Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.

A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We present a set of integrated experiments that investigate the effects of common genetic variability on DNA methylation and mRNA expression in four human brain regions each from 150 individuals (600 samples total). We find an abundance of genetic cis regulation of mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation across the genome. We show peak enrichment for cis expression QTLs to be approximately 68,000 bp away from individual transcription start sites; however, the peak enrichment for cis CpG methylation QTLs is located much closer, only 45 bp from the CpG site in question. We observe that the largest magnitude quantitative trait loci occur across distinct brain tissues. Our analyses reveal that CpG methylation quantitative trait loci are more likely to occur for CpG sites outside of islands. Lastly, we show that while we can observe individual QTLs that appear to affect both the level of a transcript and a physically close CpG methylation site, these are quite rare. We believe these data, which we have made publicly available, will provide a critical step toward understanding the biological effects of genetic variation.

An astrocytic basis of epilepsy.

Hypersynchronous neuronal firing is a hallmark of epilepsy, but the mechanisms underlying simultaneous activation of multiple neurons remains unknown. Epileptic discharges are in part initiated by a local depolarization shift that drives groups of neurons into synchronous bursting. In an attempt to define the cellular basis for hypersynchronous bursting activity, we studied the occurrence of paroxysmal depolarization shifts after suppressing synaptic activity using tetrodotoxin (TTX) and voltage-gated Ca(2+) channel blockers. Here we report that paroxysmal depolarization shifts can be initiated by release of glutamate from extrasynaptic sources or by photolysis of caged Ca(2+) in astrocytes. Two-photon imaging of live exposed cortex showed that several antiepileptic agents, including valproate, gabapentin and phenytoin, reduced the ability of astrocytes to transmit Ca(2+) signaling. Our results show an unanticipated key role for astrocytes in seizure activity. As such, these findings identify astrocytes as a proximal target for the treatment of epileptic disorders.

Sudden unexpected death due to inflammatory myofibroblastic tumor of the heart: a case report and review of the literature.

Inflammatory myofibroblastic tumor (IMT) or inflammatory pseudotumor is a rare primary cardiac tumor that may result in sudden death. We report a sudden unexpected death due to occlusion of the coronary arteries by IMT arising from the left coronary cusp of the aortic valve. An 8-year-old child suddenly woke up from his sleep with complaint of severe chest pain to his parents, and shortly he became unresponsive. He expired 40 min later in the hospital despite resuscitation efforts. The postmortem examination revealed a 2.5 × 2 × 1-cm mass composed of multiple entangled slender cylindrical fronts, filling the coronary sinus and obstructing the coronary ostia. The patient had complained of recurrent chest pains about 2 weeks prior to his death. Echocardiogram was conducted on the patient but did not recognize the mass. Histological examination of the mass established the diagnosis of primary cardiac IMT. The detailed pathological findings are described. In addition, the literature is reviewed, and pathogenesis, clinical presentation, and the importance of forensic autopsy examination are discussed.

Gene expression changes in the course of normal brain aging are sexually dimorphic.

Gene expression profiles were assessed in the hippocampus, entorhinal cortex, superior-frontal gyrus, and postcentral gyrus across the lifespan of 55 cognitively intact individuals aged 20-99 years. Perspectives on global gene changes that are associated with brain aging emerged, revealing two overarching concepts. First, different regions of the forebrain exhibited substantially different gene profile changes with age. For example, comparing equally powered groups, 5,029 probe sets were significantly altered with age in the superior-frontal gyrus, compared with 1,110 in the entorhinal cortex. Prominent change occurred in the sixth to seventh decades across cortical regions, suggesting that this period is a critical transition point in brain aging, particularly in males. Second, clear gender differences in brain aging were evident, suggesting that the brain undergoes sexually dimorphic changes in gene expression not only in development but also in later life. Globally across all brain regions, males showed more gene change than females. Further, Gene Ontology analysis revealed that different categories of genes were predominantly affected in males vs. females. Notably, the male brain was characterized by global decreased catabolic and anabolic capacity with aging, with down-regulated genes heavily enriched in energy production and protein synthesis/transport categories. Increased immune activation was a prominent feature of aging in both sexes, with proportionally greater activation in the female brain. These data open opportunities to explore age-dependent changes in gene expression that set the balance between neurodegeneration and compensatory mechanisms in the brain and suggest that this balance is set differently in males and females, an intriguing idea.

