bluuebunny/crossref_metadata_2025 huggingface dataset:
An efficient protocol for inducing pseudopregnancy using estradiol dipropionate and follicular development associated with changes in reproductive hormones after prostaglandin F2alpha treatment in pseudopregnant sows
Authors: Noguchi Michiko , Yoshioka Koji , Suzuki Chie , Itoh Seigo , Kaneko Hiroyuki
Published: December 2011

Background

Utilization of estrus synchronization program in livestock industry would provide greater options for reproductive management in herd. To develop a convenient method for estrus synchronization in pigs, we determined the effective protocol using estradiol dipropionate (EDP) for the establishment of pseudopregnancy and investigated follicular development during the estrus synchronization with prostaglandin F2alpha (PGF2alpha) in association with reproductive hormone profiles in pseudopregnant sows.

Methods

In Experiment 1, the effective dose (0, 10, 20, or 30 mg) and timing (5, 8, 11 or 13 days after ovulation) of a single administration of EDP in cyclic pigs for the induction of pseudopregnancy were investigated. In Experiment 2, four pseudopregnant sows were treated with PGF2alpha twice at a 24-h interval between 24 and 28 days after EDP treatment. The changes in plasma concentrations of reproductive hormones were analyzed by time-resolved fluoroimmunoassay. Follicular development and ovulation following PGF2alpha administration were monitored by transrectal ultrasonography.

Results

High efficiency (greater than 80%) of pseudopregnancy was achieved with a single treatment with 20 mg of EDP at 8 and 11 days after ovulation (equivalent to 9-13 days after the onset of estrus). Plasma estradiol-17beta concentrations in pseudopregnant sows were significantly higher between 12 h and 7 days than before EDP treatment. Total inhibin concentrations significantly decreased following EDP treatment and remained low for 14 days. The number of small follicles was increased from 6.3 +/- 2.6 at PGF2alpha treatment to 22.8 +/- 4.8 at 3 days later; this was associated with increased plasma concentrations of inhibin. Onset of estrus was detectable in all sows on 5.3 +/- 0.3 days after PGF2alpha treatment and the number of ovulated follicles was 15.5 +/- 1.4 detected at 7.6 +/- 0.2 days after the treatment.

Conclusions

This study has defined the effective dose and timing of EDP treatment for inducing pseudopregnancy in cyclic pigs. Our results also indicated that EDP caused a lowering of inhibin concentrations during pseudopregnancy and small numbers of follicles from 20 to 28 days after EDP. In contrast, EDP-induced pseudopregnancy appears to have no adverse effect on follicular development and subsequent ovulation following PGF2alpha administration.
A methodology for multivariate phenotype-based genome-wide association studies to mine pleiotropic genes
Authors: Park Sung Hee , Lee Ji Young , Kim Sangsoo
Published: December 2011

Background

Current Genome-Wide Association Studies (GWAS) are performed in a single trait framework without considering genetic correlations between important disease traits. Hence, the GWAS have limitations in discovering genetic risk factors affecting pleiotropic effects.

Results

This work reports a novel data mining approach to discover patterns of multiple phenotypic associations over 52 anthropometric and biochemical traits in KARE and a new analytical scheme for GWAS of multivariate phenotypes defined by the discovered patterns. This methodology applied to the GWAS for multivariate phenotype highLDLhighTG derived from the predicted patterns of the phenotypic associations. The patterns of the phenotypic associations were informative to draw relations between plasma lipid levels with bone mineral density and a cluster of common traits (Obesity, hypertension, insulin resistance) related to Metabolic Syndrome (MS). A total of 15 SNPs in six genes (PAK7, C20orf103, NRIP1, BCL2, TRPM3, and NAV1) were identified for significant associations with highLDLhighTG. Noteworthy findings were that the significant associations included a mis-sense mutation (PAK7:R335P), a frame shift mutation (C20orf103) and SNPs in splicing sites (TRPM3).

Conclusions

The six genes corresponded to rat and mouse quantitative trait loci (QTLs) that had shown associations with the common traits such as the well characterized MS and even tumor susceptibility. Our findings suggest that the six genes may play important roles in the pleiotropic effects on lipid metabolism and the MS, which increase the risk of Type 2 Diabetes and cardiovascular disease. The use of the multivariate phenotypes can be advantageous in identifying genetic risk factors, accounting for the pleiotropic effects when the multivariate phenotypes have a common etiological pathway.
Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer
Authors: Kim Sangwoo , Nam Hojung , Lee Doheon
Published: December 2011

Background

Lymph node invasion is one of the most powerful clinical factors in cancer prognosis. However, molecular level signatures of their correlation are remaining poorly understood. Here, we propose a new approach, monotonically expressed gene analysis (MEGA), to correlate transcriptional patterns of lymph node invasion related genes with clinical outcome of breast cancer patients.

Results

Using MEGA, we scored all genes with their transcriptional patterns over progression levels of lymph node invasion from 278 non-metastatic breast cancer samples. Applied on 65 independent test data, our gene sets of top 20 scores (positive and negative correlations) showed significant associations with prognostic measures such as cancer metastasis, relapse and survival. Our method showed better accuracy than conventional two class comparison methods. We could also find that expression patterns of some genes are strongly associated with stage transition of pathological T and N at specific time. Additionally, some pathways including T-cell immune response and wound healing serum response are expected to be related with cancer progression from pathway enrichment and common motif binding site analyses of the inferred gene sets.

