Substantial performance discrepancies among commercially available kits for reverse transcription quantitative polymerase chain reaction: a systematic comparative investigator-driven approach

Reverse transcription followed by quantitative polymerase chain reaction (rt-qPCR) has become the state-of-the-art tool for quantification of nucleic acids. However, there are still significant problems associated with its sensitivity, reproducibility, and efficiency and the choice of an appropriate rt-qPCR kit. The purpose of this article is to give insights into strategies to optimize and validate the performance of currently available kits for rt-qPCR and to provide up-to-date information about the benefits, potentials, and pitfalls of rt-qPCR assays. A selection of 9 complementary DNA (cDNA) synthesis and 12 qPCR kits were tested using samples obtained from three species (mouse, rat, and human) and three transcripts (Gapdh, Actb, and Hmbs) under highly standardized conditions. Kits with outstanding performance were further analyzed to identify the dynamic range for a reliable quantification of messenger RNA (mRNA). Reverse transcription efficiency varied up to 90-fold depending on the choice of reverse transcriptase, priming strategy, and assay volume. The qPCR kit test revealed variations in mean relative amplification efficiency ranging from 54% to 171%. We conclude that currently available kits for rt-qPCR vary considerably. However, with an appropriate validation strategy and knowledge about capabilities of a particular kit, sensitivity, efficiency, and reliability could be improved significantly.

Downregulation of potassium chloride cotransporter KCC2 after transient focal cerebral ischemia

BACKGROUND AND PURPOSE

The potassium chloride cotransporter 2 (KCC2) is the main neuronal chloride extruder in the adult nervous system. Therefore, KCC2 is responsible for an inwardly directed electrochemical gradient of chloride that leads to hyperpolarizing GABA-mediated responses. Under some pathophysiological conditions, GABA has been reported to be depolarizing because of a downregulation of KCC2. This is the first study to our knowledge analyzing the expression of KCC2 after a focal cerebral ischemia.

METHODS

Mild and severe ischemia were induced in rats by a transient occlusion of the middle cerebral artery for 30 and 120 minutes, respectively. KCC2 mRNA and protein expression were studied in the ischemic hemisphere after different reperfusion times (2 hour, 1 day, 7 days, 30 days, 168 days) by using quantitative polymerase chain reaction, Western blotting, and immunohistological staining.

RESULTS

We found a substantial decrease of KCC2 mRNA and protein levels in the ischemic hemisphere, with a stronger downregulation of KCC2 after severe vs mild ischemia. Long-term surviving cells expressing KCC2 could be detected in the infarct core. These cells were identified as GABAergic interneurons mainly expressing parvalbumin.

CONCLUSIONS

Our study revealed a substantial neuron-specific downregulation of KCC2 after focal cerebral ischemia.

Adult and embryonic GAD transcripts are spatiotemporally regulated during postnatal development in the rat brain

Background

GABA (gamma-aminobutyric acid), the main inhibitory neurotransmitter in the brain, is synthesized by glutamic acid decarboxylase (GAD). GAD exists in two adult isoforms, GAD65 and GAD67. During embryonic brain development at least two additional transcripts exist, I-80 and I-86, which are distinguished by insertions of 80 or 86 bp into GAD67 mRNA, respectively. Though it was described that embryonic GAD67 transcripts are not detectable during adulthood there are evidences suggesting re-expression under certain pathological conditions in the adult brain. In the present study we systematically analyzed for the first time the spatiotemporal distribution of different GADs with emphasis on embryonic GAD67 mRNAs in the postnatal brain using highly sensitive methods.

