Identification of calcium- and nitric oxide-regulated genes by differential analysis of library expression (DAzLE)

Neurophysiologic implications of neuronal nitric oxide synthase

The molecular and chemical properties of neuronal nitric oxide synthase (nNOS) have made it a key mediator in many physiological functions and signaling transduction. The NOS monomer is inactive, but the dimer form is active. There are three forms of NOS, which are neuronal (nNOS), inducible (iNOS), and endothelial (eNOS) nitric oxide synthase. nNOS regulates nitric oxide (NO) synthesis which is the mechanism used mostly by neurons to produce NO. nNOS expression and activation is regulated by some important signaling proteins, such as cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB), calmodulin (CaM), heat shock protein 90 (HSP90)/HSP70. nNOS-derived NO has been implicated in modulating many physiological functions, such as synaptic plasticity, learning, memory, neurogenesis, etc. In this review, we have summarized recent studies that have characterized structural features, subcellular localization, and factors that regulate nNOS function. Finally, we have discussed the role of nNOS in the developing brain under a wide range of physiological conditions, especially long-term potentiation and depression.

Isolated Bacillus subtilis strain 330-2 and its antagonistic genes identified by the removing PCR

Plant growth-promoting bacteria (PGPB) may trigger tolerance against biotic/abiotic stresses and growth enhancement in plants. In this study, an endophytic bacterial strain from rapeseed was isolated to assess its role in enhancing plant growth and tolerance to abiotic stresses, as well as banded leaf and sheath blight disease in maize. Based on 16S rDNA and BIOLOG test analysis, the 330-2 strain was identified as Bacillus subtilis. The strain produced indole-3-acetic acid, siderophores, lytic enzymes and solubilized different sources of organic/inorganic phosphates and zinc. Furthermore, the strain strongly suppressed the in vitro growth of Rhizoctonia solani AG1-IA, Botrytis cinerea, Fusarium oxysporum, Alternaria alternata, Cochliobolus heterostrophus, and Nigrospora oryzae. The strain also significantly increased the seedling growth (ranging 14–37%) of rice and maize. Removing PCR analysis indicated that 114 genes were differentially expressed, among which 10%, 32% and 10% were involved in antibiotic production (e.g., srfAA, bae, fen, mln, and dfnI), metabolism (e.g., gltA, pabA, and ggt) and transportation of nutrients (e.g., fhu, glpT, and gltT), respectively. In summary, these results clearly indicate the effectiveness and mechanisms of B. subtilis strain 330-2 in enhancing plant growth, as well as tolerance to biotic/abiotic stresses, which suggests that the strain has great potential for commercialization as a vital biological control agent.

Identification of low Ca(2+) stress-induced embryo apoptosis response genes in Arachis hypogaea by SSH-associated library lift (SSHaLL)

Calcium is a universal signal in the regulation of wide aspects in biology, but few are known about the function of calcium in the control of early embryo development. Ca(2+) deficiency in soil induces early embryo abortion in peanut, producing empty pods, which is a general problem; however, the underlying mechanism remains unclear. In this study, embryo abortion was characterized to be caused by apoptosis marked with cell wall degradation. Using a method of SSH cDNA libraries associated with library lift (SSHaLL), 62 differentially expressed genes were isolated from young peanut embryos. These genes were classified to be stress responses, catabolic process, carbohydrate and lipid metabolism, embryo morphogenesis, regulation, etc. The cell retardation with cell wall degradation was caused by up-regulated cell wall hydrolases and down-regulated cellular synthases genes. HsfA4a, which was characterized to be important to embryo development, was significantly down-regulated under Ca(2+) -deficient conditions from 15 days after pegging (DAP) to 30 DAP. Two AhCYP707A4 genes, encoding abscisic acid (ABA) 8'-hydroxylases, key enzymes for ABA catabolism, were up-regulated by 21-fold under Ca(2+) -deficient conditions upstream of HsfA4a, reducing the ABA level in early embryos. Over-expression of AhCYP707A4 in Nicotiana benthamiana showed a phenotype of low ABA content with high numbers of aborted embryos, small pods and less seeds, which confirms that AhCYP707A4 is a key player in regulation of Ca(2+) deficiency-induced embryo abortion via ABA-mediated apoptosis. The results elucidated the mechanism of low Ca(2+) -induced embryo abortion and described the method for other fields of study.

