Detection of two mRNA species at single-cell resolution by double-fluorescence in situ hybridization

Cloning of fatty acid-binding protein 2 (fabp2) in loach (Misgurnus anguillicaudatus) and its expression in response to dietary oxidized fish oil

Fatty acid-binding protein 2 (FABP2) is involved in the uptake of dietary fatty acids and intracellular fatty acid transport. In the present study, cDNA of fabp2 in loach (Misgurnus anguillicaudatus) was cloned and its full length was 956 bp, encoding 134 amino acids. Gene expression of fabp2 was investigated in different development stages and different tissues of loach, showing that the expression of fabp2 was recorded at 2 days after hatching (DAH), 10DAH, 20DAH and 35DAH, and higher in loach intestine, muscle and brain, compared with other tissues. We also investigated the effects of dietary oxidized fish oil (OFO) on the expression of intestinal fabp2 in loach juveniles by using fluorescence in situ hybridization (FISH) and real-time quantitative PCR. Fabp2 gene was expressed mainly by the intestinal epithelium cells of loach juveniles. The expression of intestinal fabp2 in loaches fed with OFO diet was significantly up-regulated on day 1 and 3, and down-regulated on day 10 after feeding, compared with those loaches fed with dietary fresh fish oil (FO), which were in accordance with the fluorescence intensities of FISH exhibiting in the corresponding feeding time. The present study indicated that dietary oxidized fish oil could affect the expression of fabp2 in the loach. Our results serve as reference to better understand the functional characterization of fabp2 in loach and other fish species.

Overexpression of protocadherin 7 inhibits neuronal survival by downregulating BIRC5 in vitro

Protocadherins (Pcdhs) are widely-expressed transmembrane proteins in the nervous system. Recent studies suggest that Pcdhs play multiple critical roles during neuronal development. However, the cellular mechanisms of Pcdh7 in neurons are still largely unknown. In the current study, we demonstrated that the expression of Pcdh7 during mouse brain development was regulated spatiotemporally. We observed that the elevated expression of Pcdh7 led to activation of the intrinsic apoptotic pathway in primary cortical neurons. Whole transcriptome sequencing revealed that 12 genes were involved in the apoptotic pathway including baculoviral inhibitor of apoptosis (IAP) repeat containing 5 (BIRC5). The neuronal apoptosis caused by Pcdh7 overexpression could be significantly inhibited by either a missense mutation in the conserved motif CM2 domain of Pcdh7 or BIRC5 overexpression. These results suggest the existence of Pcdh7-BIRC5 signaling cascade in the cortical neurons and represent a potential therapeutic area for further investigation.

Considerations for optimal use of postmortem human brains for molecular psychiatry: lessons from schizophrenia

Schizophrenia is a disabling disease impacting millions of people around the world, for which there is no known cure. Current antipsychotic treatments for schizophrenia mainly target psychotic symptoms, do little to ameliorate social or cognitive deficits, have side-effects that cause weight gain, and diabetes and 30% of people do not respond. Thus, better therapeutics for schizophrenia aimed at the route biologic changes are needed and discovering the underlying neurobiology is key to this quest. Postmortem brain studies provide the most direct and detailed way to determine the pathophysiology of schizophrenia. This chapter outlines steps that can be taken to ensure the best-quality molecular data from postmortem brain tissue are obtained. In this chapter, we also discuss targeted and high-throughput methods for examining gene and protein expression and some of the strengths and limitations of each method. We briefly consider why gene and protein expression changes may not always concur within brain tissue. We conclude that postmortem brain research that investigates gene and protein expression in well-characterized and matched brain cohorts provides an important foundation to be considered when interpreting data obtained from studies of living schizophrenia patients.