Conclusions

By applying MEGA, we can find possible molecular links between lymph node invasion and cancer prognosis in human breast cancer, supported by evidences of feasible gene expression patterns and significant results of meta-analysis tests.
Constitutive expression of a grapevine polygalacturonase-inhibiting protein affects gene expression and cell wall properties in uninfected tobacco
Authors: Alexandersson Erik , Becker John VW , Jacobson Dan , Nguema-Ona Eric , Steyn Cobus , Denby Katherine J , Vivier Melané A
Published: December 2011

Background

Polygalacturonase-inhibiting proteins (PGIPs) directly limit the effective ingress of fungal pathogens by inhibiting cell wall-degrading endopolygalacturonases (ePGs). Transgenic tobacco plants over-expressing grapevine (Vitis vinifera) Vvpgip1 have previously been shown to be resistant to Botrytis infection. In this study we characterized two of these PGIP over-expressing lines with known resistance phenotypes by gene expression and hormone profiling in the absence of pathogen infection.

Results

Global gene expression was performed by a cross-species microarray approach using a potato cDNA microarray. The degree of potential cross-hybridization between probes was modeled by a novel computational workflow designed in-house. Probe annotations were updated by predicting probe-to-transcript hybridizations and combining information derived from other plant species. Comparing uninfected Vvpgip1-overexpressing lines to wild-type (WT), 318 probes showed significant change in expression. Functional groups of genes involved in metabolism and associated to the cell wall were identified and consequent cell wall analysis revealed increased lignin-levels in the transgenic lines, but no major differences in cell wall-derived polysaccharides. GO enrichment analysis also identified genes responsive to auxin, which was supported by elevated indole-acetic acid (IAA) levels in the transgenic lines. Finally, a down-regulation of xyloglucan endotransglycosylase/hydrolases (XTHs), which are important in cell wall remodeling, was linked to a decrease in total XTH activity.

Conclusions

This evaluation of PGIP over-expressing plants performed under pathogen-free conditions to exclude the classical PGIP-ePG inhibition interaction indicates additional roles for PGIPs beyond the inhibition of ePGs.
Social Status Predicts How Sex Steroid Receptors Regulate Complex Behavior across Levels of Biological Organization
Authors: O'Connell Lauren A. , Hofmann Hans A.
Published: December 2011

Social status strongly affects behavior and physiology, in part mediated by gonadal hormones, although how each sex steroid acts across levels of biological organization is not well understood. We examine the role of sex steroids in modulating social behavior in dominant (DOM) and subordinate (SUB) males of a highly social fish, Astatotilapia burtoni. We first used agonists and antagonists to each sex steroid receptor and found that androgens and progestins modulate courtship behavior only in DOM, whereas estrogens modulate aggressive behavior independent of social status. We then examined the hormonal and physiological responses to sex steroid receptor antagonist treatment and uncovered substantial changes in circulating steroid hormone levels and gonad size only in SUB, not in DOM. Consistent with status-based physiological sensitivities to drug manipulation, we found that neuropeptide and steroid receptor gene expression in the preoptic area was sensitive only in SUB. However, when we compared the transcriptomes of males that received either vehicle or an estrogen receptor antagonist, 8.25% of all genes examined changed expression in DOM in comparison with only 0.56% in SUB. Finally, we integrate behavior, physiology, and brain gene expression to infer functional modules that underlie steroid receptor regulation of behavior. Our work suggests that environmentally induced changes at one level of biological organization do not simply affect changes of similar magnitude at other levels, but that instead very few key pathways likely serve as conduits for executing plastic responses across multiple levels.
Defining POMC Neurons Using Transgenic Reagents: Impact of Transient Pomc Expression in Diverse Immature Neuronal Populations
Authors: Padilla Stephanie L. , Reef Daniel , Zeltser Lori M.
Published: December 2011

Melanocortin signaling plays a central role in the regulation of phenotypes related to body weight and energy homeostasis. To specifically target and study the function of proopiomelanocortin (POMC) neurons, Pomc promoter elements have been utilized to generate reporter and Cre recombinase transgenic reagents. Across gestation, we find that Pomc is dynamically expressed in many sites in the developing mouse forebrain, midbrain, hindbrain, spinal cord, and retina. Although Pomc expression in most embryonic brain regions is transient, it is sufficient to direct Cre-mediated recombination of floxed alleles. We visualize the populations affected by this transgene by crossing Pomc-Cre mice to ROSA reporter strains and identify 62 sites of recombination throughout the adult brain, including several nuclei implicated in energy homeostasis regulation. To compare the relationship between acute Pomc promoter activity and Pomc-Cre-mediated recombination at the single cell level, we crossed Pomc-enhanced green fluorescent protein (eGFP) and Pomc-Cre;ROSA-tdTomato lines. We detect the highest concentration of Pomc-eGFP+ cells in the arcuate nucleus of the hypothalamus and dentate gyrus but also observe smaller populations of labeled cells in the nucleus of the solitary tract, periventricular zone of the third ventricle, and cerebellum. Consistent with the dynamic nature of Pomc expression in the embryo, the vast majority of neurons marked with the tdTomato reporter do not express eGFP in the adult. Thus, recombination in off-target sites could contribute to physiological phenotypes using Pomc-Cre transgenics. For example, we find that approximately 83% of the cells in the arcuate nucleus of the hypothalamus immunoreactive for leptin-induced phosphorylated signal transducer and activator of transcription 3 are marked with Pomc-Cre;ROSA-tdTomato; only 13% of these are eGFP+ POMC neurons.
Belief and Indeterminacy
Authors: Caie Michael
Published: December 2011