NRC-interacting factor directs neurite outgrowth in an activity-dependent manner

Nuclear hormone receptor coregulator-interacting factor 1 (NIF-1) is a zinc finger nuclear protein that was initially identified to enhance nuclear hormone receptor transcription via its interaction with nuclear hormone receptor coregulator (NRC). NIF-1 may regulate gene transcription either by modulating general transcriptional machinery or remodeling chromatin structure through interactions with specific protein partners. We previously reported that the cytoplasmic/nuclear localization of NIF-1 is regulated by the neuronal Cdk5 activator p35, suggesting potential neuronal functions for NIF-1. The present study reveals that NIF-1 plays critical roles in regulating neuronal morphogenesis at early stages. NIF-1 was prominently expressed in the nuclei of developing rat cortical neurons. Knockdown of NIF-1 expression attenuated both neurite outgrowth in cultured cortical neurons and retinoic acid (RA)-treated Neuro-2a neuroblastoma cells. Furthermore, activity-induced Ca(2+) influx, which is critical for neuronal morphogenesis, stimulated the nuclear localization of NIF-1 in cortical neurons. Suppression of NIF-1 expression reduced the up-regulation of neuronal activity-dependent gene transcription. These findings collectively suggest that NIF-1 directs neuronal morphogenesis during early developmental stages through modulating activity-dependent gene transcription.

The neuronal activity-driven transcriptome

Activity-driven transcription is a key event associated with long-lasting forms of neuronal plasticity. Despite the efforts to investigate the regulatory mechanisms that control this complex process and the important advances in the knowledge of the function of many activity-induced genes in neurons, as well as the specific contribution of activity-regulated transcription factors, our understanding of how activity-driven transcription operates at the systems biology level is still very limited. This review focuses on the research of neuronal activity-driven transcription from an "omics" perspective. We will discuss the different high-throughput approaches undertaken to characterize the gene programs downstream of specific activity-regulated transcription factors, including CREB, SRF, MeCP2, Fos, Npas4, and others, and the interplay between epigenetic and transcriptional mechanisms underlying neuronal plasticity changes. Although basic questions remain unanswered and important challenges still lie ahead, the refinement of genome-wide techniques for investigating the neuronal transcriptome and epigenome promises great advances.

Research progress on neurobiology of neuronal nitric oxide synthase

Neuronal nitric oxide synthase (nNOS) is mainly expressed in neurons, to some extent in astrocytes and neuronal stem cells. The alternative splicing of nNOS mRNA generates 5 isoforms of nNOS, including nNOS-α, nNOS-β, nNOS-µ, nNOS-γ and nNOS-2. Monomer of nNOS is inactive, and dimer is the active form. Dimerization requires tetrahydrobiopterin (BH4), heme and L-arginine binding. Regulation of nNOS expression relies largely on cAMP response element-binding protein (CREB) activity, and nNOS activity is regulated by heat shock protein 90 (HSP90)/HSP70, calmodulin (CaM), phosphorylation and dephosphorylation at Ser847 and Ser1412, and the protein inhibitor of nNOS (PIN). There are primarily 9 nNOS-interacting proteins, including post-synaptic density protein 95 (PSD95), clathrin assembly lymphoid leukemia (CALM), calcium/calmodulin-dependent protein kinase II alpha (CAMKIIA), Disks large homolog 4 (DLG4), DLG2, 6-phosphofructokinase, muscle type (PFK-M), carboxy-terminal PDZ ligand of nNOS (CAPON) protein, syntrophin and dynein light chain (LC). Among them, PSD95, CAPON and PFK-M are important nNOS adapter proteins in neurons. The interaction of PSD95 with nNOS controls synapse formation and is implicated in N-methyl-D-aspartic acid-induced neuronal death. nNOS-derived NO is implicated in synapse loss-mediated early cognitive/motor deficits in several neuropathological states, and negatively regulates neurogenesis under physiological and pathological conditions.

