Unexpected regulation of miRNA abundance during adaptation of early-somite mouse embryos to diabetic pregnancy.

Maternal diabetes is one of major causes of congenital malformations in offspring, but the underlying mechanism is still unclear. MiRNAs play an important role in transcriptional and post-transcriptional regulation of gene expression. However, no miRNA expression profiling of hyperglycemic offspring are thus far available. Female mice were made diabetic with streptozotocin, treated with slow-release insulin tablets, and mated. MiRNA expression profiling with Next Generation Sequencing on the SOLiD5 platform was performed on 8 control and 5 hyperglycemic embryonic day (ED)8.5 and 9 control and 6 hyperglycemic ED9.5 embryos. Differential expression was analyzed with the Wald test. On ED8.5, the abundance of expressed miRNAs was similar in control and hyperglycemic ED8.5 embryos. The spectrum of expressed miRNAs had not changed in ED9.5 embryos, but the abundance of most miRNAs increased ∼5-fold in control embryos. However, hyperglycemic D9.5 embryos were unable to mount this increase in prevalence. Only 3 miRNAs were differentially expressed in control and hyperglycemic ED9.5 embryos, but their putative target genes were underrepresented in the Jackson database of genes causing cardiovascular or neural malformations.

The dimensions of the tarsal sinus and canal in different foot positions and its clinical implications.

This study presents a reference for the dimensions of the tarsal sinus and canal in healthy adults in different foot positions to facilitate understanding of the kinematics of the subtalar joint, the effect of an implant, and other clinical issues. In a 3D CT stress test on 20 subjects, the right foot was forced into a neutral and eight different extreme foot positions while CT scans were obtained. The bones were segmented in the neutral foot position. The kinematics of the bones in the extreme positions were determined relative to the neutral position. The dimensions of the tarsal sinus and canal were calculated by determining the radii of the maximal inscribed spheres at 20 equidistant locations along an axis in 3D surface models of the tali and calcanei in each foot position. The radii were small on the medial side and increased laterally. Medial from the middle, the radii were small and not significantly different among the various foot positions. At the lateral side, the dimensions were affected mainly by eversion or inversion and less by dorsiflexion or plantarflexion. The pattern was reproducible among subjects, but there were between-subject differences. The dimensions are mostly determined by rotation in the frontal plane. A pivot point was found medial from the middle. These data serve as a reference and model for predicting the effect of sinus implants and understanding such clinical problems as sinus tarsi syndrome. Between-subjects differences have to be taken into account. Clin. Anat. 30:1049-1057, 2017. © 2017 Wiley Periodicals, Inc.

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data.

Despite the central role of quantitative PCR (qPCR) in the quantification of mRNA transcripts, most analyses of qPCR data are still delegated to the software that comes with the qPCR apparatus. This is especially true for the handling of the fluorescence baseline. This article shows that baseline estimation errors are directly reflected in the observed PCR efficiency values and are thus propagated exponentially in the estimated starting concentrations as well as 'fold-difference' results. Because of the unknown origin and kinetics of the baseline fluorescence, the fluorescence values monitored in the initial cycles of the PCR reaction cannot be used to estimate a useful baseline value. An algorithm that estimates the baseline by reconstructing the log-linear phase downward from the early plateau phase of the PCR reaction was developed and shown to lead to very reproducible PCR efficiency values. PCR efficiency values were determined per sample by fitting a regression line to a subset of data points in the log-linear phase. The variability, as well as the bias, in qPCR results was significantly reduced when the mean of these PCR efficiencies per amplicon was used in the calculation of an estimate of the starting concentration per sample.

Reducing soft-tissue shrinkage artefacts caused by staining with Lugol's solution.

