on the processing of sensory information underlying the generation of defensive reactions.     

A novel experimental chamber for single-cell voltage-clamp and patch-clamp applications with low electrical noise and excellent temperature and flow control

We describe a simple and inexpensive experimental chamber that is designed to overcome several problems encountered when doing electrical and optical studies on single cells or on isolated membrane patches. The bath is small enough to fit on the stage of a standard inverted microscope. It includes a novel solution level-detector, the output of which is used to actively control the level of solution in the experimental chamber. A Peltier-effect device is located adjacent to the flow-chamber and heats or cools the inflowing solution. Solutions can be rapidly switched using two electrically actuated microvalves. The attraction of this system is that, with appropriately quiet power supplies, not only is the bath solution-level held at a fixed height, but the temperature of the bathing solution can also be set over a wide temperature range (minimum range is 15 to 45°C), and solutions can be rapidly changed. All of the construction details are supplied as are appropriate electrical circuits. Without modification, the chamber can be used for applications as diverse as fluorescence microscopy of living cells, time-lapse photomicroscopy and single-cell motion detection as well as single cell voltage-clamp and isolated membrane patch-clamp. With simple modification the system can be adapted for use in experiments on multicellular preparations.     

Microarray profiling of antiviral antibodies for the development of diagnostics, vaccines, and therapeutics

Multiplex analysis of antiviral antibody (Ab) responses provides a potentially powerful strategy for viral diagnosis, prognostication, and development of vaccines and prophylactic Abs. In the coming years, advancements in proteomic technologies will provide even more robust methods to characterize antiviral Ab responses. Biomedical researchers will be faced with the exciting challenge of identifying antiviral Ab specificities that correlate with improved outcomes and efficacious interventions, and translating the findings into more effective diagnostics, prophylactics, and therapeutics.     

Heterokaryon Formation as a Method for Neuron Regeneration in Postischemic Injury to Cerebral Cortex in Rats

Rat prefrontal cortex was examined by light and electron microscopy after stroke induced by photothrombosis. An appreciable number of binuclear neurons with morphologically similar and different nuclei was detected in the perifocal zone and adjacent intact tissue. The satellite oligodendrocyte nucleus was frequently the second nucleus in binuclear neuron. Control specimens also had binuclear neurons, but their number was much lower. It is hypothesized that neuron fusion normally and after injury is a manifestation of physiological and reparative regeneration of these cells. Translated from Byulleten’ Eksperimental’noi Biologii i Meditsiny, Vol. 146, No. 10, pp. 467–470, October, 2008