Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins.

DNA replication origins are fundamental to chromosome organization and duplication, but understanding of these elements is limited because only a small fraction of these sites have been identified in eukaryotic genomes. Origin Recognition Complex (ORC) and minichromosome maintenance (MCM) proteins form prereplicative complexes at origins of replication. Using these proteins as molecular landmarks for origins, we identified ORC- and MCM-bound sites throughout the yeast genome. Four hundred twenty-nine sites in the yeast genome were predicted to contain replication origins, and approximately 80% of the loci identified on chromosome X demonstrated origin function. A substantial fraction of the predicted origins are associated with repetitive DNA sequences, including subtelomeric elements (X and Y') and transposable element-associated sequences (long terminal repeats). These findings identify the global set of yeast replication origins and open avenues of investigation into the role(s) ORC and MCM proteins play in chromosomal architecture and dynamics.

Genome-wide location and function of DNA binding proteins.

Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We developed a microarray method that reveals the genome-wide location of DNA-bound proteins and used this method to monitor binding of gene-specific transcription activators in yeast. A combination of location and expression profiles was used to identify genes whose expression is directly controlled by Gal4 and Ste12 as cells respond to changes in carbon source and mating pheromone, respectively. The results identify pathways that are coordinately regulated by each of the two activators and reveal previously unknown functions for Gal4 and Ste12. Genome-wide location analysis will facilitate investigation of gene regulatory networks, gene function, and genome maintenance.

Localization of P2X2 and P2X3 receptors in rat trigeminal ganglion neurons.

Purine receptors have been implicated in central neurotransmission from nociceptive primary afferent neurons, and ATP-mediated currents in sensory neurons have been shown to be mediated by both P2X3 and P2X2/3 receptors. The aim of the present study was to quantitatively examine the distribution of P2X2 and P2X3 receptors in primary afferent cell bodies in the rat trigeminal ganglion, including those innervating the dura. In order to determine the classes of neurons that express these receptor subtypes, purine receptor immunoreactivity was examined for colocalization with markers of myelinated (neurofilament 200; NF200) or mostly unmyelinated, non-peptidergic fibers (Bandeiraea simplicifolia isolectin B4; IB4). Forty percent of P2X2 and 64% of P2X3 receptor-expressing cells were IB4 positive, and 33% of P2X2 and 31% of P2X3 receptor-expressing cells were NF200 positive. Approximately 40% of cells expressing P2X2 receptors also expressed P2X3 receptors and vice versa. Trigeminal ganglion neurons innervating the dura mater were retrogradely labeled and 52% of these neurons expressed either P2X2 or P2X3 or both receptors. These results are consistent with electrophysiological findings that P2X receptors exist on the central terminals of trigeminal afferent neurons, and provide evidence that afferents supplying the dura express both receptors. In addition, the data suggest specific differences exist in P2X receptor expression between the spinal and trigeminal nociceptive systems.

Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme.

Activation of protein-encoding genes involves recruitment of an RNA polymerase II holoenzyme to promoters. Since the Srb4 subunit of the holoenzyme is essential for expression of most class II genes and is a target of at least one transcriptional activator, we reasoned that suppressors of a temperature-sensitive mutation in Srb4 would identify other factors generally involved in regulation of gene expression. We report here that MED6 and SRB6, both of which encode essential components of the holoenzyme, are among the dominant suppressors and that the products of these genes interact physically with Srb4. The recessive suppressors include NCB1 (BUR6), NCB2, NOT1, NOT3, NOT5, and CAF1, which encode subunits of NC2 and the Not complex. NC2 and Not proteins are general negative regulators which interact with TATA box binding protein (TBP). Taken together, these results suggest that transcription initiation involves a dynamic balance between activation mediated by specific components of the holoenzyme and repression by multiple TBP-associated regulators.

A novel and in situ technique for the quantitative detection of MTBE and benzene degrading bacteria in contaminated matrices.

A novel and in situ technique is presented here as a better alternative to culture-dependent and PCR-based techniques for the quantitative detection of predominant bacterial species involved in the bioremediation of contaminants. It allowed rapid, specific and in situ identification of Biosep-immobilized eubacteria from MTBE- and benzene-contaminated matrices.

Remodeling of yeast genome expression in response to environmental changes.