An attractive approach to the semantic paradoxes holds that cases of semantic pathology give rise to indeterminacy. What attitude should a rational agent have toward a proposition that it takes to be indeterminate in this sense? Orthodoxy holds that rationality requires that an agent disbelieve such a proposition. I argue that a rational agent should be such that it is indeterminate whether it believes the proposition in question. For rational agents, indeterminacy in the objects of their attitudes will filter up to the attitudes themselves.
Copper-catalyzed alkyne-azide cycloaddition for the functionalization of fullerene building blocks
Authors: Nierengarten Jean-François
Published: December 2011

In this paper, we report our ongoing progress in the preparation of fullerene-azide or fullerene-alkyne building blocks, allowing their further chemical transformation under the copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction conditions.
Specificity Characteristics of 7 Commercial Creatinine Measurement Procedures by Enzymatic and Jaffe Method Principles
Authors: Greenberg Neil , Roberts William L , Bachmann Lorin M , Wright Elizabeth C , Dalton R Neil , Zakowski Jack J , Greg Miller W
Published: December 2011

BACKGROUND

Standardized calibration does not change a creatinine measurement procedure's susceptibility to potentially interfering substances.

METHODS

We obtained individual residual serum or plasma samples (n = 365) from patients with 19 different disease categories associated with potentially interfering substances and from healthy controls. Additional sera at 0.9 mg/dL (80 μmol/L) and 3.8 mg/dL (336 μmol/L) creatinine were supplemented with acetoacetate, acetone, ascorbate, and pyruvate. We measured samples by 4 enzymatic and 3 Jaffe commercially available procedures and by a liquid chromatography/isotope dilution/mass spectrometry measurement procedure against which biases were determined.

RESULTS

The number of instances when 3 or more results in a disease category had biases greater than the limits of acceptability was 28 of 57 (49%) for Jaffe and 14 of 76 (18%) for enzymatic procedures. For the aggregate group of 59 diabetes samples with increased β-hydroxybutyrate, glucose, or glycosylated hemoglobin (Hb A1c), the enzymatic procedures had 10 biased results of 236 (4.2%) compared with 89 of 177 (50.3%) for the Jaffe procedures, and these interferences were highly procedure dependent. For supplemented sera, interferences were observed in 11 of 24 (46%) of groups for Jaffe and 8 of 32 (25%) of groups for enzymatic procedures and were different at low or high creatinine concentrations.

CONCLUSIONS

There were differences in both magnitude and direction of bias among measurement procedures, whether enzymatic or Jaffe. The influence of interfering substances was less frequent with the enzymatic procedures, but no procedure was unaffected. The details of implementation of a method principle influenced its susceptibility to potential interfering substances.
Neurosteroidogenesis Is Required for the Physiological Response to Stress: Role of Neurosteroid-Sensitive GABAAReceptors
Authors: Sarkar Jhimly , Wakefield Seth , MacKenzie Georgina , Moss Stephen J. , Maguire Jamie
Published: December 2011

The hypothalamic-pituitary-adrenal (HPA) axis, which mediates the body's response to stress, is largely under GABAergic control. Here we demonstrate that corticotropin-releasing hormone (CRH) neurons are modulated by the stress-derived neurosteroid, tetrahydrodeoxycorticosterone (THDOC), acting on δ subunit-containing GABAAreceptors (GABAARs). Under normal conditions, THDOC potentiates the inhibitory effects of GABA on CRH neurons, decreasing the activity of the HPA axis. Counterintuitively, following stress, THDOC activates the HPA axis due to dephosphorylation of KCC2 residue Ser940, resulting in a collapse of the chloride gradient and excitatory GABAergic transmission. The effects of THDOC on CRH neurons are mediated by actions on GABAAR δ subunit-containing receptors since these effects are abolished inGabrd−/−mice under both control and stress conditions. Interestingly, blocking neurosteroidogenesis with finasteride is sufficient to block the stress-induced elevations in corticosterone and prevent stress-induced anxiety-like behaviors in mice. These data demonstrate that positive feedback of neurosteroids onto CRH neurons is required to mount the physiological response to stress. Further, GABAAR δ subunit-containing receptors and phosphorylation of KCC2 residue Ser940 may be novel targets for control of the stress response, which has therapeutic potential for numerous disorders associated with hyperexcitability of the HPA axis, including Cushing's syndrome, epilepsy, and major depression.
The Chemokine CCL2 Increases Nav1.8 Sodium Channel Activity in Primary Sensory Neurons through a Gβγ-Dependent Mechanism
Authors: Belkouch Mounir , Dansereau Marc-André , Réaux-Le Goazigo Annabelle , Van Steenwinckel Juliette , Beaudet Nicolas , Chraibi Ahmed , Melik-Parsadaniantz Stéphane , Sarret Philippe
Published: December 2011

