Measures of Heart Rate Variability in Individuals With Somatic Symptom Disorder.

PubMed

Huang, Wei-Lieh; Liao, Shih-Cheng; Yang, Cheryl C H; Kuo, Terry B J; Chen, Tzu-Ting; Chen, I-Ming; Gau, Susan Shur-Fen

2017-01-01

Little is known about autonomic nervous system activity in individuals with somatic symptom disorder (SSD) as defined by DSM-V criteria. The aims of this study were to investigate whether individuals with SSD differ from healthy controls in heart rate variability (HRV) measures of autonomic nervous system activity and whether sex has a moderating effect on this association. We recruited 168 individuals with SSD (35.1% men) and 106 healthy controls (27.4% men). Demographics, HRV, and psychological factors were measured using the Patient Health Questionnaire-15, Health Anxiety Questionnaire, Beck Depression Inventory-II (BDI-II), and Beck Anxiety Inventory. Multiple regression analysis was used to examine the association of SSD with HRV, adjusting for demographic and psychological measures. Individuals with SSD had lower levels of total-power HRV and low-frequency HRV, but no differences in high-frequency (HF)-HRV were found. HRV differences between SSD and controls varied by sex and age (triple interaction TP-HRV β = -0.222, p < .001; low-frequency HRV β = -0.332, p < .001; and HF-HRV β = -0.167, p = .006). Whole-sample multiple regression analyses revealed significant sex differences in the magnitudes of the association between BDI-II with HF-HRV (β of sex*BDI-II: 0.761, p = .005) and analyses stratified by sex indicated that HF-HRV was significantly correlated with depression in men with SSD (r = -0.491, p < .001) but not in women with SSD (r = 0.057, p = .558). These results suggest that patients with SSD demonstrate different patterns of HRV and the patterns of association between HRV indices and psychological factors vary between men and women.

Down-regulation of the detoxifying enzyme NAD(P)H:quinone oxidoreductase 1 by vanadium in Hepa 1c1c7 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anwar-Mohamed, Anwar; El-Kadi, Ayman O.S.

2009-05-01

Recent data suggest that vanadium (V{sup 5+}) compounds exert protective effects against chemical-induced carcinogenesis, mainly through modifying various xenobiotic metabolizing enzymes. In fact, we have shown that V{sup 5+} down-regulates the expression of Cyp1a1 at the transcriptional level through an ATP-dependent mechanism. However, incongruously, there is increasing evidence that V{sup 5+} is found in higher amounts in cancer cells and tissues than in normal cells or tissues. Therefore, the current study aims to address the possible effect of this metal on the regulation of expression of an enzyme that helps maintain endogenous antioxidants used to protect tissues/cells from mutagens, carcinogens,more » and oxidative stress damage, NAD(P)H:quinone oxidoreductase 1 (Nqo1). In an attempt to examine these effects, Hepa 1c1c7 cells and its AhR-deficient version, c12, were treated with increasing concentrations of V{sup 5+} in the presence of two distinct Nqo1 inducers, the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and isothiocyanate sulforaphane (SUL). Our results showed that V{sup 5+} inhibits the TCDD- and SUL-mediated induction of Nqo1 at mRNA, protein, and catalytic activity levels. At transcriptional level, V{sup 5+} was able to decrease the TCDD- and SUL-induced nuclear accumulation of Nrf2 and the subsequent binding to antioxidant responsive element (ARE) without affecting Nrf2 protein levels. Looking at post-transcriptional level; we found that V{sup 5+} did not affect Nqo1 mRNA transcripts turn-over rates. However, at the post-translational level V{sup 5+} increased Nqo1 protein half-life. In conclusion, the present study demonstrates that V{sup 5+} down-regulates Nqo1 at the transcriptional level, possibly through inhibiting the ATP-dependent activation of Nrf2.« less

Androgen Receptor and its Splice Variant, AR-V7, Differentially Regulate FOXA1 Sensitive Genes in LNCaP Prostate Cancer Cells

PubMed Central

Krause, William C.; Shafi, Ayesha A.; Nakka, Manjula; Weigel, Nancy L.

2014-01-01

Prostate cancer (PCa) is an androgen-dependent disease, and tumors that are resistant to androgen ablation therapy often remain androgen receptor (AR) dependent. Among the contributors to castration-resistant PCa are AR splice variants that lack the ligand-binding domain (LBD). Instead, they have small amounts of unique sequence derived from cryptic exons or from out of frame translation. The AR-V7 (or AR3) variant is constitutively active and is expressed under conditions consistent with CRPC. AR-V7 is reported to regulate a transcriptional program that is similar but not identical to that of AR. However, it is unknown whether these differences are due to the unique sequence in AR-V7, or simply to loss of the LBD. To examine transcriptional regulation by AR-V7, we have used lentiviruses encoding AR-V7 (amino acids 1-627 of AR with the 16 amino acids unique to the variant) to prepare a derivative of the androgen-dependent LNCaP cells with inducible expression of AR-V7. An additional cell line was generated with regulated expression of AR-NTD (amino acids 1-660 of AR); this mutant lacks the LBD but does not have the AR-V7 specific sequence. We find that AR and AR-V7 have distinct activities on target genes that are co-regulated by FOXA1. Transcripts regulated by AR-V7 were similarly regulated by AR-NTD, indicating that loss of the LBD is sufficient for the observed differences. Differential regulation of target genes correlates with preferential recruitment of AR or AR-V7 to specific cis-regulatory DNA sequences providing an explanation for some of the observed differences in target gene regulation. PMID:25008967

Clinical implementation of MOSFET detectors for dosimetry in electron beams.

PubMed

Bloemen-van Gurp, Esther J; Minken, Andre W H; Mijnheer, Ben J; Dehing-Oberye, Cary J G; Lambin, Philippe

2006-09-01

To determine the factors converting the reading of a MOSFET detector placed on the patient's skin without additional build-up to the dose at the depth of dose maximum (D(max)) and investigate their feasibility for in vivo dose measurements in electron beams. Factors were determined to relate the reading of a MOSFET detector to D(max) for 4 - 15 MeV electron beams in reference conditions. The influence of variation in field size, SSD, angle and field shape on the MOSFET reading, obtained without additional build-up, was evaluated using 4, 8 and 15 MeV beams and compared to ionisation chamber data at the depth of dose maximum (z(max)). Patient entrance in vivo measurements included 40 patients, mostly treated for breast tumours. The MOSFET reading, converted to D(max), was compared to the dose prescribed at this depth. The factors to convert MOSFET reading to D(max) vary between 1.33 and 1.20 for the 4 and 15 MeV beams, respectively. The SSD correction factor is approximately 8% for a change in SSD from 95 to 100 cm, and 2% for each 5-cm increment above 100 cm SSD. A correction for fields having sides smaller than 6 cm and for irregular field shape is also recommended. For fields up to 20 x 20 cm(2) and for oblique incidence up to 45 degrees, a correction is not necessary. Patient measurements demonstrated deviations from the prescribed dose with a mean difference of -0.7% and a standard deviation of 2.9%. Performing dose measurements with MOSFET detectors placed on the patient's skin without additional build-up is a well suited technique for routine dose verification in electron beams, when applying the appropriate conversion and correction factors.

Dissecting Daily and Circadian Expression Rhythms of Clock-Controlled Genes in Human Blood.

PubMed

Lech, Karolina; Ackermann, Katrin; Revell, Victoria L; Lao, Oscar; Skene, Debra J; Kayser, Manfred

2016-02-01

The identification and investigation of novel clock-controlled genes (CCGs) has been conducted thus far mainly in model organisms such as nocturnal rodents, with limited information in humans. Here, we aimed to characterize daily and circadian expression rhythms of CCGs in human peripheral blood during a sleep/sleep deprivation (S/SD) study and a constant routine (CR) study. Blood expression levels of 9 candidate CCGs (SREBF1, TRIB1, USF1, THRA1, SIRT1, STAT3, CAPRIN1, MKNK2, and ROCK2), were measured across 48 h in 12 participants in the S/SD study and across 33 h in 12 participants in the CR study. Statistically significant rhythms in expression were observed for STAT3, SREBF1, TRIB1, and THRA1 in samples from both the S/SD and the CR studies, indicating that their rhythmicity is driven by the endogenous clock. The MKNK2 gene was significantly rhythmic in the S/SD but not the CR study, which implies its exogenously driven rhythmic expression. In addition, we confirmed the circadian expression of PER1, PER3, and REV-ERBα in the CR study samples, while BMAL1 and HSPA1B were not significantly rhythmic in the CR samples; all 5 genes previously showed significant expression in the S/SD study samples. Overall, our results demonstrate that rhythmic expression patterns of clock and selected clock-controlled genes in human blood cells are in part determined by exogenous factors (sleep and fasting state) and in part by the endogenous circadian timing system. Knowledge of the exogenous and endogenous regulation of gene expression rhythms is needed prior to the selection of potential candidate marker genes for future applications in medical and forensic settings. © 2015 The Author(s).

MO-AB-BRA-08: Rapid Treatment Field Uniformity Optimization for Total Skin Electron Beam Therapy Using Cherenkov Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andreozzi, J; Zhang, R; Glaser, A

Purpose: To evaluate treatment field heterogeneity resulting from gantry angle choice in total skin electron beam therapy (TSEBT) following a modified Stanford dual-field technique, and determine a relationship between source to surface distance (SSD) and optimized gantry angle spread. Methods: Cherenkov imaging was used to image 62 treatment fields on a sheet of 1.2m x 2.2m x 1.2cm polyethylene following standard TSEBT setup at our institution (6 MeV, 888 MU/min, no spoiler, SSD=441cm), where gantry angles spanned from 239.5° to 300.5° at 1° increments. Average Cherenkov intensity and coefficient of variation in the region of interest were compared for themore » set of composite Cherenkov images created by summing all unique combinations of angle pairs to simulate dual-field treatment. The angle pair which produced the lowest coefficient of variation was further studied using an ionization chamber. The experiment was repeated at SSD=300cm, and SSD=370.5cm. Cherenkov imaging was also implemented during TSEBT of three patients. Results: The most uniform treatment region from a symmetric angle spread was achieved using gantry angles +/−17.5° about the horizontal axis at SSD=441cm, +/−18.5° at SSD=370.5cm, and +/−19.5° at SSD=300cm. Ionization chamber measurements comparing the original treatment spread (+/−14.5°) and the optimized angle pair (+/−17.5°) at SSD=441cm showed no significant deviation (r=0.999) in percent depth dose curves, and chamber measurements from nine locations within the field showed an improvement in dose uniformity from 24.41% to 9.75%. Ionization chamber measurements correlated strongly (r=0.981) with Cherenkov intensity measured concurrently on the flat Plastic Water phantom. Patient images and TLD results also showed modest uniformity improvements. Conclusion: A decreasing linear relationship between optimal angle spread and SSD was observed. Cherenkov imaging offers a new method of rapidly analyzing and optimizing TSEBT setup geometry by providing a 2D image of the treatment plane as a sum of the two fields. This study has been funded by NIH grants R21EB17559 and R01CA109558 as well as Norris Cotton Cancer Center Pilot funding.« less

No auditory experience, no tinnitus: Lessons from subjects with congenital- and acquired single-sided deafness.

PubMed

Lee, Sang-Yeon; Nam, Dong Woo; Koo, Ja-Won; De Ridder, Dirk; Vanneste, Sven; Song, Jae-Jin

2017-10-01

Recent studies have adopted the Bayesian brain model to explain the generation of tinnitus in subjects with auditory deafferentation. That is, as the human brain works in a Bayesian manner to reduce environmental uncertainty, missing auditory information due to hearing loss may cause auditory phantom percepts, i.e., tinnitus. This type of deafferentation-induced auditory phantom percept should be preceded by auditory experience because the fill-in phenomenon, namely tinnitus, is based upon auditory prediction and the resultant prediction error. For example, a recent animal study observed the absence of tinnitus in cats with congenital single-sided deafness (SSD; Eggermont and Kral, Hear Res 2016). However, no human studies have investigated the presence and characteristics of tinnitus in subjects with congenital SSD. Thus, the present study sought to reveal differences in the generation of tinnitus between subjects with congenital SSD and those with acquired SSD to evaluate the replicability of previous animal studies. This study enrolled 20 subjects with congenital SSD and 44 subjects with acquired SSD and examined the presence and characteristics of tinnitus in the groups. None of the 20 subjects with congenital SSD perceived tinnitus on the affected side, whereas 30 of 44 subjects with acquired SSD experienced tinnitus on the affected side. Additionally, there were significant positive correlations between tinnitus characteristics and the audiometric characteristics of the SSD. In accordance with the findings of the recent animal study, tinnitus was absent in subjects with congenital SSD, but relatively frequent in subjects with acquired SSD, which suggests that the development of tinnitus should be preceded by auditory experience. In other words, subjects with profound congenital peripheral deafferentation do not develop auditory phantom percepts because no auditory predictions are available from the Bayesian brain. Copyright © 2017 Elsevier B.V. All rights reserved.

Risk of schizophrenia and minority status: a comparison of the Swedish-speaking minority and the Finnish-speaking majority in Finland.

PubMed

Suvisaari, Jaana; Opler, Mark; Lindbohm, Marja-Liisa; Sallmén, Markku

2014-11-01

Approximately five percent of the Finnish population are Swedish-speaking and have higher socioeconomic position and longer life expectancy than the Finnish-speaking majority. Previous studies have not investigated whether Swedish-speaking Finns have lower risk of schizophrenia spectrum disorders (SSD) than Finnish-speaking Finns. We investigated this in a representative sample of 47 445 Finns born in 1972-1984. Hazard ratios of SSD between language groups were assessed with conditional proportional hazards regression. Sex, parental ages at birth, paternal employment around conception, parental psychosis and place and residence in the capital area were used as other explanatory variables. The prevalence of SSD was 0.7% in the Swedish-speaking minority and 1.5% in the Finnish-speaking majority. In the adjusted regression model, belonging to the Swedish-speaking minority was associated with lower risk of SSD (hazard ratio (HR) 0.41, 95% confidence interval (CI) 0.24-0.69). In a subset analysis by gender, the protective effect was evident among Swedish-speaking males (HR 0.32, 95% CI 0.15-0.68) but marginal in females (HR 0.75, 95% CI 0.41-1.37). Parental psychosis and place of birth in the capital area were associated with higher risk of SSD, whereas paternal employment at the time of conception was associated with lower risk of SSD. Our results support the role of social factors in the etiology of schizophrenia. Belonging to a minority with high socioeconomic status and social capital may be protective against schizophrenia, especially for males. Copyright © 2014 Elsevier B.V. All rights reserved.

Tyrosine kinase oncogenes abrogate interleukin-3 dependence of murine myeloid cells through signaling pathways involving c-myc: conditional regulation of c-myc transcription by temperature-sensitive v-abl.

PubMed Central

Cleveland, J L; Dean, M; Rosenberg, N; Wang, J Y; Rapp, U R

1989-01-01

Retroviral expression vectors carrying the tyrosine kinase oncogenes abl, fms, src, and trk abrogate the requirements of murine myeloid FDC-P1 cells for interleukin-3 (IL-3). Factor-independent clones constitutively express c-myc in the absence of IL-3, whereas in parental cultures c-myc transcription requires the presence of the ligand. To directly test the effect of a tyrosine kinase oncogene on c-myc expression, retroviral constructs containing three different temperature-sensitive mutants of v-abl were introduced into myeloid IL-3-dependent FDC-P1 and 32D cells. At the permissive temperature, clones expressing temperature-sensitive abl behaved like wild-type abl-containing cells in their growth properties and expressed c-myc constitutively. Temperature shift experiments demonstrated that both IL-3 abrogation and the regulation of c-myc expression correlated with the presence of functional v-abl. Induction of c-myc expression by reactivation of temperature-sensitive v-abl mimicked c-myc induction by IL-3 in that it did not require protein synthesis and occurred at the level of transcription, with effects on both initiation and a transcription elongation block. However, v-abl-regulated FDC-P1 cell growth differed from IL-3-regulated growth in that c-fos and junB, which are normally induced by IL-3, were not induced by activation of v-abl. Images PMID:2555703

Output calculation of electron therapy at extended SSD using an improved LBR method.

PubMed

Alkhatib, Hassaan A; Gebreamlak, Wondesen T; Tedeschi, David J; Mihailidis, Dimitris; Wright, Ben W; Neglia, William J; Sobash, Philip T; Fontenot, Jonas D

2015-02-01

To calculate the output factor (OPF) of any irregularly shaped electron beam at extended SSD. Circular cutouts were prepared from 2.0 cm diameter to the maximum possible size for 15 × 15 applicator cone. In addition, two irregular cutouts were prepared. For each cutout, percentage depth dose (PDD) at the standard SSD and doses at different SSD values were measured using 6, 9, 12, and 16 MeV electron beam energies on a Varian 2100C LINAC and the distance at which the central axis electron fluence becomes independent of cutout size was determined. The measurements were repeated with an ELEKTA Synergy LINAC using 14 × 14 applicator cone and electron beam energies of 6, 9, 12, and 15 MeV. The PDD measurements were performed using a scanning system and two diodes-one for the signal and the other a stationary reference outside the tank. The doses of the circular cutouts at different SSDs were measured using PTW 0.125 cm(3) Semiflex ion-chamber and EDR2 films. The electron fluence was measured using EDR2 films. For each circular cutout, the lateral buildup ratio (LBR) was calculated from the measured PDD curve using the open applicator cone as the reference field. The effective SSD (SSDeff) of each circular cutout was calculated from the measured doses at different SSD values. Using the LBR value and the radius of the circular cutout, the corresponding lateral spread parameter [σR(z)] was calculated. Taking the cutout size dependence of σR(z) into account, the PDD curves of the irregularly shaped cutouts at the standard SSD were calculated. Using the calculated PDD curve of the irregularly shaped cutout along with the LBR and SSDeff values of the circular cutouts, the output factor of the irregularly shaped cutout at extended SSD was calculated. Finally, both the calculated PDD curves and output factor values were compared with the measured values. The improved LBR method has been generalized to calculate the output factor of electron therapy at extended SSD. The percentage difference between the calculated and the measured output factors of irregularly shaped cutouts in a clinical useful SSD region was within 2%. Similar results were obtained for all available electron energies of both Varian 2100C and ELEKTA Synergy machines.

