Imaging Transcription: Past, Present, and Future

Transcription, the first step of gene expression, is exquisitely regulated in higher eukaryotes to ensure correct development and homeostasis. Traditional biochemical, genetic, and genomic approaches have proved successful at identifying factors, regulatory sequences, and potential pathways that modulate transcription. However, they typically only provide snapshots or population averages of the highly dynamic, stochastic biochemical processes involved in transcriptional regulation. Single-molecule live-cell imaging has, therefore, emerged as a complementary approach capable of circumventing these limitations. By observing sequences of molecular events in real time as they occur in their native context, imaging has the power to derive cause-and-effect relationships and quantitative kinetics to build predictive models of transcription. Ongoing progress in fluorescence imaging technology has brought new microscopes and labeling technologies that now make it possible to visualize and quantify the transcription process with single-molecule resolution in living cells and animals. Here we provide an overview of the evolution and current state of transcription imaging technologies. We discuss some of the important concepts they uncovered and present possible future developments that might solve long-standing questions in transcriptional regulation.

Human-based systems in drug and chemical safety testing--toward replacement, the 'single R'

The Three Rs was a concept originally conceived as a means of reducing the suffering of laboratory animals that are used largely in identifying any potential safety issues with chemicals to which humans may be exposed. However, with growing evidence of the shortcomings of laboratory animal testing to reliably predict human responsiveness to such chemicals, questions are now being asked as to whether it is appropriate to use animals as human surrogates at all. This raises the question of whether, of the original Three Rs, two--Reduction and Refinement--are potentially redundant, and whether, instead, we should concentrate on the third R: Replacement. And if this is the best way forward, it is inevitable that this R should be based firmly on human biology. The present review outlines the current state-of-the-art regarding our access to human biology through in vitro, in silico and in vivo technologies, identifying strengths, weaknesses and opportunities, and goes on to address the prospect of achieving a single R, with some suggestions as to how to progress toward this goal.

A Review of Transplantation Practice of the Urologic Organs: Is It Only Achievable for the Kidney?

Transplantation is a viable treatment option for failure of most major organs. Within urology, transplantation of the kidney and ureter are well documented; however, evidence supporting transplantation of other urologic organs is limited. Failure of these organs carries significant morbidity, and transplantation may have a role in management. This article reviews the knowledge, research, and literature surrounding transplantation of each of the urologic organs. Transplantation of the penis, testicle, urethra, vas deferens, and bladder is discussed. Transplantation attempts have been made individually with each of these organs. Penile transplantation has only been performed once in a human. Testicular transplantation research was intertwined with unethical lucrative pursuits. Interest in urethra, bladder, and vas deferens transplantation has decreased as a result of successful surgical reconstructive techniques. Despite years of effort, transplantations of the penis, testicle, urethra, vas deferens, and bladder are not established in current practice. Recent research has shifted toward techniques of reconstruction, tissue engineering, and regenerative medicine.

Spinal cord dopamine D2/D3 receptors: in vivo and ex vivo imaging in the rat using (18)F/(11)C-fallypride

OBJECTIVES

The spinal cord is known to be innervated with dopaminergic cells with catecholaminergic projections arising from the medulla and pons and dopaminergic transmission in the spinal cord is vital for sensory and motor function. Our goal was to evaluate and compare the imaging capability of dopamine D2/D3 receptors in the rat spinal cord using PET ligands (18)F-fallypride and (11)C-fallypride.

METHODS

Male Sprague-Dawley rats were used in all in vitro and in vivo studies. Spinal cord and brain sections were used for in vitro autoradiography and ex vivo autoradiography. For in vivo studies animals received a (18)F-fallypride scan or a (11)C-fallypride PET scan. The spinal cord and the brain were then harvested, flash-frozen and imaged ex vivo. For in vivo analysis Logan plots with cerebellum as a reference was used to evaluate binding potentials (BP). Tissue ratios were used for ex vivo analysis. Drug effects were evaluated using clozapine, haloperidol and dopamine were evaluated on spinal cord sections in vitro.