Changes in function of voltage-gated sodium channels in nociceptive primary sensory neurons participate in the development of peripheral hyperexcitability that occurs in neuropathic and inflammatory chronic pain conditions. Among them, the tetrodotoxin-resistant (TTX-R) sodium channel Nav1.8, primarily expressed by small- and medium-sized dorsal root ganglion (DRG) neurons, substantially contributes to the upstroke of action potential in these neurons. Compelling evidence also revealed that the chemokine CCL2 plays a critical role in chronic pain facilitation via its binding to CCR2 receptors. In this study, we therefore investigated the effects of CCL2 on the density and kinetic properties of TTX-R Nav1.8 currents in acutely small/medium dissociated lumbar DRG neurons from naive adult rats. Whole-cell patch-clamp recordings demonstrated that CCL2 concentration-dependently increased TTX-resistant Nav1.8 current densities in both small- and medium-diameter sensory neurons. Incubation with CCL2 also shifted the activation and steady-state inactivation curves of Nav1.8 in a hyperpolarizing direction in small sensory neurons. No change in the activation and inactivation kinetics was, however, observed in medium-sized nociceptive neurons. Our electrophysiological recordings also demonstrated that the selective CCR2 antagonist INCB3344 [N-[2-[[(3S,4S)-1-E4-(1,3-benzodioxol-5-yl)-4-hydroxycyclohexyl]-4-ethoxy-3-pyrrolidinyl]amino]-2-oxoethyl]-3-(trifluoromethyl)benzamide] blocks the potentiation of Nav1.8 currents by CCL2 in a concentration-dependent manner. Furthermore, the enhancement in Nav1.8 currents was prevented by pretreatment with pertussis toxin (PTX) or gallein (a Gβγ inhibitor), indicating the involvement of Gβγ released from PTX-sensitive Gi/o-proteins in the cross talk between CCR2 and Nav1.8. Together, our data clearly demonstrate that CCL2 may excite primary sensory neurons by acting on the biophysical properties of Nav1.8 currents via a CCR2/Gβγ-dependent mechanism.
Ceruloplasmin Oxidation, a Feature of Parkinson's Disease CSF, Inhibits Ferroxidase Activity and Promotes Cellular Iron Retention
Authors: Olivieri Stefano , Conti Antonio , Iannaccone Sandro , Cannistraci Carlo V. , Campanella Alessandro , Barbariga Marco , Codazzi Franca , Pelizzoni Ilaria , Magnani Giuseppe , Pesca Mariasabina , Franciotta Diego , Cappa Stefano F. , Alessio Massimo
Published: December 2011

Parkinson's disease is a neurodegenerative disorder characterized by oxidative stress and CNS iron deposition. Ceruloplasmin is an extracellular ferroxidase that regulates cellular iron loading and export, and hence protects tissues from oxidative damage. Using two-dimensional electrophoresis, we investigated ceruloplasmin patterns in the CSF of human Parkinson's disease patients. Parkinson's disease ceruloplasmin profiles proved more acidic than those found in healthy controls and in other human neurological diseases (peripheral neuropathies, amyotrophic lateral sclerosis, and Alzheimer's disease); degrees of acidity correlated with patients' pathological grading. Applying an unsupervised pattern recognition procedure to the two-dimensional electrophoresis images, we identified representative pathological clusters.In vitrooxidation of CSF in two-dimensional electrophoresis generated a ceruloplasmin shift resembling that observed in Parkinson's disease and co-occurred with an increase in protein carbonylation. Likewise, increased protein carbonylation was observed in Parkinson's disease CSF, and the same modification was directly identified in these samples on ceruloplasmin. These results indicate that ceruloplasmin oxidation contributes to pattern modification in Parkinson's disease. From the functional point of view, ceruloplasmin oxidation caused a decrease in ferroxidase activity, which in turn promotes intracellular iron retention in neuronal cell lines as well as in primary neurons, which are more sensitive to iron accumulation. Accordingly, the presence of oxidized ceruloplasmin in Parkinson's disease CSF might be used as a marker for oxidative damage and might provide new insights into the underlying pathological mechanisms.
Optimizing the Decoding of Movement Goals from Local Field Potentials in Macaque Cortex
Authors: Markowitz David A. , Wong Yan T. , Gray Charles M. , Pesaran Bijan
Published: December 2011

The successful development of motor neuroprosthetic devices hinges on the ability to accurately and reliably decode signals from the brain. Motor neuroprostheses are widely investigated in behaving non-human primates, but technical constraints have limited progress in optimizing performance. In particular, the organization of movement-related neuronal activity across cortical layers remains poorly understood due, in part, to the widespread use of fixed-geometry multielectrode arrays. In this study, we use chronically implanted multielectrode arrays with individually movable electrodes to examine how the encoding of movement goals depends on cortical depth. In a series of recordings spanning several months, we varied the depth of each electrode in the prearcuate gyrus of frontal cortex in two monkeys as they performed memory-guided eye movements. We decode eye movement goals from local field potentials (LFPs) and multiunit spiking activity recorded across a range of depths up to 3 mm from the cortical surface. We show that both LFP and multiunit signals yield the highest decoding performance at superficial sites, within 0.5 mm of the cortical surface, while performance degrades substantially at sites deeper than 1 mm. We also analyze performance by varying bandpass filtering characteristics and simulating changes in microelectrode array channel count and density. The results indicate that the performance of LFP-based neuroprostheses strongly depends on recording configuration and that recording depth is a critical parameter limiting system performance.
Conduction Failure following Spinal Cord Injury: Functional and Anatomical Changes from Acute to Chronic Stages
Authors: James Nicholas D. , Bartus Katalin , Grist John , Bennett David L. H. , McMahon Stephen B. , Bradbury Elizabeth J.
Published: December 2011