SU-F-T-75: Dosimetry Considerations in the Use of Hanging-Eye Block for Lesions of the Conjunctiva

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grelewicz, Z; Lee, B; Cutright, D

Purpose: Superficial lesions in the conjunctiva are frequently treated with en face electrons, using a hanging block to spare dose to the lens of the eye. Dose to the tumor and lens depend on the design and setup of the block and supporting apparatus. We performed in phantom measurements in order to characterize the dose sparing effects of the block as well as the under-dosing effect under the supporting apparatus for 6 MeV treatment. Methods: The commercial hanging block studied uses a 1.2 cm diameter tungsten cylinder supported by a 3 mm diameter acrylic rod. Point dose measurements under themore » hanging block, under an unblocked part of the field, and under the acrylic rod were performed using MOSFET detectors. In addition, EBT3 film was used for both PDD and profile measurements at a depth in phantom of 3 mm for both 105 and 103 cm SSD. Results: MOSFET measurements reported a dose reduction of 95% under the tungsten block when using an SSD of 103 cm, and 86% when using an SSD of 105 cm at a depth in phantom of 3 mm. Film measurements showed that the area under the acrylic rod may be under-dosed by as much as 30% when using 103 SSD. MOSFET measurements confirmed that when using an SSD of 103 cm, the area under the acrylic rod is under-dosed by up to 30% at 3mm depth, compared to the unblocked part of the field. Conclusion: The effectiveness of the commercial hanging block apparatus depends on setup, with 95% lens sparing possible with an SSD of 103 cm. This short SSD is necessary for sharp penumbra. At this SSD, substantial under-dosing under the acrylic support rod is possible. This must be mitigated with either feathering, or using an alternative method of support for the tungsten block.« less

Synergistic activation of the chicken mim-1 gene by v-myb and C/EBP transcription factors.

PubMed Central

Burk, O; Mink, S; Ringwald, M; Klempnauer, K H

1993-01-01

The retroviral oncogene v-myb encodes a transcriptional activator which is responsible for the activation of the mim-1 gene in myelomonocytic cells transformed by v-myb. The mim-1 promoter contains several myb consensus binding sites and has previously been shown to be regulated directly by v-myb. Here we report that the mim-1 gene is activated synergistically by v-myb and different C/EBP transcription factors. We have cloned a chicken C/EBP-related gene that is highly expressed in myeloid cells and identified it as the chicken homolog of C/EBP beta. A dominant-negative variant of chicken C/EBP beta interferes with the v-myb induced activation of the mim-1 gene in these cells, suggesting that C/EBP beta or another C/EBP transcription factor is required for the activation of mim-1 by v-myb. We found that C/EBP beta and other C/EBP transcription factors confer to fibroblasts the ability to induce the mim-1 gene in the presence of v-myb. Finally we show that, in contrast to v-myb, c-myb synergizes with C/EBP transcription factors only at low concentrations of c-myb protein. Our results suggest a role for C/EBP beta, and possibly for other C/EBP transcription factors, in v-myb function and in myeloid-specific gene activation. Images PMID:8491193

Loss of Vacuolar H+-ATPase (V-ATPase) Activity in Yeast Generates an Iron Deprivation Signal That Is Moderated by Induction of the Peroxiredoxin TSA2 *

PubMed Central

Diab, Heba I.; Kane, Patricia M.

2013-01-01

Vacuolar H+-ATPases (V-ATPases) acidify intracellular organelles and help to regulate overall cellular pH. Yeast vma mutants lack V-ATPase activity and allow exploration of connections between cellular pH, iron, and redox homeostasis common to all eukaryotes. A previous microarray study in a vma mutant demonstrated up-regulation of multiple iron uptake genes under control of Aft1p (the iron regulon) and only one antioxidant gene, the peroxiredoxin TSA2 (Milgrom, E., Diab, H., Middleton, F., and Kane, P. M. (2007) Loss of vacuolar proton-translocating ATPase activity in yeast results in chronic oxidative stress. J. Biol. Chem. 282, 7125–7136). Fluorescent biosensors placing GFP under transcriptional control of either an Aft1-dependent promoter (PFIT2-GFP) or the TSA2 promoter (PTSA2-GFP) were constructed to monitor transcriptional signaling. Both biosensors were up-regulated in the vma2Δ mutant, and acute V-ATPase inhibition with concanamycin A induced coordinate up-regulation from both promoters. PTSA2-GFP induction was Yap1p-dependent, indicating an oxidative stress signal. Total cell iron measurements indicate that the vma2Δ mutant is iron-replete, despite up-regulation of the iron regulon. Acetic acid up-regulated PFIT2-GFP expression in wild-type cells, suggesting that loss of pH control contributes to an iron deficiency signal in the mutant. Iron supplementation significantly decreased PFIT2-GFP expression and, surprisingly, restored PTSA2-GFP to wild-type levels. A tsa2Δ mutation induced both nuclear localization of Aft1p and PFIT2-GFP expression. The data suggest a novel function for Tsa2p as a negative regulator of Aft1p-driven transcription, which is induced in V-ATPase mutants to limit transcription of the iron regulon. This represents a new mechanism bridging the antioxidant and iron-regulatory pathways that is intimately linked to pH homeostasis. PMID:23457300

Trends of the sunshine duration and diffuse radiation percentage on sunny days in urban agglomerations of China during 1960-2005.

PubMed

Fu, Chuanbo; Dan, Li; Chen, Youlong; Tang, Jiaxiang

2015-08-01

The long-term observational data of sunshine duration (SD) and diffuse radiation percentage (defined as diffuse solar radiation/total solar radiation, DRP) on sunny days during 1960-2005 were analyzed in 7 urban agglomerations and the whole of China. The results show that the sunny sunshine duration (SSD) has decreased significantly except at a few stations over northwestern China in the past 46 years. An obvious decrease of the SSD is found in eastern China, with the trend coefficients lower than -0.8. Accompanied by the SSD decline, the sunny diffuse radiation percentage (SDRP) in most stations shows obvious increasing trends during the 46 years. The averaged SDRP over China has increased 2.33% per decade, while the averaged SSD shows a decrease of -0.13 hr/day per decade. The correlation coefficient between SDRP and SSD is -0.88. SSD decreased over urban agglomerations (small to large city clusters) in the past 46 years, especially in large cities and medium cities, due to the strong anthropogenic activities and air pollution represented by aerosol option depth (AOD) and tropospheric column NO2 (TroNO2). On the regional scale, SSD has an opposite trend from SDRP during 1960 to 2005, and the variation trends of regional mean values of SSD and SDRP in southeastern China are more pronounced than those in northwestern China. Copyright © 2015. Published by Elsevier B.V.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, H; Guerrero, M; Chen, S

Purpose: The TG-71 report was published in 2014 to present standardized methodologies for MU calculations and determination of dosimetric quantities. This work explores the clinical implementation of a TG71-based electron MU calculation algorithm and compares it with a recently released commercial secondary calculation program–Mobius3D (Mobius Medical System, LP). Methods: TG-71 electron dosimetry data were acquired, and MU calculations were performed based on the recently published TG-71 report. The formalism in the report for extended SSD using air-gap corrections was used. The dosimetric quantities, such PDD, output factor, and f-air factors were incorporated into an organized databook that facilitates data accessmore » and subsequent computation. The Mobius3D program utilizes a pencil beam redefinition algorithm. To verify the accuracy of calculations, five customized rectangular cutouts of different sizes–6×12, 4×12, 6×8, 4×8, 3×6 cm{sup 2}–were made. Calculations were compared to each other and to point dose measurements for electron beams of energy 6, 9, 12, 16, 20 MeV. Each calculation / measurement point was at the depth of maximum dose for each cutout in a 10×10 cm{sup 2} or 15×15cm{sup 2} applicator with SSDs 100cm and 110cm. Validation measurements were made with a CC04 ion chamber in a solid water phantom for electron beams of energy 9 and 16 MeV. Results: Differences between the TG-71 and the commercial system relative to measurements were within 3% for most combinations of electron energy, cutout size, and SSD. A 5.6% difference between the two calculation methods was found only for the 6MeV electron beam with 3×6 cm{sup 2}cutout in the 10×10{sup 2}cm applicator at 110cm SSD. Both the TG-71 and the commercial calculations show good consistency with chamber measurements: for 5 cutouts, <1% difference for 100cm SSD, and 0.5–2.7% for 110cm SSD. Conclusions: Based on comparisons with measurements, a TG71-based computation method and a Mobius3D program produce reasonably accurate MU calculations for electron-beam therapy.« less

Impaired verbal learning in forensic inpatients with Schizophrenia Spectrum Disorder.

PubMed

Corbett, Lasha; Karyadi, Kenny A; Kinney, Dominique; Nitch, Stephen R; Bayan, Stacey Marie; Williams, Mark

2018-01-01

The present study aimed to: (a) examine verbal learning performances among forensic inpatients diagnosed with Schizophrenia Spectrum Disorder (SSD); and (b) compare verbal learning performances among forensic SSD inpatients, SSD outpatients, and a small control sample. Participants included forensic SSD inpatients (n = 71), SSD outpatients (n = 305; see Stone et al.), and a control sample from the California Verbal Learning Test-II (CVLT-II) manual (n = 78; see Delis, Kramer, Kaplan, & Ober). Five verbal learning outcomes were measured using the CVLT-II. The average forensic SSD inpatients performed 1 to 1.5 standard deviations below the mean across the five verbal learning outcomes, many of whom (26.8% to 36.6%) performed in the impaired range across the five outcomes. Forensic SSD inpatients performed significantly lower than the SSD outpatients on three verbal learning outcomes and significantly lower than healthy controls on all five verbal learning outcomes. Results indicated forensically committed SSD inpatients have diminished verbal learning performances. Study findings could help define normative verbal learning performances in different types of SSD patients, may guide the development of compensatory strategies for verbal learning deficits, and could subsequently lead to more successful clinical outcomes in this population.

An Exploratory Study of the Influence of Load and Practice on Segmental and Articulatory Variability in Children with Speech Sound Disorders

PubMed Central

Vuolo, Janet; Goffman, Lisa

2017-01-01

This exploratory treatment study used phonetic transcription and speech kinematics to examine changes in segmental and articulatory variability. Nine children, ages 4- to 8-years-old, served as participants, including two with childhood apraxia of speech (CAS), five with speech sound disorder (SSD), and two who were typically developing (TD). Children practised producing agent + action phrases in an imitation task (low linguistic load) and a retrieval task (high linguistic load) over five sessions. In the imitation task in session one, both participants with CAS showed high degrees of segmental and articulatory variability. After five sessions, imitation practice resulted in increased articulatory variability for five participants. Retrieval practice resulted in decreased articulatory variability in three participants with SSD. These results suggest that short-term speech production practice in rote imitation disrupts articulatory control in children with and without CAS. In contrast, tasks that require linguistic processing may scaffold learning for children with SSD but not CAS. PMID:27960554

Gene end-like sequences within the 3' non-coding region of the Nipah virus genome attenuate viral gene transcription.

PubMed

Sugai, Akihiro; Sato, Hiroki; Yoneda, Misako; Kai, Chieko

2017-08-01

The regulation of transcription during Nipah virus (NiV) replication is poorly understood. Using a bicistronic minigenome system, we investigated the involvement of non-coding regions (NCRs) in the transcriptional re-initiation efficiency of NiV RNA polymerase. Reporter assays revealed that attenuation of NiV gene expression was not constant at each gene junction, and that the attenuating property was controlled by the 3' NCR. However, this regulation was independent of the gene-end, gene-start and intergenic regions. Northern blot analysis indicated that regulation of viral gene expression by the phosphoprotein (P) and large protein (L) 3' NCRs occurred at the transcription level. We identified uridine-rich tracts within the L 3' NCR that are similar to gene-end signals. These gene-end-like sequences were recognized as weak transcription termination signals by the viral RNA polymerase, thereby reducing downstream gene transcription. Thus, we suggest that NiV has a unique mechanism of transcriptional regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

SU-E-T-191: Commissioning and Dosimetric Characteristics of Elekta Agility for Total Skin Electron Beam (TSEB) Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayler, E; Charpentier, P; Micaily, B

2015-06-15

Purpose The purpose of this work is to publish beam data from Elekta Synergy(R) linear accelerators with Agility(TM) MLC for total skin electron beam (TSEB) therapy using the HDRE1 (High Dose Rate Electron 6MeV) energy. Method & Materials The optimal gantry angles for TSEB were determined using ion chamber measurements along a vertical profile at 450cm SSD. After gantry angles were chosen, field uniformity was measured over the entire treatment area. Uniformity was measured with and without the patient support device, allowing the dosimetric effect of the support device to be determined. Beam output and PDD were measured at themore » calibration point (450cm SSD) for a dual beam using a parallel plate chamber in solid water. These measurements were repeated with the chamber and phantom rotated about the patient isocenter at various angles, in order to measure the contribution from oblique beams. This technique provides a precise measurement of the treatment skin dose (TSD). Lastly, ion chamber measurements were verified by film and diodes. Results The optimal gantry angle for 450 cm SSD was determined to be 90±16°. This achieved uniformity better than 96% on the vertical axis, and 92% along the horizontal axis. HDRE1 was calibrated to deliver 10 cGy/MU at standard geometry (100 cm SSD, 1.2 cm depth). Thus at TSEB geometry (450 cm SSD, 0.1 cm depth) the output of the AP dual field was measured to be 0.35 cGy/MU. The TSD of a 20 cm radius cylinder for six (equally, 60° spaced) dual fields was measured to be 1.19 cGy/MU. Percent Depth Dose data for the AP dual field and TSD are shown in Figure 2. Conclusion This paper provides a modern procedure for commissioning TSEB therapy on a linear accelerator, and clinical beam data for the Elekta Synergy(R) with Agility(TM) MLC.« less

DBC1 promotes castration-resistant prostate cancer by positively regulating DNA binding and stability of AR-V7.

PubMed

Moon, Sue Jin; Jeong, Byong Chang; Kim, Hwa Jin; Lim, Joung Eun; Kwon, Ghee Young; Kim, Jeong Hoon

2018-03-01

Constitutively active AR-V7, one of the major androgen receptor (AR) splice variants lacking the ligand-binding domain, plays a key role in the development of castration-resistant prostate cancer (CRPC) and anti-androgen resistance. However, our understanding of the regulatory mechanisms of AR-V7-driven transcription is limited. Here we report DBC1 as a key regulator of AR-V7 transcriptional activity and stability in CRPC cells. DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression. DBC1 is required for recruitment of AR-V7 to its target enhancers and for long-range chromatin looping between the CDH2 enhancer and promoter. Mechanistically, DBC1 enhances DNA-binding activity of AR-V7 by direct interaction and inhibits CHIP E3 ligase-mediated ubiquitination and degradation of AR-V7 by competing with CHIP for AR-V7 binding, thereby stabilizing and activating AR-V7. Importantly, DBC1 depletion suppresses the tumorigenic and metastatic properties of CRPC cells. Our results firmly establish DBC1 as a critical AR-V7 coactivator that plays a key role in the regulation of DNA binding and stability of AR-V7 and has an important physiological role in CRPC progression.

Loss of vacuolar H+-ATPase (V-ATPase) activity in yeast generates an iron deprivation signal that is moderated by induction of the peroxiredoxin TSA2.

PubMed

Diab, Heba I; Kane, Patricia M

2013-04-19

Vacuolar H(+)-ATPases (V-ATPases) acidify intracellular organelles and help to regulate overall cellular pH. Yeast vma mutants lack V-ATPase activity and allow exploration of connections between cellular pH, iron, and redox homeostasis common to all eukaryotes. A previous microarray study in a vma mutant demonstrated up-regulation of multiple iron uptake genes under control of Aft1p (the iron regulon) and only one antioxidant gene, the peroxiredoxin TSA2 (Milgrom, E., Diab, H., Middleton, F., and Kane, P. M. (2007) Loss of vacuolar proton-translocating ATPase activity in yeast results in chronic oxidative stress. J. Biol. Chem. 282, 7125-7136). Fluorescent biosensors placing GFP under transcriptional control of either an Aft1-dependent promoter (P(FIT2)-GFP) or the TSA2 promoter (P(TSA2)-GFP) were constructed to monitor transcriptional signaling. Both biosensors were up-regulated in the vma2Δ mutant, and acute V-ATPase inhibition with concanamycin A induced coordinate up-regulation from both promoters. PTSA2-GFP induction was Yap1p-dependent, indicating an oxidative stress signal. Total cell iron measurements indicate that the vma2Δ mutant is iron-replete, despite up-regulation of the iron regulon. Acetic acid up-regulated P(FIT2)-GFP expression in wild-type cells, suggesting that loss of pH control contributes to an iron deficiency signal in the mutant. Iron supplementation significantly decreased P(FIT2)-GFP expression and, surprisingly, restored P(TSA2)-GFP to wild-type levels. A tsa2Δ mutation induced both nuclear localization of Aft1p and P(FIT2)-GFP expression. The data suggest a novel function for Tsa2p as a negative regulator of Aft1p-driven transcription, which is induced in V-ATPase mutants to limit transcription of the iron regulon. This represents a new mechanism bridging the antioxidant and iron-regulatory pathways that is intimately linked to pH homeostasis.

Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations.

PubMed

Emerick, Mark C; Stein, Rebecca; Kunze, Robin; McNulty, Megan M; Regan, Melissa R; Hanck, Dorothy A; Agnew, William S

2006-08-01

We describe the regulated transcriptome of CACNA1G, a human gene for T-type Ca(v)3.1 calcium channels that is subject to extensive alternative RNA splicing. Fifteen sites of transcript variation include 2 alternative 5'-UTR promoter sites, 2 alternative 3'-UTR polyadenylation sites, and 11 sites of alternative splicing within the open reading frame. A survey of 1580 fetal and adult human brain full-length complementary DNAs reveals a family of 30 distinct transcripts, including multiple functional forms that vary in expression with development. Statistical analyses of fetal and adult transcript populations reveal patterns of linkages among intramolecular splice site configurations that change dramatically with development. A shift from nearly independent, biased splicing in fetal transcripts to strongly concerted splicing in adult transcripts suggests progressive activation of multiple "programs" of splicing regulation that reorganize molecular structures in differentiating cells. Patch-clamp studies of nine selected variants help relate splicing regulation to permutations of the gating parameters most likely to modify T-channel physiology in expressing neurons. Gating behavior reflects combinatorial interactions between variable domains so that molecular phenotype depends on ensembles of coselected domains, consistent with the observed emergence of concerted splicing during development. We conclude that the structural gene and networks of splicing regulatory factors define an integrated system for the phenotypic variation of Ca(v)3.1 biophysics during nervous system development. Copyright 2006 Wiley-Liss, Inc.

Phonological Processing and Reading in Children with Speech Sound Disorders

ERIC Educational Resources Information Center

Rvachew, Susan

2007-01-01

Purpose: To examine the relationship between phonological processing skills prior to kindergarten entry and reading skills at the end of 1st grade, in children with speech sound disorders (SSD). Method: The participants were 17 children with SSD and poor phonological processing skills (SSD-low PP), 16 children with SSD and good phonological…

Selenium effect on selenoprotein transcriptome in chondrocytes.