RESULTS

In vitro studies showed (18)F-fallypride binding to superficial dorsal horn (SDH), dorsal horn (DH), ventral horn (VH) and the pars centralis (PC). In the cervical section, the greatest amount of binding appeared to be in the SDH. Ex vivo studies showed approximately 6% of (18)F-fallypride in SDH compared to that observed in the striatum. In vivo analysis of both (18)F-fallypride and (11)C-fallypride in the spinal cord were comparable to that in the extrastriatal regions. Haloperidol and clozapine displaced more than 75% of the (18)F-fallypride in spinal cord sections.

CONCLUSIONS

Our studies showed (18)F-fallypride and (11)C-fallypride binding in the spinal cord in vitro and in vivo. The binding pattern correlates well with the known distribution of dopamine D2/D3 receptors in the spinal cord.

Evaluation of serotonin 5-HT(1A) receptors in rodent models using [¹⁸F]mefway PET

INTRODUCTION

Serotonin 5-HT(1A) receptors have been investigated in various CNS disorders, including epilepsy, mood disorders, and neurodegeneration. [¹⁸F]Mefway (N-{2-[4-(2'-methoxyphenyl)piperazinyl]ethyl}-N-(2-pyridyl)-N-(cis/trans-4'-[¹⁸F]fluoromethylcyclohexane)-carboxamide) has been developed as a suitable positron emission tomography (PET) imaging agent for these receptors. We have now evaluated the suitability of [¹⁸F]trans-mefway in rat and mouse models using PET and computerized tomography (CT) imaging and corroborated with ex vivo and in vitro autoradiographic studies.

METHODS

Normal Sprague-Dawley rats and Balb/C mice were used for PET/CT imaging using intravenously injected [¹⁸F]trans-mefway. Brain PET data were coregistered with rat and mouse magnetic resonance imaging template and regional distribution of radioactivity was quantitated. Selected animals were used for ex vivo autoradiographic studies to confirm regional brain distribution and quantitative measures of binding, using brain region to cerebellum ratios. Binding affinity of trans-mefway and WAY-100635 was measured in rat brain homogenates. Distribution of [¹⁸F]trans-4-fluoromethylcyclohexane carboxylate ([¹⁸F]FMCHA), a major metabolite of [¹⁸F] trans-mefway, was assessed in the rat by PET/CT.

RESULTS

The inhibition constant, K(i) for trans-mefway was 0.84 nM and that for WAY-100635 was 1.07 nM. Rapid brain uptake of [¹⁸F]trans-mefway was observed in all rat brain regions and clearance from cerebellum was fast and was used as a reference region in all studies. Distribution of [¹⁸F]trans-mefway in various brain regions was consistent in PET and in vitro studies. The dorsal raphe was visualized and quantified in the rat PET but identification in the mouse was difficult. The rank order of binding to the various brain regions was hippocampus > frontal cortex > anterior cingulate cortex > lateral septal nuclei > dorsal raphe nuclei.

CONCLUSION

[¹⁸F]trans-Mefway appears to be an effective 5-HT(1A) receptor imaging agent in rodents for studies of various disease models.

Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae)

Genetic markers are widely used to define and manage populations of threatened species based on the notion that populations with unique lineages of mtDNA and well-differentiated nuclear marker frequencies should be treated separately. However, a danger of this approach is that genetic uniqueness might be emphasized at the cost of genetic diversity, which is essential for adaptation and is potentially boosted by mixing geographically separate populations. Here, we re-explore the issue of defining management units, focussing on a detailed study of Galaxiella pusilla, a small freshwater fish of national conservation significance in Australia. Using a combination of microsatellite and mitochondrial markers, 51 populations across the species range were surveyed for genetic structure and diversity. We found an inverse relationship between genetic differentiation and genetic diversity, highlighting a long-term risk of deliberate isolation of G. pusilla populations based on protection of unique lineages. Instead, we adopt a method for identifying genetic management units that takes into consideration both uniqueness and genetic variation. This produced a management framework to guide future translocation and re-introduction efforts for G. pusilla, which contrasted to the framework based on a more traditional approach that may overlook important genetic variation in populations.