In the majority of spinal cord injuries (SCIs), some axonal projections remain intact. We examined the functional status of these surviving axons since they represent a prime therapeutic target. Using a novel electrophysiological preparation, adapted from techniques used to study primary demyelination, we quantified conduction failure across a SCI and studied conduction changes over time in adult rats with a moderate severity spinal contusion (150 kdyn; Infinite Horizon impactor). By recording antidromically activated single units from teased dorsal root filaments, we demonstrate complete conduction block in ascending dorsal column axons acutely (1–7 d) after injury, followed by a period of restored conduction over the subacute phase (2–4 weeks), with no further improvements in conduction at chronic stages (3–6 months). By cooling the lesion site, additional conducting fibers could be recruited, thus revealing a population of axons that are viable but unable to conduct under normal physiological conditions. Importantly, this phenomenon is still apparent at the most chronic (6 month) time point. The time course of conduction changes corresponded with changes in behavioral function, and ultrastructural analysis of dorsal column axons revealed extensive demyelination during the period of conduction block, followed by progressive remyelination. A proportion of dorsal column axons remained chronically demyelinated, suggesting that these are the axons recruited with the cooling paradigm. Thus, using a clinically relevant SCI model, we have identified a population of axons present at chronic injury stages that are intact but fail to conduct and are therefore a prime target for therapeutic strategies to restore function.
Attention for Learning Signals in Anterior Cingulate Cortex
Authors: Bryden Daniel W. , Johnson Emily E. , Tobia Steven C. , Kashtelyan Vadim , Roesch Matthew R.
Published: December 2011

Learning theory suggests that animals attend to pertinent environmental cues when reward contingencies unexpectedly change so that learning can occur. We have previously shown that activity in basolateral nucleus of amygdala (ABL) responds to unexpected changes in reward value, consistent with unsigned prediction error signals theorized by Pearce and Hall. However, changes in activity were present only at the time of unexpected reward delivery, not during the time when the animal needed to attend to conditioned stimuli that would come to predict the reward. This suggested that a different brain area must be signaling the need for attention necessary for learning. One likely candidate to fulfill this role is the anterior cingulate cortex (ACC). To test this hypothesis, we recorded from single neurons in ACC as rats performed the same behavioral task that we have used to dissociate signed from unsigned prediction errors in dopamine and ABL neurons. In this task, rats chose between two fluid wells that produced varying magnitudes of and delays to reward. Consistent with previous work, we found that ACC detected errors of commission and reward prediction errors. We also found that activity during cue sampling encoded reward size, but not expected delay to reward. Finally, activity in ACC was elevated during trials in which attention was increased following unexpected upshifts and downshifts in value. We conclude that ACC not only signals errors in reward prediction, as previously reported, but also signals the need for enhanced neural resources during learning on trials subsequent to those errors.
Non-Equilibrium Kinetic Studies of Plasma-Assisted Combustion using Laser-Based Diagnostics
Authors: Grisch F. , Grandin G. A. , Messina D. , Attal-Tretout B.
Published: December 2011

Experimental investigation of nanosecond pulsed discharge in premixed CH4/air mixtures at atmospheric pressure has been carried out using laser diagnostics. Electron temperature and number density are measured using laser Thomson scattering. Temperature of neutral molecules is measured by CARS. Finally, OH, CH and CH2O are probed using PLIF to identify their role in the reduction of ignition delay and in the improvement of lean burn capability relative to conventional spark ignition. Measurements are compared with numerical simulations performed using CHEMKIN-based code.
Process Control of CVD Deposition of Nanocrystalline Diamond Films by Plasma Diagnostics
Authors: Woehrl Nicolas , Buck Volker
Published: December 2011

Ultrananocrystalline Diamond (UNCD) Films were deposited by MW-CVD from an Ar/H2/CH4 plasma. The plasma properties were measured in situ by optical emission spectroscopy and mass spectroscopy. The intensity of the C2 emission line was systematically varied as a key plasma parameter and a correlation with resulting film properties was found.
Single Acetone Droplets at Supercritical Pressure: Droplet Generation and Characterization of PLIFP
Authors: Weckenmann F. , Bork B. , Oldenhof E. , Lamanna G. , Weigand B. , Böhm B. , Dreizler A.
Published: December 2011

An experimental investigation of isolated acetone droplets under supercritical pressure is presented. An optically accessible pressure chamber was set up for pressures ranging up to 60 bar and temperatures of up to 530 K. A novel method for the generation of acetone droplets on demand in the vicinity of the critical point is presented. High speed shadowgraphy imaging revealed remarkable reproducibility of the droplet generation regarding their size and shape and the timing of the detachment.