Autocrine activation of neuronal NMDA receptors by aspartate mediates dopamine- and cAMP-induced CREB-dependent gene transcription.

cAMP can stimulate the transcription of many activity-dependent genes via activation of the transcription factor, cAMP response element-binding protein (CREB). However, in mouse cortical neuron cultures, prior to synaptogenesis, neither cAMP nor dopamine, which acts via cAMP, stimulated CREB-dependent gene transcription when NR2B-containing NMDA receptors (NMDARs) were blocked. Stimulation of transcription by cAMP was potentiated by inhibitors of excitatory amino acid uptake, suggesting a role for extracellular glutamate or aspartate in cAMP-induced transcription. Aspartate was identified as the extracellular messenger: enzymatic scavenging of l-aspartate, but not glutamate, blocked stimulation of CREB-dependent gene transcription by cAMP; moreover, cAMP induced aspartate but not glutamate release. Together, these results suggest that cAMP acts via an autocrine or paracrine pathway to release aspartate, which activates NR2B-containing NMDARs, leading to Ca(2+) entry and activation of transcription. This cAMP/aspartate/NMDAR signaling pathway may mediate the effects of transmitters such as dopamine on axon growth and synaptogenesis in developing neurons or on synaptic plasticity in mature neural networks.

Direct measurement of oxidative metabolism in the living brain by microdialysis: a review.

This review summarizes microdialysis studies that address the question of which compounds serve as energy sources in the brain. Microdialysis was used to introduce 14C-labeled glucose, lactate, pyruvate, glutamate, glutamine, and acetate into the interstitial fluid of the brain to observe their metabolism to 14CO2. Although glucose uptake from the systemic system supplies the carbon source for these compounds, compounds synthesized from glucose by the brain are subject to recycling including complete metabolism to CO2. Therefore, the brain utilizes multiple compounds in its domain to provide the energy needed to fulfill its function. The physiological conditions controlling metabolism and the contribution of compartmentation into different brain regions, cell types, and subcellular spaces are still unresolved. The aconitase inhibitor fluorocitrate, with a lower inhibition threshold in glial cells, was used to identify the proportion of lactate and glucose that was oxidized in glial cells versus neurons. The fluorocitrate data suggest that glial and neuronal cells are capable of utilizing both lactate and glucose for energy metabolism.

Online lectures for students in dermatology: a replacement for traditional teaching or a valuable addition?

INTRODUCTION/OBJECTIVE: Although the Internet, podcasts and multimedia have become a natural part of our life, these instruments still do not find widespread use in medical education. We aimed to increase the percentage of students benefiting from our lectures during their 6-month principal training period in dermatology by making lectures available online. METHODS: To establish a baseline, we started to count and calculate the average percentage of students attending face to face classes. For the next semester, with a new student generation, we made recordings of about half of the lectures and made them available online. After this testing period, we informed the next new student population at the beginning of the following semester that all lectures would be recorded and made available online. Students' attendance was documented during these periods, and in addition, questionnaires were used to assess students' acceptance and use of the online lectures. RESULTS: At the end of the project, 66% of the students (n = 256) indicated that they had used the online lectures, and 12% of all students stated that they were usually unable to attend lectures due to conflicting obligations, but could now participate thanks to the e-learning programme. An additional 44.9% of all respondents indicated that they welcomed the e-learning programme as a way to view specific lectures. The average attendance of face-to-face lectures did not decrease. CONCLUSION: Online lectures in dermatology were highly welcomed by our students and may be a good means to improve the education of students in dermatology.

A review of brain biorepository management and operations.

Brain biospecimen banking requires centralized resources, national networks for referral of donors, trained personnel to interact with grieving families, and scientific staff to process the biospecimens. Process development of quality control standards is needed to meet the specific requirements of emerging genomic and proteomic technologies. Attention has to be paid to agonal factors and postmortem interval, tissue processing, neuropathology review, and long-term storage. Samples of both diseased and unaffected normal tissues are required with age- and gender-matched control tissues. Data management is vital to store and retrieve quality control measures, clinical and pathologic data linked to the biospecimens. Customized solutions for managing the acquisition and long-term storage of high-quality brain and tissue biospecimens is necessary to support neuroscience research programs, biomarker discovery and genome scale technologies. Biorepositories that operate according to best-practice policies and procedures guarantee the final wish of the families who donate tissue to support neuroscience research and discovery science.

Astrocytic control of glutamatergic activity: astrocytes as stars of the show.