Effects of zinc on microalgal biofilms in intertidal and subtidal habitats

Microalgal biofilms are sensitive to environmental conditions. Impacts of contaminants on assemblages of marine biofilm are often investigated in laboratories or in mesocosms. Such experiments are rarely representative of the effects of contaminants on biofilms under natural conditions. Studies in field situations, with enough power to detect impacts, are necessary to develop a better understanding of the effects of contaminants on ecological processes. Metals are a common contaminant of marine systems and can cause disturbances to assemblages. Using a new technique to experimentally deliver contaminants to microalgal assemblages, hypotheses were tested regarding the effects of zinc on microalgal biofilms growing on settlement panels in subtidal and intertidal habitats. PAM fluorometry was used to assess the amount and physiological state of biofilms on panels. Control panels deployed for 1 month in each habitat had significantly greater amounts of biofilm than those exposed to zinc. After deployment for 3 months, the results varied with location. The observed effects on the biofilm did not, however, cause significant changes in the macro-invertebrate assemblages that developed on the panels.

Human tissue in the evaluation of safety and efficacy of new medicines: a viable alternative to animal models?

The pharma Industry's ability to develop safe and effective new drugs to market is in serious decline. Arguably, a major contributor to this is the Industry's extensive reliance on nonhuman biology-based test methods to determine potential safety and efficacy, objective analysis of which reveals poor predictive value. An obvious alternative approach is to use human-based tests, but only if they are available, practical, and effective. While in vivo (phase 0 microdosing with high sensitivity mass spectroscopy) and in silico (using established human biological data), technologies are increasingly being used, in vitro human approaches are more rarely employed. However, not only are increasingly sophisticated in vitro test methods now available or under development, but the basic ethically approved infrastructure through which human cells and tissues may be acquired is established. Along with clinical microdosing and in silico approaches, more effective access to and use of human cells and tissues in vitro provide exciting and potentially more effective opportunities for the assessment of safety and efficacy of new medicines.

A human approach to drug development: opportunities and limitations

The pharmaceutical industry is failing in its primary function, with increasing expenditure and decreased output in terms of new medicines brought to market. It cannot carry on as it is, without sliding into a terminal decline. It must, therefore, take some positive steps toward addressing its problems. We do not have to look far to see one very obvious problem, namely, the industry's continuing reliance on nonhuman biology as the basis of its evaluation of potential safety and efficacy. The time has come to focus on the relevant, and to realise that more human-based testing is essential, if the industry is to survive as a source of innovation in drug therapy. This can incorporate earlier clinical testing, in the form of microdosing, and promotion of the development of more-powerful computational approaches based on human information. Fortunately, headway is being made in both approaches. However, a problem remains in the lack of functional evaluation of human tissues, where the lack of commitment, and the inadequacy of the tissue resource itself, are hampering any serious developments. An outline of a collaborative scheme is proposed, that will address this issue, central to which is improved access to research tissues from heart-beating organ donors.

Striatal and extrastriatal microPET imaging of D2/D3 dopamine receptors in rat brain with [¹⁸F]fallypride and [¹⁸F]desmethoxyfallypride