The photo-physical properties of acetone in nitrogen as well as nitrogen-oxygen mixtures were investigated using planar laser induced fluorescence and phosphorescence (PLIFP). The measurements revealed a strong sensitivity and selectivity of the phosphorescence-fluorescence-ratio relative to the oxygen concentration. This demonstrates the potential of PLIFP to distinguish between the liquid and gaseous phase of acetone injected into mixtures of nitrogen and oxygen.
Dispersed Fluorescence Spectra of 1H- and 1D-Indazole
Authors: Nicken Hauke , Temps Friedrich , Jalviste Erko
Published: December 2011

Dispersed fluorescence (DF) spectra of jet-cooled indazole (Ia-h) and its singly-deuterated isotopologue (Ia-d) were recorded following excitation of the origin band of the S
1(1
A´) ← S
0(1
A´) electronic transition. The spectra were analyzed and assigned with the help of vibrational frequency calculations by density functional theory (DFT) at the TPSS/aug-cc-pVTZ level. The calculated and measured S
0 state vibrations are in agreement within ≤ 3%. The obtained results for the two Ia monomers form the basis for an analysis of the electronic spectra of the hydrogen-bonded dimers Ia2-hh, Ia2-dd and Ia2-hd and a determination of the exciton splitting in the dimer in a forthcoming paper.
Embryonic epithelial Pten deletion through Nkx2.1-cre leads to thyroid tumorigenesis in a strain-dependent manner
Authors: Tiozzo Caterina , Danopoulos Soula , Lavarreda-Pearce Maria , Baptista Sheryl , Varimezova Radka , Al Alam Denise , Warburton David , Virender Rehan , De Langhe Stijn , Di Cristofano Antonio , Bellusci Saverio , Minoo Parviz
Published: December 2011

Even though the role of the tyrosine phosphatasePtenas a tumor suppressor gene has been well established in thyroid cancer, its role during thyroid development is still elusive. We therefore targetedPtendeletion in the thyroid epithelium by crossingPtenflox/floxwith a newly developedNkx2.1-credriver line in the BALB/c and C57BL/6 genetic backgrounds. C57BL/6 homozygousPtenmutant mice died around 2 weeks of age due to tracheal and esophageal compression by a hyperplasic thyroid. By contrast, BALB/c homozygousPtenmutant mice survived up to 2 years, but with a slightly increased thyroid volume. Characterization of the thyroid glands from C57BL/6 homozygousPtenmutant mice at postnatal day 14 (PN14) showed abnormally enlarged tissue with areas of cellular hyperplasia, disruption of the normal architecture, and follicular degeneration. In addition, differing degrees of hypothyroidism, thyroxine (T4) decrease, and thyroid-stimulating hormone elevation between the strains in the mutants and the heterozygous mutant were detected at PN14. Finally, C57BL/6 heterozygousPtenmutant mice developed thyroid tumors after 2 years of age. Our results indicate thatPtenhas a pivotal role in thyroid development and its deletion results in thyroid tumor formation, with the timing and severity of the tumor depending on the particular genetic background.
Fluorescence In Situ Hybridization–Based Karyotyping of Soybean Translocation Lines
Authors: Findley Seth D , Pappas Allison L , Cui Yaya , Birchler James A , Palmer Reid G , Stacey Gary
Published: December 2011

Soybean (Glycine max [L.] Merr.) is a major crop species and, therefore, a major target of genomic and genetic research. However, in contrast to other plant species, relatively few chromosomal aberrations have been identified and characterized in soybean. This is due in part to the difficulty of cytogenetic analysis of its small, morphologically homogeneous chromosomes. The recent development of a fluorescence in situ hybridization –based karyotyping system for soybean has enabled our characterization of most of the chromosomal translocation lines identified to date. Utilizing genetic data from existing translocation studies in soybean, we identified the chromosomes and approximate breakpoints involved in five translocation lines.
Variability of Gene Expression After Polyhaploidization in Wheat (Triticum aestivumL.)
Authors: Wang Jiali , Liu Dongcheng , Guo Xiaoli , Yang Wenlong , Wang XiuJie , Zhan Kehui , Zhang Aimin
Published: December 2011

Interspecific hybridization has a much greater effect than chromosome doubling on gene expression; however, the associations between homeologous gene expression changes and polyhaploidization had rarely been addressed. In this study, cDNA–single strand conformation polymorphism analysis was applied to measure the expression of 30 homeologous transcripts in naturally occurring haploid (ABD, 2n = 21) and its polyploid maternal parent Yumai 21A (AABBDD, 2n = 42) in wheat. Only one gene (TC251989) showed preferentially silenced homoeoalleles in haploids. Further analyses of 24 single-copy genes known to be silenced in the root and/or leaf also found no evidence of homeologous silencing in 1-month-old haploids and two ESTs (BF484100 and BF473379) exhibit different expression patterns between 4-month-old haploids and hexaploids. Global analysis of the gene expression patterns using the Affymetrix GeneChip showed that of the 55,052 genes probed, only about 0.11% in the shoots and 0.25% in the roots were activated by polyhaploidization. The results demonstrate that activation and silencing of homoeoalleles were not widespread in haploid seedlings.
High-Resolution Genotyping of Wild Barley Introgression Lines and Fine-Mapping of the Threshability Locus thresh-1 Using the Illumina GoldenGate Assay
Authors: Schmalenbach Inga , March Timothy J , Bringezu Thomas , Waugh Robbie , Pillen Klaus
Published: December 2011