PubMed

Yan, Jidong; Zheng, Yuewen; Min, Zixin; Ning, Qilan; Lu, Shemin

2013-04-01

Selenium is an essential micronutrient and exerts its biological functions predominantly through selenoproteins. Selenium deficiency is associated with cartilage function. This study demonstrated that all 24 selenoprotein transcripts in mouse genome were detectable in ATDC5 chondrocytes except deiodinase 1 (DIO1), DIO2, and selenoprotein V (Sel V), while all 25 selenoprotein transcripts in human genome were detectable in C28/I2 chondrocytes except glutathione peroxidase 6 (GPx6) and DIO1. In addition, gene expression of five selenoproteins (GPx1, Sel H, Sel N, Sel P, and Sel W) was up-regulated and two selenoproteins (SPS2 and Sel O) was down-regulated by sodium selenite (Se) in both ATDC5 and C28/I2 cells. Gene expression of six selenoproteins (TrxR1, Sel I, Sel M, Sel R, Sel S, Sel T) and one selenoprotein (GPx3) was up-regulated by Se in ATDC5 and C28/I2 cells, respectively. Gene expression of one selenoprotein (TrxR2) was down-regulated by Se only in ATDC5 cells. Further transcription inhibition assay showed that both transcriptional and posttranscriptional mechanisms involved in Se-regulated gene expression of GPx1, TrxR1, TrxR2, SPS2, Sel O, and Sel S. However, Se-regulated gene expression of Sel H, Sel I, Sel M, Sel N, Sel P, Sel R, Sel T, and Sel W mainly at posttranscriptional level. Moreover, new protein synthesis inhibition assay indicated that Se-mediated new protein synthesis also played roles in Se-regulated gene expression of GPx1, TrxR1, TrxR2, Sel H, Sel O, Sel P, Sel R, and Sel W. In summary, this study described the selenoprotein transcriptome, Se-regulated selenoproteins and possible mechanisms involved in chondrocytes.

"When he's around his brothers … he's not so quiet": the private and public worlds of school-aged children with speech sound disorder.

PubMed

McLeod, Sharynne; Daniel, Graham; Barr, Jacqueline

2013-01-01

Children interact with people in context: including home, school, and in the community. Understanding children's relationships within context is important for supporting children's development. Using child-friendly methodologies, the purpose of this research was to understand the lives of children with speech sound disorder (SSD) in context. Thirty-four interviews were undertaken with six school-aged children identified with SSD, and their siblings, friends, parents, grandparents, and teachers. Interview transcripts, questionnaires, and children's drawings were analyzed to reveal that these children experienced the world in context dependent ways (private vs. public worlds). Family and close friends typically provided a safe, supportive environment where children could be themselves and participate in typical childhoods. In contrast, when out of these familiar contexts, the children often were frustrated, embarrassed, and withdrawn, their relationships changed, and they were unable to get their message across in public contexts. Speech-language pathology assessment and intervention could be enhanced by interweaving the valuable insights of children, siblings, friends, parents, teachers, and other adults within children's worlds to more effectively support these children in context. 1. Recognize that children with SSD experience the world in different ways, depending on whether they are in private or public contexts. 2. Describe the changes in the roles of family and friends when children with SSD are in public contexts. 3. Discover the position of the child as central in Bronfenbrenner’s bioecological model. 4. Identify principles of child-friendly research. 5. Recognize the importance of considering the child in context during speech-language pathology assessment and intervention. Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.

Novel down-regulatory mechanism of the surface expression of the vasopressin V2 receptor by an alternative splice receptor variant.

PubMed

Sarmiento, José M; Añazco, Carolina C; Campos, Danae M; Prado, Gregory N; Navarro, Javier; González, Carlos B

2004-11-05

In rat kidney, two alternatively spliced transcripts are generated from the V2 vasopressin receptor gene. The large transcript (1.2 kb) encodes the canonical V2 receptor, whereas the small transcript encodes a splice variant displaying a distinct sequence corresponding to the putative seventh transmembrane domain and the intracellular C terminus of the V2 receptor. This work showed that the small spliced transcript is translated in the rat kidney collecting tubules. However, the protein encoded by the small transcript (here called the V2b splice variant) is retained inside the cell, in contrast to the preferential surface distribution of the V2 receptor (here called the V2a receptor). Cells expressing the V2b splice variant do not exhibit binding to 3H-labeled vasopressin. Interestingly, we found that expression of the splice variant V2b down-regulates the surface expression of the V2a receptor, most likely via the formation of V2a.V2b heterodimers as demonstrated by co-immunoprecipitation and fluorescence resonance energy transfer experiments between the V2a receptor and the V2b splice variant. The V2b splice variant would then be acting as a dominant negative. The effect of the V2b splice variant is specific, as it does not affect the surface expression of the G protein-coupled interleukin-8 receptor (CXCR1). Furthermore, the sequence encompassing residues 242-339, corresponding to the C-terminal domain of the V2b splice variant, also down-regulates the surface expression of the V2a receptor. We suggest that some forms of nephrogenic diabetes insipidus are due to overexpression of the splice variant V2b, which could retain the wild-type V2a receptor inside the cell via the formation of V2a.V2b heterodimers.

Right Ear Advantage of Speech Audiometry in Single-sided Deafness.

PubMed

Wettstein, Vincent G; Probst, Rudolf

2018-04-01

Postlingual single-sided deafness (SSD) is defined as normal hearing in one ear and severely impaired hearing in the other ear. A right ear advantage and dominance of the left hemisphere are well established findings in individuals with normal hearing and speech processing. Therefore, it seems plausible that a right ear advantage would exist in patients with SSD. The audiometric database was searched to identify patients with SSD. Results from the German monosyllabic Freiburg word test and four-syllabic number test in quiet were evaluated. Results of right-sided SSD were compared with left-sided SSD. Statistical calculations were done with the Mann-Whitney U test. Four hundred and six patients with SSD were identified, 182 with right-sided and 224 with left-sided SSD. The two groups had similar pure-tone thresholds without significant differences. All test parameters of speech audiometry had better values for right ears (SSD left) when compared with left ears (SSD right). Statistically significant results (p < 0.05) were found for a weighted score (social index, 98.2 ± 4% right and 97.5 ± 4.7% left, p < 0.026), for word understanding at 60 dB SPL (95.2 ± 8.7% right and 93.9 ± 9.1% left, p < 0.035), and for the level at which 100% understanding was reached (61.5 ± 10.1 dB SPL right and 63.8 ± 11.1 dB SPL left, p < 0.022) on a performance-level function. A right ear advantage of speech audiometry was found in patients with SSD in this retrospective study of audiometric test results.

Competition through dimerization between antiapoptotic and proapoptotic HS-1-associated protein X-1 (Hax-1).

PubMed

Koontz, Jason; Kontrogianni-Konstantopoulos, Aikaterini

2014-02-07

Studies on Hax-1 have mainly focused on variant (v) 1, demonstrating its antiapoptotic properties. However, HAX1 is heavily spliced, generating structurally distinct isoforms. We sought to characterize the Hax-1 isoforms expressed in rat heart before and after insult. We confirmed the presence of at least four Hax-1 transcripts in healthy rat cardiac muscle. These exhibited differential expression before and after induction of myocardial infarction, with v2 being up-regulated 12-fold at the transcript level and 1.5-fold at the protein level post-insult. Contrary to antiapoptotic rat and human v1, overexpression of rat v2 or human v4 (the human homologue of rat v2) in epithelial cells exacerbated cell death by 30% following H2O2 treatment compared with control vector. Coexpression of rat v1 and v2 or human v1 and v4 neutralized the protective effects of rat and human v1 and the proapoptotic effects of rat v2 and human v4 by modulating cytochrome c release. This is, at least partly, mediated by the ability of Hax-1 proteins to form homotypic and heterotypic dimers with binding affinities ranging from ~3.8 nm for v1 dimers to ~97 nm for v1/v2 dimers. The minimal binding region supporting these interactions lies between amino acids 97-278, which are shared by nearly all Hax-1 proteins, indicating that additional factors regulate the preferential formation of Hax-1 homo- or heterodimers. Our studies are the first to show that Hax-1 is a family of anti- and proapoptotic regulators that may modulate cell survival and death through homo- or heterodimerization.

Corrected and Republished from: BCL11A Is a Critical Component of a Transcriptional Network That Activates Recombinase Activating Gene Expression and V(D)J Recombination

PubMed Central

Lee, Baeck-Seung; Lee, Bum-Kyu; Iyer, Vishwanath R.; Sleckman, Barry P.; Shaffer, Arthur L.; Ippolito, Gregory C.

2017-01-01

ABSTRACT Recombination activating gene 1 (RAG1) and RAG2 are critical enzymes for initiating variable-diversity-joining [V(D)J] segment recombination, an essential process for antigen receptor expression and lymphocyte development. The BCL11A transcription factor is required for B cell and plasmacytoid dendritic cell (pDC) development, but its molecular function(s) in early B cell fate specification and commitment is unknown. We show here that the major B cell isoform, BCL11A-XL, binds directly to the RAG1 promoter as well as directly to regulatory regions of transcription factors previously implicated in both B cell and pDC development to activate RAG1 and RAG2 gene transcription in pro- and pre-B cells. We employed BCL11A overexpression with recombination substrates to demonstrate direct consequences of BCL11A/RAG modulation on V(D)J recombination. We conclude that BCL11A is a critical component of a transcriptional network that regulates B cell fate by controlling V(D)J recombination. PMID:29038163

Electric-acoustic stimulation suppresses tinnitus in a subject with high-frequency single-sided deafness.

PubMed

Mertens, Griet; Van Rompaey, Vincent; Van de Heyning, Paul

2018-05-17

A suggested solution to suppress tinnitus is to restore the normal sensory input. This is based on the auditory deprivation hypothesis. It is known that hearing aids can provide sufficient activation of the auditory nervous system and reduce tinnitus in subjects with mild to moderate hearing loss and that cochlear implantation can reduce tinnitus in subjects with severe to profound hearing loss. This applies to subjects with single-sided deafness (SSD) or bilateral hearing loss. To investigate if electric-acoustic stimulation (EAS) can reduce severe tinnitus in a subject with residual hearing in the ipsilateral ear and contralateral normal hearing (high-frequency SSD) by restoring the auditory input. Tinnitus reduction was investigated for 1 year after implantation in a subject with high-frequency SSD, who uses EAS, and was compared to 11 subjects with a cochlear implant (CI) with SSD. The Visual Analogue Scale (VAS) and the Tinnitus Questionnaire (TQ) were administered pre-operatively and at 1, 3, 6, and 12 months after implantation. Significant tinnitus reduction was observed 1 month after implantation on the VAS in the subjects with SSD using a CI. Tinnitus reduction was also observed in the subject with high-frequency SSD using EAS. A further decrease was observed 3 months after implantation. The TQ and VAS scores remained stable up to 1 year after implantation. A CI can significantly reduce ipsilateral severe tinnitus in a subject with SSD. Ipsilateral severe tinnitus can also be reduced using EAS in subjects with high-frequency SSD.

Exploration of G-quadruplex function in c-Myb gene and its transcriptional regulation by topotecan.

PubMed

Li, Fangyuan; Zhou, Jiang; Xu, Ming; Yuan, Gu

2018-02-01

Our bioinformatics research shows that there are four G-rich sequences (S1-S4) in the upstream region of the transcription start site of c-Myb gene, and we have proved that these sequences have the ability to form G-quadruplex structures. This work mainly focuses on G-quadruplex function, recognition and transcription regulation in c-Myb gene, revealing a novel regulatory element in c-Myb proximal promoter region, and its transcription regulation by G-quadruplex binder. The research has identified that the enhancer effect in c-Myb transcription was primarily affected by the G-quadruplex formed by S1 sequence, and the up-regulation effect may due to the removal of repressive progress of MZF-1 by stabilizing G-quadruplex. Attentions were being paid to the development of G-quadruplex binders for selective recognition, and topotecan was found to have high binding affinity in vitro and could effectively affect the c-Myb transcription activities in cells. The regulation of G-quadruplex with binders in transcriptional, translational levels by Q-RT-PCR and western blot was in expectation of providing a strategy for gene expression modulation. In conclusion, our study revealed a G-quadruplex structure in c-Myb proximal promoter region, which was of great importance in the regulation of c-Myb function. Copyright © 2017 Elsevier B.V. All rights reserved.

Working memory span in Persian-speaking children with speech sound disorders and normal speech development.

PubMed

Afshar, Mohamad Reza; Ghorbani, Ali; Rashedi, Vahid; Jalilevand, Nahid; Kamali, Mohamad

2017-10-01

The aim of this study was to compare working memory span in Persian-speaking preschool children with speech sound disorder (SSD) and their typically speaking peers. Additionally, the study aimed to examine Non-Word Repetition (NWR), Forward Digit Span (FDS) and Backward Digit Span (BDS) in four groups of children with varying severity levels of SSD. The participants in this study comprised 35 children with SSD and 35 typically developing (TD) children -matched for age and sex-as a control group. The participants were between the age range of 48 and 72 months. Two components of working memory including phonological loop and central executive were compared between two groups. We used two tasks (NWR and FDS) to assess phonological loop component, and one task (BDS) to assess central executive component. Percentage of correct consonants (PCC) was used to calculate the severity of SSD. Significant differences were observed between the two groups in all tasks that assess working memory (p < 0.001). In addition, the comparison of the phonological loop of working memory between the various severity groups indicated significant differences between different severities of both NWR and FDS tasks among the SSD children (p < 0.001). Nevertheless, comparison of the central executive between various severity groups, which was assessed with the BDS task, did not show any significant differences (p > 0.05). The result showed that PCC scores in TD children were associated with NWR (p < 0.001), FDS (p = 0.001), and BDS (p < 0.001). Furthermore, PCC scores in SSD children were associated with NWR and FDS (p < 0.001), but not with BDS (p > 0.05). The working memory skills were weaker in SSD children, in comparison to TD children. In addition, children with varying levels of severity of SSD differed in terms of NWR and FSD, but not BDS. Copyright © 2017 Elsevier B.V. All rights reserved.

Social security work disability and its predictors in patients with fibromyalgia.

PubMed

Wolfe, Frederick; Walitt, Brian T; Katz, Robert S; Häuser, Winfried

2014-09-01

To determine prevalence and incidence of US Social Security Disability and Supplemental Security Income (SSD) in patients with fibromyalgia and to investigate prediction of SSD. Over a mean of 4 years (range 1-13 years), we studied 2,321 patients with physician-diagnosed fibromyalgia (prevalent cases) and applied modified American College of Rheumatology (ACR) 2010 research criteria to identify criteria-positive patients. During the study, 34.8% (95% confidence interval [95% CI] 32.9-36.8%) of fibromyalgia patients received SSD. The annual incidence of SSD among patients not receiving SSD at study enrollment was 3.4% (95% CI 3.0-3.9%), and 25% were estimated to be work disabled at 9.0 years of followup. By comparison, the prevalence of SSD in rheumatoid arthritis (RA) patients with concomitant fibromyalgia was 55.6% (95% CI 54.3-57.0%) and was 42.4% in osteoarthritis (OA). By study conclusion, 31.4% of SSD awardees were no longer receiving SSD. In univariate models, incident SSD in patients with fibromyalgia was predicted by sociodemographic measures and by symptom burden; but the strongest predictor was functional status (Health Assessment Questionnaire disability index [HAQ DI]). In multivariable models, the HAQ DI and the Short Form 36-item health survey physical and mental component summary scores, but no other variables, predicted SSD. Fibromyalgia criteria-positive patients had more SSD, but the continuous scale, polysymptomatic distress index derived from the ACR criteria was a substantially better predictor of SSD than a criteria-positive diagnosis. The prevalence of SSD is high in fibromyalgia, but not higher than in RA and OA patients who satisfy fibromyalgia criteria. The best predictors of work disability are functional status variables. Copyright © 2014 by the American College of Rheumatology.

Low maternal retinol as a risk factor for schizophrenia in adult offspring

PubMed Central

Bao, YuanYuan; Ibram, Ghionul; Blaner, William S.; Quesenberry, Charles P.; Shen, Ling; McKeague, Ian W.; Schaefer, Catherine A.; Susser, Ezra S.; Brown, Alan S.

2012-01-01

Background Prenatal micronutrient deficiency has been linked to later development of schizophrenia among offspring; however, no study has specifically investigated the association between vitamin A and this disorder. Vitamin A is an essential nutrient which is required by the early embryo and fetus for gene expression and regulation, cell differentiation, proliferation and migration. Previous work suggests that vitamin A deficiency in the second trimester may be particularly relevant to the etiopathogenesis of neurobehavioral phenotypes some of which are observed in schizophrenia. Methods We examined whether low maternal vitamin A levels in the second trimester are associated with the risk of schizophrenia and other schizophrenia spectrum disorders (SSD) in the Prenatal Determinants of Schizophrenia study; third trimester vitamin A levels were also examined in relation to SSD. The cases were derived from a population-based birth cohort; all cohort members belonged to a prepaid health plan. Archived maternal serum samples were assayed for vitamin A in cases (N=55) and up to 2 controls per case (N=106) matched on length of membership in the health plan, date of birth (±28 days), sex, and gestational timing and availability of archived maternal sera. Results For the second trimester, low maternal vitamin A, defined as values in the lowest tertile of the distribution among controls, was associated with a greater than threefold increased risk of SSD, adjusting for maternal education and age (OR=3.04, 95% CI=1.06, 8.79, p=.039). No association between third trimester maternal vitamin A and SSD was observed. Conclusions Although further investigations are warranted, this is the first birth cohort study to our knowledge to report an association between low maternal vitamin A levels and SSD among offspring. PMID:22381190

Hippocampal activation and memory performance in schizophrenia depend on strategy use in a virtual maze.

PubMed

Wilkins, Leanne K; Girard, Todd A; Herdman, Katherine A; Christensen, Bruce K; King, Jelena; Kiang, Michael; Bohbot, Veronique D

2017-10-30

Different strategies may be spontaneously adopted to solve most navigation tasks. These strategies are associated with dissociable brain systems. Here, we use brain-imaging and cognitive tasks to test the hypothesis that individuals living with Schizophrenia Spectrum Disorders (SSD) have selective impairment using a hippocampal-dependent spatial navigation strategy. Brain activation and memory performance were examined using functional magnetic resonance imaging (fMRI) during the 4-on-8 virtual maze (4/8VM) task, a human analog of the rodent radial-arm maze that is amenable to both response-based (egocentric or landmark-based) and spatial (allocentric, cognitive mapping) strategies to remember and navigate to target objects. SSD (schizophrenia and schizoaffective disorder) participants who adopted a spatial strategy performed more poorly on the 4/8VM task and had less hippocampal activation than healthy comparison participants using either strategy as well as SSD participants using a response strategy. This study highlights the importance of strategy use in relation to spatial cognitive functioning in SSD. Consistent with a selective-hippocampal dependent deficit in SSD, these results support the further development of protocols to train impaired hippocampal-dependent abilities or harness non-hippocampal dependent intact abilities. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of a spliced variant of human IRF-3 promoter and its regulation by the transcription factor Sp1.