Diffusible iodine-based contrast-enhanced computed tomography (diceCT) is progressively used in clinical and morphological research to study developmental anatomy. Lugol's solution (Lugol) has gained interest as an effective contrast agent; however, usage is limited due to extensive soft-tissue shrinkage. The mechanism of Lugol-induced shrinkage and how to prevent it is largely unknown, hampering applications of Lugol in clinical or forensic cases where tissue shrinkage can lead to erroneous diagnostic conclusions. Shrinkage was suggested to be due to an osmotic imbalance between tissue and solution. Pilot experiments pointed to acidification of Lugol, but the relation of acidification and tissue shrinkage was not evaluated. In this study, we analyzed the relation between tissue shrinkage, osmolarity and acidification of the solution during staining. Changes in tissue volume were measured on 2D-segmented magnetic resonance and diceCT images using AMIRA software. Partial correlation and stepwise regression analysis showed that acidification of Lugol is the main cause of tissue shrinkage. To prevent acidification, we developed a buffered Lugol's solution (B-Lugol) and showed that stabilizing its pH almost completely prevented shrinkage without affecting staining. Changing from Lugol to B-Lugol is a major improvement for clinical and morphological research and only requires a minor adaptation of the staining protocol.

Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers.

Since the discovery of microRNAs (miRNAs), circulating miRNAs have been proposed as biomarkers for disease. Consequently, many groups have tried to identify circulating miRNA biomarkers for various types of diseases including cardiovascular disease and cancer. However, the replicability of these experiments has been disappointingly low. In order to identify circulating miRNA candidate biomarkers, in general, first an unbiased high-throughput screen is performed in which a large number of miRNAs is detected and quantified in the circulation. Because these are costly experiments, many of such studies have been performed using a low number of study subjects (small sample size). Due to lack of power in small sample size experiments, true effects are often missed and many of the detected effects are wrong. Therefore, it is important to have a good estimate of the appropriate sample size for a miRNA high-throughput screen. In this review, we discuss the effects of small sample sizes in high-throughput screens for circulating miRNAs. Using data from a miRNA high-throughput experiment on isolated monocytes, we illustrate that the implementation of power calculations in a high-throughput miRNA discovery experiment will avoid unnecessarily large and expensive experiments, while still having enough power to be able to detect clinically important differences.

Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources.

We describe a genome-wide characterization of mRNA transcript levels in yeast grown on the fatty acid oleate, determined using Serial Analysis of Gene Expression (SAGE). Comparison of this SAGE library with that reported for glucose grown cells revealed the dramatic adaptive response of yeast to a change in carbon source. A major fraction (>20%) of the 15,000 mRNA molecules in a yeast cell comprised differentially expressed transcripts, which were derived from only 2% of the total number of approximately 6300 yeast genes. Most of the mRNAs that were differentially expressed code for enzymes or for other proteins participating in metabolism (e.g., metabolite transporters). In oleate-grown cells, this was exemplified by the huge increase of mRNAs encoding the peroxisomal beta-oxidation enzymes required for degradation of fatty acids. The data provide evidence for the existence of redox shuttles across organellar membranes that involve peroxisomal, cytoplasmic, and mitochondrial enzymes. We also analyzed the mRNA profile of a mutant strain with deletions of the PIP2 and OAF1 genes, encoding transcription factors required for induction of genes encoding peroxisomal proteins. Induction of genes under the immediate control of these factors was abolished; other genes were up-regulated, indicating an adaptive response to the changed metabolism imposed by the genetic impairment. We describe a statistical method for analysis of data obtained by SAGE.

The 3'-UTR of the glutamine-synthetase gene interacts specifically with upstream regulatory elements, contains mRNA-instability elements and is involved in glutamine sensing.