Activated Hedgehog-GLI Signaling Causes Congenital Ureteropelvic Junction Obstruction

Intrinsic ureteropelvic junction obstruction is the most common cause of congenital hydronephrosis, yet the underlying pathogenesis is undefined. Hedgehog proteins control morphogenesis by promoting GLI-dependent transcriptional activation and inhibiting the formation of the GLI3 transcriptional repressor. Hedgehog regulates differentiation and proliferation of ureteric smooth muscle progenitor cells during murine kidney-ureter development. Histopathologic findings of smooth muscle cell hypertrophy and stroma-like cells, consistently observed in obstructing tissue at the time of surgical correction, suggest that Hedgehog signaling is abnormally regulated during the genesis of congenital intrinsic ureteropelvic junction obstruction. Here, we demonstrate that constitutively active Hedgehog signaling in murine intermediate mesoderm-derived renal progenitors results in hydronephrosis and failure to develop a patent pelvic-ureteric junction. Tissue obstructing the ureteropelvic junction was marked as early as E13.5 by an ectopic population of cells expressing Ptch2, a Hedgehog signaling target. Constitutive expression of GLI3 repressor in Ptch1-deficient mice rescued ectopic Ptch2 expression and obstructive hydronephrosis. Whole transcriptome analysis of isolated Ptch2⁺ cells revealed coexpression of genes characteristic of stromal progenitor cells. Genetic lineage tracing indicated that stromal cells blocking the ureteropelvic junction were derived from intermediate mesoderm-derived renal progenitors and were distinct from the smooth muscle or epithelial lineages. Analysis of obstructive ureteric tissue resected from children with congenital intrinsic ureteropelvic junction obstruction revealed a molecular signature similar to that observed in Ptch1-deficient mice. Together, these results demonstrate a Hedgehog-dependent mechanism underlying mammalian intrinsic ureteropelvic junction obstruction.

Tbx15 Defines a Glycolytic Subpopulation and White Adipocyte Heterogeneity

Tbx15 is a member of the T-box gene family of mesodermal developmental genes. We have recently shown that Tbx15 plays a critical role in the formation and metabolic programming of glycolytic myofibers in skeletal muscle. Tbx15 is also differentially expressed among white adipose tissue (WAT) in different body depots. In the current study, using three independent methods, we show that even within a single WAT depot, high Tbx15 expression is restricted to a subset of preadipocytes and mature white adipocytes. Gene expression and metabolic profiling demonstrate that the Tbx15^Hi preadipocyte and adipocyte subpopulations of cells are highly glycolytic, whereas Tbx15^Low preadipocytes and adipocytes in the same depot are more oxidative and less glycolytic. Likewise, in humans, expression of TBX15 in subcutaneous and visceral WAT is positively correlated with markers of glycolytic metabolism and inversely correlated with obesity. Furthermore, overexpression of Tbx15 is sufficient to reduce oxidative and increase glycolytic metabolism in cultured adipocytes. Thus, Tbx15 differentially regulates oxidative and glycolytic metabolism within subpopulations of white adipocytes and preadipocytes. This leads to a functional heterogeneity of cellular metabolism within WAT that has potential impact in the understanding of human metabolic diseases.

Variant Ionotropic Receptors in the Malaria Vector Mosquito Anopheles gambiae Tuned to Amines and Carboxylic Acids

The principal Afrotropical human malaria vector mosquito, Anopheles gambiae, remains a significant threat to global health. A critical component in the transmission of malaria is the ability of An. gambiae females to detect and respond to human-derived chemical kairomones in their search for blood meal hosts. The basis for host odor responses resides in olfactory receptor neurons (ORNs) that express chemoreceptors encoded by large gene families, including the odorant receptors (ORs) and the variant ionotropic receptors (IRs). While ORs have been the focus of extensive investigation, functional IR complexes and the chemical compounds that activate them have not been identified in An. gambiae. Here we report the transcriptional profiles and functional characterization of three An. gambiae IR (AgIr) complexes that specifically respond to amines or carboxylic acids - two classes of semiochemicals that have been implicated in mediating host-seeking by adult females but are not known to activate An. gambiae ORs (AgOrs). Our results suggest that AgIrs play critical roles in the detection and behavioral responses to important classes of host odors that are underrepresented in the AgOr chemical space.