Methodology/Principal Findings

QPCR was used to precisely investigate the postnatal expression level of GAD related mRNAs in cortex, hippocampus, cerebellum, and olfactory bulb of rats from P1 throughout adulthood. Within the first three postnatal weeks the expression of both GAD65 and GAD67 mRNAs reached adult levels in hippocampus, cortex, and cerebellum. The olfactory bulb showed by far the highest expression of GAD65 as well as GAD67 transcripts. Embryonic GAD67 splice variants were still detectable at birth. They continuously declined to barely detectable levels during postnatal development in all investigated regions with exception of a comparatively high expression in the olfactory bulb. Radioactive in situ hybridizations confirmed the occurrence of embryonic GAD67 transcripts in the olfactory bulb and furthermore detected their localization mainly in the subventricular zone and the rostral migratory stream.

Conclusions/Significance

Embryonic GAD67 transcripts can hardly be detected in the adult brain, except for specific regions associated with neurogenesis and high synaptic plasticity. Therefore a functional role in processes like proliferation, migration or synaptogenesis is suggested.

Loss of GABAergic neurons in the subiculum and its functional implications in temporal lobe epilepsy

Clinical and experimental evidence suggest that the subiculum plays an important role in the maintenance of temporal lobe seizures. Using the pilocarpine-model of temporal lobe epilepsy (TLE), the present study examines the vulnerability of GABAergic subicular interneurons to recurrent seizures and determines its functional implications. In the subiculum of pilocarpine-treated animals, the density of glutamic acid decarboxylase (GAD) mRNA-positive cells was reduced in all layers. Our data indicate a substantial loss of parvalbumin-immunoreactive neurons in the pyramidal cell and molecular layer whereas calretinin-immunoreactive cells were predominantly reduced in the molecular layer. Though the subiculum of pilocarpine-treated rats showed an increased intensity of GAD65 immunoreactivity, the density of GAD65 containing synaptic terminals in the pyramidal cell layer was decreased indicating an increase in the GAD65 intensity of surviving synaptic terminals. We observed a decrease in evoked inhibitory post-synaptic currents that mediate dendritic inhibition as well as a decline in the frequency of miniature inhibitory post-synaptic currents (mIPSCs) that are restricted to the perisomatic region. The decrease in mIPSC frequency (-30%) matched with the reduced number of perisomatic GAD-positive terminals (-28%) suggesting a decrease of pre-synaptic GABAergic input onto pyramidal cells in epileptic animals. Though cell loss in the subiculum has not been considered as a pathogenic factor in human and experimental TLE, our data suggest that the vulnerability of subicular GABAergic interneurons causes an input-specific disturbance of the subicular inhibitory system.

Up-regulation of Connexin43 in the glial scar following photothrombotic ischemic injury

Several types of CNS injury and various diseases are associated with the development of a glial scar. Astrocytes are major components of the glial scar. They are interconnected by gap junctions, with connexin43 (Cx43) being the most prominent channel protein. We applied a model of focal cerebral ischemia to study the spatio-temporal expression of glial fibrillary acidic protein, as well as of Cx43 mRNA and protein in gliotic tissue up to 60 days after injury. Reactive astrocytes enveloping the lesion up-regulated their Cx43 mRNA and protein. A band of reactive astrocytes filling in the lesion exhibited elevated Cx43 and showed a high degree of proliferation. Because of these findings, we hypothesize a role for Cx43 in glial scar formation, specifically in the proliferation of astrocytes.

Synaptic responses in superficial layers of medial entorhinal cortex from rats with kainate-induced epilepsy

Mesial temporal lobe epilepsy patients often display shrinkage of the entorhinal cortex, which has been attributed to neuronal loss in medial entorhinal cortex layer III (MEC-III). MEC-III neuronal loss is reproduced in chronic epileptic rats after kainate-induced (KA) status epilepticus. Here we examined, in vitro, functional changes in superficial entorhinal cortex layers. Alterations in superficial layer circuitry were suggested by showing that presubiculum, parasubiculum and deep MEC stimulation evoked 100-300 Hz field potential transients and prolonged EPSPs (superimposed on IPSPs) in superficial MEC which were partially blocked by APV (in contrast to control) and fully blocked by CNQX. Contrary to controls, bicuculline (5 and 30 microM) had minor effects on evoked field potentials in KA rats. GAD65/67 in situ hybridization revealed preserved interneurons in MEC-III. In conclusion, hyperexcitability in superficial MEC neurons is not due to loss of GABAergic interneurons and probably results from alterations in synaptic connectivity within superficial MEC.