Glutamine synthetase (GS) is expressed at various levels in a wide range of tissues, suggesting that a complex network of modules regulates its expression. We explored the interactions between the upstream enhancer, regulatory regions in the first intron, and the 3'-untranslated region and immediate downstream genomic sequences of the GS gene (the GS "tail"), and compared the results with those obtained previously in conjunction with the bovine growth hormone (bGH) tail. The statistical analysis of these interactions revealed that the GS tail was required for full enhancer activity of the combination of the upstream enhancer and either the middle or the 3'-intron element. The GS tail also prevented a productive interaction between the upstream enhancer and the 5'-intron element, whereas the bGH tail did not, suggesting that the 5'-intron element is a regulatory element that needs to be silenced for full GS expression. Using the CMV promoter/enhancer and transfection experiments, we established that the 2.8 kb GS mRNA polyadenylation signal is approximately 10-fold more efficient than the 1.4 kb mRNA signal. Because the steady-state levels of both mRNAs are similar, the intervening conserved elements destabilize the long mRNA. Indeed, one but not all constructs containing these elements had a shorter half life in FTO-2B cells. A construct containing only 300 bases before and 100 bases after the 2.8 kb mRNA polyadenylation site sufficed for maximal expression. A stretch of 21 adenines inside this fragment conferred, in conjunction with the upstream enhancer and the 3'-part of the first intron, sensitivity of GS expression to ambient glutamine.

Melatonin generates an outward potassium current in rat suprachiasmatic nucleus neurones in vitro independent of their circadian rhythm.

The present study investigated the membrane mechanisms underlying the inhibitory influence of melatonin on suprachiasmatic nucleus (SCN) neurones in a hypothalamic slice preparation. Perforated-patch recordings were performed to prevent the rapid rundown of spontaneous firing rate as observed during whole cell recordings and to preserve circadian rhythmicity in SCN neurones. In current-clamp mode melatonin (1 microM or 1 nM) application, in the presence of agents that block action potential generation and fast synaptic transmission, resulted in a membrane hyperpolarisation accompanied with a decrease in input resistance in the majority of SCN neurones (71-86%). The amplitude of the hyperpolarisation was not found to be significantly different between circadian time 5-12 and 14-21. In voltage-clamp mode melatonin (1 microM or 1 nM) induced an outward current accompanied with an increase in membrane conductance. The current was found to be mainly potassium driven with voltage kinetics resembling those of an open rectifying potassium conductance. Investigations into the signal transduction mechanism revealed melatonin-induced inhibition of SCN neurones to be sensitive to pertussis toxin but independent of intracellular cAMP levels and phospholipase C activity. The present study shows that melatonin, at night-time physiological concentrations, reduces the neuronal excitability of the majority of SCN neurones independent of the time of application in the circadian cycle. Thus in vivo melatonin may be important for circadian time-keeping by amplifying the circadian rhythm in SCN neurones, by lowering their sensitivity to phase-shifting stimuli occurring at night.

RNA content differs in slow and fast muscle fibers: implications for interpretation of changes in muscle gene expression.

Quantification of a specific muscle mRNA per total RNA (e.g., by Northern blot analysis) plays a crucial role in assessment of developmental, experimental, or pathological changes in gene expression. However, total RNA content per gram of a particular fiber type may differ as well. We have tested this possibility in the distinct fiber types of adult rat skeletal muscle. Sections of single fibers were hybridized against 28S rRNA as a marker for RNA content. Quantification of the hybridization showed that the 28S rRNA content decreases in the order I>IIA>IIX>IIB, where Type I fibers show a five- to sixfold higher expression level compared to Type IIB fibers. Results were verified with an independent biochemical determination of total RNA content performed on pools of histochemically defined freeze-dried single fibers. In addition, the proportion of myosin heavy chain (MHC) mRNA per microgram of total RNA was similar in slow and fast fibers, as demonstrated by Northern blot analysis. Consequently, Type I fibers contain five- to sixfold more MHC mRNA per microgram of tissue than IIB fibers. These differences are not reflected in the total fiber protein content. This study implies that proper assessment of mRNA levels in skeletal muscle requires evaluation of total RNA levels according to fiber type composition.

Outflow characteristics of isolated anterior segments of human eyes.