Hippocampal gene profiling: toward a systems biology of the hippocampus

Transcriptomics and proteomics approaches give a unique perspective for understanding brain and hippocampal functions but also pose unique challenges because of the singular complexity of the nervous system. The proliferation of genome-wide expression studies during the last decade has provided important insight into the molecular underpinnings of brain anatomy, neural plasticity, and neurological diseases. Microarray technology has dominated transcriptomics research, but this situation is rapidly changing with the recent technological advances in high-throughput sequencing. The full potential of transcriptomics in the neurosciences will be achieved as a result of its integration with other "-omics" disciplines as well as the development of novel analytical bioinformatics and systems biology tools for meta-analysis. Here, we review some of the most relevant advances in the gene profiling of the hippocampus, its relationship with proteomics approaches, and the promising perspectives for the future.

Calcium dynamics in gonadotropin-releasing hormone neurons

The gonadotropin-releasing hormone (GnRH) neurons represent the key output cells of the neuronal network controlling fertility. Intracellular calcium ion concentration ([Ca(2+)](i)) is likely to be a key signaling tool used by GnRH neurons to regulate and co-ordinate multiple cell processes. This review examines the dynamics and control of [Ca(2+)](i) in GT1 cells, embryonic GnRH neurons in the nasal placode culture, and adult GnRH neurons in the acute brain slice preparation. GnRH neurons at all stages of development display spontaneous [Ca(2+)](i) transients driven, primarily, by their burst firing. However, the intracellular mechanisms generating [Ca(2+)](i) transients, and the control of [Ca(2+)](i) by neurotransmitters, varies markedly across the different developmental stages. The functional roles of [Ca(2+)](i) transients are beginning to be unraveled with one key action being that of regulating the dynamics of GnRH neuron burst firing.

p38 mitogen-activated protein kinase and calcium channels mediate signaling in depolarization-induced activation of peroxisome proliferator-activated receptor gamma coactivator-1alpha in neurons

Peroxisome proliferator-activated receptor gamma coactivator 1alpha (PGC-1alpha) coactivates a number of transcription factors critical for mitochondrial biogenesis. Previously, we found that the expression of PGC-1alpha is governed by neuronal activity, but the signaling mechanism is poorly understood. The present study aimed at testing our hypothesis that depolarizing activation of PGC-1alpha in neurons is mediated by p38 mitogen-activated protein kinase (MAPK) and calcium channels. Cultured primary neurons and N2a cells were depolarized with 20 mM KCl for varying times, and increases in PGC-1alpha mRNA and protein levels were found after 0.5 and 1 hr of stimulation, respectively. These levels returned to those of controls after the withdrawal of KCl. Significantly, 15 min of KCl stimulation induced an up-regulation of both p38 MAPK and phosphorylated p38 MAPK that were suppressed by 30 min of pretreatment with SB203580, a blocker of p38 MAPK that also blocked the up-regulation of PGC-1alpha by KCl. Likewise, 30 min of pretreatment with nifedipine, a calcium channel blocker, also prevented the up-regulation of PGC-1alpha mRNA and proteins by KCl. Furthermore, a knockdown of p38 MAPK with small interference hairpin RNA significantly suppressed PGC-1alpha mRNA and protein levels. Our results indicate that both p38 MAPK and calcium play important roles in mediating signaling in depolarization-induced activation of PGC-1alpha at the protein and message levels in neurons.