Genetically well-characterized mapping populations are a key tool for rapid and precise localization of quantitative trait loci (QTL) and subsequent identification of the underlying genes. In this study, a set of 73 introgression lines (S42ILs) originating from a cross between the spring barley cultivar Scarlett (Hordeum vulgare ssp. vulgare) and the wild barley accession ISR42-8 (H. v. ssp. spontaneum) was subjected to high-resolution genotyping with an Illumina 1536-SNP array. The array enabled a precise localization of the wild barley introgressions in the elite barley background. Based on 636 informative SNPs, the S42IL set represents 87.3% of the wild barley genome, where each line contains on average 3.3% of the donor genome. Furthermore, segregating high-resolution mapping populations (S42IL-HRs) were developed for 70 S42ILs in order to facilitate QTL fine-mapping and cloning. As a case study, we used the developed genetic resources to rapidly identify and fine-map the novel locus thresh-1 on chromosome 1H that controls grain threshability. Here, the recessive wild barley allele confers a difficult to thresh phenotype, suggesting that thresh-1 played an important role during barley domestication. Using a S42IL-HR population, thresh-1 was fine-mapped within a 4.3cM interval that was predicted to contain candidate genes involved in regulation of plant cell wall composition. The set of wild barley introgression lines and derived high-resolution populations are ideal tools to speed up the process of mapping and further dissecting QTL, which ultimately clears the way for isolating the genes behind QTL effects.
Sequence Analysis of the Segmental Duplication Responsible for ParisSex-RatioDrive inDrosophila simulans
Authors: Fouvry Lucie , Ogereau David , Berger Anne , Gavory Frederick , Montchamp-Moreau Catherine
Published: December 2011

Sex-ratio distorters are X-linked selfish genetic elements that facilitate their own transmission by subverting Mendelian segregation at the expense of the Y chromosome. Naturally occurring cases of sex-linked distorters have been reported in a variety of organisms, including several species of Drosophila; they trigger genetic conflict over the sex ratio, which is an important evolutionary force. However, with a few exceptions, the causal loci are unknown. Here, we molecularly characterize the segmental duplication involved in the Paris sex-ratio system that is still evolving in natural populations of Drosophila simulans. This 37.5 kb tandem duplication spans six genes, from the second intron of the Trf2 gene (TATA box binding protein-related factor 2) to the first intron of the org-1 gene (optomotor-blind-related-gene-1). Sequence analysis showed that the duplication arose through the production of an exact copy on the template chromosome itself. We estimated this event to be less than 500 years old. We also detected specific signatures of the duplication mechanism; these support the Duplication-Dependent Strand Annealing model. The region at the junction between the two duplicated segments contains several copies of an active transposable element, Hosim1, alternating with 687 bp repeats that are noncoding but transcribed. The almost-complete sequence identity between copies made it impossible to complete the sequencing and assembly of this region. These results form the basis for the functional dissection of Paris sex-ratio drive and will be valuable for future studies designed to better understand the dynamics and the evolutionary significance of sex chromosome drive.
A Synthetic Human Kinase Can Control Cell Cycle Progression in Budding Yeast
Authors: Davey Megan J , Andrighetti Heather J , Ma Xiaoli , Brandl Christopher J
Published: December 2011

The DDK kinase complex, composed of Cdc7 and Dbf4, is required for S-phase progression. The two component proteins show different degrees of sequence conservation between human and yeast. Here, we determine that Saccharomyces cerevisiae bearing human CDC7 and DBF4 grows comparably to cells with yeast DDK under standard growth conditions. HsDrf1 (a second human Dbf4-like protein) does not support growth, suggesting that HsDbf4 is the true ortholog of ScDbf4. Both human subunits are required to complement yeast cdc7Δ or dbf4Δ due to the inability of human Cdc7 or Dbf4 to interact with the corresponding yeast protein. Flow cytometry indicates normal cell cycle progression for yeast containing human DDK. However, yeast containing human DDK is sensitive to long-term exposure to hydroxyurea and fails to sporulate, suggesting that human DDK substitutes for some, but not all, of yeast DDK’s functions. We mapped the region of Cdc7 required for species-specific function of DDK to the C-terminus of Cdc7 by substituting the yeast C-terminal 55 amino acid residues in place of the equivalent human residues. The resulting hybrid protein supported growth of a cdc7Δ strain only in the presence of ScDBF4. The strain supported by the hybrid CDC7 was not sensitive to HU and formed tetrads. Together, our data indicate that DDK’s targeting of its essential substrate is conserved between species, whereas the interactions within DDK are species specific.
High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly UsedCandida albicansStrains
Authors: Abbey Darren , Hickman Meleah , Gresham David , Berman Judith
Published: December 2011

Phenotypic diversity can arise rapidly through loss of heterozygosity (LOH) or by the acquisition of copy number variations (CNV) spanning whole chromosomes or shorter contiguous chromosome segments. In Candida albicans, a heterozygous diploid yeast pathogen with no known meiotic cycle, homozygosis and aneuploidy alter clinical characteristics, including drug resistance. Here, we developed a high-resolution microarray that simultaneously detects ∼39,000 single nucleotide polymorphism (SNP) alleles and ∼20,000 copy number variation loci across the C. albicans genome. An important feature of the array analysis is a computational pipeline that determines SNP allele ratios based upon chromosome copy number. Using the array and analysis tools, we constructed a haplotype map (hapmap) of strain SC5314 to assign SNP alleles to specific homologs, and we used it to follow the acquisition of loss of heterozygosity (LOH) and copy number changes in a series of derived laboratory strains. This high-resolution SNP/CGH microarray and the associated hapmap facilitated the phasing of alleles in lab strains and revealed detrimental genome changes that arose frequently during molecular manipulations of laboratory strains. Furthermore, it provided a useful tool for rapid, high-resolution, and cost-effective characterization of changes in allele diversity as well as changes in chromosome copy number in new C. albicans isolates.
Physical Mapping in a Triplicated Genome: Mapping the Downy Mildew Resistance LocusPp523inBrassica oleraceaL.
Authors: Carlier Jorge D , Alabaça Claudia S , Sousa Nelson H , Coelho Paula S , Monteiro António A , Paterson Andrew H , Leitão José M
Published: December 2011