PURPOSE: To evaluate the relationship between intraocular pressure (IOP) and flow through the trabecular meshwork in isolated anterior segments of human eyes. Outflow facility (C) is thought to decrease proportionally with increasing IOP in human eyes in vivo and in vitro. METHODS: Twenty-nine eviscerated human anterior segments were perfused with ascending and descending pressure sequences in a stepwise fashion (range, 4 to 40 mm Hg); 11 of the 29 eyes were treated similarly after 20 hours of perfusion at 12 mm Hg. Pressure-flow sequences of individual eyes were evaluated with a linear (constant C) and a nonlinear regression method (C decreasing with increasing IOP). In addition, in eight intact postmortem eyes, pressure-flow characteristics were determined, followed by perfusion of their isolated anterior segments. RESULTS: Pressure-flow sequences as determined by linear regression had an average correlation coefficient of 0.99. Average C (slope of the plot) was 0.26 +/- 0.03 microliter minute-1 mm Hg-1. There was no influence of direction of pressure sequence or time on C. To test for linearity, the hypothetical outflow obstruction coefficient (Q) was determined for each plot. Median Q of 29 eyes was 0.003 mm Hg-1, and in 45% (13 eyes) Q was negative, suggesting facilitation instead of obstruction. This indicates that the outflow obstruction coefficient is not a physiological parameter in isolated anterior segments. CONCLUSIONS: The relationship between IOP and flow through perfused isolated anterior segments of human eyes is linear between 4 and 40 mm Hg, indicating that within this range outflow facility is constant and does not decrease with increasing IOP.

A procedure for culturing rat neocortex explants in a serum-free nutrient medium.

A procedure is described for long-term culturing of rat neocortex explants in a serum-free growth medium. Slices spanning the entire cortical depth from pial to ventricular side are prepared from 6-day-old rat pups. After preincubation in Hanks' balanced salt solution with extra glucose, the explants are placed on polyamide gauze carriers in plastic culture dishes containing serum-free medium. The dishes are continuously rocked during the culture period. After 3 weeks in vitro the explants consist of a three-dimensional network of neural tissue with a mean thickness above the gauze of ca. 100 micron which corresponds with about 8 cell layers. Central necrosis is either fully absent (in one-third of the explants) or restricted to a minimal strip or patch located close to the gauze. From pial to ventricular side, 5 layers can be distinguished which, with respect to cell size and cell density, reflect a histiotypic architecture. The dense neuropil shows abundant axo-dendritic synapses (both on shafts and spines), myelinated fibers, and spontaneous bioelectric activity.

Chronic blockade of bioelectric activity in neonatal rat neocortex in vitro: physiological effects.

We have examined what effect the loss of spontaneous bioelectric activity has on neural network formation in organotypic rat neocortical explants grown under serum-free culture conditions. Explants were taken from dorsal midline (presumptive visual) and lateral (presumptive auditory) occipital cortex and chronically exposed to tetrodotoxin which blocked all measurable bioelectric activity between change of medium. Extracellular recordings revealed complex, rhythmic spontaneous and evoked multiunit discharges in all explants examined (following tetrodotoxin washout in the experimental group). Control auditory explants had significantly more sites from which electric activity could be recorded compared with control visual explants. Auditory cultures showed no effect of the tetrodotoxin treatment, whereas visual explants showed significant increases over control values, equalling the auditory values. This increased level of spontaneous bioelectric activity was maintained for at least 10 days following transfer of the cultures to control growth medium. There was no significant difference between control visual and auditory explants regarding the number of sites from which evoked activity was seen. Nor did either cortex group show an effect of tetrodotoxin on the number of sites from which evoked activity was seen. The frequency with which spontaneous bioelectric discharges occurred per site increased with age in auditory vs visual cortex. These differences, however, were abolished in the tetrodotoxin-treated groups. It was concluded that neocortical explants which have experienced chronic suppression of spontaneous electric activity did not suffer deficits in neural network formation, though there is an effect on the incidence and frequency with which such activity is given.