In this study, we compared two different D(2/3) receptor ligands, [¹⁸F]fallypride and [¹⁸F]desmethoxyfallypride ([¹⁸F]DMFP) with respect to the duration of the scan, visualization of extrastriatal receptors, and binding potentials (BP(ND) ) in the rat brain. In addition, we studied the feasibility of using these tracers following a period of awake tracer uptake, during which the animal may perform a behavioral task. Male Sprague-Dawley rats were imaged with [¹⁸F]fallypride and with [¹⁸F]DMFP in four different studies using microPET. All scans were performed under isoflurane anesthesia. The first (test) and second (retest) study were 150-min baseline scans. No retest scans were performed with [¹⁸F]DMFP. A third study was a 60-min awake uptake of radiotracer followed by a 90-min scan. A fourth study was a 150-min competition scan with haloperidol (0.2 mg/kg) administered via tail vein at 90-min post-[¹⁸F]fallypride injection and 60-min post-[¹⁸F]DMFP. For the test-retest studies, BP(ND) was measured using both Logan noninvasive (LNI) method and the interval ratios (ITR) method. Cerebellum was used as a reference region. For the third study, the binding was measured only with the ITR method, and the results were compared to the baseline results. Studies showed that the average transient equilibrium time in the dorsal striatum (DSTR) was at 90 min for [¹⁸F]fallypride and 30 min for [¹⁸F]DMFP. The average BP(ND) for [¹⁸F]fallypride was 14.4 in DSTR, 6.8 in ventral striatum (VSTR), 1.3 in substantia nigra/ventral tegmental area (SN/VTA), 1.4 in colliculi (COL), and 1.5 in central gray area. In the case of [¹⁸F]DMFP, the average BP(ND) values were 2.2 in DSTR, 2.7 in VSTR, and 0.8 in SN/VTA. The haloperidol blockade showed detectable decrease in binding of both tracers in striatal regions with a faster displacement of [¹⁸F]DMFP. No significant changes in BP(ND) of [¹⁸F]fallypride due to the initial awake state of the animal were found, whereas BP(ND) of [¹⁸F]DMFP was significantly higher in the awake state compared to baseline. We were able to demonstrate that dynamic PET using MicroPET Inveon allows quantification of both striatal and extrastriatal [¹⁸F]fallypride binding in rats in vivo. Quantification of the striatal regions could be achieved with [¹⁸F]DMFP.

Immunocytochemical localization of phytochrome

An immunocytochemical assay, which localizes phytochrome in situ, indicates that this plant chromoprotein is associated with both nuclei and plastids, in addition to the cytoplasm. In an etiolated oat shoot, phytochrome is most abundant just behind the apex of the coleoptile, where it is associated with parenchyma cells; it is apparently absent at the extreme apx of the coleoptile. Further back from the tip, phytochrome is found in the epidermal cells of the coleoptile; it decreases in concentration toward the node, where it is again abundant. Phytochrome is also abundant in the extreme apical cells of young adventitious roots and in association with the procambium of the mesocotyl.

On the mechanism of the persistent action of salmeterol: what is the current position?

The mechanism of the long duration of action of salmeterol at beta(2)-adrenoceptors has long been a matter of debate, and is still unresolved. Szczuka and colleagues have both summarized the position to date and suggested a new mechanistic contender, receptor rebinding. Despite this, they still do not come to any clear conclusion. Much of the literature data that they have drawn upon appears contradictory, and mathematical models are inevitably flawed by the questionable validity of key values applied to them. Although the issue will undoubtedly eventually be resolved, it will probably require investigators to apply carefully designed studies on simple experimental systems such as isolated membranes or cultured cells. Only then should studies be extended to more complex systems such as isolated preparations of airways smooth muscle, where tissue bulk inevitably presents a complicating factor, particularly where relatively lipophilic compounds are concerned.

Urethral duplication: cases of ventral and dorsal complete duplication and review of the literature

Urethral duplication is a rare congenital anomaly, with multiple described anatomical variants. Duplications in the sagittal plane can be complete or partial, dorsal or ventral, and may be associated with other congenital urogenital anomalies. The anatomy of the duplication should be defined, and the functional urethra identified prior to any corrective surgical intervention. Correction aims to restore normal cosmesis, provide functional voiding and maintain continence. We describe two cases of urethral duplication in the sagittal plane, outline our approach to surgical correction, and review the literature.