We used genome-wide expression analysis to explore how gene expression in Saccharomyces cerevisiae is remodeled in response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity. The results demonstrate that more than half of the genome is involved in various responses to environmental change and identify the global set of genes induced and repressed by each condition. These data implicate a substantial number of previously uncharacterized genes in these responses and reveal a signature common to environmental responses that involves approximately 10% of yeast genes. The results of expression analysis with MSN2/MSN4 mutants support the model that the Msn2/Msn4 activators induce the common response to environmental change. These results provide a global description of the transcriptional response to environmental change and extend our understanding of the role of activators in effecting this response.

Pleural Fluid Analysis in Chronic Hemothorax: A Mimicker of Infection.

OBJECTIVES: Timing to video-assisted thoracoscopic surgery (VATS) in hemothorax is based on preventing acute and long-term complications of retained blood products in the pleural space, including pleural space infection. We propose that the persistence of blood in the pleural space induces a proinflammatory state, independent of active infection. METHODS: We identified six patients with a hemothorax by clinical history, radiographic imaging, and pleural fluid analysis from a database of 1133 patients undergoing thoracentesis from 2002 to 2010 at the Medical University of South Carolina. RESULTS: In four of the six patients identified, the time from injury to thoracentesis was one, four, four, and five days, respectively. The fluid pH range was 7.32-7.41. The lactate dehydrogenase (LDH) range was 210-884 IU/L (mean 547 IU/L), and the absolute neutrophil count (ANC) range was 1196-3631 cells/µL. In two patients, the time from injury to thoracentesis was 7 and 60 days. In these two patients, the pH was 7.18 and 6.91, LDH was 1679 and 961 IU/L, and the ANC was 8134 and 5943 cells/µL. Microbiology and pathology were negative in all patients. CONCLUSIONS: The persistence of blood outside the vascular compartment, and within the pleural space, biochemically mirrors infection. We will explore the multiple mechanisms that account for development of pleural fluid acidosis, inflammation, and neutrophil recruitment.

C-fos can be induced in the neonatal rat spinal cord by both noxious and innocuous peripheral stimulation.

The development of spinal cord nociceptive pathways has been investigated in neonatal rat pups using the expression of Fos immunoreactivity in laminae I and II cells produced by high and low intensity skin stimulation. Noxious pinch of the hindpaw evoked a clear response in the newborn rat pup, which was not significantly different from that seen at postnatal day (P) 21. Low intensity touch stimulation also produced a significant fos response in laminae I and II cells at P3 which was 60% that of the pinch response. This was reduced to 27% of the pinch response by P10 and was gone by P21. Electrical stimulation through percutaneous electrodes showed that A beta fibre stimulation also produced a fos response at P3 that was not significantly different from that produced by C fibre stimulation. By P21 and P30 the response to C fibre stimulation was much greater and the response to A fibre stimulation was not significantly above background. The results suggest that in the neonatal spinal cord, low threshold A fibres are able to activate pathways in lamina I and II of the dorsal horn that in the adult are predominantly nociceptive.

Effects of sumatriptan on rat medullary dorsal horn neurons.

This study examined the cellular actions of the anti-migraine drug sumatriptan, on neurons in the substantia gelatinosa of the spinal trigeminal nucleus pars caudalis. Sumatriptan inhibited the miniature EPSC (mEPSC) rate in a dose dependent fashion, with an EC(50) of 250 nM. Sumatriptan (3 microM) inhibited the mEPSC rate by 36%, without altering the mEPSC amplitude. This effect was partially reversed by the 5HT(1D) specific antagonist BRL15572 (10 microM). In contrast, the 5HT(1B) agonist CP93129 (10 microm) did not alter the mEPSC rate. Furthermore, sumatriptan (3 microM) decreased the amplitude of electrically evoked EPSCs (eEPSC) by 40%. After incubating the slices in ketanserin (an antagonist which shows selectivity for 5HT(1D) over 5HT(1B) receptors) sumatriptan had little effect on eEPSC amplitude. In control conditions paired stimuli resulted in paired pulse depression (PPD; the ratio eEPSC(2)/eEPSC(1)=0.7+/-0.01), whilst in the presence of sumatriptan the PPD was blocked (ratio eEPSC(2)/eEPSC(1)=0.9+/-0.1). Sumatriptan produced no post-synaptic membrane current and had no significant effect on membrane conductance over a range of membrane potentials (-60 to -130 mV). RT-PCR experiments revealed the presence of mRNA for both 5HT(1D) and 5HT(1B) receptor subtypes in the trigeminal ganglia and subnucleus caudalis. These data suggest that sumatriptan acts pre-synaptically on trigeminal primary afferent central terminals to reduce the probability of release of glutamate, and that this action is mediated through 5HT(1D) receptors.