Fluorescence resonance energy transfer-based hybridization chain reaction for in situ visualization of tumor-related mRNA

The ability to visualize tumor-related mRNA in situ in single cells would distinguish whether they are cancer cells or normal cells, which holds great promise for cancer diagnosis at an early stage. Fluorescence resonance energy transfer (FRET) and hybridization chain reactions (HCRs) were combined with amplified sense tumor-related mRNA (TK1 mRNA) in situ with high sensitivity in single cells and tissue sections. Using this strategy, each copy of the target mRNA can propagate a chain reaction of hybridization events between two alternating hairpins to form a nicked duplex that contains repeated FRET units, amplifying the fluorescent signal. The detection limit of 18 pM is about three orders of magnitude lower than that of a non-HCR method (such as the binary-probe-system). Meanwhile, due to the FRET strategy, complicated washing steps are not necessary and experimental time is sharply reduced. As far as we know, this is the first report of a fluorescence in situ hybridization (FISH) strategy that can simultaneously fulfil signal amplification and is wash-free. We believe that this FRET-based HCR strategy has great potential as a powerful tool in basic research and clinical diagnosis.

Persistent Hyperactivity of Hippocampal Dentate Interneurons After a Silent Period in the Rat Pilocarpine Model of Epilepsy

Profile of GABAergic interneuron activity after pilocarpine-induced status epilepticus (SE) was examined in the rat hippocampal dentate gyrus by analyzing immediate early gene expression and recording spontaneous firing at near resting membrane potential (REM). SE for exact 2 h or more than 2 h was induced in the male Sprague-Dawley rats by an intraperitoneal injection of pilocarpine. Expression of immediate early genes (IEGs) was examined at 1 h, 1 week, 2 weeks or more than 10 weeks after SE. For animals to be examined at 1 h after SE, SE lasted for exact 2 h was terminated by an intraperitoneal injection of diazepam. Spontaneous firing at near the REM was recorded in interneurons located along the border between the granule cell layer and the hilus more than 10 weeks after SE. Results showed that both c-fos and activity-regulated cytoskeleton associated protein (Arc) in hilar GABAergic interneurons were up-regulated after SE in a biphasic manner; they were increased at 1 h and more than 2 weeks, but not at 1 week after SE. Ten weeks after SE, nearly 60% of hilar GABAergic cells expressed c-fos. With the exception of calretinin (CR)-positive cells, percentages of hilar neuronal nitric oxide synthase (nNOS)-, neuropeptide Y (NPY)-, parvalbumin (PV)-, and somatostatin (SOM)-positive cells with c-fos expression are significantly higher than those of controls more than 10 weeks after SE. Without the REM to be more depolarizing and changed threshold potential level in SE-induced rats, cell-attached recording revealed that nearly 90% of hilar interneurons fired spontaneously at near the REM while only 22% of the same cell population did so in the controls. In conclusion, pilocarpine-induced SE eventually leads to a state in which surviving dentate GABAergic interneurons become hyperactive with a subtype-dependent manner; this implies that a fragile balance between excitation and inhibition exists in the dentate gyrus and in addition, the activity-dependent up-regulation of IEGs may underlie plastic changes seen in some types of GABAergic cells in the pilocarpine model of epilepsy.

"Nanofiltration" Enabled by Super-Absorbent Polymer Beads for Concentrating Microorganisms in Water Samples

Detection and quantification of pathogens in water is critical for the protection of human health and for drinking water safety and security. When the pathogen concentrations are low, large sample volumes (several liters) are needed to achieve reliable quantitative results. However, most microbial identification methods utilize relatively small sample volumes. As a consequence, a concentration step is often required to detect pathogens in natural waters. Herein, we introduce a novel water sample concentration method based on superabsorbent polymer (SAP) beads. When SAP beads swell with water, small molecules can be sorbed within the beads, but larger particles are excluded and, thus, concentrated in the residual non-sorbed water. To illustrate this approach, millimeter-sized poly(acrylamide-co-itaconic acid) (P(AM-co-IA)) beads are synthesized and successfully applied to concentrate water samples containing two model microorganisms: Escherichia coli and bacteriophage MS2. Experimental results indicate that the size of the water channel within water swollen P(AM-co-IA) hydrogel beads is on the order of several nanometers. The millimeter size coupled with a negative surface charge of the beads are shown to be critical in order to achieve high levels of concentration. This new concentration procedure is very fast, effective, scalable, and low-cost with no need for complex instrumentation.