Temporal profile of connexin 43 expression after photothrombotic lesion in rat brain

Following focal ischemic injury, several mechanisms lead to secondary expansion of the affected area and therefore increase the initial damage. We thoroughly investigated the expression of astrocytic connexin 43 (Cx43) after photothrombosis in rat brain. The temporal profile of Cx43 mRNA as well as protein expression was studied in remote, structurally uninjured cortical and hippocampal areas. The hippocampal formation revealed an increased number of Cx43 mRNA positive astrocytes and an up-regulated protein expression exclusively in the ipsilateral stratum oriens. We assume a participation of this region in glia scar formation. While Cx43 mRNA positive cells were transiently increased, immunoreactivity was reduced in the somatosensory cortex of injured hemispheres. The observed decrease of Cx43 protein in the post-ischemic cerebral cortex implies an impairment of gap junctional intercellular communication which might be detrimental to the brain.

The combined use of non-radioactive in situ hybridization and real-time RT-PCR to assess gene expression in cryosections

Gene expression changes in pathophysiological states can be spatiotemporally monitored by in situ hybridization and reliably quantified by real-time RT-PCR. Here we developed a new method whereby adjacent slides of frozen sections can be used for gene expression analysis by in situ hybridization and real-time RT-PCR. We applied this method to assess the mRNA expression of connexin 43 (Cx43), the major astrocytic connexin, after kainate-induced seizures in rat hippocampus. Gap junction-building connexins play a role in the pathogenesis of several diseases of the brain, including epilepsy. The number of Cx43 mRNA-positive cells in the hippocampus of kainate-treated and control rats was automatically quantified by computerized image analysis of brain sections hybridized with DIG-labeled RNA probes. In parallel, real-time RT-PCR was used to examine the relative Cx43 mRNA levels in hippocampal tissue from adjacent brain sections. Applying these two very sensitive methods we showed that kainate induced seizures do not affect hippocampal connexin 43 mRNA expression.

Value of fat-suppressed proton-density-weighted turbo spin-echo sequences in detecting meniscal lesions: comparison with arthroscopy

PURPOSE

To evaluate fat-suppressed (FS) proton-density-weighted (PDw) turbo spin-echo (TSE) magnetic resonance imaging (MRI) compared to arthroscopy in the detection of meniscal lesions.

MATERIAL AND METHODS

In a prospective study, 31 knee joints were imaged on a 1.5T MR scanner before arthroscopy using the following sequences: (a) coronal and sagittal FS-PDw TSE (TR/TE: 4009/15 ms); (b) coronal T1w SE (TR/TE: 722/20 ms), and sagittal PDw TSE (TR/TE: 3800/15 ms). Other imaging parameters were: slice thickness 3 mm, FOV 160 mm, matrix 256 x 256. A total of 186 meniscal regions (62 menisci; anterior horn, body, posterior horn) were evaluated. Standard of reference was arthroscopy. Sensitivity, specificity, negative predictive value (npv), positive predictive value (ppv), and accuracy were calculated.

RESULTS

Arthroscopically, meniscal lesions were detected in 55/186 segments (35 medial and 20 lateral meniscal lesions). Sensitivity, specificity, npv, ppv, and accuracy for combination of coronal and sagittal FS PDw TSE were 91.4%, 98.3%, 95%, 97%, and 93.5% for the medial meniscus, and 90%, 98.6%, 97.3%, 94.7%, and 96.8% for the lateral. The results were comparable to the combination of coronal T1w SE and sagittal PDw TSE for the medial (88.6%, 98.3%, 93.4%, 96.9%, 91.4%) and the lateral (90%, 95.9%, 97.2%, 85.7%, 92.5%) meniscus.