From synapse to nucleus: calcium-dependent gene transcription in the control of synapse development and function

One of the unique characteristics of higher organisms is their ability to learn and adapt to changes in their environment. This plasticity is largely a result of the brain's ability to convert transient stimuli into long-lasting alterations in neuronal structure and function. This process is complex and involves changes in receptor trafficking, local mRNA translation, protein turnover, and new gene synthesis. Here, we review how neuronal activity triggers calcium-dependent gene expression to regulate synapse development, maturation, and refinement. Interestingly, many components of the activity-dependent gene expression program are mutated in human cognitive disorders, which suggest that this program is essential for proper brain development and function.

Signaling mechanisms linking neuronal activity to gene expression and plasticity of the nervous system

Sensory experience and the resulting synaptic activity within the brain are critical for the proper development of neural circuits. Experience-driven synaptic activity causes membrane depolarization and calcium influx into select neurons within a neural circuit, which in turn trigger a wide variety of cellular changes that alter the synaptic connectivity within the neural circuit. One way in which calcium influx leads to the remodeling of synapses made by neurons is through the activation of new gene transcription. Recent studies have identified many of the signaling pathways that link neuronal activity to transcription, revealing both the transcription factors that mediate this process and the neuronal activity-regulated genes. These studies indicate that neuronal activity regulates a complex program of gene expression involved in many aspects of neuronal development, including dendritic branching, synapse maturation, and synapse elimination. Genetic mutations in several key regulators of activity-dependent transcription give rise to neurological disorders in humans, suggesting that future studies of this gene expression program will likely provide insight into the mechanisms by which the disruption of proper synapse development can give rise to a variety of neurological disorders.

The endoplasmic reticulum exit of glutamate transporter is regulated by the inducible mammalian Yip6b/GTRAP3-18 protein

GTRAP3-18 interacts with and reduces the activity of the neuronal specific Na(+)/K(+) glutamate transporter, EAAC1 both in vitro and in vivo. GTRAP3-18 and the related isoform, JM4, are distant relatives of the Rab GTPase-interacting factor PRA1, and share a topology of four transmembrane domains and cytosolic termini. GTRAP3-18 and JM4 are resident endoplasmic reticulum (ER) proteins. The physiological role of GTRAP3-18 is poorly understood. We demonstrate for the first time that GTRAP3-18 is a regulator of ER protein trafficking. Expression of GTRAP3-18 delays the ER exit of EAAC1, as well as other members of the excitatory amino acid transporter family. GTRAP3-18 uses hydrophobic domain interactions in the ER membrane to self-associate and cytoplasmic interactions at the C terminus to regulate trafficking. The features of GTRAP3-18 activity are consistent with recent phylogenic sequence analyses suggesting GTRAP3-18 and JM4 be reclassified as mammalian isoforms of the yeast protein family Yip, Yip6b, and Yip6a, respectively.

Exon expression profiling reveals stimulus-mediated exon use in neural cells

BACKGROUND

Neuronal cells respond to changes in intracellular calcium ([Ca2+]i) by affecting both the abundance and architecture of specific mRNAs. Although calcium-induced transcription and transcript variation have both been recognized as important sources of gene regulation, the interplay between these two phenomena has not been evaluated on a genome-wide scale.

RESULTS

Here, we show that exon-centric microarrays can be used to resolve the [Ca2+]i-modulated gene expression response into transcript-level and exon-level regulation. Global assessments of affected transcripts reveal modulation within distinct functional gene categories. We find that transcripts containing calcium-modulated exons exhibit enrichment for calcium ion binding, calmodulin binding, plasma membrane associated, and metabolic proteins. Additionally, we uncover instances of regulated exon use in potassium channels, neuroendocrine secretory proteins and metabolic enzymes, and demonstrate that regulated changes in exon expression give rise to distinct transcript variants.