It is a major recent finding that astrocytes can influence synaptic activity by release of glutamate, but many other glutamate-mediated activities are also controlled by astrocytes. Even the most obvious neuronal function of glutamate - its release as a transmitter - is regulated by astrocytes; these cells are needed for formation of precursors for glutamate synthesis, for reuptake of released transmitter, and for disposal of excess glutamate. Without astrocytic involvement, normal function of glutamatergic neurons is not possible, as exemplified by almost instantaneous abrogation of normal vision and learning upon inhibition of astrocyte-specific metabolic pathways. In addition, astrocytes are essential for production of the neuroprotectant glutathione, yet they can also contribute to neuronal death during ischemia by maintaining glutamine synthesis, enabling neuronal formation of neurotoxic glutamate.

Concentration of carbon monoxide (CO) in postmortem human tissues: effect of environmental CO exposure.

We studied how carbon monoxide (CO) is distributed within the human body through quantitation of CO concentrations in postmortem tissue samples from fatalities including possible CO exposure. Stored, frozen tissues were diced, sonicated in water, and 0.01-8.0 mg wet weight (ww) tissues were incubated with sulfosalicylic acid in CO-purged, septum-sealed vials. CO released into the headspace was quantitated by reduction gas chromatography. Mean tissue CO concentrations (pmol/mg ww) from subjects diagnosed to have no known CO exposure (control, N=14), died from fire (N=13), and CO asphyxiation (N=7), respectively, were: adipose (2;13;9), brain (3;13;65), muscle (15;97;297), heart (30;99;371), kidney (22;432;709, lung (54;690;2638), spleen (73;1366;3548), and blood (162;2238;5070). Carboxyhemoglobin concentrations were 1.4%, 25.2%, and 69.1% of total hemoglobin, respectively. We conclude that measurements of CO concentration in a variety of tissues can be used as markers for the degree of exogenous CO exposure and the identification of possible causes of death.

Isolation of thymidine-resistant cells from a thymidine-sensitive acute lymphoblastic leukemia cell line.

Malignant cells have enhanced sensitivity to inhibition of growth by thymidine. Cell growth of the permanent lymphoid cell line CCRF-CEM, originating from a patient with acute lymphoblastic leukemia, is inhibited by 3 x 10(-5) M thymidine, compared to 1 to 5 x 10(-3) M thymidine required to inhibit growth of normal lymphoid lines. Thymidine-resistant cells were isolated at a frequency of approximately 1/100,000 cells after cloning CCRF-CEM cells in medium containing 5 x 10(-4) M thymidine. The resistant cells lacked the enzyme thymidine kinase, had a 20-fold decrease of thymidine uptake, and were resistant to 1 x 10(-4) M 5-bromo-2-deoxyuridine. The cells were sensitive to 1 x 10(-5) M methotrexate, even in the presence of exogenously added thymidine and hypoxanthine. The data indicate that a small fraction of malignant cells may escape the toxic effect of high thymidine therapy and therefore, require additional chemotherapy for their control.

Translational Research in Pediatrics IV: Solid Tissue Collection and Processing.

Solid tissues are critical for child-health research. Specimens are commonly obtained at the time of biopsy/surgery or postmortem. Research tissues can also be obtained at the time of organ retrieval for donation or from tissue that would otherwise have been discarded. Navigating the ethics of solid tissue collection from children is challenging, and optimal handling practices are imperative to maximize tissue quality. Fresh biopsy/surgical specimens can be affected by a variety of factors, including age, gender, BMI, relative humidity, freeze/thaw steps, and tissue fixation solutions. Postmortem tissues are also vulnerable to agonal factors, body storage temperature, and postmortem intervals. Nonoptimal tissue handling practices result in nucleotide degradation, decreased protein stability, artificial posttranslational protein modifications, and altered lipid concentrations. Tissue pH and tryptophan levels are 2 methods to judge the quality of solid tissue collected for research purposes; however, the RNA integrity number, together with analyses of housekeeping genes, is the new standard. A comprehensive clinical data set accompanying all tissue samples is imperative. In this review, we examined: the ethical standards relating to solid tissue procurement from children; potential sources of solid tissues; optimal practices for solid tissue processing, handling, and storage; and reliable markers of solid tissue quality.

Comprehensive cellular-resolution atlas of the adult human brain.

Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127-3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Comparison of the oxidation of glutamine, glucose, ketone bodies and fatty acids by human diploid fibroblasts.