CONCLUSION

FS PDw TSE-MR sequences are an excellent alternative for the detection of meniscal lesions in comparison with diagnostic arthroscopy.

Evidence that errors made by DNA polymerase alpha are corrected by DNA polymerase delta

Eukaryotic replication begins at origins and on the lagging strand with RNA-primed DNA synthesis of a few nucleotides by polymerase alpha, which lacks proofreading activity. A polymerase switch then allows chain elongation by proofreading-proficient pol delta and pol epsilon. Pol delta and pol epsilon are essential, but their roles in replication are not yet completely defined . Here, we investigate their roles by using yeast pol alpha with a Leu868Met substitution . L868M pol alpha copies DNA in vitro with normal activity and processivity but with reduced fidelity. In vivo, the pol1-L868M allele confers a mutator phenotype. This mutator phenotype is strongly increased upon inactivation of the 3' exonuclease of pol delta but not that of pol epsilon. Several nonexclusive explanations are considered, including the hypothesis that the 3' exonuclease of pol delta proofreads errors generated by pol alpha during initiation of Okazaki fragments. Given that eukaryotes encode specialized, proofreading-deficient polymerases with even lower fidelity than pol alpha, such intermolecular proofreading could be relevant to several DNA transactions that control genome stability.

Stable expression of the vesicular GABA transporter following photothrombotic infarct in rat brain

Before exocytotic release of the inhibitory neurotransmitter GABA, this amino acid has to be stored in synaptic vesicles. Accumulation of GABA in vesicles is achieved by a specific membrane-integrated transporter termed vesicular GABA transporter. This vesicular protein is mainly located at presynaptic terminals of GABAergic interneurons. In the present study we investigated the effects of focal ischemia on the expression of the vesicular GABA transporter. Vesicular GABA transporter mRNA and protein expression was examined after photothrombosis in different cortical and hippocampal brain regions of Wistar rats. In situ hybridization and quantitative real-time RT-PCR were performed to analyze vesicular GABA transporter mRNA. Both vesicular GABA transporter mRNA-stained perikarya and mRNA expression levels remained unaffected. Vesicular GABA transporter protein-containing synaptic terminals and somata were visualized by immunohistochemistry. The pattern of vesicular GABA transporter immunoreactivity as well as the protein expression level revealed by semiquantitative image analysis and by Western blot remained stable after stroke. The steady expression of vesicular GABA transporter mRNA and protein after photothrombosis indicates that the exocytotic release mechanism of GABA is not affected by ischemia.

Regulation of GABA transporter mRNA and protein after photothrombotic infarct in rat brain

Animal models of focal ischemic infarcts reveal an impaired GABAergic (gamma-aminobutyric acid) neurotransmission. GABA, the main inhibitory neurotransmitter, is primarily taken up by specific sodium-dependent transporters. As these transporters play a crucial role in maintaining levels of GABA concentration, they may be functionally involved in ischemic processes. We investigated whether the mRNA and protein expression of GAT-1, the dominant neuronal GABA transporter, is altered after cortical infarct induced by photothrombosis in Wistar rats. In situ hybridization was performed to analyze GAT-1 mRNA-positive cells in cortical brain regions and the hippocampus. The lesion dramatically raised the number of GABA transporter mRNA-expressing cells in all investigated cortical regions. Double-labeling studies with a general neuronal marker and a marker for astrocytes revealed that cells expressing GAT-1 mRNA after photothrombosis are neurons. The mRNA expression pattern of all hippocampal subfields remained unchanged. In contrast, cortical GAT-1 protein density was only slightly affected and surprisingly in the opposite way. In the primary and secondary somatosensory cortex, density values were significantly reduced. Immunoreactivity was not altered in all investigated hippocampal areas. We found a marked discordance between the increased number of cells expressing GAT-1 mRNA in the cortex and the reduced tissue GAT-1 protein content. Focal brain ischemia obviously triggers mechanisms that interfere with GAT-1 transcriptional regulation and protein synthesis or turnover.