Methods to Study Long Noncoding RNA Biology in Cancer

Thousands of long noncoding RNAs (lncRNAs) have been discovered in recent years. The functions of lncRNAs range broadly from regulating chromatin structure and gene expression in the nucleus to controlling messenger RNA (mRNA) processing, mRNA posttranscriptional regulation, cellular signaling, and protein activity in the cytoplasm. Experimental and computational techniques have been developed to characterize lncRNAs in high-throughput scale, to study the lncRNA function in vitro and in vivo, to map lncRNA binding sites on the genome, and to capture lncRNA-protein interactions with the identification of lncRNA-binding partners, binding sites, and interaction determinants. In this chapter, we will discuss these technologies and their applications in decoding the functions of lncRNAs. Understanding these techniques including their advantages and disadvantages and developing them in the future will be essential to elaborate the roles of lncRNAs in cancer and other diseases.

A supersandwich fluorescence in situ hybridization strategy for highly sensitive and selective mRNA imaging in tumor cells

This strategy uses two fluorophore-labeled signal probes to generate a supersandwich product, which in turn generates numerous signal probes located at the target mRNA position, resulting in thein situfluorescence signal amplification.

Different mechanisms are responsible for dishabituation of electrophysiological auditory responses to a change in acoustic identity than to a change in stimulus location

Repeated exposure to an auditory stimulus leads to habituation of the electrophysiological and immediate-early-gene (IEG) expression response in the auditory system. A novel auditory stimulus reinstates this response in a form of dishabituation. This has been interpreted as the start of new memory formation for this novel stimulus. Changes in the location of an otherwise identical auditory stimulus can also dishabituate the IEG expression response. This has been interpreted as an integration of stimulus identity and stimulus location into a single auditory object, encoded in the firing patterns of the auditory system. In this study, we further tested this hypothesis. Using chronic multi-electrode arrays to record multi-unit activity from the auditory system of awake and behaving zebra finches, we found that habituation occurs to repeated exposure to the same song and dishabituation with a novel song, similar to that described in head-fixed, restrained animals. A large proportion of recording sites also showed dishabituation when the same auditory stimulus was moved to a novel location. However, when the song was randomly moved among 8 interleaved locations, habituation occurred independently of the continuous changes in location. In contrast, when 8 different auditory stimuli were interleaved all from the same location, a separate habituation occurred to each stimulus. This result suggests that neuronal memories of the acoustic identity and spatial location are different, and that allocentric location of a stimulus is not encoded as part of the memory for an auditory object, while its acoustic properties are. We speculate that, instead, the dishabituation that occurs with a change from a stable location of a sound is due to the unexpectedness of the location change, and might be due to different underlying mechanisms than the dishabituation and separate habituations to different acoustic stimuli.

Genomics and proteomics in solving brain complexity

The human brain is extraordinarily complex, composed of billions of neurons and trillions of synaptic connections. Neurons are organized into circuit assemblies that are modulated by specific interneurons and non-neuronal cells, such as glia and astrocytes. Data on human genome sequences predicts that each of these cells in the human brain has the potential of expressing ∼20 000 protein coding genes and tens of thousands of noncoding RNAs. A major challenge in neuroscience is to determine (1) how individual neurons and circuitry utilize this potential during development and maturation of the nervous system, and for higher brain functions such as cognition, and (2) how this potential is altered in neurological and psychiatric disorders. In this review, we will discuss how recent advances in next generation sequencing, proteomics and bioinformatics have transformed our understanding of gene expression and the functions of neural circuitry, memory storage, and disorders of cognition.

Combined FISH and immunofluorescent staining methods to co-localize proteins and mRNA in neurons and brain tissue

Combining multicolor fluorescent in situ hybridization (FISH) and immunofluorescent staining (IFS) presents a powerful method for visualizing the spatial relationship between mRNA and proteins in different neural compartments. Although seemingly straightforward, the combination of IFS/FISH and quantitative co-localization analysis of mRNA and proteins can be difficult to perform successfully, often generating variable results. Here we describe a combined method of multicolor IFS and FISH in concert with two-dimensional (2D) and three-dimensional (3D) co-localization analysis for determining the expression of individual molecules in rat neurons and brain sections. Using this approach, we have analyzed interactions of the Huntington's disease protein huntingtin with select proteins and mRNA.