PubMed

Ren, Wei; Zhu, Liang-Hua; Xu, Hua-Guo; Jin, Rui; Zhou, Guo-Ping

2012-06-01

Interferon regulatory factor 3 (IRF-3), an essential transcriptional regulator of the interferon genes, plays an important role in host defense against viral and microbial infection as well as in cell growth regulation. Promoter plays a crucial role in gene transcription. We have reported the characterization of the wide type of human IRF-3 promoter, but the characterization of the spliced variant of human IRF-3 Int2V1 promoter has not been systematically analyzed. To observe the spliced variant of human IRF-3 promoter, we have cloned the human IRF-3 gene promoter region containing 300 nucleotides upstream the transcription start site (TSS). Transient transfection of 5' deleted promoter-reporter constructs and luciferase assay illustrated the region -159/-100 relative to the TSS is sufficient for full promoter activity. This region contains GATA1 and specific protein-1 (Sp1) transcription factor binding sites. Interestingly, mutation of this Sp1 site reduced the promoter activity by 50%. However, overexpression of Sp1 increased the transcription activity by 2.4-fold. These results indicated that the spliced variant of human IRF-3 gene core promoter was located within the region -159/-100 relative to the TSS. Sp1 transcription factor upregulates the spliced variant of human IRF-3 gene promoter.

Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation

PubMed Central

Giloteaux, Ludovic; Holmes, Dawn E; Williams, Kenneth H; Wrighton, Kelly C; Wilkins, Michael J; Montgomery, Alison P; Smith, Jessica A; Orellana, Roberto; Thompson, Courtney A; Roper, Thomas J; Long, Philip E; Lovley, Derek R

2013-01-01

The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the α-subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative reverse transcription-PCR. Most of the arrA (>60%) and acr3-1 (>90%) sequences that were recovered were most similar to Geobacter species, while the majority of acr3-2 (>50%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated the transcription of arrA in situ, even though the presence of As(V) increased the transcription of arrA in cultures of Geobacter lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry. PMID:23038171

The plant-specific transcription factors CBP60g and SARD1 are targeted by a Verticillium secretory protein VdSCP41 to modulate immunity

PubMed Central

Qin, Jun; Wang, Kailun; Sun, Lifan; Xing, Haiying; Wang, Sheng; Li, Lin; Chen, She

2018-01-01

The vascular pathogen Verticillium dahliae infects the roots of plants to cause Verticillium wilt. The molecular mechanisms underlying V. dahliae virulence and host resistance remain elusive. Here, we demonstrate that a secretory protein, VdSCP41, functions as an intracellular effector that promotes V. dahliae virulence. The Arabidopsis master immune regulators CBP60g and SARD1 and cotton GhCBP60b are targeted by VdSCP41. VdSCP41 binds the C-terminal portion of CBP60g to inhibit its transcription factor activity. Further analyses reveal a transcription activation domain within CBP60g that is required for VdSCP41 targeting. Mutations in both CBP60g and SARD1 compromise Arabidopsis resistance against V. dahliae and partially impair VdSCP41-mediated virulence. Moreover, virus-induced silencing of GhCBP60b compromises cotton resistance to V. dahliae. This work uncovers a virulence strategy in which the V. dahliae secretory protein VdSCP41 directly targets plant transcription factors to inhibit immunity, and reveals CBP60g, SARD1 and GhCBP60b as crucial components governing V. dahliae resistance. PMID:29757140

Transcription factor Sp1 regulates T-type Ca(2+) channel CaV 3.1 gene expression.

PubMed

González-Ramírez, Ricardo; Martínez-Hernández, Elizabeth; Sandoval, Alejandro; Felix, Ricardo

2014-05-01

Voltage-gated T-type Ca(2+) (CaV 3) channels mediate a number of physiological events in developing and mature cells, and are implicated in neurological and cardiovascular diseases. In mammals, there are three distinct T-channel genes (CACNA1G, CACNA1H, and CACNA1I) encoding proteins (CaV 3.1-CaV 3.3) that differ in their localization as well as in molecular, biophysical, and pharmacological properties. The CACNA1G is a large gene that contains 38 exons and is localized in chromosome 17q22. Only basic characteristics of the CACNA1G gene promoter region have been investigated classifying it as a TATA-less sequence containing several potential transcription factor-binding motifs. Here, we cloned and characterized a proximal promoter region and initiated the analysis of transcription factors that control CaV 3.1 channel expression using the murine Cacna1g gene as a model. We isolated a ∼1.5 kb 5'-upstream region of Cacna1g and verified its transcriptional activity in the mouse neuroblastoma N1E-115 cell line. In silico analysis revealed that this region possesses a TATA-less minimal promoter that includes two potential transcription start sites and four binding sites for the transcription factor Sp1. The ability of one of these sites to interact with the transcription factor was confirmed by electrophoretic mobility shift assays. Consistent with this, Sp1 over-expression enhanced promoter activity while siRNA-mediated Sp1 silencing significantly decreased the level of CaV 3.1 protein and reduced the amplitude of whole-cell T-type Ca(2+) currents expressed in the N1E-115 cells. These results provide new insights into the molecular mechanisms that control CaV 3.1 channel expression. © 2013 Wiley Periodicals, Inc.

The Rsb Phosphoregulatory Network Controls Availability of the Primary Sigma Factor in Chlamydia trachomatis and Influences the Kinetics of Growth and Development

PubMed Central

Thompson, Christopher C.; Griffiths, Cherry; Nicod, Sophie S.; Lowden, Nicole M.; Wigneshweraraj, Sivaramesh; Fisher, Derek J.; McClure, Myra O.

2015-01-01

Chlamydia trachomatis is an obligate intracellular human pathogen that exhibits stage-specific gene transcription throughout a biphasic developmental cycle. The mechanisms that control modulation in transcription and associated phenotypic changes are poorly understood. This study provides evidence that a switch-protein kinase regulatory network controls availability of σ66 , the main sigma subunit for transcription in Chlamydia. In vitro analysis revealed that a putative switch-protein kinase regulator, RsbW, is capable of interacting directly with σ66, as well as phosphorylating its own antagonist, RsbV1, rendering it inactive. Conversely, the putative PP2C-like phosphatase domain of chlamydial RsbU was capable of reverting RsbV1 into its active state. Recent advances in genetic manipulation of Chlamydia were employed to inactivate rsbV1, as well as to increase the expression levels of rsbW or rsbV1, in vivo. Representative σ66-dependent gene transcription was repressed in the absence of rsbV1 or upon increased expression of RsbW, and increased upon elevated expression of RsbV1. These effects on housekeeping transcription were also correlated to several measures of growth and development. A model is proposed where the relative levels of active antagonist (RsbV1) and switch-protein anti-sigma factor (RsbW) control the availability of σ66 and subsequently act as a molecular 'throttle' for Chlamydia growth and development. PMID:26313645

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9.

PubMed

Huang, Hua; Kapeli, Katannya; Jin, Wenhao; Wong, Yuk Peng; Arumugam, Thiruma Valavan; Koh, Joanne Huifen; Srimasorn, Sumitra; Mallilankaraman, Karthik; Chua, John Jia En; Yeo, Gene W; Soong, Tuck Wah

2018-05-04

Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of voltage-gated calcium channel CaV1.3 are subject to brain-selective A-to-I RNA editing by ADAR2. Here, we show that editing of CaV1.3 mRNA is dependent on a 40 bp RNA duplex formed between exon 41 and an evolutionarily conserved editing site complementary sequence (ECS) located within the preceding intron. Heterologous expression of a mouse minigene that contained the ECS, intermediate intronic sequence and exon 41 with ADAR2 yielded robust editing. Interestingly, editing of CaV1.3 was potently inhibited by serine/arginine-rich splicing factor 9 (SRSF9). Mechanistically, the inhibitory effect of SRSF9 required direct RNA interaction. Selective down-regulation of SRSF9 in neurons provides a basis for the neuron-specific editing of CaV1.3 transcripts.

Functional Characterization of a Bidirectional Plant Promoter from Cotton Leaf Curl Burewala Virus Using an Agrobacterium-Mediated Transient Assay

PubMed Central

Ashraf, Muhammad Aleem; Shahid, Ahmad Ali; Rao, Abdul Qayyum; Bajwa, Kamran Shehzad; Husnain, Tayyab

2014-01-01

The C1 promoter expressing the AC1 gene, and V1 promoter expressing the AV1 gene are located in opposite orientations in the large intergenic region of the Cotton leaf curl Burewala virus (CLCuBuV) genome. Agro-infiltration was used to transiently express putative promoter constructs in Nicotiana tabacum and Gossypium hirsutum leaves, which was monitored by a GUS reporter gene, and revealed that the bidirectional promoter of CLCuBuV transcriptionally regulates both the AC1 and AV1 genes. The CLCuBuV C1 gene promoter showed a strong, consistent transient expression of the reporter gene (GUS) in N. tabacum and G. hirsutum leaves and exhibited GUS activity two- to three-fold higher than the CaMV 35S promoter. The CLCuBuV bidirectional genepromoter is a nearly constitutive promoter that contains basic conserved elements. Many cis-regulatory elements (CREs) were also analyzed within the bidirectional plant promoters of CLCuBuV and closely related geminiviruses, which may be helpful in understanding the transcriptional regulation of both the virus and host plant. PMID:24424501

Polo-like kinase 1 expression is suppressed by CCAAT/enhancer-binding protein α to mediate colon carcinoma cell differentiation and apoptosis.

PubMed

Dasgupta, Nirmalya; Thakur, Bhupesh Kumar; Ta, Atri; Das, Sayan; Banik, George; Das, Santasabuj

2017-07-01

Human polo-like kinase 1 (PLK1), a highly conserved serine/threonine kinase is a key player in several essential cell-cycle events. PLK1 is considered an oncogene and its overexpression often correlates with poor prognosis of cancers, including colorectal cancer (CRC). However, regulation of PLK1 expression in colorectal cells was never studied earlier and it is currently unknown if PLK1 regulates differentiation and apoptosis of CRC. PLK1 expression was analyzed by real-time PCR and western blotting. Transcriptional regulation was studied by reporter assay, gene knock-down, EMSA and ChIP. PLK1 expression was down-regulated during butyrate-induced differentiation of HT-29 and other CRC cells. Also, PLK1 down-regulation mediated the role of butyrate in CRC differentiation and apoptosis. We report here a novel transcriptional regulation of PLK1 by butyrate. Transcription factors CCAAT/enhancer-binding protein α (C/EBPα) and Oct-1 share an overlapping binding site over the PLK1 promoter. Elevated levels of C/EBPα by butyrate treatment of CRC cells competed out the activator protein Oct-1 from binding to the PLK1 promoter and sequestered it. Binding of C/EBPα was associated with increased deacetylation near the transcription start site (TSS) of the PLK1 promoter, which abrogated transcription through reduced recruitment of RNA polymerase II. We also found a synergistic role between the synthetic PLK1-inhibitor SBE13 and butyrate on the apoptosis of CRC cells. This study offered a novel p53-independent regulation of PLK1 during CRC differentiation and apoptosis. Down-regulation of PLK1 is one of the mechanisms underlying the anti-cancer role of dietary fibre-derived butyrate in CRC. Copyright © 2017 Elsevier B.V. All rights reserved.

Troponin T3 regulates nuclear localization of the calcium channel Ca{sub v}β{sub 1a} subunit in skeletal muscle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Tan; Taylor, Jackson; Jiang, Yang

The voltage-gated calcium channel (Ca{sub v}) β{sub 1a} subunit (Ca{sub v}β{sub 1a}) plays an important role in excitation–contraction coupling (ECC), a process in the myoplasm that leads to muscle-force generation. Recently, we discovered that the Ca{sub v}β{sub 1a} subunit travels to the nucleus of skeletal muscle cells where it helps to regulate gene transcription. To determine how it travels to the nucleus, we performed a yeast two-hybrid screening of the mouse fast skeletal muscle cDNA library and identified an interaction with troponin T3 (TnT3), which we subsequently confirmed by co-immunoprecipitation and co-localization assays in mouse skeletal muscle in vivo andmore » in cultured C2C12 muscle cells. Interacting domains were mapped to the leucine zipper domain in TnT3 COOH-terminus (160–244 aa) and Ca{sub v}β{sub 1a} NH{sub 2}-terminus (1–99 aa), respectively. The double fluorescence assay in C2C12 cells co-expressing TnT3/DsRed and Ca{sub v}β{sub 1a}/YFP shows that TnT3 facilitates Ca{sub v}β{sub 1a} nuclear recruitment, suggesting that the two proteins play a heretofore unknown role during early muscle differentiation in addition to their classical role in ECC regulation. - Highlights: • Previously, we demonstrated that Ca{sub v}β{sub 1a} is a gene transcription regulator. • Here, we show that TnT3 interacts with Ca{sub v}β{sub 1a}. • We mapped TnT3 and Ca{sub v}β{sub 1a} interaction domain. • TnT3 facilitates Ca{sub v}β{sub 1a} nuclear enrichment. • The two proteins play a heretofore unknown role during early muscle differentiation.« less

Circulating miR-142-3p levels in patients with systemic sclerosis.

PubMed

Makino, K; Jinnin, M; Kajihara, I; Honda, N; Sakai, K; Masuguchi, S; Fukushima, S; Inoue, Y; Ihn, H

2012-01-01

Recently, increased evidence has shown that serum micro (mi)RNA levels are a useful biomarker for the diagnosis, prognosis and therapeutic value of various diseases. However, serum miRNA has not been investigated in patients with systemic sclerosis (SSc), to our knowledge. To investigate the possibility that serum levels of Homo sapiens miR-142 stem-loop (hsa-miR-142-3p), one of the miRNAs regulating the expression of integrin αV, could be a specific disease marker for SSc. Serum samples were obtained from 61 patients with SSc and 20 healthy controls. Patients with systemic lupus erythematosus (SLE), dermatomyositis (DM) and scleroderma spectrum disorder (SSD), who did not fulfil American College of Rheumatology criteria for SSc but might develop SSc in the future, were included as disease controls in this study. miRNAs were purified from serum, and miR-142-3p levels were measured with a quantitative real-time PCR assay. Serum miR-142-3p levels in patients with SSc were significantly higher than in patients with SSD, SLE or DM, and healthy control groups. Patients with increased miR-142-3p levels tended to have a short sublingual frenulum. Our data indicate that serum levels of miR-142-3p may be elevated specifically in patients with SSc, correlating with the severity of this disease, and may be useful diagnostic markers for the presence of SSc and for the differentiation of SSc from SSD. © The Author(s). CED © 2011 British Association of Dermatologists.

Methylation of an intragenic alternative promoter regulates transcription of GARP.

PubMed

Haupt, Sonja; Söntgerath, Viktoria Sophie Apollonia; Leipe, Jan; Schulze-Koops, Hendrik; Skapenko, Alla

2016-02-01

Alternative promoter usage has been proposed as a mechanism regulating transcriptional and translational diversity in highly elaborated systems like the immune system in humans. Here, we report that transcription of human glycoprotein A repetitions predominant (GARP) in regulatory CD4 T cells (Tregs) is tightly regulated by two alternative promoters. An intragenic promoter contains several CpGs and acts as a weak promoter that is demethylated and initiates transcription Treg-specifically. The strong up-stream promoter containing a CpG-island is, in contrast, fully demethylated throughout tissues. Transcriptional activity of the strong promoter was surprisingly down-regulated upon demethylation of the weak promoter. This demethylation-induced transcriptional attenuation regulated the magnitude of GARP expression and correlated with disease activity in rheumatoid arthritis. Treg-specific GARP transcription was initiated by synergistic interaction of forkhead box protein 3 (Foxp3) with nuclear factor of activated T cells (NFAT) and was underpinned by permissive chromatin remodeling caused by release of the H3K4 demethylase, PLU-1. Our findings describe a novel function of alternative promoters in regulating the extent of transcription. Moreover, since GARP functions as a transporter of transforming growth factor β (TGFβ), a cytokine with broad pleiotropic traits, GARP transcriptional attenuation by alternative promoters might provide a mechanism regulating peripheral TGFβ to avoid unwanted harmful effects. Copyright © 2015 Elsevier B.V. All rights reserved.

Research of beam smoothing technology on the technical integration line

NASA Astrophysics Data System (ADS)

Zhang, Rui; Su, Jingqin; Li, Ping; Zhang, Ying; Wang, Jianjun; Dong, Jun; Yang, Dong; Jing, Feng; Xu, Lixin; Ming, Hai

2013-05-01

This paper is focused on the research of SSD and CPP carried out on TIL. A bulk phase modulator with 9.2-GHz modulation frequency is adopted in SSD. The output spectrum of the phase modulator is stable and the residual amplitude modulation is small. FM-to-AM effect caused by free-space propagation after using smoothing by spectral dispersion is theoretically and experimentally studied. Results indicate inserting a dispersion grating in places with larger beam aperture alleviates the FM-to-AM effect, suggesting minimizing free-space propagation and adopting image relay. Experiments indicate when the number of color cycles (Nc) adopts 1, imposing of SSD with 4.26 times diffraction limit (TDL) did not lead to pinhole closure in the spatial filters of the preamplifier with 20 TDL and main amplifier with 26 TDL. Experimental results also indicate SSD didn't influence the load capacity of the laser facility. The contrast of the 440-μm diameter focal spot with 95% energy included using SSD and CPP drops to 0.47, comparing to 1.71 not using SSD and CPP. When the pulse width of the third harmonic wave is 1 ns and the energy is 1115 J, no damage is found in CPP and other final optics. The experiments solves some key technical problems using SSD and CPP on high-power laser facilities, and provides a flexible platform for the laser-plasma interaction experiments.

The BCL11A Transcription Factor Directly Activates RAG Gene Expression and V(D)J Recombination

PubMed Central

Lee, Baeck-seung; Dekker, Joseph D.; Lee, Bum-kyu; Iyer, Vishwanath R.; Sleckman, Barry P.; Shaffer, Arthur L.; Ippolito, Gregory C.