Drug discovery and development tomorrow -- changing the mindset

Today's drug discovery and development paradigm is not working, and something needs to be done about it. There is good reason to believe that a move away from reliance on animal surrogates for human subjects in the Pharma Industry's R&D programmes could provide an important step forward. However, no serious move will be made in that direction until there is some hard evidence that it will be rewarded with improved productivity outcomes. The Safer Medicines Trust are proposing that a study be undertaken, involving a range of drugs that have been approved for human use, but have subsequently proved to have limitations in terms of safety and/or efficacy. The aim is to determine the efficiency of a battery of human-based test methods to identify a compound's safety and efficacy profiles, and to compare this with that of the more traditional, largely animal-based methods that were employed in their original development. Should such an approach prove more reliable, the authorities will be faced with important decisions relating to the role of human biological test data in regulatory submissions, while the Pharma Industry will be faced with the key logistical issue of how to acquire the human biomaterials necessary to make possible the routine application of such test methods.

Structures of three distinct activator-TFIID complexes

Sequence-specific DNA-binding activators, key regulators of gene expression, stimulate transcription in part by targeting the core promoter recognition TFIID complex and aiding in its recruitment to promoter DNA. Although it has been established that activators can interact with multiple components of TFIID, it is unknown whether common or distinct surfaces within TFIID are targeted by activators and what changes if any in the structure of TFIID may occur upon binding activators. As a first step toward structurally dissecting activator/TFIID interactions, we determined the three-dimensional structures of TFIID bound to three distinct activators (i.e., the tumor suppressor p53 protein, glutamine-rich Sp1 and the oncoprotein c-Jun) and compared their structures as determined by electron microscopy and single-particle reconstruction. By a combination of EM and biochemical mapping analysis, our results uncover distinct contact regions within TFIID bound by each activator. Unlike the coactivator CRSP/Mediator complex that undergoes drastic and global structural changes upon activator binding, instead, a rather confined set of local conserved structural changes were observed when each activator binds holo-TFIID. These results suggest that activator contact may induce unique structural features of TFIID, thus providing nanoscale information on activator-dependent TFIID assembly and transcription initiation.

BGC20-1531, a novel, potent and selective prostanoid EP receptor antagonist: a putative new treatment for migraine headache

BACKGROUND AND PURPOSE

Prostanoid EP(4) receptor antagonists may have therapeutic utility in the treatment of migraine since EP(4) receptors have been shown to be involved in prostaglandin (PG)E(2)-induced cerebral vascular dilatation, which may be an important contributor to migraine pain. This study reports the pharmacological characterization of BGC20-1531, a novel EP(4) receptor antagonist.

EXPERIMENTAL APPROACH

BGC20-1531 was characterized in radioligand binding and in vitro functional assays employing recombinant and native EP(4) receptors. Changes in canine carotid haemodynamics were used to assess the pharmacodynamic profile of BGC20-1531 in vivo.

KEY RESULTS

BGC20-1531 exhibited high affinity at recombinant human EP(4) receptors expressed in cell lines (pK(B) 7.6) and native EP(4) receptors in human cerebral and meningeal artery (pK(B) 7.6-7.8) but showed no appreciable affinity at a wide range of other receptors (including other prostanoid receptors), channels, transporters and enzymes (pKi < 5). BGC20-1531 competitively antagonized PGE(2)-induced vasodilatation of human middle cerebral (pK(B) 7.8) and meningeal (pK(B) 7.6) arteries in vitro, but had no effect on responses induced by PGE(2) on coronary, pulmonary or renal arteries in vitro. BGC20-1531 (1-10 mg.kg(-1) i.v.) caused a dose-dependent antagonism of the PGE(2)-induced increase in canine carotid blood flow in vivo.

CONCLUSIONS AND IMPLICATIONS

BGC20-1531 is a potent and selective antagonist at EP(4) receptors in vitro and in vivo, with the potential to alleviate the symptoms of migraine that result from cerebral vasodilatation. BGC20-1531 is currently in clinical development for the treatment of migraine headache.