Analysis of single-cell gene transcription by RNA fluorescent in situ hybridization (FISH)

Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 protein variants encoded by the var genes. The haploid P. falciparum genome harbors approximately 60 different var genes of which only one has been believed to be transcribed per cell at a time during the blood stage of the infection. How such mutually exclusive regulation of var gene transcription is achieved is unclear, as is the identification of individual var genes or sub-groups of var genes associated with different receptors and the consequence of differential binding on the clinical outcome of P. falciparum infections. Recently, the mutually exclusive transcription paradigm has been called into doubt by transcription assays based on individual P. falciparum transcript identification in single infected erythrocytic cells using RNA fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE(1). Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human erythrocytes. The method is based on the use of digoxigenin- and biotin- labeled antisense RNA probes using the TSA Plus Fluorescence Palette System(2) (Perkin Elmer), microscopic analyses and freshly selected P. falciparum IE. The in situ hybridization method can be used to monitor transcription and regulation of a variety of genes expressed during the different stages of the P. falciparum life cycle and is adaptable to other malaria parasite species and other organisms and cell types.

CAG expansion induces nucleolar stress in polyglutamine diseases

The cell nucleus is a major site for polyglutamine (polyQ) toxicity, but the underlying mechanisms involved have yet been fully elucidated. Here, we report that mutant RNAs that carry an expanded CAG repeat (expanded CAG RNAs) induce apoptosis by activating the nucleolar stress pathway in both polyQ patients and transgenic animal disease models. We showed that expanded CAG RNAs interacted directly with nucleolin (NCL), a protein that regulates rRNA transcription. Such RNA-protein interaction deprived NCL of binding to upstream control element (UCE) of the rRNA promoter, which resulted in UCE DNA hypermethylation and subsequently perturbation of rRNA transcription. The down-regulation of rRNA transcription induced nucleolar stress and provoked apoptosis by promoting physical interaction between ribosomal proteins and MDM2. Consequently, p53 protein was found to be stabilized in cells and became concentrated in the mitochondria. Finally, we showed that mitochondrial p53 disrupted the interaction between the antiapoptotic protein, Bcl-xL, and the proapoptotic protein, Bak, which then caused cytochrome c release and caspase activation. Our work provides in vivo evidence that expanded CAG RNAs trigger nucleolar stress and induce apoptosis via p53 and describes a polyQ pathogenic mechanism that involves the nucleolus.

Expression and rapid experience-dependent regulation of type-A GABAergic receptors in the songbird auditory forebrain

GABAergic transmission influences sensory processing and experience-dependent plasticity in the adult brain. Little is known about the functional organization of inhibitory circuits in the auditory forebrain of songbirds, a robust model extensively used in the study of central auditory processing of behaviorally relevant communication signals. In particular, no information is currently available on the expression and organization of GABAA receptor-expressing neurons. Here, we studied the distribution and regulation of GABAA receptors in the songbird auditory forebrain, with a specific focus on α5, a subunit implicated in tonic inhibition and sensory learning. We obtained a zebra finch cDNA that encodes the α5-subunit (GABRA5) and carried out a detailed analysis of its expression via in situ hybridization. GABRA5 was highly expressed in the caudomedial nidopallium (NCM), caudomedial mesopallium, and field L2. Using double fluorescence in situ hybridization, we demonstrate that a large fraction of GABRA5-expressing neurons is engaged by auditory experience, as revealed by the song-induced expression of the activity-dependent gene zenk. Remarkably, we also found that α5 expression is rapidly regulated by sensory stimulation: 30 min of conspecific song playbacks significantly increase the number of GABRA5-expressing neurons in NCM, but not in other auditory areas. This effect is selective for α5, but not γ2 transcripts. Our results suggest that α5-containing GABAA receptors likely play a key role in central auditory processing and may contribute to the experience-dependent plasticity underlying auditory learning.