CONCLUSION

Our findings connect extracellular stimuli to specific exon behavior, and suggest that changes in transcript and exon abundance are reflective of a coordinated gene expression response to elevated [Ca2+]i. The technology we describe here lends itself readily to the resolution of stimulus-induced gene expression at both the transcript and exon levels.

The untranslated region of exon 2 of the human neuronal nitric oxide synthase (NOS1) gene exerts regulatory activity

Expressional dysregulation of the human neuronal nitric oxide synthase (NOS1) gene represents an important mechanism in the pathogenesis of certain neuronal disease states. The structure and regulation of the human NOS1 gene is highly complex based on cell type- and stimulus-dependent usage of multiple exon 1 variants. Here we demonstrate that the untranslated region of exon 2 exerts promoter and enhancer functions as well, facilitated in large part by cooperative interaction of two conserved adjacent CREB/AP-1 binding sites. In human neuronal A673 cells, NOS1 expression is stimulated by several compounds which act through these sites, but also stimulate the combined promoter region of exons 1f and 1g. While stimulation of NOS1 expression by dibutyryl-cAMP is mediated by protein kinase A (blocked by H-89), the antiepileptic drug valproic acid is likely to activate phosphatidylinositol-3 kinase (inhibited by LY 294002).

Extrasynaptic NMDA receptors reshape gene ranks

The N-methyl-D-aspartate (NMDA) subtype of glutamate receptors (NMDAR) plays a key role in the control of neuronal plasticity and cell survival by modifying the activity of different signaling pathways and numerous genes. However, it remains unclear how the activation of this one class of glutamate receptors can lead to different functional consequences, such as enhancement of neuronal survival or induction of neuronal death. Recent work further refines the hypothesis that synaptic and extrasynaptic NMDARs have distinct roles in neuronal survival and death by showing that these two subpopulations of NMDARs differentially modify whole-genome activity.

Mining for survival genes

Many stressful, but not lethal, stimuli activate endogenous protective mechanisms that significantly decrease the degree of injury to subsequent injurious stimuli. This protective mechanism is termed preconditioning and tolerance. It occurs across organ systems including the brain and nervous system. Preconditioning has been investigated in cell and animal models and recently been shown to potentially occur in human brain. Learning more about these powerful endogenous neuroprotective mechanisms could help identify new approaches to treat patients with stroke and other central nervous system disorders or injury. Cell and animal models are helping us to better understand the network response of gene and protein expression that activates the neuroprotective response.

Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus

Gene transcription is required for establishing and maintaining the enduring form of long term potentiation (LTP). However, the transcriptome and its associated molecular programs that support LTP are not well understood. The purpose of this study was to identify activity-regulated genes (ARGs) and their molecular pathways that are modulated by LTP induction and to investigate the genomic mechanism for coordinating the transcription of ARGs. We performed time course DNA microarray analyses on the mouse dentate gyrus to determine the temporal genomic expression profiles of ARGs in response to LTP-inducing tetanic stimulation. Our studies uncovered ARGs that regulate various cellular processes, including the structure and function of the synapse, and offered an overview of the dynamic molecular programs that are probably important for LTP. Surprisingly, we found that ARGs are clustered on chromosomes, and ARG clusters are conserved during evolution. Although ARGs in the same cluster have apparently different molecular properties, they are functionally correlated by regulating LTP. In addition, ARGs in specific clusters are co-regulated by the cAMP-response element-binding protein. We propose that chromosomal clustering provides a genomic mechanism for coordinating the transcription of ARGs involved in LTP.