We describe the construction of a BAC contig and identification of a minimal tiling path that encompass the dominant and monogenically inherited downy mildew resistance locus Pp523 of Brassica oleracea L. The selection of BAC clones for construction of the physical map was carried out by screening gridded BAC libraries with DNA overgo probes derived from both genetically mapped DNA markers flanking the locus of interest and BAC-end sequences that align to Arabidopsis thaliana sequences within the previously identified syntenic region. The selected BAC clones consistently mapped to three different genomic regions of B. oleracea. Although 83 BAC clones were accurately mapped within a ∼4.6 cM region surrounding the downy mildew resistance locus Pp523, a subset of 33 BAC clones mapped to another region on chromosome C8 that was ∼60 cM away from the resistance gene, and a subset of 63 BAC clones mapped to chromosome C5. These results reflect the triplication of the Brassica genomes since their divergence from a common ancestor shared with A. thaliana, and they are consonant with recent analyses of the C genome of Brassica napus. The assembly of a minimal tiling path constituted by 13 (BoT01) BAC clones that span the Pp523 locus sets the stage for map-based cloning of this resistance gene.
A Geographically Diverse Collection ofSchizosaccharomyces pombeIsolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity
Authors: Brown William R A , Liti Gianni , Rosa Carlos , James Steve , Roberts Ian , Robert Vincent , Jolly Neil , Tang Wen , Baumann Peter , Green Carter , Schlegel Kristina , Young Jonathan , Hirchaud Fabienne , Leek Spencer , Thomas Geraint , Blomberg Anders , Warringer Jonas
Published: December 2011

The fission yeast Schizosaccharomyces pombe has been widely used to study eukaryotic cell biology, but almost all of this work has used derivatives of a single strain. We have studied 81 independent natural isolates and 3 designated laboratory strains of Schizosaccharomyces pombe. Schizosaccharomyces pombe varies significantly in size but shows only limited variation in proliferation in different environments compared with Saccharomyces cerevisiae. Nucleotide diversity, π, at a near neutral site, the central core of the centromere of chromosome II is approximately 0.7%. Approximately 20% of the isolates showed karyotypic rearrangements as detected by pulsed field gel electrophoresis and filter hybridization analysis. One translocation, found in 6 different isolates, including the type strain, has a geographically widespread distribution and a unique haplotype and may be a marker of an incipient speciation event. All of the other translocations are unique. Exploitation of this karyotypic diversity may cast new light on both the biology of telomeres and centromeres and on isolating mechanisms in single-celled eukaryotes.
Genotype Imputation with Thousands of Genomes
Authors: Howie Bryan , Marchini Jonathan , Stephens Matthew
Published: December 2011

Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. These panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 Genomes Project produce larger and more diverse reference sets, which led us to develop an alternative framework. Our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. This approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. Using data from HapMap 3, we show that our framework produces accurate results in a wide range of human populations. We also use data from the Malaria Genetic Epidemiology Network (MalariaGEN) to provide recommendations for imputation-based studies in Africa. We demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. Genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. New methodology from this study is implemented in the IMPUTE2 software package.
A avaliação do custo eficácia das intervenções em organizações de saúde
Authors: Lima Clóvis Ricardo Montenegro de , Lima Carlos Rogério Montenegro de
Published: December 2011

Os principais problemas das organizações de saúde são má alocação de recursos, ineficiência, custos crescentes e desigualdade nas condições de acesso dos usuários. A rentabilidade expressa resultados por recursos aplicados. A avaliação custo-eficácia das intervenções das organizações de saúde busca soluções de menor despesa para obter resultado esperado e de melhor resultado com determinada despesa. O ABC - activity-based costing- é o método de custeio que melhor subsidia a decisão sobre composição de atividades, custo de recursos e consumo de recursos. A avaliação custo-eficácia mostra-se, portanto, uma ferramenta útil para a melhoria da qualidade das organizações de saúde.
Descripción del postcráneo de Rhipidomys austrinus y Graomys griseoflavus (Rodentia, Cricetidae, Sigmodontinae)
Authors: Carrizo Luz V. , Díaz Mónica
Published: December 2011

Se describe el esqueleto postcraneal de dos especies de roedores sigmodontinos Rhipidomys austrinus Thomas, 1921 y Graomys griseoflavus (Waterhouse, 1837). Se detalla cada estructura del esqueleto postcraneal sobre la base de la forma, tamaño, superficie y orientación de cada elemento esqueletal. La anatomía postcraneal de estas dos especies muestra caracteres asociados a patrones morfológicos diferentes, vinculados a su modo de locomoción. Es así que R. austrinus exhibe características en varios elementos del postcráneo consistente con una locomoción arborícola, mientras G. griseoflavus muestra atributos en su esqueleto relacionados a una locomoción de tipo terrestre.