The effects of potassium-induced depolarization, glutamate receptor antagonists and N-methyl-D-aspartate on neuronal survival in cultured neocortex explants.

The effects of elevating the potassium concentration of the growth medium of neocortical explants was studied. Under control conditions, 10 mM potassium resulted in ca 20% decrease in the number of surviving neurons. The same potassium concentration, however, was clearly neurotrophic in tetrodotoxin-grown cultures: tetrodotoxin-induced neuronal death was significantly reduced. Both effects could be mimicked by the addition of 10 microM N-methyl-D-aspartate (NMDA); lower concentrations were without effect; higher concentrations were neurotoxic under both control and tetrodotoxin conditions. The neurotoxic, as well as the neurotrophic effects of 10 mM potassium appear to be mediated through depolarization-induced glutamate release since they could be influenced by the application of glutamate receptor antagonists. The addition of the NMDA receptor antagonist D-2-amino-7-phosphonoheptanoate (APH) blocked the trophic effect of 10 mM potassium in tetrodotoxin-grown cultures, resulting in low survival. On the other hand, the addition of the non-NMDA antagonist 6,7-dinitroquinoxaline-2,3-dione (DNQX) resulted in neuronal survival similar to control cultures, indicating that it blocked the toxic effects of glutamate, leaving the trophic effects on the NMDA receptor untouched. Under control (non-TTX) conditions, neither DNQX nor APH showed significant effects on 10 mM potassium-induced cell death, indicating that stimulation of the non-NMDA, as well as the NMDA receptors is neurotoxic. This differential effect of NMDA receptor stimulation on neuronal survival is discussed with respect to the maturational and/or functional state of the neurons in the culture.

Elevated potassium prevents neuronal death but inhibits network formation in neocortical cultures.

Chronic depolarization is inimical to neuronal growth and synaptogenesis so that spontaneous action potential generation appears to be required for the normal cytomorphological maturation of neocortical networks. The efficacy of 25 mM K in suppressing spontaneous bioelectric activity was monitored by extra- and intracellular recording from the explants. Intracellular recording from individual neurons showed that membrane potentials were reduced to ca -30 mV in potassium cultures but rapidly repolarized to ca -50 mV when returned to normal growth medium. Though action potentials could be readily evoked from these explants, spontaneous discharges and postsynaptic potentials were absent from potassium-treated cultures. Both spontaneous bioelectric activity and postsynaptic potentials returned to the cultures by 5 days after returning the explants to normal growth medium. Extracellular recordings also showed that the explants were bioelectrically silent in the presence of 25 mM K or 25 mM K plus tetrodotoxin. In contrast to tetrodotoxin alone, bioelectric activity was absent when the cultures (with or without tetrodotoxin) were returned to normal growth medium. The explants gradually began to evince spontaneous bioelectric activity between 3 and 5 days after being returned to normal growth medium. Massive cell death induced by chronic exposure to tetrodotoxin was totally prevented by concomitant addition of 25 mM potassium, though these explants were significantly thinner than controls due to a large decrease in neuropil. We conclude that chronic depolarization of neonatal cortical explants by potassium results in a delayed return of spontaneous bioelectric discharges. Chronic depolarization results in a retardation of network formation in these explants apparently due to a lack of neurite and/or synapse formation.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of chronic exposure to high magnesium on neuron survival in long-term neocortical explants of neonatal rats in vitro.