Activity-dependent transcriptional regulation of nuclear respiratory factor-1 in cultured rat visual cortical neurons

Nuclear respiratory factor 1 is a transcription factor involved in the regulation of mitochondrial biogenesis by activating the transcription of subunit genes of cytochrome oxidase and other respiratory enzymes. Very little is known of its role in neurons. To determine if neuronal activity regulates nuclear respiratory factor 1 expression, cultured primary neurons from postnatal rat visual cortex were subjected to 20 mM KCl depolarizing treatment for 1, 3, 5, and 7 h, or exposed to 7 h of KCl followed by withdrawal for 1, 3, 5, and 7 h. Nuclear respiratory factor 1 expression was analyzed by immunoblots, immunocytochemistry, quantitative electron microscopy, real-time quantitative PCR, and in situ hybridization. Nuclear respiratory factor 1 protein was expressed at relatively low basal levels in both the nucleus, where it was associated primarily with euchromatin, and in the cytoplasm, where it was localized to free ribosomes and occasionally to the Golgi apparatus and the outer nuclear membrane. Depolarizing treatment progressively up-regulated both nuclear respiratory factor 1 protein and mRNA in a time-dependent manner, increasing above controls after 1 h and remaining high at 3, 5, and 7 h. Both nuclear and cytoplasmic mRNA levels increased with stimulation, and there was an apparent cytoplasmic-to-nuclear translocation of protein. Following the withdrawal of KCl, both nuclear respiratory factor 1 message and protein were significantly reduced after 1 h. The message returned to basal levels by 5 h and the protein by 7 h. These results strongly indicate that the expression and compartmental redistribution of nuclear respiratory factor 1 protein and mRNA in visual cortical neurons are dynamic processes tightly controlled by neuronal activity.

A cDNA macroarray approach to parasite-induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticum

In 1994, the bacterial parasite Mycoplasma gallisepticum expanded its host range and swept through populations of a novel host--eastern US populations of the house finch (Carpodacus mexicanus). This epizootic caused a dramatic decline in finch population numbers, has been shown to have caused strong selection on house finch morphology, and presumably caused evolutionary change at the molecular level as finches evolved enhanced resistance. As a first step toward identifying finch genes that respond to infection by Mycoplasma and which may have experienced natural selection by this parasite, we used suppression subtractive hybridization (SSH) and cDNA macroarray approaches to identify differentially expressed genes regulated by the Mycoplasma parasite. Two subtractive cDNA libraries consisting of 16,512 clones were developed from spleen using an experimentally uninfected bird as the 'tester' and an infected bird as 'driver', and vice versa. Two hundred and twenty cDNA clones corresponding 34 genes with known vertebrate homologues and a large number of novel transcripts were found to be qualitatively up- or down-regulated genes by high-density filter hybridization. These gene expression changes were further confirmed by a high throughout reverse Northern blot approach and in specific cases by targeted Northern analysis. blast searches show that heat shock protein (HSP) 90, MHC II-associated invariant chain (CD74), T-cell immunoglobulin mucin 1 (TIM1), as well as numerous novel expressed genes not found in the databases were up- or down-regulated by the host in response to this parasite. Our results and macroarray resources provide a foundation for molecular co-evolutionary studies of the Mycoplasma parasite and its recently colonized avian host.

Brain cholinergic vulnerability: Relevance to behavior and disease

The major populations of cholinergic neurons in the brain include two "projection" systems, located in the pontine reticular formation and in the basal forebrain. These two complexes comprise, in part, the anatomical substrates for the "ascending reticular activating system" (ARAS). The pontine cholinergic system relays its rostral influences mainly through thalamic intralaminar nuclei, but it also connects to the basal forebrain and provides a minor innervation of cortex. The basal forebrain cholinergic complex (BFCC) projects directly to cortex and hippocampus, and has a minor connection with the thalamus. Recent data reveal that a parallel system of basal forebrain GABAergic projection neurons innervates cortex/hippocampus in a way that seems to complement the BFCC. Generally, the picture developed from more than 50 years of research is consistent with a "global" influence of these two ascending cholinergic projections on cortical and hippocampal regions. Seemingly, the BFCC acts in tandem or in parallel with the pontine cholinergic projection to activate the electro-encephalogram, increase cerebral blood flow, regulate sleep-wake cycling, and modulate cognitive function. There are quite a number and variety of human brain conditions, notably including Alzheimer's disease, in which degeneration of basal forebrain cholinergic neurons has been documented. Whether the corticopetal GABA system is affected by disease has not been established. Studies of degeneration of the pontine projection are limited, but the available data suggest that it is relatively preserved in Alzheimer's disease. Hypotheses of BFCC degeneration include growth factor deprivation, intracellular calcium dysfunction, amyloid excess, inflammation, and mitochondrial abnormalities/oxidative stress. But, despite considerable research conducted over several decades, the exact mechanisms underlying brain cholinergic vulnerability in human disease remain unclear.