Nociceptin, Phe(1)psi-nociceptin(1 - 13), nocistatin and prepronociceptin(154 - 181) effects on calcium channel currents and a potassium current in rat locus coeruleus in vitro.

1. The actions of the neuropeptide nociceptin, the putative nociceptin receptor antagonist [Phe1psi(CH(2)-NH)Gly(2)]-nociceptin-(1 - 13)NH(2) (Phe(1)psi-nociceptin(1 - 13)) and the putative nociceptin precursor products nocistatin (rat prepronociceptin(125 - 132)) and rat prepronociceptin(154 - 181) were examined on membrane properties of rat locus coeruleus (LC) neurons using whole cell patch clamp techniques. 2. Nociceptin inhibited I(Ba) in all LC neurons, (pD(2) of 8.9, maximum inhibition 50%). The inhibition of I(Ba) by nociceptin was associated with slowing of the activation of I(Ba) and could be significantly reversed by a strong depolarizing prepulse. Phe(1)psi-nociceptin(1 - 13) also inhibited I(Ba) in LC neurons (notional pD(2) of 7.6, maximum inhibition 18%). Application of Phe(1)psi-nociceptin(1 - 13) (1 microM) significantly occluded the subsequent effects of a co-application of nociceptin (3 nM) on I(Ba). 3. As previously reported for nociceptin, Phe(1)psi-nociceptin(1 - 13) caused an outward current in LC neurons voltage clamped at -60 mV (pD(2) of 7.1, maximum current 50% of that of methionine enkephalin, 10 microM). The Phe(1)psi-nociceptin(1 - 13) induced current reversed polarity at -112 mV and exhibited pronounced inward rectification. Phe(1)psi-nociceptin(1 - 13) (1 microM) reversibly inhibited the current caused by nociceptin (300 nM) by 30%. 4. Neither nocistatin nor rat prepronociceptin(154 - 181) inhibited I(Ba) in LC neurons, or prevented the subsequent inhibition by nociceptin. Neither nocistatin or prepronociceptin(154 - 181) affected the membrane properties of LC neurons. 5. This study demonstrates that nociceptin modulates somatic I(Ba) in rat LC neurons. The putative ORL1 antagonist Phe(1)psi-nociceptin(1 - 13) exhibited partial agonist activity at inhibiting I(Ba) and opening K(+) channels in LC. Other putative nociceptin precursor products were without effect on LC cells.

Mechanisms regulating differential activation of membrane-mediated signaling by 1alpha,25(OH)2D3 and 24R,25(OH)2D3.

Vitamin D metabolites 1alpha,25(OH)(2)D(3) and 24R,25(OH)(2)D(3) regulate endochondral ossification in a cell maturation-dependent manner via membrane-mediated mechanisms. 24R,25(OH)(2)D(3) stimulates PKC activity in chondrocytes from the growth plate resting zone, whereas 1alpha,25(OH)(2)D(3) stimulates PKC in growth zone chondrocytes. We used the rat costochondral growth plate cartilage cell model to study how these responses are differentially regulated. 1alpha,25(OH)(2)D(3) acts on PKC, MAP kinase, and downstream physiological responses via phosphatidylinositol-specific PLC-beta; 24R,25(OH)(2)D(3) acts via PLD. In both cases, diacylglycerol (DAG) is increased, activating PKC. Both cell types possess membrane and nuclear receptors for 1alpha,25(OH)(2)D(3), but the mechanisms that render the 1alpha,25(OH)(2)D(3) pathway silent in resting zone cells or the 24R,25(OH)(2)D(3) pathway silent in growth zone cells are unclear. PLA(2) is pivotal in this process. 1alpha,25(OH)(2)D(3) stimulates PLA(2) activity in growth zone cells and 24R,25(OH)(2)D(3) inhibits PLA(2) activity in resting zone cells. Both processes result in PKC activation. To understand how negative regulation of PLA(2) results in increased PKC activity in resting zone cells, we used PLA(2) activating peptide to stimulate PLA(2) activity and examined cell response. PLAP is not expressed in resting zone cells in vivo, supporting the hypothesis that PLA(2) activation is inhibitory to 24R,25(OH)(2)D(3) action in these cells.

