The UNC-Wisconsin Rhesus Macaque Neurodevelopment Database: A Structural MRI and DTI Database of Early Postnatal Development.

Rhesus macaques are commonly used as a translational animal model in neuroimaging and neurodevelopmental research. In this report, we present longitudinal data from both structural and diffusion MRI images generated on a cohort of 34 typically developing monkeys from 2 weeks to 36 months of age. All images have been manually skull stripped and are being made freely available via an online repository for use by the research community.

Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics.

Magnetic resonance imaging (MRI) of rodent brains enables study of the development and the integrity of the brain under certain conditions (alcohol, drugs etc.). However, these images are difficult to analyze for biomedical researchers with limited image processing experience. In this paper we present an image processing pipeline running on a Midas server, a web-based data storage system. It is composed of the following steps: rigid registration, skull-stripping, average computation, average parcellation, parcellation propagation to individual subjects, and computation of region-based statistics on each image. The pipeline is easy to configure and requires very little image processing knowledge. We present results obtained by processing a data set using this pipeline and demonstrate how this pipeline can be used to find differences between populations.

Expression of the γ2-subunit distinguishes synaptic and extrasynaptic GABA(A) receptors in NG2 cells of the hippocampus.

NG2 cells are equipped with transmitter receptors and receive direct synaptic input from glutamatergic and GABAergic neurons. The functional impact of these neuron-glia synapses is still unclear. Here, we combined functional and molecular techniques to analyze properties of GABA(A) receptors in NG2 cells of the juvenile mouse hippocampus. GABA activated slowly desensitizing responses in NG2 cells, which were mimicked by muscimol and inhibited by bicuculline. To elucidate the subunit composition of the receptors we tested its pharmacological properties. Coapplication of pentobarbital, benzodiazepines, and zolpidem all significantly increased the GABA-evoked responses. The presence of small tonic currents indicated the presence of extrasynaptic GABA(A) receptors. To further analyze the subunit expression, single cell transcript analysis was performed subsequent to functional characterization of NG2 cells. The subunits α1, α2, ß3, γ1, and γ2 were most abundantly expressed, matching properties resulting from pharmacological characterization. Importantly, lack of the γ2-subunit conferred a high Zn²âº sensitivity to the GABA(A) receptors of NG2 cells. Judging from the zolpidem sensitivity, postsynaptic GABA(A) receptors in NG2 cells contain the γ2-subunit, in contrast to extrasynaptic receptors, which were not modulated by zolpidem. To determine the effect of GABA(A) receptor activation on membrane potential, perforated patch recordings were obtained from NG2 cells. In the current-clamp mode, GABA depolarized the cells to approximately -30 mV, indicating a higher intracellular Cl⁻ concentration (∼50 mM) than previously reported. GABA-induced depolarization in NG2 cells might trigger Ca²âº influx through voltage-activated Ca²âº channels.

A midas plugin to enable construction of reproducible web-based image processing pipelines.

Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline.

Mitochondrial genome sequence analysis: a custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy.

BACKGROUND: Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. We used this custom pipeline to analyze MitoChip v2.0 data from 24 DNA samples representing a broad range of tissue types (18 whole blood, 3 skeletal muscle, 3 cell lines), mutations (a 5.8 kilobase pair deletion and 6 known heteroplasmic mutations), and haplogroup origins. All results were compared to those obtained by at least one other mitochondrial DNA sequence analysis method, including Sanger sequencing, denaturing HPLC-based heteroduplex analysis, and/or the Illumina Genome Analyzer II next generation sequencing platform. RESULTS: An average call rate of 99.75% was achieved across all samples with our custom pipeline. Comparison of calls for 15 samples characterized previously by Sanger sequencing revealed a total of 29 discordant calls, which translates to an estimated 0.012% for the base call error rate. We successfully identified 4 known heteroplasmic mutations and 24 other potential heteroplasmic mutations across 20 samples that passed quality control. CONCLUSIONS: Affymetrix MitoChip v2.0 analysis using our optimized MitoChip Filtering Protocol (MFP) bioinformatics pipeline now offers the high sensitivity and accuracy needed for reliable, high-throughput and cost-efficient whole mitochondrial genome sequencing. This approach provides a viable alternative of potential utility for both clinical diagnostic and research applications to traditional Sanger and other emerging sequencing technologies for whole mitochondrial genome analysis.

Lack of P2X receptor mediated currents in astrocytes and GluR type glial cells of the hippocampal CA1 region.

Purinergic signalling plays a major role in intercellular communication between neurons and glial cells. Glial cells express metabotropic receptors for ATP and adenosine, the latter being activated after ATP cleavage through extracellular ecto-ATPase activity. Ionotropic receptors for extracellular ATP, so called P2X receptors, might contribute to neuron-glia signalling. However, experimental evidence for the presence of these receptors in glial cells is less convincing so far. In a previous study, immunohistochemistry was used to identify P2X(1-4,6,7) receptor protein in S100beta-positive hippocampal glial cells. Applying patch clamp and fast application techniques, here we challenged the question of the functional expression of these receptors. Time correlated membrane currents served as test criterion for receptor function, since P2X receptor activation leads to the opening of unspecific cation channels in a millisecond time scale. Agonists were applied via short pressure puffs, with a fast concentration clamp method and through UV flash triggered photolysis of caged ATP. Two types of murine hippocampal macroglial cells, both labelled by the expression of green fluorescence protein driven by the human glial fibrillary acid protein promoter, were analysed in acute brain slices and in freshly dissociated cell suspensions. Surprisingly, ATP or related agonists completely failed to activate currents. Additionally, changes in spontaneously occurring glial postsynaptic currents were never observed. These results have been verified using rat and human hippocampal tissue as well as investigating cells from P2X7 knock out mice. It is concluded that in acute preparations, astroglial cells of the hippocampal CA1 subfield do not express functional P2X receptors.