Organization of Estrogen-Associated Circuits in the Mouse Primary Auditory Cortex

Sex steroid hormones influence the perceptual processing of sensory signals in vertebrates. In particular, decades of research have shown that circulating levels of estrogen correlate with hearing function. The mechanisms and sites of action supporting this sensory-neuroendocrine modulation, however, remain unknown. Here we combined a molecular cloning strategy, fluorescence in-situ hybridization and unbiased quantification methods to show that estrogen-producing and -sensitive neurons heavily populate the adult mouse primary auditory cortex (AI). We also show that auditory experience in freely-behaving animals engages estrogen-producing and -sensitive neurons in AI. These estrogen-associated networks are greatly stable, and do not quantitatively change as a result of acute episodes of sensory experience. We further demonstrate the neurochemical identity of estrogen-producing and estrogen-sensitive neurons in AI and show that these cell populations are phenotypically distinct. Our findings provide the first direct demonstration that estrogen-associated circuits are highly prevalent and engaged by sensory experience in the mouse auditory cortex, and suggest that previous correlations between estrogen levels and hearing function may be related to brain-generated hormone production. Finally, our findings suggest that estrogenic modulation may be a central component of the operational framework of central auditory networks.

Neurochemical organization and experience-dependent activation of estrogen-associated circuits in the songbird auditory forebrain

The classic steroid hormone estradiol is rapidly produced by central auditory neurons in the songbird brain and instantaneously modulates auditory coding to enhance the neural and behavioral discrimination of acoustic signals. Although recent advances highlight novel roles for estradiol in the regulation of central auditory processing, current knowledge on the functional and neurochemical organization of estrogen-associated circuits, as well as the impact of sensory experience in these auditory forebrain networks, remains very limited. Here we show that both estrogen-producing and -sensitive neurons are highly expressed in the caudomedial nidopallium (NCM), the zebra finch analog of the mammalian auditory association cortex, but not other auditory forebrain areas. We further demonstrate that auditory experience primarily engages estrogen-producing, and to a lesser extent, estrogen-responsive neurons in NCM, that these neuronal populations moderately overlap and that acute episodes of sensory experience do not quantitatively affect these circuits. Finally, we show that whereas estrogen-producing cells are neurochemically heterogeneous, estrogen-sensitive neurons are primarily glutamatergic. These findings reveal the neurochemical and functional organization of estrogen-associated circuits in the auditory forebrain, demonstrate their activation and stability in response to sensory experience in behaving animals, and highlight estrogenic circuits as fundamental components of central networks supporting sensory processing.

The mouse primary visual cortex is a site of production and sensitivity to estrogens

The classic female estrogen, 17β-estradiol (E2), has been repeatedly shown to affect the perceptual processing of visual cues. Although gonadal E2 has often been thought to influence these processes, the possibility that central visual processing may be modulated by brain-generated hormone has not been explored. Here we show that estrogen-associated circuits are highly prevalent in the mouse primary visual cortex (V1). Specifically, we cloned aromatase, a marker for estrogen-producing neurons, and the classic estrogen receptors (ERs) ERα and ERβ, as markers for estrogen-responsive neurons, and conducted a detailed expression analysis via in-situ hybridization. We found that both monocular and binocular V1 are highly enriched in aromatase- and ER-positive neurons, indicating that V1 is a site of production and sensitivity to estrogens. Using double-fluorescence in-situ hybridization, we reveal the neurochemical identity of estrogen-producing and -sensitive cells in V1, and demonstrate that they constitute a heterogeneous neuronal population. We further show that visual experience engages a large population of aromatase-positive neurons and, to a lesser extent, ER-expressing neurons, suggesting that E2 levels may be locally regulated by visual input in V1. Interestingly, acute episodes of visual experience do not affect the density or distribution of estrogen-associated circuits. Finally, we show that adult mice dark-reared from birth also exhibit normal distribution of aromatase and ERs throughout V1, suggesting that the implementation and maintenance of estrogen-associated circuits is independent of visual experience. Our findings demonstrate that the adult V1 is a site of production and sensitivity to estrogens, and suggest that locally-produced E2 may shape visual cortical processing.