Ionotropic GABA receptors with mixed pharmacological properties of GABAA and GABAC receptors

Ionotropic gamma-aminobutyric acid (GABA) receptors form a large family of molecular isoforms with distinct properties. We have characterized a distinct new type of GABA receptors in CA1 pyramidal cells in rat hippocampal slices. Somatic application of GABA induced currents which were partially suppressed by (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid (TPMPA), a specific antagonist of GABA(C) receptors. This sensitivity was enhanced when we evoked the currents by the GABA(C) receptor agonist cis-4-aminocrotonic acid (CACA). However, both GABA- and CACA-evoked currents were sensitive towards bicuculline and thus lack the defining feature of GABA(C) receptors, which are insensitive towards this antagonist. Spontaneous miniature post-synaptic currents (mIPSCs) revealed a similar pharmacological behaviour. We conclude that juvenile CA1 pyramidal cells express a fraction of ionotropic GABA receptors with mixed pharmacological properties of both, GABA(A) and GABA(C) receptors.

GABA neurons survive focal ischemic injury

Focal cerebral lesions in rat brain induced by photothrombosis lead to an impaired inhibitory neurotransmission. A reduced gamma-aminobutyric acid (GABA)-mediated inhibition has been revealed by electrophysiological recordings associated with a diminished immunostaining of GABA handling proteins. Changes were found in ipsi- as well as in contralateral brain areas. Inhibition is mediated by interneurons using GABA as neurotransmitter. These cells use GAD (glutamate decarboxylase) to synthesize GABA. To analyze the vulnerability of GABAergic neurons in rats with a lesioned hindlimb area, cells expressing GAD65/67 mRNA were labeled using in situ hybridization. Positive somata were counted 7 and 30 days after focal ischemia in different cortical (hindlimb cortex, frontal cortex, primary and secondary somatosensory cortex) and hippocampal subsectors (pyramidal cell layer, stratum oriens and stratum radiatum/lacunosum-moleculare). The lesioned hemispheres were compared with the intact brain sides and with control brains. GABAergic interneurons survived the injury for up to 30 days in all investigated brain regions. Therefore it is unlikely that a loss of GABAergic neurons contributes to the reduced inhibition.

Unaltered control of extracellular GABA-concentration through GAT-1 in the hippocampus of rats after pilocarpine-induced status epilepticus

The uptake of the inhibitory transmitter GABA (gamma-aminobutyric acid) limits the efficacy of synaptic and tonic inhibition in brain tissue. It has been reported that GABA-uptake is down-regulated in temporal lobe epilepsy. This down-regulation may increase the inhibitory action of GABA but may also limit the anticonvulsant activity of GABA-uptake blockers. We have directly compared the function of GABA-uptake in hippocampal slices from normal and chronically epileptic rats. We raised the global extracellular concentration of GABA by bath-application of the agonist in the absence and presence of the GABA-uptake blocker tiagabine. GABA-induced currents were measured in dentate granule cells and CA1 pyramidal neurons in hippocampal slices. The potentiation of currents by tiagabine was taken as a measure for the efficacy of GABA-uptake in the hippocampal tissue. There was no difference between cells from control- or pilocarpine-treated animals in the response to GABA or in the conductance increase following application of tiagabine. Our data show that in the chronic phase of the pilocarpine-model GABA-uptake maintains its ability to control the extracellular background concentration of GABA.

Gadobutrol: an alternative contrast agent for digital subtraction dacryocystography

We report the application of gadobutrol as a contrast medium for digital subtraction dacryocystography (DS-DCG) in patients with known allergy to iodinated contrast agent. Gadobutrol has the double gadolinium concentration (1.0 mmol/ml) of other gadolinium-based contrast agents. Quality of the DS-DCG images obtained with gadobutrol was comparable to DS-DCG images obtained with iodinated contrast medium. Radiodensity measurements using a micro-CT scanner confirmed a high radiodensity of gadobutrol which was comparable to the radiodensity of iopentol with a iodine concentration of 250 mg/ml and only approximately 20% lower than the radiodensity of iopentol with a concentration of 300 mg/l. Gadobutrol is a well-suited substitute for DS-DCG in patients with allergy to iodinated contrast agents.