The contribution of glutamine, glucose, ketone bodies and fatty acids to the oxidative energy metabolism of human diploid fibroblasts ws studied. The rate of glutamine oxidation by fibroblasts was 98 nmol/h per mg cell protein compared to 2 nmol/h per mg cell protein or less for glucose, acetoacetate, D-3-hydroxybutyrate, octanoic acid and palmitic acid. Glucose inhibited glutamine oxidation by 85%, while the other substrates had no effect. Therefore, these cells meet their energy requirement almost solely by anaerobic glycolysis and glutamine oxidation.

Formation of extracellular glutamate from glutamine: exclusion of pyroglutamate as an intermediate.

A 4.6-fold increase in interstitial glutamate was observed following the reverse microdialysis of 5 mM glutamine into the rat hippocampus. Two possible mechanisms of glutamine hydrolysis were examined: (a) an enzymatic glutaminase activity and (b) a non-enzymatic mechanism. Injection of 14C-glutamine at the site of microdialysis followed by microdialysis with artificial cerebral spinal fluid allowed isolation of 14C-glutamine (63%), 14C-glutamate (14%), and a compound tentatively identified as pyroglutamate (22%). In this study, we determined if non-enzymatic pyroglutamate formation from glutamine contributed to the synthesis of glutamate. Pyroglutamate is in chemical equilibrium with glutamate, although under physiological conditions, the chemical equilibrium is strongly in the direction of pyroglutamate. In vitro stability studies indicated that 14C-glutamine and 14C-pyroglutamate are not subject to significant non-enzymatic breakdown at pH 6.5-7.5 at 37 degrees C for up to 8 h. Reverse microdialysis with 1 mM pyroglutamate did not increase interstitial glutamate levels. Following injection of 14C-pyroglutamate and microdialysis, radioactivity was recovered in 14C-pyroglutamate (88%) and 14C-glutamine (11%). Less than 1% of the radioactivity was recovered as glutamate. Our data do not support a role of pyroglutamate as an intermediate in the formation of extracellular glutamate following the infusion of glutamine. However, it confirms that pyroglutamate, a known constituent in brain, is actively metabolized in brain cells and contributes to glutamine in the interstitial space.

Bioaccumulation and molecular effects of sediment-bound metals in zebrafish embryos.

Predicting the bioavailability and effects of metals in sediments is of major concern in context with sediment risk assessment. This study aimed to investigate the bioavailability and molecular effects of metals spiked into riverine sediments to zebrafish (Danio rerio) embryos. Embryos were exposed to a natural and an artificial sediment spiked with cadmium (Cd), copper (Cu), nickel (Ni) and zinc (Zn) individually or as a mixture at concentrations ranging from 150 to 3000 mg/kg dry weight (dw) over 48 h, and uptake of metals was determined. Furthermore, transcript abundances of the metallothioneins MT1 and MT2, the metal-responsive element-binding transcription factor (MTF) and the genes sod1, hsp70 and hsp90α1 were measured as indicators of metal-induced or general cellular stress. D. rerio embryos accumulated metals from sediments at concentrations up to 100 times greater than those spiked to the sediment with the greatest bioaccumulation factor (BAF) for Cu from artificial sediment (275.4 ± 41.9 (SD)). Embryos accumulated greater concentrations of all metals from artificial than from natural sediment, and accumulation was greater when embryos were exposed to individual metals than when they were exposed to the mixture. Exposure of embryos to Zn or the mixture exhibited up to 30-fold greater transcript abundances of MT1, MT2 and hsp70 compared to controls which is related to significant uptake of Zn from the sediment. Further changes in transcript abundances could not be related to a significant uptake of metals from sediments. These studies reveal that metals from spiked sediments are bioavailable to D. rerio embryos directly exposed to sediments and that the induction of specific genes can be used as biomarkers for the exposure of early life stages of zebrafish to metal-contaminated sediments.

Chronic exposure to subcutaneously implanted methylxanthines. Differential elevation of A1-adenosine receptors in mouse cerebellar and cerebral cortical membranes.

Upregulation of brain adenosine receptors in DBA/2J mice as affected by theophylline and caffeine, adenosine antagonists, was examined following subcutaneous drug implantation to ensure chronic exposure. Scatchard analysis of binding to membranes of cerebral cortex and cerebellum from individual mice showed a differential upregulation of (-)-N6-R-[G-3H]phenylisopropyladenosine ([3H]-L-PIA) binding density by theophylline. After 14 days of exposure to theophylline (serum concentration of 1.2 +/- 0.01 micrograms/ml measured by HPLC analysis), the Bmax for L-PIA binding to cerebellar membranes increased 22% over the control mice (statistically significant at P less than 0.01 level). Theophylline had no effect on the Bmax for L-PIA binding to cerebral cortical membranes. The observed increases in Bmax values of cerebellar (13.2%) and cerebral cortical membrane binding (14.2%) on chronic exposure to caffeine (7.1 +/- 0.5 micrograms/ml) were not statistically significant at the P less than or equal to 0.05 level. Neither methylxanthine affected the dissociation constant, KD, for L-PIA. The increased potential for adenosine receptor upregulation by theophylline compared to caffeine following chronic, low level exposure suggests that caffeine treatment for sleep apnea may be preferred to the standard theophylline therapy.