Relationship Between Bicarbonate Retention and Bone Characteristics in Broiler Chickens

Determination of the bicarbonate retention factor (BRF) is an important step during development of the indicator amino acid oxidation technique for use in a new model. A series of 4-h oxidation experiments were performed to determine the BRF of broilers aged 7, 14, 21, 28, 35, and 42 d using 4 birds per age group. A priming dose of 1.2 microCi of NaH(14)CO(3), followed by eight half-hourly doses of 1 microCi of NaH(14)CO(3) were given orally to each of 4 birds per age. The percentage of (14)C dose expired by the bird at a steady state was measured. These birds, as well as 12 additional birds matched for age and BW, were killed, and femur bone mineral density was measured by quantitative computed tomography to determine the relationship between bone development and bicarbonate retention at each age. There was a correlation (r = 0.50; P < 0.05) between total cross-sectional femur bone mineral density and bicarbonate retention at each age. A prediction equation (Y = 6.95 x 10(-2)X - 3.51 x 10(-5)X(2) + 27.58; P < 0.0001, R(2) = 0.79) where Y = bicarbonate retention and X = BW was generated to predict Y as a function of X. Bicarbonate retention values peaked at 28 d, during the stage of the most rapid bone deposition and the highest growth rate. A constant BRF was found from 1,900 to 2,700 g of BW of 35.15 +/- 1.095% (mean +/- SEM). This retention factor will allow the accurate correction of oxidation of (14)C-labeled substrates in broilers of different ages and BW in future indicator amino acid oxidation studies.

GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues

Quantitative gene expression data are often normalized to the expression levels of control or so-called “housekeeping” genes. An inherent assumption in the use of housekeeping genes is that expression of the genes remains constant in the cells or tissues under investigation. Although exceptions to this assumption are well documented, housekeeping genes are of value in fully characterized systems. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the most commonly used housekeeping genes used in comparisons of gene expression data. To investigate the value of GAPDH as a housekeeping gene in human tissues, the expression of GAPDH mRNA was measured in a panel of 72 different pathologically normal human tissue types. Measurements were obtained from 371,088 multiplexed, quantitative real-time RT-PCRs with specific target genes. Significant differences in the expression levels of GAPDH mRNA were observed between tissue types and between donors of the same tissue. A 15-fold difference in GAPDH mRNA copy numbers was observed between the highest and lowest expressing tissue types, skeletal muscle and breast, respectively. No specific effect of either age or gender was observed on GAPDH mRNA expression. These data provide an extensive analysis of GAPDH mRNA expression in human tissues and confirm previous reports of the marked variability of GAPDH expression between tissue types. These data establish comparative levels of expression and can be used to add value to gene expression data in which GAPDH is used as the internal control.

Expression and Functions of the Duodenal Peptide Secretin and its Receptor in Human Lung

The physiological role of the duodenal peptide secretin is as a potent stimulant of electrolyte and water movement in pancreatic and biliary epithelium, via activation of G protein-coupled secretin receptors (hSCTR). However, the distribution and potential function of hSCTR in human lung has not previously been addressed. Using real-time quantitative reverse transcriptase-polymerase chain reaction profiling, in situ hybridization, and immunohistochemistry, we demonstrated that the hSCTR is abundantly expressed within the distal regions of human lung (tertiary bronchus and parenchyma), with negligible expression detected in more proximal regions (trachea, primary, and secondary bronchus). Expression was observed predominantly on the basolateral membrane of the bronchial epithelial layer, with some expression also observed in bronchial smooth muscle. In primary cultures of human tertiary bronchial epithelial cells, secretin was demonstrated to potently stimulate channel-mediated Cl- efflux in a concentration-dependent manner. Secretin was also shown to cause concentration-dependent relaxation of human tertiary bronchial smooth muscle. In summary, these data demonstrate that secretin receptors are present in human lung, and that activation of these receptors with human secretin potently stimulates concentration-dependent Cl- efflux from bronchial epithelial cells and bronchorelaxation.