Postsynaptic K+ current induced by nociceptin in medullary dorsal horn neurons.

The actions of the endogenous ORL1 receptor (opioid receptor-like1) ligand nociceptin on the membrane properties of rat trigeminal nucleus caudalis neurons were examined by use of whole cell and perforated patch clamp recording in brain slices. Nociceptin produced an outward current in all neurons tested (EC50 112 nM). The outward current produced by nociceptin was completely reversed with the addition of the non-peptide ORL1 antagonist J-113397. Outward currents reversed polarity at -99+/-2 mV, close to the potential for K+ of -102 mV, suggesting that they were mediated by an increased K+ conductance. These results suggest that the analgesic action of nociceptin might be mediated by direct postsynaptic inhibition within the dorsal horn.

Evidence that large myelinated primary afferent fibers make synaptic contacts in lamina II of neonatal rats.

Choleragenoid horseradish peroxidase (B-HRP) is a retrogradely transported marker that selectively labels large cutaneous myelinated primary afferent fibers. In adults, B-HRP labelled large afferent fibers are seen to enter laminae III-V, and to a lesser extent lamina I, whereas lamina II, which is the major termination site of unmyelinated primary afferents, remains unlabelled. In the neonate, however, there is extensive B-HRP label in lamina II. The present study shows that the B-HRP labelled fibers in the neonate make many synaptic contacts in lamina II. This supports the idea that large primary afferent fibers in neonatal animals make synaptic contact with post-synaptic targets that presumably process nociceptive information. Accordingly to ameliorate pain in neonates it may be more important to block low threshold sensory input whereas in adults it would be more important to block the high threshold inputs.

The onset of diffuse noxious inhibitory controls in postnatal rat pups: a C-Fos study.

The development of diffuse noxious inhibitory controls (DNIC) was studied in postnatal rats aged 12, 21 and 42-days-old, using immunoreactive localization of the c-fos protein products induced in the dorsal horn by noxious stimulation. The presence of DNIC was revealed by the reduction in the levels of Fos-like immunoreactivity that are normally induced by a standardized primary pinch stimulus when this stimulus was accompanied by a concurrent noxious stimulus (formalin) to a heterotopic body part. Significant reductions were seen at postnatal day 42 (P42; 15% reduction) and P21 (17% reduction), but concurrent stimulation had no significant effect at P12. These results suggest that the system subserving DNIC is functionally mature by P21, but not effective at P12. This delayed maturation of an inhibitory system may underlie the extreme sensitivity to somatosensory stimulation seen in neonatal pups and premature infants.

Multiple sulfa compounds: high-pressure liquid chromatographic assay and mobile phase correlation.

A mixture of sulfacetamide, sulfathiazole, and sulfabenzamide was used to develop a rapid high-pressure liquid chromatographic assay. In addition, this study provided a means to develop concepts relating solvent molar polarization parameters and retention times. A linear correlation between molar polarization and retention time was observed and will permit reasonably rapid predictions about the dependent variable.

Folic acid as a cancer-preventing agent.

Higher intakes of folic acid-rich foods such as vegetables, legumes, and whole grains are associated with lower incidence of carcinomas in international comparisons and case-control studies. Deficiency of folic acid in experimental studies causes DNA damage that resembles the DNA damage seen in cancer cells. The requirement for folic acid in DNA synthesis and DNA methylation provides a plausible mechanism for a mutagenic effect of a low-folate diet. It is suggested that cancer can be initiated by DNA damage that results from folic acid deficiency. The relatively low level of folic acid in North American diets might be the underlying reason for high rates of many cancers in North America.

A process economic approach to develop a dilute-acid cellulose hydrolysis process to produce ethanol from biomass.