2013-01-01

Recombination-activating gene 1 protein (RAG1) and RAG2 are critical enzymes for initiating variable-diversity-joining (VDJ) segment recombination, an essential process for antigen receptor expression and lymphocyte development. The transcription factor BCL11A is required for B cell development, but its molecular function(s) in B cell fate specification and commitment is unknown. We show here that the major B cell isoform, BCL11A-XL, binds the RAG1 promoter and Erag enhancer to activate RAG1 and RAG2 transcription in pre-B cells. We employed BCL11A overexpression with recombination substrates in a cultured pre-B cell line as well as Cre recombinase-mediated Bcl11alox/lox deletion in explanted murine pre-B cells to demonstrate direct consequences of BCL11A/RAG modulation on V(D)J recombination. We conclude that BCL11A is a critical component of a transcriptional network that regulates B cell fate by controlling V(D)J recombination. PMID:23438597

A-MUPS score to differentiate patients with somatic symptom disorder from those with medical disease for complaints of non-acute pain

PubMed Central

Suzuki, Shingo; Ohira, Yoshiyuki; Noda, Kazutaka; Ikusaka, Masatomi

2017-01-01

Purpose To develop a clinical score to discriminate patients with somatic symptom disorder (SSD) from those with medical disease (MD) for complaints of non-acute pain. Methods We retrospectively examined the clinical records of consecutive patients with pain for a duration of ≥1 month in our department from April 2003 to March 2015. We divided the subjects according to the diagnoses of definite SSD (as diagnosed and tracked by psychiatrists in our hospital), probable SSD (without evaluation by psychiatrists in our hospital), matched MD (randomly matched two patients by age, sex, and pain location for each definite SSD patient), unmatched MD, other mental disease, or functional somatic syndrome (FSS). We investigated eight clinical factors for definite SSD and matched MD, and developed a diagnostic score to identify SSD. We subsequently validated the model with cases of probable SSD and unmatched MD. Results The number of patients with definite SSD, probable SSD, matched MD, unmatched MD, other mental disease, and FSS was 104 (3.5%), 214 (7.3%), 197 (6.7%), 742 (25%), 708 (24%), and 978 (33%), respectively. In a conditional logistic regression analysis, the following five factors were included as independent predictors of SSD: Analgesics ineffective, Mental disorder history, Unclear provocative/palliative factors, Persistence without cessation, and Stress feelings/episodes (A-MUPS). The area under the receiver operating characteristic curve (AUC) of the model was 0.900 (95% CI: 0.864–0.937, p<0.001), and the McFadden’s pseudo-R-squared was 0.709. For internal validation, the AUC between probable SSD and unmatched MD was 0.930 (95% CI: 0.910–0.950, p<0.001). The prevalence and the likelihood ratio of SSD increased as the score increased. Conclusion The A-MUPS score was useful for discriminating patients with SSD from those with MD for complaints of non-acute pain, although external validation and refinement should be needed. PMID:28652807

A-MUPS score to differentiate patients with somatic symptom disorder from those with medical disease for complaints of non-acute pain.

PubMed

Suzuki, Shingo; Ohira, Yoshiyuki; Noda, Kazutaka; Ikusaka, Masatomi

2017-01-01

To develop a clinical score to discriminate patients with somatic symptom disorder (SSD) from those with medical disease (MD) for complaints of non-acute pain. We retrospectively examined the clinical records of consecutive patients with pain for a duration of ≥1 month in our department from April 2003 to March 2015. We divided the subjects according to the diagnoses of definite SSD (as diagnosed and tracked by psychiatrists in our hospital), probable SSD (without evaluation by psychiatrists in our hospital), matched MD (randomly matched two patients by age, sex, and pain location for each definite SSD patient), unmatched MD, other mental disease, or functional somatic syndrome (FSS). We investigated eight clinical factors for definite SSD and matched MD, and developed a diagnostic score to identify SSD. We subsequently validated the model with cases of probable SSD and unmatched MD. The number of patients with definite SSD, probable SSD, matched MD, unmatched MD, other mental disease, and FSS was 104 (3.5%), 214 (7.3%), 197 (6.7%), 742 (25%), 708 (24%), and 978 (33%), respectively. In a conditional logistic regression analysis, the following five factors were included as independent predictors of SSD: Analgesics ineffective, Mental disorder history, Unclear provocative/palliative factors, Persistence without cessation, and Stress feelings/episodes (A-MUPS). The area under the receiver operating characteristic curve (AUC) of the model was 0.900 (95% CI: 0.864-0.937, p <0.001), and the McFadden's pseudo- R -squared was 0.709. For internal validation, the AUC between probable SSD and unmatched MD was 0.930 (95% CI: 0.910-0.950, p <0.001). The prevalence and the likelihood ratio of SSD increased as the score increased. The A-MUPS score was useful for discriminating patients with SSD from those with MD for complaints of non-acute pain, although external validation and refinement should be needed.

SU-E-T-219: Comprehensive Validation of the Electron Monte Carlo Dose Calculation Algorithm in RayStation Treatment Planning System for An Elekta Linear Accelerator with AgilityTM Treatment Head

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yi; Park, Yang-Kyun; Doppke, Karen P.

2015-06-15

Purpose: This study evaluated the performance of the electron Monte Carlo dose calculation algorithm in RayStation v4.0 for an Elekta machine with Agility™ treatment head. Methods: The machine has five electron energies (6–8 MeV) and five applicators (6×6 to 25×25 cm {sup 2}). The dose (cGy/MU at d{sub max}), depth dose and profiles were measured in water using an electron diode at 100 cm SSD for nine square fields ≥2×2 cm{sup 2} and four complex fields at normal incidence, and a 14×14 cm{sup 2} field at 15° and 30° incidence. The dose was also measured for three square fields ≥4×4more » cm{sup 2} at 98, 105 and 110 cm SSD. Using selected energies, the EBT3 radiochromic film was used for dose measurements in slab-shaped inhomogeneous phantoms and a breast phantom with surface curvature. The measured and calculated doses were analyzed using a gamma criterion of 3%/3 mm. Results: The calculated and measured doses varied by <3% for 116 of the 120 points, and <5% for the 4×4 cm{sup 2} field at 110 cm SSD at 9–18 MeV. The gamma analysis comparing the 105 pairs of in-water isodoses passed by >98.1%. The planar doses measured from films placed at 0.5 cm below a lung/tissue layer (12 MeV) and 1.0 cm below a bone/air layer (15 MeV) showed excellent agreement with calculations, with gamma passing by 99.9% and 98.5%, respectively. At the breast-tissue interface, the gamma passing rate is >98.8% at 12–18 MeV. The film results directly validated the accuracy of MU calculation and spatial dose distribution in presence of tissue inhomogeneity and surface curvature - situations challenging for simpler pencil-beam algorithms. Conclusion: The electron Monte Carlo algorithm in RayStation v4.0 is fully validated for clinical use for the Elekta Agility™ machine. The comprehensive validation included small fields, complex fields, oblique beams, extended distance, tissue inhomogeneity and surface curvature.« less

Characterization and Transcription of Arsenic Respiration and Resistance Genes During In Situ Uranium Bioremediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giloteaux, L.; Holmes, Dawn E.; Williams, Kenneth H.

2013-02-04

The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the alpha subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative RT-PCR. Most of the arrA (> 60%) and acr3-1 (> 90%) sequencesmore » that were recovered were most similar to Geobacter species, while the majority of acr3-2 (>50%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated transcription of arrA in situ even though the presence of As(V) increased transcription of arrA in cultures of G. lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry.« less

Regional contextual influences on short sleep duration: a 50 universities population-based multilevel study in China.

PubMed

Yang, Tingzhong; Peng, Sihui; Barnett, Ross; Zhang, Chichen

2018-01-01

Ecological models have emphasized that short sleep duration (SSD) is influenced by both individual and environmental variables. However, few studies have considered the latter. The present study explores the influence of urban and regional contextual factors, net of individual characteristics, on the prevalence of SSD among university students in China. Participants were 11,954 students, who were identified through a multistage survey sampling process conducted in 50 universities. Individual data were obtained through a self-administered questionnaire, and contextual variables were retrieved from a national database. Multilevel logistic regression models were used to examine urban and regional variations in high and moderate levels of SSD. Overall the prevalence of high SSD (<6 hours sleep duration) was 2.8% (95% CI: 1.7%,3.9%) and moderate SSD (<7 hours) 24.7% (95% CI: 19.5%, 29.8%). Multilevel logistic regressions confirmed that home region gross domestic product (GDP) and the university regional unemployment rate were associated with SSD, net of other individual- and city-level covariates. Students attending high-level universities also recorded the highest levels of SSD. Of the individual characteristcs, only mother's occupation and student mental health status were related to SSD. The results of this study add important insights about the role of contextual factors affecting SSD among young adults and indicate the need to take into account both past, as well as present, environmental influences to control SSD.

A single point mutation in cyclin T1 eliminates binding to Hexim1, Cdk9 and RNA but not to AFF4 and enforces repression of HIV transcription

PubMed Central

2014-01-01

Background Human immunodeficiency virus (HIV) gene expression is primarily regulated at the step of transcription elongation. The viral Tat protein recruits the Positive Transcription Elongation Factor b (P-TEFb) and the Super Elongation Complex (SEC) to the HIV promoter and enhances transcription by host RNA polymerase II. Results To map residues in the cyclin box of cyclin T1 that mediate the binding of P-TEFb to its interacting host partners and support HIV transcription, a pool of N-terminal cyclin T1 mutants was generated. Binding and functional assays in cells identified specific positions in cyclin T1 that are important for (i) association of P-TEFb with Hexim1, Cdk9 and SEC/AFF4 (ii) supporting Tat-transactivation in murine cells and (iii) inhibition of basal and Tat-dependent HIV transcription in human cells. Significantly, a unique cyclin T1 mutant where a Valine residue at position 107 was mutated to Glutamate (CycT1-V107E) was identified. CycT1-V107E did not bind to Hexim1 or Cdk9, and also could not assemble on HIV TAR or 7SK-snRNA. However, it bound strongly to AFF4 and its association with HIV Tat was slightly impaired. CycT1-V107E efficiently inhibited HIV replication in human T cell lines and in CD4(+) primary cells, and enforced HIV transcription repression in T cell lines that harbor a transcriptionally silenced integrated provirus. Conclusions This study outlines the mechanism by which CycT1-V107E mutant inhibits HIV transcription and enforces viral latency. It defines the importance of N-terminal residues of cyclin T1 in mediating contacts of P-TEFb with its transcription partners, and signifies the requirement of a functional P-TEFb and SEC in mediating HIV transcription. PMID:24985467

A single point mutation in cyclin T1 eliminates binding to Hexim1, Cdk9 and RNA but not to AFF4 and enforces repression of HIV transcription.

PubMed

Kuzmina, Alona; Verstraete, Nina; Galker, Sigal; Maatook, Maayan; Bensaude, Olivier; Taube, Ran

2014-07-01

Human immunodeficiency virus (HIV) gene expression is primarily regulated at the step of transcription elongation. The viral Tat protein recruits the Positive Transcription Elongation Factor b (P-TEFb) and the Super Elongation Complex (SEC) to the HIV promoter and enhances transcription by host RNA polymerase II. To map residues in the cyclin box of cyclin T1 that mediate the binding of P-TEFb to its interacting host partners and support HIV transcription, a pool of N-terminal cyclin T1 mutants was generated. Binding and functional assays in cells identified specific positions in cyclin T1 that are important for (i) association of P-TEFb with Hexim1, Cdk9 and SEC/AFF4 (ii) supporting Tat-transactivation in murine cells and (iii) inhibition of basal and Tat-dependent HIV transcription in human cells. Significantly, a unique cyclin T1 mutant where a Valine residue at position 107 was mutated to Glutamate (CycT1-V107E) was identified. CycT1-V107E did not bind to Hexim1 or Cdk9, and also could not assemble on HIV TAR or 7SK-snRNA. However, it bound strongly to AFF4 and its association with HIV Tat was slightly impaired. CycT1-V107E efficiently inhibited HIV replication in human T cell lines and in CD4(+) primary cells, and enforced HIV transcription repression in T cell lines that harbor a transcriptionally silenced integrated provirus. This study outlines the mechanism by which CycT1-V107E mutant inhibits HIV transcription and enforces viral latency. It defines the importance of N-terminal residues of cyclin T1 in mediating contacts of P-TEFb with its transcription partners, and signifies the requirement of a functional P-TEFb and SEC in mediating HIV transcription.

DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

PubMed Central

Zhong, Xuehua; Hale, Christopher J.; Nguyen, Minh; Ausin, Israel; Groth, Martin; Hetzel, Jonathan; Vashisht, Ajay A.; Henderson, Ian R.; Wohlschlegel, James A.; Jacobsen, Steven E.

2015-01-01

DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase DOMAINS REARRANGED METHYLASE 2 (DRM2) controls RNA-directed DNA methylation in a pathway that also involves the plant-specific RNA Polymerase V (Pol V). Additionally, the Arabidopsis genome encodes an evolutionarily conserved but catalytically inactive DNA methyltransferase, DRM3. Here, we show that DRM3 has moderate effects on global DNA methylation and small RNA abundance and that DRM3 physically interacts with Pol V. In Arabidopsis drm3 mutants, we observe a lower level of Pol V-dependent noncoding RNA transcripts even though Pol V chromatin occupancy is increased at many sites in the genome. These findings suggest that DRM3 acts to promote Pol V transcriptional elongation or assist in the stabilization of Pol V transcripts. This work sheds further light on the mechanism by which long noncoding RNAs facilitate RNA-directed DNA methylation. PMID:25561521

Derivation of predicted no effect concentration (PNEC) for HHCB to terrestrial species (plants and invertebrates).

PubMed

Wang, Xiaonan; Liu, Zhengtao; Wang, Wanhua; Zhang, Cong; Chen, Lihong

2015-03-01

The 1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta-(γ)-2-benzopyrane (HHCB) is a synthetic musk which is used as a fragrance in a variety of personal care products, and due to this it is widely spread in the environment. However, there is no paper dealing with the predicted no effect concentration (PNEC) for HHCB to terrestrial species using the species sensitivity distribution (SSD) method, mainly results from the shortage of species toxicity data of different taxonomic levels. In this study, toxicity data were obtained from 10 chronic toxicity tests using 10 terrestrial species (3 dicotyledonous plants, 5 monocotyledonous plants and 2 terrestrial invertebrates) from 3 Phyla and 9 Families. The PNEC of HHCB was derived using the SSD method. The result of present research showed that the dicotyledonous Solanum lycopersicum was the most sensitive plants to HHCB contamination. The PNEC ranged between 0.70 and 3.52 mg HHCB/kg when using the log-logistic SSD method. It is recommended to use toxicity data of different taxonomic levels for the development of PNEC values in terrestrial environment due to different species sensitivity. Copyright © 2014 Elsevier B.V. All rights reserved.

MEGA: the next generation Medium Energy Gamma-ray Telescope

NASA Astrophysics Data System (ADS)

Paciesas, W.; Miller, R. S.; Andritschke, R.; Kanbach, G.; Zoglauer, A.; Bloser, P.; Hunter, S.; Cravens, J.; Cherry, M.; Guzik, T. G.; Stacy, J. G.; Wefel, J. P.; Di Cocco, G.; Hartmann, D.; Kippen, R. M.; Vestrand, W. T.; Kurfess, J.; Phlips, B.; Strickman, M.; Wulf, E.; Macri, J. R.; McConnell, M. L.; Ryan, J. M.; Reglero, V.; Zych, A. D.

2004-08-01

The MEGA mission would enable a sensitive all-sky survey of the medium-energy gamma-ray sky (0.3-50 MeV). This mission will bridge the huge sensitivity gap between the COMPTEL and OSSE experiments on the Compton Gamma Ray Observatory, the SPI and IBIS instruments on INTEGRAL and the visionary ACT mission. It will, among other things, serve to compile a much larger catalog of sources in this energy range, perform far deeper searches for supernovae, better measure the galactic continuum emission as well as identify the components of the cosmic diffuse emission. It will accomplish these goals with a stack of Si-strip detector (SSD) planes surrounded by a dense high-Z calorimeter. At lower photon energies (below ˜ 30 MeV), the design is sensitive to Compton interactions, with the SSD system serving as a scattering medium that also detects and measures the Compton recoil energy deposit. If the energy of the recoil electron is sufficiently high (> 2 MeV), the track of the recoil electron can also be defined. At higher photon energies (above ˜ 10 MeV), the design is sensitive to pair production events, with the SSD system measuring the tracks of the electron and positron. We will discuss the various types of event signatures in detail and describe the advantages of this design over previous Compton telescope designs. Effective area, sensitivity and resolving power estimates are also presented along with simulations of expected scientific results and beam calibration results from the prototype instrument.

c-Abl phosphorylation of Yin Yang 1's conserved tyrosine 254 in the spacer region modulates its transcriptional activity.

PubMed

Daraiseh, Susan I; Kassardjian, Ari; Alexander, Karen E; Rizkallah, Raed; Hurt, Myra M

2018-05-25

Yin Yang 1 (YY1) is a multifunctional transcription factor that can activate or repress transcription depending on the promotor and/or the co-factors recruited. YY1 is phosphorylated in various signaling pathways and is critical for different biological functions including embryogenesis, apoptosis, proliferation, cell-cycle regulation and tumorigenesis. Here we report that YY1 is a substrate for c-Abl kinase phosphorylation at conserved residue Y254 in the spacer region. Pharmacological inhibition of c-Abl kinase by imatinib, nilotinib and GZD824, knock-down of c-Abl using siRNA, and the use of c-Abl kinase-dead drastically reduces tyrosine phosphorylation of YY1. Both radioactive and non-radioactive in vitro kinase assays, as well as co-immunoprecipitation in different cell lines, show that the target of c-Abl phosphorylation is tyrosine residue 254. c-Abl phosphorylation has little effect on YY1 DNA binding ability or cellular localization in asynchronous cells. However, functional studies reveal that c-Abl mediated phosphorylation of YY1 regulates YY1's transcriptional ability in vivo. In conclusion, we demonstrate the novel role of c-Abl kinase in regulation of YY1's transcriptional activity, linking YY1 regulation with c-Abl tyrosine kinase signaling pathways. Copyright © 2018. Published by Elsevier B.V.

The Transcriptional Regulator, CosR, Controls Compatible Solute Biosynthesis and Transport, Motility and Biofilm Formation in Vibrio cholerae

PubMed Central

Shikuma, Nicholas J.; Davis, Kimberly R.; Fong, Jiunn N. C.; Yildiz, Fitnat H.

2012-01-01

SUMMARY Vibrio cholerae inhabits aquatic environments and colonizes the human digestive tract to cause the disease cholera. In these environments, V. cholerae copes with fluctuations in salinity and osmolarity by producing and transporting small, organic, highly soluble molecules called compatible solutes, which counteract extracellular osmotic pressure. Currently, it is unclear how V. cholerae regulates the expression of genes important for the biosynthesis or transport of compatible solutes in response to changing salinity or osmolarity conditions. Through a genome-wide transcriptional analysis of the salinity response of V. cholerae, we identified a transcriptional regulator we name CosR for compatible solute regulator. The expression of cosR is regulated by ionic strength and not osmolarity. A transcriptome analysis of a ΔcosR mutant revealed that CosR represses genes involved in ectoine biosynthesis and compatible solute transport in a salinity-dependent manner. When grown in salinities similar to estuarine environments, CosR activates biofilm formation and represses motility independently of its function as an ectoine regulator. This is the first study to characterize a compatible solute regulator in V. cholerae and couples the regulation of osmotic tolerance with biofilm formation and motility. PMID:22690884

DSM-5 somatic symptom disorder in patients with vertigo and dizziness symptoms.