Large neutral amino acids auto exchange when infused by microdialysis into the rat brain: implication for maple syrup urine disease and phenylketonuria.

Maple syrup urine disease (MSUD) and phenylketonuria (PKU) are associated with accumulation of large neutral amino acids (LNAA) in blood and tissues and a decrease of other LNAA not directly related to the enzyme defects. One characteristic shared by both the elevated and decreased amino acids is that all are substrates for transport via the large neutral amino acid transporter. In this study, the blood brain barrier was effectively bypassed using microdialysis to determine the immediate effect of infused phenylalanine, tyrosine, 2-amino-2-norborane-carboxylic acid (BCH), and leucine and alpha-ketoisocaproate on extracellular levels of LNAA. The concentration of non-infused LNAA increased in the interstitial fluid, presumably due to trans-stimulated exchange of these LNAA from intracellular pools as the infused LNAA entered the cells. Such trans-stimulated exchange can potentially deplete cells of multiple essential LNAA. It is proposed that brain cells in disorders such as MSUD and PKU may be subject to two mechanisms that limit the availability of a full complement of these amino acids: competition for transport of LNAAs at the blood brain barrier and trans-stimulated exchange out of neuronal cells for subsequent metabolism or sequestration in the periphery.

Glutamate-pyruvate transaminase protects against glutamate toxicity in hippocampal slices.

Elimination of glutamate through enzymatic degradation is an alternative to glutamate receptor blockade in preventing excitotoxic neuronal injury. Glutamate pyruvate transaminase (GPT) is a highly active glutamate degrading enzyme that requires pyruvate as a co-substrate. This study examined the ability of GPT to protect neurons of the hippocampal slice preparation against glutamate toxicity. Two methods were used to elevate the concentration of glutamate in the peri-neuronal space. In an endogenous release paradigm, slices were incubated with 100-500 microM L-trans-pyrrolidine-2,4-dicarboxylate (PDC), an inhibitor of glutamate re-uptake. One hour of exposure to PDC in normal, pyruvate-free slice maintenance medium caused a dose dependent increase in neuronal death assessed 24 h later by propidium iodide uptake in dead cell nuclei. GPT (10 U/ml) decreased neuronal death caused by exposure to PDC at all PDC concentrations tested. Neuroprotection in this model was not dependent on added or non-physiologic levels of pyruvate. In a different paradigm, glutamate was added directly to the normal, pyruvate-free slice maintenance medium and not rinsed away, exposing the slices to a range of 1-5 mM glutamate for an extended period. Twenty-four hours later, neuronal death was again assessed by propidium iodide uptake. GPT was again neuroprotective, decreasing neuronal death in the range from 3 to 5 mM glutamate. In the setting of incubation with this large load of glutamate, neuroprotection by GPT was enhanced by adding pyruvate to the medium. GPT is an effective neuroprotectant against glutamate excitotoxicity. When exposure is limited to endogenously released glutamate, neuroprotection by GPT is not dependent on added pyruvate.

Synthesis of glutamate and glutamine in dibutyryl cyclic AMP-treated astrocytes.

The relative contributions of radioactively labeled fatty acids and glucose to synthesis of glutamate and glutamine were compared in native and dibutyryl cyclic AMP (diBcAMP)-treated primary rat astrocytes. The intracellular specific activities of glutamate and glutamine were 10-fold greater than the specific activities of aspartate or alanine. Butyrate, octanoate and palmitate were equally as effective as precursors for glutamate and glutamine while glucose was 50% as effective as the fatty acids. The specific activity of glutamate and glutamine were identical in the absence of diBcAMP. In diBcAMP treated cells the specific activity of glutamine was greater than that of glutamate when octanoate and palmitate were the labeled precursors. This suggests that cultured astrocytes preferentially utilize free fatty acids for glutamate/glutamine synthesis and that diBcAMP-treated astrocytes contain more than one glutamate compartment.