Successful deployment of a bioethanol process depends on the integration of technologies that can be economically commercialized. Pretreatment and fermentation operations of the traditional enzymatic bioethanol-production process constitute the largest portion of the capital and operating costs. Cost reduction in these areas, through improved reactions and reduced capital, will improve the economic feasibility of a large-scale plant. A technoeconomic model was developed using the ASPEN Plus modeling software package. This model included a two-stage pretreatment operation with a co-current first stage and countercurrent second stage, a lignin adsorption unit, and a cofermentation unit. Data from kinetic modeling of the pretreatment reactions, verified by bench-scale experiments, were used to create the ASPEN Plus base model. Results from the initial pretreatment and fermentation yields of the two-stage system correlated well to the performance targets established by the model. The ASPEN Plus model determined mass and energy-balance information, which was supplied to an economic module to determine the required selling price of the ethanol. Several pretreatment process variables such as glucose yield, liquid: solid ratio, additional pretreatment stages, and lignin adsorption were varied to determine which parameters had the greatest effect on the process economics. Optimized values for these key variables became target values for the bench-scale research, either to achieve or identify as potential obstacles in the future commercialization process. Results from this modeling and experimentation sequence have led to the design of an advanced two-stage engineering- scale reactor for a dilute-acid hydrolysis process.

Managed bioremediation of soil contaminated with crude oil soil chemistry and microbial ecology three years later.

Analysis of samples taken from three experimental soil lysimeters demonstrated marked long-term effects of managed bioremediation on soil chemistry and on bacterial and fungal communities 3 yr after the application of crude oil or crude oil and fertilizer. The lysimeters were originally used to evaluate the short-term effectiveness of managed (application of fertilizer and water, one lysimeter) vs unmanaged bioremediation (one lysimeter) of Michigan Silurian crude oil compared to one uncontaminated control lysimeter. Three years following the original experiment, five 2-ft-long soil cores were extracted from each lysimeter, each divided into three sections, and the like sections mixed together to form composited soil samples. All subsequent chemical and microbiological analyses were performed on these nine composited samples. Substantial variation was found among the lysimeters for certain soil chemical characteristics (% moisture, pH, total Kjeldahl nitrogen [TKN], ammonia nitrogen [NH4-N], phosphate phosphorous [PO4-P], and sulfate [SO4 (-2)]). The managed lysimeter had 10% the level of total petroleum hydrocarbons (TPH-IR) found in the unmanaged lysimeter. Assessment of the microbial community was performed for heterotropic bacteria, fungi, and aromatic hydrocarbon-degrading bacteria (toluene, naphthalene, and phenanthrene) by dilution onto solid media. There was little difference in the number of heterotrophic bacteria, in contrast to counts of fungi, which were markedly higher in the contaminated lysimeters. Hydrocarbon-degrading bacteria were elevated in both oil-contaminated lysimeters. In terms of particular hydrocarbons as substrates, phenanthrene degraders were greater in number than naphthalene degraders, which outnumbered toluene degraders. Levels of sulfate-reducing bacteria seem to have been stimulated by hydrocarbon degradation.

Microbial dynamics in oil-impacted prairie soil.

A remote site in the Tallgrass Prairie Preserve (Osage County, OK) was contaminated with crude oil by a pipeline break in 1992. In 1996, the contaminated soil was bioremediated by blending with uncontaminated soil, prairie hay, buffalo manure, and commercial fertilizers, and spreading in a shallow layer over uncontaminated soil to create a landfarm. The landfarm was monitored for two years for aerobic and anaerobic bacteria, soil gases indicative of microbial activity, and for changes in the concentration of total petroleum hydrocarbons (TPH). Levels of hydrocarbon degraders and soil gas indicators of aerobic degradation were stimulated in the landfarm during the first warm season relative to uncontaminated prairie soil. However, these same indicators were less conclusive during the second warm season, indicating depletion of the more easily degradable hydrocarbons, although the landfarm still contained 6,800 mg/kg TPH on the average at the beginning of the second warm season. Methane formation and methanogen counts were clearly stimulated in the first warm season relative to uncontaminated prairie soil, indicating that methanogenesis plays an important role in the mineralization of hydrocarbons even in these shallow soils.