PubMed

Limburg, Karina; Sattel, Heribert; Radziej, Katharina; Lahmann, Claas

2016-12-01

DSM-5 somatic symptom disorder (SSD) could potentially be a highly relevant diagnosis for patients with vertigo and dizziness. The criteria of SSD, particularly the B-criterion with its three components (cognitive, affective, behavioral), have however not yet been investigated in this patient group. We evaluated a large sample (n=399) of outpatients presenting in a neurological setting. Physical examinations and a psychometric assessment (SCID-I) were conducted; patients completed self-report questionnaires. The diagnosis of SSD was assigned retrospectively. The prevalence of SSD, its diagnostic criteria, and its overlap with former DSM-IV somatoform disorders were evaluated; comparisons were drawn between (1) patients fulfilling different components of the B-criterion and (2) patients with diagnoses after DSM-IV vs. DSM-5. SSD was almost twice as common as DSM-IV somatoform disorders. Patients with all three components of the B-criterion reported the highest impairment levels. Patients with both DSM-IV somatoform disorders and DSM-5 SSD were more impaired compared to groups with one of the diagnoses; patients with DSM-IV somatoform disorders only were more impaired than those with SSD only. Our findings demonstrate that SSD is highly prevalent in patients with vertigo and dizziness. The classification of severity based on the number of psychological symptoms appears valid and may assist in finding suitable treatment options according to clinical practice guidelines. Future studies should investigate the overlap of SSD and other psychiatric disorders, this may assist in better defining the diagnostic criteria of SSD. Copyright © 2016 Elsevier Inc. All rights reserved.

Matching extended-SSD electron beams to multileaf collimated photon beams in the treatment of head and neck cancer.

PubMed

Steel, Jared; Stewart, Allan; Satory, Philip

2009-09-01

Matching the penumbra of a 6 MeV electron beam to the penumbra of a 6 MV photon beam is a dose optimization challenge, especially when the electron beam is applied from an extended source-to-surface distance (SSD), as in the case of some head and neck treatments. Traditionally low melting point alloy blocks have been used to define the photon beam shielding over the spinal cord region. However, these are inherently time consuming to construct and employ in the clinical situation. Multileaf collimators (MLCs) provide a fast and reproducible shielding option but generate geometrically nonconformal approximations to the desired beam edge definition. The effects of substituting Cerrobend for the MLC shielding mode in the context of beam matching with extended-SSD electron beams are the subject of this investigation. Relative dose beam data from a Varian EX 2100 linear accelerator were acquired in a water tank under the 6 MeV electron beam at both standard and extended-SSD and under the 6 MV photon beam defined by Cerrobend and a number of MLC stepping regimes. The effect of increasing the electron beam SSD on the beam penumbra was assessed. MLC stepping was also assessed in terms of the effects on both the mean photon beam penumbra and the intraleaf dose-profile nonuniformity relative to the MLC midleaf. Computational techniques were used to combine the beam data so as to simulate composite relative dosimetry in the water tank, allowing fine control of beam abutment gap variation. Idealized volumetric dosimetry was generated based on the percentage depth-dose data for the beam modes and the abutment geometries involved. Comparison was made between each composite dosimetry dataset and the relevant ideal dosimetry dataset by way of subtraction. Weighted dose-difference volume histograms (DDVHs) were produced, and these, in turn, summed to provide an overall dosimetry score for each abutment and shielding type/angle combination. Increasing the electron beam SSD increased the penumbra width (defined as the lateral distance of the 80% and 20% isodose contours) by 8-10 mm at the depths of 10-20 mm. Mean photon beam penumbra width increased with increased MLC stepping, and the mean MLC penumbra was approximately 1.5 times greater than that across the corresponding Cerrobend shielding. Intraleaf dose discrepancy in the direction orthogonal to the beam edge also increased with MLC stepping. The weighted DDVH comparison techniques allowed the composite dosimetry resulting from the interplay of the abovementioned variables to be ranked. The MLC dosimetry ranked as good or better than that resulting from beam matching with Cerrobend for all except large field overlaps (-2.5 mm gap). The results for the linear-weighted DDVH comparison suggest that optimal MLC abutment dosimetry results from an optical surface gap of around 1 +/- 0.5 mm. Furthermore, this appears reasonably lenient to abutment gap variation, such as that arising from uncertainty in beam markup or other setup errors.

Expression and responses to dehydration and salinity stresses of V-PPase gene members in wheat.

PubMed

Wang, Yuezhi; Xu, Haibin; Zhang, Guangxiang; Zhu, Huilan; Zhang, Lixia; Zhang, Zhengzhi; Zhang, Caiqin; Ma, Zhengqiang

2009-12-01

Vacuolar H(+)-translocating pyrophosphatase (V-PPase) is a key enzyme related to plant growth as well as abiotic stress tolerance. In this work, wheat V-PPase genes TaVP1, TaVP2 and TaVP3 were identified. TaVP1 and TaVP2 are more similar to each other than to TaVP3. Their deduced polypeptide sequences preserve the topological structure and essential residues of V-PPases. Phylogenetic studies suggested that monocot plants, at least monocot grasses, have three VP paralogs. TaVP3 transcripts were only detected in developing seeds, and no TaVP2 transcripts were found in germinating seeds. TaVP2 was mainly expressed in shoot tissues and down-regulated in leaves under dehydration. Its expression was up-regulated in roots under high salinity. TaVP1 was relatively more ubiquitously and evenly expressed than TaVP2. Its expression level in roots was highest among the tissues examined, and was inducible by salinity stress. These results indicated that the V-PPase gene paralogs in wheat are differentially regulated spatially and in response to dehydration and salinity stresses. 2009 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Control of lysosomal biogenesis and Notch-dependent tissue patterning by components of the TFEB-V-ATPase axis in Drosophila melanogaster.

PubMed

Tognon, Emiliana; Kobia, Francis; Busi, Ilaria; Fumagalli, Arianna; De Masi, Federico; Vaccari, Thomas

2016-01-01

In vertebrates, TFEB (transcription factor EB) and MITF (microphthalmia-associated transcription factor) family of basic Helix-Loop-Helix (bHLH) transcription factors regulates both lysosomal function and organ development. However, it is not clear whether these 2 processes are interconnected. Here, we show that Mitf, the single TFEB and MITF ortholog in Drosophila, controls expression of vacuolar-type H(+)-ATPase pump (V-ATPase) subunits. Remarkably, we also find that expression of Vha16-1 and Vha13, encoding 2 key components of V-ATPase, is patterned in the wing imaginal disc. In particular, Vha16-1 expression follows differentiation of proneural regions of the disc. These regions, which will form sensory organs in the adult, appear to possess a distinctive endolysosomal compartment and Notch (N) localization. Modulation of Mitf activity in the disc in vivo alters endolysosomal function and disrupts proneural patterning. Similar to our findings in Drosophila, in human breast epithelial cells we observe that impairment of the Vha16-1 human ortholog ATP6V0C changes the size and function of the endolysosomal compartment and that depletion of TFEB reduces ligand-independent N signaling activity. Our data suggest that lysosomal-associated functions regulated by the TFEB-V-ATPase axis might play a conserved role in shaping cell fate.

Sub-surface mechanical damage distributions during grinding of fused silica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suratwala, T I; Wong, L L; Miller, P E

2005-11-28

The distribution and characteristics of surface cracking (i.e. sub-surface damage or SSD) formed during standard grinding processes has been investigated on fused silica glass. The SSD distributions of the ground surfaces were determined by: (1) creating a shallow (18-108 {micro}m) wedge/taper on the surface by magneto-rheological finishing; (2) exposing the SSD by HF acid etching; and (3) performing image analysis of the observed cracks from optical micrographs taken along the surface taper. The observed surface cracks are characterized as near-surface lateral and deeper trailing indent type fractures (i.e., chatter marks). The SSD depth distributions are typically described by a singlemore » exponential distribution followed by an asymptotic cutoff in depth (c{sub max}). The length of the trailing indent is strongly correlated with a given process. Using established fracture indentation relationships, it is shown that only a small fraction of the abrasive particles are being mechanically loaded and causing fracture, and it is likely the larger particles in the abrasive particle size distribution that bear the higher loads. The SSD depth was observed to increase with load and with a small amount of larger contaminant particles. Using a simple brittle fracture model for grinding, the SSD depth distribution has been related to the SSD length distribution to gain insight into ''effective'' size distribution of particles participating in the fracture. Both the average crack length and the surface roughness were found to scale linearly with the maximum SSD depth (c{sub max}). These relationships can serve as useful rules-of-thumb for nondestructively estimating SSD depth and to identify the process that caused the SSD. In certain applications such as high intensity lasers, SSD on the glass optics can serve as a reservoir for minute amounts of impurities that absorb the high intensity laser light and lead to subsequent laser-induced surface damage. Hence a more scientific understanding of SSD formation can provide a means to establish recipes to fabricate SSD-free, laser damage resistant optical surfaces.« less

Involvement of Human Estrogen Related Receptor Alpha 1 (hERR 1) in Breast Cancer and Hormonally Insensitive Disease

DTIC Science & Technology

2000-08-01

SV40 early-to-late switch involves titration of cellular transcriptional repressors, Genes Dev. 7: 2206-19, 1993. 6. Bonnelye, E., Vanacker , J. M ...transcriptional regulator of the human medium-chain acyl coenzyme A dehydrogenase gene, Mol Cell Biol. 17: 5400-9, 1997. 8. Vanacker , J. M ., Bonnelye, E...related receptor-alpha), Mol Endocrinol. 13: 764-73, 1999. 9. Vanacker , J. M ., Pettersson, K., Gustafsson, J. A., and Laudet, V. Transcriptional

The small-animal radiation research platform (SARRP): dosimetry of a focused lens system.

PubMed

Deng, Hua; Kennedy, Christopher W; Armour, Elwood; Tryggestad, Erik; Ford, Eric; McNutt, Todd; Jiang, Licai; Wong, John

2007-05-21

A small animal radiation platform equipped with on-board cone-beam CT and conformal irradiation capabilities is being constructed for translational research. To achieve highly localized dose delivery, an x-ray lens is used to focus the broad beam from a 225 kVp x-ray tube down to a beam with a full width half maximum (FWHM) of approximately 1.5 mm in the energy range 40-80 keV. Here, we report on the dosimetric characteristics of the focused beam from the x-ray lens subsystem for high-resolution dose delivery. Using the metric of the average dose within a 1.5 mm diameter area, the dose rates at a source-to-surface distance (SSD) of 34 cm are 259 and 172 cGy min(-1) at 6 mm and 2 cm depths, respectively, with an estimated uncertainty of +/-5%. The per cent depth dose is approximately 56% at 2 cm depth for a beam at 34 cm SSD.

Silver aids healing in the sterile skin wound: experimental studies in the laboratory rat.

PubMed

Lansdown, A B; Sampson, B; Laupattarakasem, P; Vuttivirojana, A

1997-11-01

Incisional wounds 15 mm long were induced surgically in the back skin of young adult Wistar rats. They were sutured and used as an experimental model in the therapeutic evaluation of daily applications of 0.5 mL of silver nitrate (SN) at 0.01, 0.1 or 1.0% w/v aqueous solution, or 0.5 g silver sulphadiazine (SSD) over a 10-day period. Control wounds received deionized water only. The silver preparations were not toxic but SN did stain the hair and superficial layers of the stratum corneum. The wounds remained microbiologically clean. Wounds exposed to SN (0.1 or 1.0%) or SSD healed more rapidly than controls. From about the fourth day of treatment, we noted a more rapid exteriorization of sutures, improved wound closure and an earlier loss of scabs and wound debris. Silver treatment appeared to reduce the inflammatory and granulation tissue phases of healing and enhance epidermal repair. Silver from SN was deposited as silver sulphide in extrafollicular hair shafts and superficial aspects of the skin and wound debris but not at deeper levels. Silver uptake was four-fold higher in damaged skin than in intact tissue. SSD was absorbed by intact and wounded skin but the silver did not precipitate as silver sulphide and its localization in the tissue is not known. Uptake of silver from SN or SSD was associated with changes in the concentrations of zinc and calcium in the skin. Zinc levels were depressed during the inflammatory and proliferative phases of healing and then increased. Zinc concentrations had normalized by 10 days when wound healing was achieved. Calcium levels remained higher than normal throughout the observation period. The mechanism of action of silver in advancing wound healing in the rat is unclear. Its ability to reduce the inflammatory and granulation phases of healing, and to invoke metallothionein production and influence metal ion binding are possibly important.

Research of beam smoothing technologies using CPP, SSD, and PS

NASA Astrophysics Data System (ADS)

Zhang, Rui; Su, Jingqin; Hu, Dongxia; Li, Ping; Yuan, Haoyu; Zhou, Wei; Yuan, Qiang; Wang, Yuancheng; Tian, Xiaocheng; Xu, Dangpeng; Dong, Jun; Zhu, Qihua

2015-02-01

Precise physical experiments place strict requirements on target illumination uniformity in Inertial Confinement Fusion. To obtain a smoother focal spot and suppress transverse SBS in large aperture optics, Multi-FM smoothing by spectral dispersion (SSD) was studied combined with continuous phase plate (CPP) and polarization smoothing (PS). New ways of PS are being developed to improve the laser irradiation uniformity and solve LPI problems in indirect-drive laser fusion. The near field and far field properties of beams using polarization smoothing were studied and compared, including birefringent wedge and polarization control array. As more parameters can be manipulated in a combined beam smoothing scheme, quad beam smoothing was also studies. Simulation results indicate through adjusting dispersion directions of one-dimensional (1-D) SSD beams in a quad, two-dimensional SSD can be obtained. Experiments have been done on SG-III laser facility using CPP and Multi-FM SSD. The research provides some theoretical and experimental basis for the application of CPP, SSD and PS on high-power laser facilities.

Design and dosimetry characteristics of a commercial applicator system for intra-operative electron beam therapy utilizing ELEKTA Precise accelerator.

PubMed

Nevelsky, Alexander; Bernstein, Zvi; Bar-Deroma, Raquel; Kuten, Abraham; Orion, Itzhak

2010-07-19

The design concept and dosimetric characteristics of a new applicator system for intraoperative radiation therapy (IORT) are presented in this work. A new hard-docking commercial system includes polymethylmethacrylate (PMMA) applicators with different diameters and applicator end angles and a set of secondary lead collimators. A telescopic device allows changing of source-to-surface distance (SSD). All measurements were performed for 6, 9, 12 and 18 MeV electron energies. Output factors and percentage depth doses (PDD) were measured in a water phantom using a plane-parallel ion chamber. Isodose contours and radiation leakage were measured using a solid water phantom and radiographic films. The dependence of PDD on SSD was checked for the applicators with the smallest and the biggest diameters. SSD dependence of the output factors was measured. Hardcopies of PDD and isodose contours were prepared to help the team during the procedure on deciding applicator size and energy to be chosen. Applicator output factors are a function of energy, applicator size and applicator type. Dependence of SSD correction factors on applicator size and applicator type was found to be weak. The same SSD correction will be applied for all applicators in use for each energy. The radiation leakage through the applicators is clinically acceptable. The applicator system enables effective collimation of electron beams for IORT. The data presented are sufficient for applicator, energy and monitor unit selection for IORT treatment of a patient.

Optical smoothing of laser imprinting in planar-target experiments on OMEGA EP using multi-FM 1-D smoothing by spectral dispersion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hohenberger, M., E-mail: mhoh@lle.rochester.edu; Shvydky, A.; Marozas, J. A.

Direct-drive ignition on the National Ignition Facility (NIF) requires single-beam smoothing to minimize imprinting of laser nonuniformities that can negatively affect implosion performance. One-dimensional, multi-FM smoothing by spectral dispersion (SSD) has been proposed to provide the required smoothing [Marozas et al., Bull. Am. Phys. Soc. 55, 294 (2010)]. A prototype multi-FM SSD system has been integrated into the NIF-like beamline of the OMEGA EP Laser System. Experiments have been performed to verify the smoothing performance by measuring Rayleigh–Taylor growth rates in planar targets of laser-imprinted and preimposed surface modulations. Multi-FM 1-D SSD has been observed to reduce imprint levels bymore » ∼50% compared to the nominal OMEGA EP SSD system. The experimental results are in agreement with 2-D DRACO simulations using realistic, time-dependent far-field spot-intensity calculations that emulate the effect of SSD.« less

Transcriptome analysis provides insights into the delayed sticky disease symptoms in Carica papaya.

PubMed

Madroñero, Johana; Rodrigues, Silas P; Antunes, Tathiana F S; Abreu, Paolla M V; Ventura, José A; Fernandes, A Alberto R; Fernandes, Patricia Machado Bueno

2018-03-21

Global gene expression analysis indicates host stress responses, mainly those mediated by SA, associated to the tolerance to sticky disease symptoms at pre-flowering stage in Carica papaya. Carica papaya plants develop the papaya sticky disease (PSD) as a result of the combined infection of papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), or PMeV complex. PSD symptoms appear only after C. papaya flowers. To understand the mechanisms involved in this phenomenon, the global gene expression patterns of PMeV complex-infected C. papaya at pre-and post-flowering stages were assessed by RNA-Seq. The result was 633 and 88 differentially expressed genes at pre- and post-flowering stages, respectively. At pre-flowering stage, genes related to stress and transport were up-regulated while metabolism-related genes were down-regulated. It was observed that induction of several salicylic acid (SA)-activated genes, including PR1, PR2, PR5, WRKY transcription factors, ROS and callose genes, suggesting SA signaling involvement in the delayed symptoms. In fact, pre-flowering C. papaya treated with exogenous SA showed a tendency to decrease the PMeV and PMeV2 loads when compared to control plants. However, pre-flowering C. papaya also accumulated transcripts encoding a NPR1-inhibitor (NPR1-I/NIM1-I) candidate, genes coding for UDP-glucosyltransferases (UGTs) and several genes involved with ethylene pathway, known to be negative regulators of SA signaling. At post-flowering, when PSD symptoms appeared, the down-regulation of PR-1 encoding gene and the induction of BSMT1 and JA metabolism-related genes were observed. Hence, SA signaling likely operates at the pre-flowering stage of PMeV complex-infected C. papaya inhibiting the development of PSD symptoms, but the induction of its negative regulators prevents the full-scale and long-lasting tolerance.

Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability.