Sub-unit Specific Regulation of Type-A GABAergic Receptors During Post-Natal Development of the Auditory Cortex

The GABA-A receptor has been strongly implicated in the organization and function of cortical sensory circuits in the adult mammal. In the present work, changes in the expression patterns of select GABA-A subunits were examined as a function of development. The RNA expression profiles for three subunit types were studied, α1, β2/3 and δ at four developmental time points, (p0, p15, p30 and p90). The α1, β2/3 subunits were present at birth and following a modest increase early in life; mRNA expression for these subunits were found at stable levels throughout life. The expression pattern for the δ subunit showed the most dramatic changes in the number of positive cells as a function of age. In early life, p0 through p15 expression of mRNA for the δ subunit was quite low but increased in later life, p30 and p90. Together these data suggest that much of the potential for inhibitory connectivity is laid down in the pre and early post-natal periods.

Surface co-expression of two different PfEMP1 antigens on single plasmodium falciparum-infected erythrocytes facilitates binding to ICAM1 and PECAM1

The Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) antigens play a major role in cytoadhesion of infected erythrocytes (IE), antigenic variation, and immunity to malaria. The current consensus on control of variant surface antigen expression is that only one PfEMP1 encoded by one var gene is expressed per cell at a time. We measured var mRNA transcript levels by real-time Q-PCR, analysed var gene transcripts by single-cell FISH and directly compared these with PfEMP1 antigen surface expression and cytoadhesion in three different antibody-selected P. falciparum 3D7 sub-lines using live confocal microscopy, flow cytometry and in vitro adhesion assays. We found that one selected parasite sub-line simultaneously expressed two different var genes as surface antigens, on single IE. Importantly, and of physiological relevance to adhesion and malaria pathogenesis, this parasite sub-line was found to bind both CD31/PECAM1 and CD54/ICAM1 and to adhere twice as efficiently to human endothelial cells, compared to infected cells having only one PfEMP1 variant on the surface. These new results on PfEMP1 antigen expression indicate that a re-evaluation of the molecular mechanisms involved in P. falciparum adhesion and of the accepted paradigm of absolutely mutually exclusive var gene transcription is required.

Plasmodium falciparum is the most pathogenic human malaria parasite and its virulence has been linked to its capacity to express different adhesion proteins that enable the developing parasitized erythrocyte to bind to capillaries of the host, thereby avoiding removal by the spleen. Each parasite has approximately 60 genes encoding different versions of this adhesion protein, and a switch in surface display of these proteins enables the parasite to evade the immune system. Here we show that different variants of these binding proteins can be found expressed simultaneously on single infected red blood cells mediating binding to different endothelial receptors.

Double fluorescence in situ hybridization in fresh brain sections

Here we describe a modified version of a double fluorescence in situ hybridization (dFISH) method optimized for detecting two mRNAs of interest in fresh frozen brain sections. Our group has successfully used this approach to study gene co-regulation. More specifically, we have used this dFISH method to explore the anatomical organization, neurochemical properties, and the impact of sensory experience in central sensory circuits, at single cell resolution. This protocol has been validated in brain tissue from mice, rats and songbirds but is expected to be easily adaptable to other vertebrate species, as well as to an array of non-neural tissues. In this film we provide a detailed demonstration of the main steps of this procedure.

Localization of BDNF mRNA with the Huntington's disease protein in rat brain

Background

Studies have implicated reduced levels of brain-derived neurotrophic factor (BDNF) in the pathogenesis of Huntington's disease. Mutant huntingtin (Htt) protein was previously reported to decrease BDNF gene transcription and axonal transport of BDNF. We recently showed that wild-type Htt is associated with the Argonaute 2 microRNA-processing enzyme involved in gene silencing. In dendrites, Htt co-localizes with components of neuronal granules and mRNAs, indicating that it might play a role in post-transcriptional processing/transport of dendritic mRNAs.