In order to assess the effect of elevated magnesium, neuronal morphology and physiology was studied in chronically cultured organotypic neonatal rat occipital neocortex. Explants grown in 10 mM magnesium were found to experience an approximate 30% cell loss (as shown by cell count and DNA-protein analysis), while 12.5 and 15 mM magnesium showed ca. 47 and 60% cell losses, respectively. Intracellular recording from 10 mM magnesium explants revealed that measurable postsynaptic potentials and action potentials could occur, apparently depending on the type of cell examined. All post-synaptic activities ceased in 12.5 mM magnesium cultures, though action potentials could be elicited by current stimulation. The effects of known depolarizing agents, viz. potassium and N-methyl-D-aspartate, on 12.5 mM magnesium-grown explants were also examined. Explants grown in the presence of 12.5 mM magnesium plus 10 mM potassium showed a dramatic increase in the loss of neurons. The simultaneous addition of 6,7-dinitro-quinoxaline-2,3-dione showed this to be due to an increase in non-N-methyl-D-aspartate mediated cell death in response to glutamate release brought about by the depolarizing effects of the potassium. The addition of 10 microM N-methyl-D-aspartate to 12.5 mM magnesium-grown cultures, on the other hand, improved cell survival to control levels. The mechanism of this reciprocal neuroprotective effect of N-methyl-D-aspartate against magnesium has yet to be elucidated. We conclude that these findings are consistent with regard to the opposing actions of N-methyl-D-aspartate and magnesium on calcium influx and various metabolic processes within the explants.

Cell number, tissue thickness and protein content as measures for development and variability in cultured neocortex explants.

The development of neuronal number, explant thickness and amount of protein was studied in several series of rat neocortex explants, cultured up to 21 days in vitro (DIV). In contrast to the dimensions of the explant, which rapidly stabilized, the amount of protein showed a prolonged increase with age in vitro. The number of neurons initially tended to decrease until a constant level was reached from 14 to 21 DIV. These findings are in good agreement with previously described cytoarchitectural characteristics. The present data also provided an opportunity to calculate the variance for various parameters within and between culture series obtained from different rats. Especially for the amount of protein, the variance between culture series appeared to be larger than within culture series. This difference was present already at the onset of culturing and persisted during development in vitro. Implications of these findings for experimental design are discussed.

Cytoarchitecture in cultured rat neocortex explants.

Neocortex explants obtained from 6-day-old rat pups and cultured in a serum-free medium from 5 hr to 13 days in vitro (DIV) show preservation of cytoarchitectural characteristics. Major changes in the size of the explants and their layers occur during the first 2 DIV. A radial arrangement of neurons within layer 2-3-4, which becomes apparent between 2 and 10 DIV, suggests an advance in maturation in culture. In contrast to the situation in vivo, a distinct layer 4 cannot be consistently identified. During the first 2 DIV, a transposition of cells into the pial direction can be seen. Individual degenerated cells are spotted especially in layer 5. The presence of these cells amidst healthy neurons suggests that their death has a functional cause. Neurons at the ventricular border of layer 6 become relatively large in comparison with other neurons. Within the cultured tissue there is a marked increase in GFA reactivity compared to the situation in vivo. The described results clearly indicate that in these cultured explants, both similarities and differences are of interest for studies on the formation of neuronal circuitry within the cerebral cortex.

Chronic blockade of bioelectric activity in neonatal rat cortex grown in vitro: morphological effects.

Culture thickness, numerical density of neurons and neuronal survival were studied in timed series of control and tetrodotoxin-silenced neocortical cultures to provide information on the role of bioelectric activity on neuronal development. In control cultures, culture thickness and number of surviving neurons decrease during the first weeks in vitro, but remain constant between 2 and 3 weeks indicating that the cultures are essentially mature. In the 4th week in vitro a further decrease in surviving neurons was observed. In tetrodotoxin-treated cultures the number of surviving neurons decreased significantly between 1 and 2 weeks in vitro, to remain constant thereafter. However, culture thickness significantly increased at 3 and 4 weeks in vitro after an initial drop between 1 and 2 weeks. Compared to age-matched controls at 2 and 3 weeks in vitro, only ca 50% of the neurons survived the loss of bioelectric activity. Similar differences were present between 1 and 2 weeks. Thus, the loss of all measurable bioelectric activity induces neuronal death in neocortical explants, but promotes neuropil formation by the surviving cells.