PubMed

Miller, Christopher B; Bartlett, Delwyn J; Mullins, Anna E; Dodds, Kirsty L; Gordon, Christopher J; Kyle, Simon D; Kim, Jong Won; D'Rozario, Angela L; Lee, Rico S C; Comas, Maria; Marshall, Nathaniel S; Yee, Brendon J; Espie, Colin A; Grunstein, Ronald R

2016-11-01

To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative ( q )-EEG and heart rate variability (HRV). Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P < 0.05). Preliminary work suggested three clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q -EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Two insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q -EEG. Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. © 2016 Associated Professional Sleep Societies, LLC.

Rabbit antithymocyte globulin–induced serum sickness disease and human kidney graft survival

PubMed Central

Couvrat-Desvergnes, Grégoire; Salama, Apolline; Le Berre, Ludmilla; Evanno, Gwénaëlle; Viklicky, Ondrej; Hruba, Petra; Vesely, Pavel; Guerif, Pierrick; Dejoie, Thomas; Rousse, Juliette; Nicot, Arnaud; Bach, Jean-Marie; Ang, Evelyn; Foucher, Yohann; Brouard, Sophie; Castagnet, Stéphanie; Giral, Magali; Harb, Jean; Perreault, Hélène; Charreau, Béatrice; Lorent, Marine; Soulillou, Jean-Paul

2015-01-01

BACKGROUND. Rabbit-generated antithymocyte globulins (ATGs), which target human T cells, are widely used as immunosuppressive agents during treatment of kidney allograft recipients. However, ATGs can induce immune complex diseases, including serum sickness disease (SSD). Rabbit and human IgGs have various antigenic differences, including expression of the sialic acid Neu5Gc and α-1-3-Gal (Gal), which are not synthesized by human beings. Moreover, anti-Neu5Gc antibodies have been shown to preexist and be elicited by immunization in human subjects. This study aimed to assess the effect of SSD on long-term kidney allograft outcome and to compare the immunization status of grafted patients presenting with SSD following ATG induction treatment. METHODS. We analyzed data from a cohort of 889 first kidney graft recipients with ATG induction (86 with SSD [SSD+] and 803 without SSD [SSD–]) from the Données Informatisées et Validées en Transplantation data bank. Two subgroups of SSD+ and SSD– patients that had received ATG induction treatment were then assessed for total anti-ATG, anti-Neu5Gc, and anti-Gal antibodies using ELISA assays on sera before and after transplantation. RESULTS. SSD was significantly associated with long-term graft loss (>10 years, P = 0.02). Moreover, SSD+ patients exhibited significantly elevated titers of anti-ATG (P = 0.043) and anti-Neu5Gc (P = 0.007) IgGs in late post-graft samples compared with SSD– recipients. CONCLUSION. In conclusion, our data indicate that SSD is a major contributing factor of late graft loss following ATG induction and that anti-Neu5Gc antibodies increase over time in SSD+ patients. FUNDING. This study was funded by Société d’Accélération du Transfert de Technologies Ouest Valorisation, the European FP7 “Translink” research program, the French National Agency of Research, Labex Transplantex, the Natural Science and Engineering Research Council of Canada, and the Canadian Foundation for Innovation. PMID:26551683

Suppression of human fibrosarcoma cell growth by transcription factor, Egr-1, involves down-regulation of Bcl-2.

PubMed

Huang, R P; Fan, Y; Peng, A; Zeng, Z L; Reed, J C; Adamson, E D; Boynton, A L

1998-09-11

Previously, we showed that the transcription factor Egr-1 suppressed the proliferation of v-sis transformed NIH3T3 cells and also a number of human tumor cells. Here, we investigate the possible mechanisms responsible for this function. We show that transfected Egr-1 in human fibrosarcoma cells HT1080 leads to down-regulation of Bcl-2. Transient CAT transfection assays reveal that expression of Egr-1 suppresses Bcl-2 promoter activity in a dose-dependent manner. Furthermore, overexpression of Bcl-2 in Egr-1-expressing HT1080 cells enhanced cell proliferation in monolayer culture and increased anchorage-independent growth. Our results suggest that suppression of tumor cell proliferation by Egr-1 may be at least partially mediated through the down-regulation of Bcl-2.

Are chemicals in articles an obstacle for reaching environmental goals? - Missing links in EU chemical management.

PubMed

Molander, Linda; Breitholtz, Magnus; Andersson, Patrik L; Rybacka, Aleksandra; Rudén, Christina

2012-10-01

It is widely acknowledged that the management of risks associated with chemicals in articles needs to be improved. The EU environmental policy states that environmental damage should be rectified at source. It is therefore motivated that the risk management of substances in articles also takes particular consideration to those substances identified as posing a risk in different environmental compartments. The primary aim of the present study was to empirically analyze to what extent the regulation of chemicals in articles under REACH is coherent with the rules concerning chemicals in the Sewage Sludge Directive (SSD) and the Water Framework Directive (WFD). We also analyzed the chemical variation of the organic substances regulated under these legislations in relation to the most heavily used chemicals. The results show that 16 of 24 substances used in or potentially present in articles and regulated by the SSD or the WFD are also identified under REACH either as a substance of very high concern (SVHC) or subject to some restrictions. However, for these substances we conclude that there is limited coherence between the legislations, since the identification as an SVHC does not in itself encompass any use restrictions, and the restrictions in REACH are in many cases limited to a particular use, and thus all other uses are allowed. Only a minor part of chemicals in commerce is regulated and these show a chemical variation that deviates from classical legacy pollutants. This warrants new tools to identify potentially hazardous chemicals in articles. We also noted that chemicals monitored in the environment under the WFD deviate in their chemistry from the ones regulated by REACH. In summary, we argue that to obtain improved resource efficiency and a sustainable development it is necessary to minimize the input of chemicals identified as hazardous to health or the environment into articles. Copyright © 2012 Elsevier B.V. All rights reserved.

SU-F-T-667: Development and Validation of Dose Calculation for An Open-Source KV Treatment Planning System for Small Animal Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prajapati, S; Mo, X; Bednarz, B

Purpose: An open-source, convolution/superposition based kV-treatment planning system(TPS) was developed for small animal radiotherapy from previously existed in-house MV-TPS. It is flexible and applicable to both step and shoot and helical tomotherapy treatment delivery. For initial commissioning process, the dose calculation from kV-TPS was compared with measurements and Monte Carlo(MC) simulations. Methods: High resolution, low energy kernels were simulated using EGSnrc user code EDKnrc, which was used as an input in kV-TPS together with MC-simulated x-ray beam spectrum. The Blue Water™ homogeneous phantom (with film inserts) and heterogeneous phantom (with film and TLD inserts) were fabricated. Phantom was placed atmore » 100cm SSD, and was irradiated with 250 kVp beam for 10mins with 1.1cm × 1.1cm open field (at 100cm) created by newly designed binary micro-MLC assembly positioned at 90cm SSD. Gafchromic™ EBT3 film was calibrated in-phantom following AAPM TG-61 guidelines, and were used for measurement at 5 different depths in phantom. Calibrated TLD-100s were obtained from ADCL. EGS and MNCP5 simulation were used to model experimental irradiation set up calculation of dose in phantom. Results: Using the homogeneous phantom, dose difference between film and kV-TPS was calculated: mean(x)=0.9%; maximum difference(MD)=3.1%; standard deviation(σ)=1.1%. Dose difference between MCNP5 and kV-TPS was: x=1.5%; MD=4.6%; σ=1.9%. Dose difference between EGS and kV-TPS was: x=0.8%; MD=1.9%; σ=0.8%. Using the heterogeneous phantom, dose difference between film and kV-TPS was: x=2.6%; MD=3%; σ=1.1%; and dose difference between TLD and kV-TPS was: x=2.9%; MD=6.4%; σ=2.5%. Conclusion: The inhouse, open-source kV-TPS dose calculation system was comparable within 5% of measurements and MC simulations in both homogeneous and heterogeneous phantoms. The dose calculation system of the kV-TPS is validated as a part of initial commissioning process for small animal radiotherapy. The kV-TPS has the potential for accurate dose calculation for any kV treatment or imaging modalities.« less

MEGA: the next generation Medium Energy Gamma-ray Telescope

NASA Astrophysics Data System (ADS)

Ryan, James M.; Andritschke, Robert; Bloser, Peter F.; Cravens, James P.; Cherry, Michael L.; Di Cocco, Guido; Guzik, T. G.; Hartmann, Dieter H.; Hunter, Stanley H.; Kanbach, Gottfried; Kippen, R. M.; Kurfess, James; Macri, John R.; McConnell, Mark L.; Miller, Richard S.; Paciesas, William S.; Phlips, Bernard; Reglero, Victor; Stacy, J. G.; Strickman, Mark; Vestrand, W. Thomas; Wefel, John P.; Wulf, Eric; Zoglauer, Andreas; Zych, Allen D.

2004-10-01

The MEGA mission would enable a sensitive all-sky survey of the medium-energy ?-ray sky (0.3-50 MeV). This mission will bridge the huge sensitivity gap between the COMPTEL and OSSE experiments on the Compton Gamma Ray Observatory, the SPI and IBIS instruments on INTEGRAL and the visionary ACT mission. It will, among other things, serve to compile a much larger catalog of sources in this energy range, perform far deeper searches for supernovae, better measure the galactic continuum emission as well as identify the components of the cosmic diffuse emission. The large field of view will allow MEGA to continuously monitor the sky for transient and variable sources. It will accomplish these goals with a stack of Si-strip detector (SSD) planes surrounded by a dense high-Z calorimeter. At lower photon energies (below ~30 MeV), the design is sensitive to Compton interactions, with the SSD system serving as a scattering medium that also detects and measures the Compton recoil energy deposit. If the energy of the recoil electron is sufficiently high (> 2 MeV), the track of the recoil electron can also be defined. At higher photon energies (above ~10 MeV), the design is sensitive to pair production events, with the SSD system measuring the tracks of the electron and positron. We will discuss the various types of event signatures in detail and describe the advantages of this design over previous Compton telescope designs. Effective area, sensitivity and resolving power estimates are also presented along with simulations of expected scientific results and beam calibration results from the prototype instrument.

Optimal Skin-to-Stone Distance Is a Positive Predictor for Successful Outcomes in Upper Ureter Calculi following Extracorporeal Shock Wave Lithotripsy: A Bayesian Model Averaging Approach

PubMed Central

Cho, Kang Su; Jung, Hae Do; Ham, Won Sik; Chung, Doo Yong; Kang, Yong Jin; Jang, Won Sik; Kwon, Jong Kyou; Choi, Young Deuk; Lee, Joo Yong

2015-01-01

Objectives To investigate whether skin-to-stone distance (SSD), which remains controversial in patients with ureter stones, can be a predicting factor for one session success following extracorporeal shock wave lithotripsy (ESWL) in patients with upper ureter stones. Patients and Methods We retrospectively reviewed the medical records of 1,519 patients who underwent their first ESWL between January 2005 and December 2013. Among these patients, 492 had upper ureter stones that measured 4–20 mm and were eligible for our analyses. Maximal stone length, mean stone density (HU), and SSD were determined on pretreatment non-contrast computed tomography (NCCT). For subgroup analyses, patients were divided into four groups. Group 1 consisted of patients with SSD<25th percentile, group 2 consisted of patients with SSD in the 25th to 50th percentile, group 3 patients had SSD in the 50th to 75th percentile, and group 4 patients had SSD≥75th percentile. Results In analyses of group 2 patients versus others, there were no statistical differences in mean age, stone length and density. However, the one session success rate in group 2 was higher than other groups (77.9% vs. 67.0%; P = 0.032). The multivariate logistic regression model revealed that shorter stone length, lower stone density, and the group 2 SSD were positive predictors for successful outcomes in ESWL. Using the Bayesian model-averaging approach, longer stone length, lower stone density, and group 2 SSD can be also positive predictors for successful outcomes following ESWL. Conclusions Our data indicate that a group 2 SSD of approximately 10 cm is a positive predictor for success following ESWL. PMID:26659086

A comparative test of adaptive hypotheses for sexual size dimorphism in lizards.

PubMed

Cox, Robert M; Skelly, Stephanie L; John-Alder, Henry B

2003-07-01

It is commonly argued that sexual size dimorphism (SSD) in lizards has evolved in response to two primary, nonexclusive processes: (1) sexual selection for large male size, which confers an advantage in intrasexual mate competition (intrasexual selection hypothesis), and (2) natural selection for large female size, which confers a fecundity advantage (fecundity advantage hypothesis). However, outside of several well-studied lizard genera, the empirical support for these hypotheses has not been examined with appropriate phylogenetic control. We conducted a comparative phylogenetic analysis to test these hypotheses using literature data from 497 lizard populations representing 302 species and 18 families. As predicted by the intrasexual selection hypothesis, male aggression and territoriality are correlated with SSD, but evolutionary shifts in these categorical variables each explain less than 2% of the inferred evolutionary change in SSD. We found stronger correlations between SSD and continuous estimates of intrasexual selection such as male to female home range ratio and female home range size. These results are consistent with the criticism that categorical variables may obscure much of the actual variation in intrasexual selection intensity needed to explain patterns in SSD. In accordance with the fecundity advantage hypothesis, SSD is correlated with clutch size, reproductive frequency, and reproductive mode (but not fecundity slope, reduced major axis estimator of fecundity slope, length of reproductive season, or latitude). However, evolutionary shifts in clutch size explain less than 8% of the associated change in SSD, which also varies significantly in the absence of evolutionary shifts in reproductive frequency and mode. A multiple regression model retained territoriality and clutch size as significant predictors of SSD, but only 16% of the variation in SSD is explained using these variables. Intrasexual selection for large male size and fecundity selection for large female size have undoubtedly helped to shape patterns of SSD across lizards, but the comparative data at present provide only weak support for these hypotheses as general explanations for SSD in this group. Future work would benefit from the consideration of alternatives to these traditional evolutionary hypotheses, and the elucidation of proximate mechanisms influencing growth and SSD within populations.

The transcriptional regulator, CosR, controls compatible solute biosynthesis and transport, motility and biofilm formation in Vibrio cholerae.

PubMed

Shikuma, Nicholas J; Davis, Kimberly R; Fong, Jiunn N C; Yildiz, Fitnat H

2013-05-01

Vibrio cholerae inhabits aquatic environments and colonizes the human digestive tract to cause the disease cholera. In these environments, V. cholerae copes with fluctuations in salinity and osmolarity by producing and transporting small, organic, highly soluble molecules called compatible solutes, which counteract extracellular osmotic pressure. Currently, it is unclear how V. cholerae regulates the expression of genes important for the biosynthesis or transport of compatible solutes in response to changing salinity or osmolarity conditions. Through a genome-wide transcriptional analysis of the salinity response of V. cholerae, we identified a transcriptional regulator we name CosR for compatible solute regulator. The expression of cosR is regulated by ionic strength and not osmolarity. A transcriptome analysis of a ΔcosR mutant revealed that CosR represses genes involved in ectoine biosynthesis and compatible solute transport in a salinity-dependent manner. When grown in salinities similar to estuarine environments, CosR activates biofilm formation and represses motility independently of its function as an ectoine regulator. This is the first study to characterize a compatible solute regulator in V. cholerae and couples the regulation of osmotic tolerance with biofilm formation and motility. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Estrogen-induced transcription factor EGR1 regulates c-Kit transcription in the mouse uterus to maintain uterine receptivity for embryo implantation.

PubMed

Park, Mira; Kim, Hye-Ryun; Kim, Yeon Sun; Yang, Seung Chel; Yoon, Jung Ah; Lyu, Sang Woo; Lim, Hyunjung Jade; Hong, Seok-Ho; Song, Haengseok

2018-07-15

Early growth response 1 (Egr1) is a key transcription factor that mediates the action of estrogen (E 2 ) to establish uterine receptivity for embryo implantation. However, few direct target genes of EGR1 have been identified in the uterus. Here, we demonstrated that E 2 induced EGR1-regulated transcription of c-Kit, which plays a crucial role in cell fate decisions. Spatiotemporal expression of c-Kit followed that of EGR1 in uteri of ovariectomized mice at various time points after E 2 treatment. E 2 activated ERK1/2 and p38 to induce EGR1, which then activated c-Kit expression in the uterus. EGR1 transfection produced rapid and transient induction of c-KIT in a time- and dose-dependent manner. Furthermore, luciferase assays to measure c-Kit promoter activity confirmed that a functional EGR1 binding site(s) (EBS) was located within -1 kb of the c-Kit promoter. Site-directed mutagenesis and chromatin immunoprecipitation-PCR for three putative EBS within -1 kb demonstrated that the EBS at -818/-805 was critical for EGR1-dependent c-Kit transcription. c-Kit expression was significantly increased in the uterus on day 4 and administration of Masitinib, a c-Kit inhibitor, effectively interfered with embryo implantation. Collectively, our results showed that estrogen induces transcription factor EGR1 to regulate c-Kit transcription for uterine receptivity for embryo implantation in the mouse uterus. Copyright © 2017 Elsevier B.V. All rights reserved.

Outcomes of Subsyndromal Depression in Older Primary Care Patients

PubMed Central

Grabovich, Andrew; Lu, Naiji; Tang, Wan; Tu, Xin; Lyness, Jeffrey M.

2010-01-01

Objectives Most older persons in primary care suffering clinically significant depressive symptoms do not meet criteria for major or minor depression. We tested the hypothesis that patients with subsyndromal depression (SSD) would have poorer psychiatric, medical, and functional outcomes at follow-up than non-depressed patients, but not as poor as those with minor or major depression. We also explored the relative outcomes of three definitions of SSD to determine their relative prognostic value. Design Prospective observational cohort study. Setting Primary care practices in Monroe County, NY. Participants 481 primary care patients age ≥65 years who completed research assessments at intake and at least one year of follow-up evaluation. Measurements Depression diagnoses and three definitions of SSD were determined by the Structured Clinical Interview for DSM-IV and the 24-item Hamilton Depression Rating Scale. Other validated measures assessed anxiety, cognition, medical burden, and functional status. Results Patients with SSD had poorer 1-year lagged outcomes than non-depressed subjects in terms of psychiatric symptoms and functional status, often not significantly different than major or minor depression. Two of the SSD definitions identified subjects with poorer psychiatric and functional outcomes than the third SSD definition. Conclusions Clinicians should be vigilant in caring for patients with SSD, monitoring for persistent or worsening depressive symptoms including suicidality, anxiety, cognitive impairment, and functional decline. Researchers may use particular SSD definitions to identify individuals at higher risk of poor outcomes, to better understand the relationships of SSD to functional disability and to test innovative preventive and therapeutic interventions. PMID:20173424

An A257V Mutation in the Bacillus subtilis Response Regulator Spo0A Prevents Regulated Expression of Promoters with Low-Consensus Binding Sites▿

PubMed Central

Seredick, Steve D.; Seredick, Barbara M.; Baker, David; Spiegelman, George B.