[Early results with a monorail-stent-balloon device for endovascular treatment of renal artery stenosis]

OBJECTIVE

To evaluate the technical feasibility of a new monorail-stent-balloon device for treatment of renal artery stenosis (RAS).

PATIENTS AND METHODS

During a study period of 18 months, 38 patients with proven RAS in 41 cases (hypertension n = 36, renal insufficiency n = 13) and indication for stenting (calicified ostial lesions n = 35, insufficient PTA n = 4, dissection n = 2) were enrolled into this prospective evaluation. Pre-mounted stents (Rx-Herculink(TM) 5 mm = 13, 6 mm = 34, 7 mm = 1) were implanted a transfemoral (n = 35) or transbrachial approach (n = 6). Mean grade and lengths of stenosis measured were 88 % plus minus 10 and 9 mm plus minus 5.

RESULTS

Renal stent implantation was technically successful in all cases (100 %). In 7 cases a second stent had to be implanted to cover the entire lesion. The transstenotic pressure drop decreased from 88 mmHg plus minus 10 before to 1 mmHg plus minus 1.8 after the procedure. Remaining stenosis measured 0.7 % plus minus 4.2. Serum creatine levels decreased from 1.9 mm/dl to 1.5 mg/dl (n. s.), blood pressure decreased from 178/94 mmHg to 148/79 mmHg (p < 0.0001) after the intervention. Primary and secondary patency rates at 6 months were 72 % (Standard Error 9.8 %) and 77 (% (Standard Error 9.2 %), respectively.

CONCLUSION

With the used monorail-stend-balloon device a technically easy, secure and exact renal stent placement is guaranteed, patency rates are similar to those described in the current literature.

GAD and GABA transporter (GAT-1) mRNA expression in the developing rat hippocampus

Synaptic inhibition in the mammalian central nervous system is mostly mediated by GABA (gamma-aminobutyric acid). Inhibitory interneurons can be identified by staining for glutamate decarboxylase (GAD), the key enzyme which produces the transmitter. After release, GABA is removed from the extracellular space by specific transporters which are localized at the presynaptic endings of interneurons, in adjacent glial processes and, possibly, also in the postsynaptic target cell membranes. The GABAergic system undergoes profound functional and structural changes during the first 2 weeks of postnatal development, including migration of interneurons and changes in the level of expression and subcellular distribution of GABA transporters. We therefore analyzed the distribution of mRNA coding for GAD and GAT-1 (the main neuronal GABA transporter) in the developing rat hippocampus. Our data show that both transcripts are present in putative interneurons from the first postnatal day and exhibit a largely similar distribution throughout postnatal ontogenesis, with some specific differences in certain hippocampal subfields. Quantification of stained somata confirmed the postnatal redistribution of putative interneurons in the area dentata from dendritic layers towards the hilus. We also found a general staining of principal cell layers for both probes, which differs with postnatal age and between GAD and GAT-1 mRNA. Together, our data reveal a profound reorganization of the GABAergic system in the rat hippocampus during the first weeks of postnatal development.

Uncommon presentation of a giant biliary cystadenoma: correlation between MRI and pathologic findings

An uncommon case of a giant mucinous biliary cystadenoma (BCA) of the liver is described. On T2-weighted and STIR images, a large hyperintense cystic mass revealed some septations and multiple intracystic masses of similar size and shape and uniform signal intensity, which was isointense to liver parenchyma. On T1-weighted images, intracystic bodies were obscured and the cyst was hyperintense. The magnetic resonance (MR) appearance of intracystic fluid and structures was not due to mucinous or proteinous or hyperproteinous material, but corresponded to clots floating within hemorrhagic fluid.