Identification and Evaluation of NO‐Regulated Genes by Differential Analysis of Primary cDNA Library Expression (DAzLE)

Nitric oxide (NO) has numerous physiological roles in the cell. One of the actions of NO is gene regulation through protein modification and signal transduction. In neurons, NO can be produced from neuronal NO synthase, which is activated by calcium following N-methyl-D-aspartate (NMDA) receptor activation. Differential analysis of cDNA library expression (DAzLE) was used to identify differentially expressed genes by NO. Fundamentally, this technique combines differential hybridization to isolate genes whose expression is differentially regulated with microarray to analyze the expression of the isolated genes. The expression of genes identified by the DAzLE method is verified further by quantitative real-time polymerase chain reaction (RT-PCR) and/or Northern blot analysis. The high selectivity and sensitivity of this technique for detecting differentially expressed gene transcripts enable the investigation and identification of a panel of genes that are regulated by NO.

Molecular pathways to neurodegeneration

The molecular bases underlying the pathogenesis of neurodegenerative diseases are gradually being disclosed. One problem that investigators face is distinguishing primary from secondary events. Rare, inherited mutations causing familial forms of these disorders have provided important insights into the molecular networks implicated in disease pathogenesis. Increasing evidence indicates that accumulation of aberrant or misfolded proteins, protofibril formation, ubiquitin-proteasome system dysfunction, excitotoxic insult, oxidative and nitrosative stress, mitochondrial injury, synaptic failure, altered metal homeostasis and failure of axonal and dendritic transport represent unifying events in many slowly progressive neurodegenerative disorders.

Suppression subtractive hybridization coupled with microarray analysis to examine differential expression of genes in virus infected cells

High throughput detection of differential expression of genes is an efficient means of identifying genes and pathways that may play a role in biological systems under certain experimental conditions. There exist a variety of approaches that could be used to identify groups of genes that change in expression in response to a particular stimulus or environment. We here describe the application of suppression subtractive hybridization (SSH) coupled with cDNA microarray analysis for isolation and identification of chicken transcripts that change in expression on infection of host cells with a paramyxovirus. SSH was used for initial isolation of differentially expressed transcripts, a large-scale validation of which was accomplished by microarray analysis. The data reveals a large group of regulated genes constituting many biochemical pathways that could serve as targets for future investigations to explore their role in paramyxovirus pathogenesis. The detailed methods described herein could be useful and adaptable to any biological system for studying changes in gene expression.

Identification and analysis of plasticity-induced late-response genes

The excitatory neurotransmitter, glutamate, activates N-methyl-d-aspartate (NMDA) receptors to induce long-lasting synaptic changes through alterations in gene expression. It is believed that these long-lasting changes contribute to learning and memory, drug tolerance, and ischemic preconditioning. To identify NMDA-induced late-response genes, we used a powerful gene-identification method, differential analysis of primary cDNA library expression (DAzLE), and cDNA microarray from primary cortical neurons. We report here that a variety of genes, which we have named plasticity-induced genes (PLINGs), are up-regulated with differential expression patterns after NMDA receptor activation, indicating that there is a broad and dynamic range of long-lasting neuronal responses that occur through NMDA receptor activation. Our results provide a molecular dissection of the activity-dependent long-lasting neuronal responses induced by NMDA receptor activation.