Results

We conducted imaging experiments in cultured cortical neurons to demonstrate the co-localization of endogenous Htt and BDNF mRNA in fixed cells, and co-trafficking of BDNF 3'UTR mRNA with endogenous and fluorescently tagged Htt in live neurons. We used an enhanced technique that combines FISH and immunofluorescent staining to co-localize BDNF mRNA with Htt, Ago2, CPEB and dynein in thick vibratome sections of the rat cortex.

Conclusions

In cultured neurons and sections of the rat cortex, we found BDNF mRNA associated with Htt and components of neuronal RNA granules, which are centers for regulating RNA transport and local translation. Htt may play a role in post-transcriptional transport/targeting of mRNA for BDNF, thus contributing to neurotrophic support and neuron survival.

Duplex in situ hybridization in the study of gene co-regulation in the vertebrate brain

We describe here a high-sensitivity in situ hybridization protocol, optimized for fresh-frozen brain sections, that enables the detection of two transcripts, at single cell resolution. Riboprobes directed against two mRNAs of interest are synthesized with nucleotides tagged with different haptens (digoxigenin- or biotin-UTP), via in vitro transcription, hybridized simultaneously to brain sections, and independently detected through immunocytochemistry. Sequential detection of each probe involves peroxidase-mediated precipitation of tyramide-linked fluorophores of separate emission wavelengths. In addition, we demonstrate how classic non-fluorescent chromogens, such as 3,3'-diaminobenzidine, can be successfully combined with fluorescence-based detection, to yield reliable detection of two transcript populations. We provide examples of representative results obtained with this protocol and describe necessary controls. Additionally, we discuss common problems associated with this methodology, and detail troubleshooting recommendations. Although this method has been optimized for brain sections, it may be useful to detect two mRNA species in a variety of tissues.

Anatomical and Functional Organization of Inhibitory Circuits in the Songbird Auditory Forebrain

Recent studies on the anatomical and functional organization of GABAergic networks in central auditory circuits of the zebra finch have highlighted the strong impact of inhibitory mechanisms on both the central encoding and processing of acoustic information in a vocal learning species. Most of this work has focused on the caudomedial nidopallium (NCM), a forebrain area postulated to be the songbird analogue of the mammalian auditory association cortex. NCM houses neurons with selective responses to conspecific songs and is a site thought to house auditory memories required for vocal learning and, likely, individual identification. Here we review our recent work on the anatomical distribution of GABAergic cells in NCM, their engagement in response to song and the roles for inhibitory transmission in the physiology of NCM at rest and during the processing of natural communication signals. GABAergic cells are highly abundant in the songbird auditory forebrain and account for nearly half of the overall neuronal population in NCM with a large fraction of these neurons activated by song in freely-behaving animals. GABAergic synapses provide considerable local, tonic inhibition to NCM neurons at rest and, during sound processing, may contain the spread of excitation away from un-activated or quiescent parts of the network. Finally, we review our work showing that GABAA-mediated inhibition directly regulates the temporal organization of song-driven responses in awake songbirds, and appears to enhance the reliability of auditory encoding in NCM.

Estradiol shapes auditory processing in the adult brain by regulating inhibitory transmission and plasticity-associated gene expression

Estradiol impacts a wide variety of brain processes, including sex differentiation, mood, and learning. Here we show that estradiol regulates auditory processing of acoustic signals in the vertebrate brain, more specifically in the caudomedial nidopallium (NCM), the songbird analog of the mammalian auditory association cortex. Multielectrode recordings coupled with local pharmacological manipulations in awake animals reveal that both exogenous and locally generated estradiol increase auditory-evoked activity in NCM. This enhancement in neuronal responses is mediated by suppression of local inhibitory transmission. Surprisingly, we also found that estradiol is both necessary and sufficient for the induction of multiple mitogen-activated protein kinase (MAPK)-dependent genes thought to be required for synaptic plasticity and memorization of birdsong. Specifically, we show that local blockade of estrogen receptors or aromatase activity in awake birds decrease song-induced MAPK-dependent gene expression. Infusions of estradiol in acoustically isolated birds induce transcriptional activation of these genes to levels comparable with song-stimulated animals. Our results reveal acute and rapid nongenomic functions for estradiol in central auditory physiology and suggest that such roles may be ubiquitously expressed across sensory systems.