2009-01-01

In Bacillus species, the master regulator of sporulation is Spo0A. Spo0A functions by both activating and repressing transcription initiation from target promoters that contain 0A boxes, the binding sites for Spo0A. Several classes of spo0A mutants have been isolated, and the molecular basis for their phenotypes has been determined. However, the molecular basis of the Spo0A(A257V) substitution, representative of an unusual phenotypic class, is not understood. Spo0A(A257V) is unusual in that it abolishes sporulation; in vivo, it fails to activate transcription from key stage II promoters yet retains the ability to repress the abrB promoter. To determine how Spo0A(A257V) retains the ability to repress but not stimulate transcription, we performed a series of in vitro and in vivo assays. We found unexpectedly that the mutant protein both stimulated transcription from the spoIIG promoter and repressed transcription from the abrB promoter, albeit twofold less than the wild type. A DNA binding analysis of Spo0A(A257V) showed that the mutant protein was less able to tolerate alterations in the sequence and arrangement of its DNA binding sites than the wild-type protein. In addition, we found that Spo0A(A257V) could stimulate transcription of a mutant spoIIG promoter in vivo in which low-consensus binding sites were replaced by high-consensus binding sites. We conclude that Spo0A(A257V) is able to bind to and regulate the expression of only genes whose promoters contain high-consensus binding sites and that this effect is sufficient to explain the observed sporulation defect. PMID:19581368

Nerve-dependent factors regulating transcript levels of glycogen phosphorylase in skeletal muscle.

PubMed

Matthews, C C; Carlsen, R C; Froman, B; Tait, R; Gorin, F

1998-06-01

1. Muscle glycogen phosphorylase (MGP), the rate-limiting enzyme for glycogen metabolism in skeletal muscle, is neurally regulated. Steady-state transcript levels of the skeletal muscle isozyme of MGP decrease significantly following muscle denervation and after prolonged muscle inactivity with an intact motor nerve. These data suggest that muscle activity has an important influence on MGP gene expression. The evidence to this point, however, does not preclude the possibility that MGP is also regulated by motor neuron-derived trophic factors. This study attempts to distinguish between regulation provided by nerve-evoked muscle contractile activity and that provided by the delivery of neurotrophic factors. 2. Steady-state MGP transcript levels were determined in rat tibialis anterior (TA) muscles following controlled interventions aimed at separating the contributions of contractile activity from axonally transported trophic factors. The innervated TA was rendered inactive by daily epineural injections of tetrodotoxin (TTX) into the sciatic nerve. Sustained inhibition of axonal transport was accomplished by applying one of three different concentrations of the antimicrotubule agent, vinblastine (VIN), to the proximal sciatic nerve for 1 hr. The axonal transport of acetylcholinesterase (AChE) was assessed 7, 14, and 28 days after the single application of VIN. 3. MGP transcript levels normalized to total RNA were reduced by 67% in rat TA, 7 days after nerve section. Daily injection of 2 microg TTX into the sciatic nerve for 7 days eliminated muscle contractile activity and reduced MGP transcript levels by 60%. 4. A single, 1-hr application of 0.10% (w/v) VIN to the sciatic nerve reduced axonal transport but did not alter MGP transcript levels in the associated TA, 7 days after treatment. Application of 0.10% VIN to the sciatic nerve also did not affect IA sensory or motor nerve conduction velocities or TA contractile function. 5. Treatment of the sciatic nerve with 0.40% (w/v) VIN for 1 hr reduced axonal transport and decreased MGP transcript levels by 50% within 7 days, but also reduced sensory and motor nerve conduction velocities and depressed TA contractile function. 6. Myogenin, a member of a family of regulatory factors shown to influence the transcription of many muscle genes, including MGP, was used as a molecular marker for muscle inactivity. Myogenin transcript levels were increased following denervation and after treatment with TTX or 0.40% VIN but not after treatment with 0.10% VIN. 7. The results suggest that MGP transcript levels in TA are regulated predominantly by muscle activity, rather than by the delivery of neurotrophic factors. Intrinsic myogenic factors, however, also play a role in MGP expression, since denervation did not reduce MGP transcript levels below 30% of control TA. The dominant influence of activity in the regulation of MGP contrasts with the proposed regulation of oxidative enzyme expression, which appears to depend on both activity and trophic factor influences.

Comparison of four methods for bioavailability-based risk assessment of mixtures of Cu, Zn, and Ni in freshwater.

PubMed

Van Regenmortel, Tina; Nys, Charlotte; Janssen, Colin R; Lofts, Stephen; De Schamphelaere, Karel A C

2017-08-01

Although chemical risk assessment is still mainly conducted on a substance-by-substance basis, organisms in the environment are typically exposed to mixtures of substances. Risk assessment procedures should therefore be adapted to fit these situations. Four mixture risk assessment methodologies were compared for risk estimations of mixtures of copper (Cu), zinc (Zn), and nickel (Ni). The results showed that use of the log-normal species sensitivity distribution (SSD) instead of the best-fit distribution and sampling species sensitivities independently for each metal instead of using interspecies correlations in metal sensitivity had little impact on risk estimates. Across 4 different monitoring datasets, between 0% and 52% of the target water samples were estimated to be at risk, but only between 0% and 15% of the target water samples were at risk because of the mixture of metals and not any single metal individually. When a natural baseline database was examined, it was estimated that 10% of the target water samples were at risk because of single metals or their mixtures; when the most conservative method was used (concentration addition [CA] applied directly to the SSD, i.e., CA SSD ). However, the issue of metal mixture risk at geochemical baseline concentrations became relatively small (2% of target water samples) when a theoretically more correct method was used (CA applied to individual dose response curves, i.e., CA DRC ). Finally, across the 4 monitoring datasets, the following order of conservatism for the 4 methods was shown (from most to least conservative, with ranges of median margin of safety [MoS] relative to CA SSD ): CA SSD  > CA DRC (MoS = 1.17-1.25) > IA DRC (independent action (IA) applied to individual dose-response curves; MoS = 1.38-1.60) > IA SSD (MoS = 1.48-1.72). Therefore, it is suggested that these 4 methods can be used in a general tiered scheme for the risk assessment of metal mixtures in a regulatory context. In this scheme, the CA SSD method could serve as a first (conservative) tier to identify situations with likely no potential risk at all, regardless of the method used (the sum toxic unit expressed relative to the 5% hazardous concentration [SumTU HC5 ] < 1) and the IA SSD method to identify situations of potential risk, also regardless of the method used (the multisubstance potentially affected fraction of species using the IA SSD method [msPAF IA,SSD ] > 0.05). The CA DRC and IA DRC methods could be used for site-specific assessment for situations that fall in between (SumTU HC5  > 1 and msPAF IA,SSD  < 0.05). Environ Toxicol Chem 2017;36:2123-2138. © 2017 SETAC. © 2017 SETAC.

Metabolic and molecular analyses of white mutant Vaccinium berries show down-regulation of MYBPA1-type R2R3 MYB regulatory factor.

PubMed

Primetta, Anja K; Karppinen, Katja; Riihinen, Kaisu R; Jaakola, Laura

2015-09-01

MYBPA1-type R2R3 MYB transcription factor shows down-regulation in white mutant berries of Vaccinium uliginosum deficient in anthocyanins but not proanthocyanidins suggesting a role in the regulation of anthocyanin biosynthesis. Berries of the genus Vaccinium are among the best natural sources of flavonoids. In this study, the expression of structural and regulatory flavonoid biosynthetic genes and the accumulation of flavonoids in white mutant and blue-colored wild-type bog bilberry (V. uliginosum) fruits were measured at different stages of berry development. In contrast to high contents of anthocyanins in ripe blue-colored berries, only traces were detected by HPLC-ESI-MS in ripe white mutant berries. However, similar profile and high levels of flavonol glycosides and proanthocyanidins were quantified in both ripe white and ripe wild-type berries. Analysis with qRT-PCR showed strong down-regulation of structural genes chalcone synthase (VuCHS), dihydroflavonol 4-reductase (VuDFR) and anthocyanidin synthase (VuANS) as well as MYBPA1-type transcription factor VuMYBPA1 in white berries during ripening compared to wild-type berries. The profiles of transcript accumulation of chalcone isomerase (VuCHI), anthocyanidin reductase (VuANR), leucoanthocyanidin reductase (VuLAR) and flavonoid 3'5' hydroxylase (VuF3'5'H) were more similar between the white and the wild-type berries during fruit development, while expression of UDP-glucose: flavonoid 3-O-glucosyltransferase (VuUFGT) showed similar trend but fourfold lower level in white mutant. VuMYBPA1, the R2R3 MYB family member, is a homologue of VmMYB2 of V. myrtillus and VcMYBPA1 of V. corymbosum and belongs to MYBPA1-type MYB family which members are shown in some species to be related with proanthocyanidin biosynthesis in fruits. Our results combined with earlier data of the role of VmMYB2 in white mutant berries of V. myrtillus suggest that the regulation of anthocyanin biosynthesis in Vaccinium species could differ from other species studied.

Vibrio parahaemolyticus CalR down regulates the thermostable direct hemolysin (TDH) gene transcription and thereby inhibits hemolytic activity.

PubMed

Zhang, Yiquan; Zhang, Ying; Gao, He; Zhang, Lingyu; Yin, Zhe; Huang, Xinxiang; Zhou, Dongsheng; Yang, Huiying; Yang, Wenhui; Wang, Li

2017-05-20

TDH, encoded by tdh gene, is a major virulent determinant of V. parahaemolyticus that controls various biological activities, such as hemolytic activity, cytotoxicity, and enterotoxicity. The hemolytic activity on Wagatsuma agar ascribed to TDH is called Kanagawa phenomenon (KP). All KP positive strains contain tdh1 and tdh2 genes, but tdh2 is predominantly responsible for KP. CalR is a regulatory protein that was originally identified as a repressor of swarming motility and T3SS1 gene expression in V. parahaemolyticus. In the present study, the regulation of tdh2 by CalR was investigated using a set of experiments including qRT-PCR, primer extension, LacZ fusion, hemolytic phenotype, EMSA, and DNase I footprinting assays. The results showed that His-CalR protected a single region from 224bp to 318bp upstream of tdh2 against DNase I digestion, and a transcriptional start site located at 42bp upstream of tdh2 was detected and its transcribed activity was inhibited by CalR. Moreover, the KP test results showed that the hemolytic activity of V. parahaemolyticus is also under negative control of CalR. The data demonstrated that CalR is a repressor of the tdh2 transcription and thereby inhibits the hemolytic activity of V. parahaemolyticus. Copyright © 2017. Published by Elsevier B.V.

Targeting chromatin binding regulation of constitutively active AR variants to overcome prostate cancer resistance to endocrine-based therapies

PubMed Central

Chan, Siu Chiu; Selth, Luke A.; Li, Yingming; Nyquist, Michael D.; Miao, Lu; Bradner, James E.; Raj, Ganesh V.; Tilley, Wayne D.; Dehm, Scott M.

2015-01-01

Androgen receptor (AR) variants (AR-Vs) expressed in prostate cancer (PCa) lack the AR ligand binding domain (LBD) and function as constitutively active transcription factors. AR-V expression in patient tissues or circulating tumor cells is associated with resistance to AR-targeting endocrine therapies and poor outcomes. Here, we investigated the mechanisms governing chromatin binding of AR-Vs with the goal of identifying therapeutic vulnerabilities. By chromatin immunoprecipitation and sequencing (ChIP-seq) and complementary biochemical experiments, we show that AR-Vs display a binding preference for the same canonical high-affinity androgen response elements (AREs) that are preferentially engaged by AR, albeit with lower affinity. Dimerization was an absolute requirement for constitutive AR-V DNA binding and transcriptional activation. Treatment with the bromodomain and extraterminal (BET) inhibitor JQ1 resulted in inhibition of AR-V chromatin binding and impaired AR-V driven PCa cell growth in vitro and in vivo. Importantly, this was associated with a novel JQ1 action of down-regulating AR-V transcript and protein expression. Overall, this study demonstrates that AR-Vs broadly restore AR chromatin binding events that are otherwise suppressed during endocrine therapy, and provides pre-clinical rationale for BET inhibition as a strategy for inhibiting expression and chromatin binding of AR-Vs in PCa. PMID:25908785

Paternal occupational lead exposure and offspring risks for schizophrenia.

PubMed

Sallmén, Markku; Suvisaari, Jaana; Lindbohm, Marja-Liisa; Malaspina, Dolores; Opler, Mark G

2016-10-01

This register-based cohort study investigated whether paternal occupational exposure to inorganic lead was related to offspring risk for schizophrenia spectrum disorder (SSD). Exposed men (n=11,863) were identified from blood lead measurements taken at the Finnish Institute of Occupational Health in 1973-1983. Data on mothers and their offspring born from 1972-1984 were obtained from the national Population Information System. Two population comparison offspring for each exposed offspring were matched on date of birth, sex and area (n=23,720). SSD cases were identified from The Finnish Hospital Discharge Register. Hazard ratios of SSD between exposed groups were analyzed using conditional proportional hazards regression, adjusted for parental history of psychoses, parental ages, language of offspring, father's employment, and father's self-employment. After 26-38years of follow up, there were no significant differences in the incidence of schizophrenia, either between the offspring of exposed (188/11,863; 1.6%) and unexposed fathers (347/23,720; 1.5%) or based on blood lead levels (adjusted hazard ratios (aHR): 0.97, CI 0.52-1.83, 1.25, CI 0.85-1.82, 0.90, CI 0.54-1.49, and 1.38, CI 0.65-2.92 for lead categories <0.5, 0.5-0.9, 1.0-1.4, and ≥1.5μmol/L, respectively, as compared to population comparison). Parental psychosis, paternal age and offspring language were associated with offspring risk. The findings suggest that paternal exposure to lead is not a risk factor for schizophrenia in offspring. However, the majority of exposed fathers had low-level exposure, and we cannot exclude the possibility of an effect for higher exposures to lead. Copyright © 2016 Elsevier B.V. All rights reserved.

Transcriptional regulation of human paraoxonase 1 by PXR and GR in human hepatoma cells.

PubMed

Ponce-Ruiz, N; Rojas-García, A E; Barrón-Vivanco, B S; Elizondo, G; Bernal-Hernández, Y Y; Mejía-García, A; Medina-Díaz, I M

2015-12-25

Human paraoxonase 1 (PON1) is A-esterase synthesized in the liver and secreted into the plasma, where it associates with HDL. PON1 acts as an antioxidant preventing lipid oxidation and detoxifies a wide range of substrates, including organophosphate compounds. The variability of PON1 (enzyme activity/serum levels) has been attributed to internal and external factors. However, the molecular mechanisms involved in the transcriptional regulation of PON1 have not been well-studied. The aim of this study was to evaluate and characterize the transcriptional activation of PON1 by nuclear receptors (NR) in human hepatoma cells. In silico analysis was performed on the promoter region of PON1 to determine the response elements of NR. Real-time PCR was used to evaluate the effect of specific NR ligands on the mRNA levels of genes regulated by NR and PON1. The results indicated that NR response elements had 95% homology to pregnenolone (PXR), glucocorticoids (GR), retinoic acid (RXR) and peroxisomes proliferator-activated receptor alpha (PPARα). Treatments with Dexamethasone (GR ligand), Rifampicin (PXR ligand) and TCDD (AhR ligand) increased the mRNA levels of PON1 at 24 and 48 h. We showed that the activation of GR by Dexamethasone results in PON1 gene induction accompanied by an increase in activity levels. In conclusion, these results demonstrate that GR regulates PON1 gene transcription through directly binding to NR response elements at -95 to -628 bp of the PON1 promoter. This study suggests new molecular mechanisms for the transcriptional regulation of PON1 through a process involving the activation of PXR. Copyright © 2015 Elsevier B.V. All rights reserved.

Prospective observational study of delirium recovery trajectories and associated short-term outcomes in older adults admitted to a specialized delirium unit.

PubMed

Lam, Ching-yu; Tay, Laura; Chan, Mark; Ding, Yew Yoong; Chong, Mei Sian

2014-09-01

To describe the recovery trajectories of delirium and to determine factors predicting the course of recovery and adverse outcome. A prospective observational study. Geriatric monitoring unit (GMU), a five-bed unit specializing in managing older adults with delirium. Individuals admitted to the GMU between December 2010 and August 2012 (N = 234; mean age 84.1 ± 7.4). Information was collected on demographic characteristics; comorbidities; severity of illness; functional status; and daily cognitive, Delirium Rating Scale, Revised-98 (DRS-R98) severity, and functional scoring. Resolution of delirium, and thus GMU discharge, was determined according to clinical assessment. The primary outcome was residual subsyndromal delirium (SSD) (DRS-R98 severity ≥13) upon GMU discharge. Univariate and multivariate methods were used to determine the predictors of residual SSD and adverse outcomes (inpatient mortality and incident nursing home admission upon discharge). Participants with residual SSD had a slower recovery in terms of delirium severity, cognition, and functional status than those with no residual SSD. Residual SSD predictors included underlying dementia, admission DRS-R98 severity, DRS-R98 severity on Day 1 minus Day 3 of GMU stay, and admission modified Barthel Index. Only presence of residual SSD at discharge predicted adverse outcomes (odds ratio = 5.27, 95% confidence interval = 1.43-19.47). Individuals with residual SSD had prolonged recovery trajectory of delirium. These new insights into the recovery trajectories of delirium may help formulate early discharge planning and provide the basis for future research on delirium treatment. © 2014, Copyright the Authors Journal compilation © 2014, The American Geriatrics Society.

Calculating the number of shock waves, expulsion time, and optimum stone parameters based on noncontrast computerized tomography characteristics.

PubMed

Foda, Khaled; Abdeldaeim, Hussein; Youssif, Mohamed; Assem, Akram

2013-11-01

To define the parameters that accompanied a successful extracorporeal shock wave lithotripsy (ESWL), namely the number of shock waves (SWs), expulsion time (ET), mean stone density (MSD), and the skin-to-stone distance (SSD). A total of 368 patients diagnosed with renal calculi using noncontrast computerized tomography had their MSD, diameter, and SSD recorded. All patients were treated using a Siemens lithotripter. ESWL success meant a stone-free status or presence of residual fragments <3 mm, ET was the time in days for the successful clearance of stone fragments. Correlation was performed between the stone characteristics, number of SWs, and ET. Two multiple regression analysis models defined the number of SWs and ET. Two receiver operating characteristic curves plotted the best MSD cutoff value and optimum SSD for a successful ESWL. Three hundred one patients were ESWL successes. A significant positive correlation was elicited between number of SWs and stone diameter, density and SSD; between ET and stone diameter and density. Multiple regressions concluded 2 equations: Number of SWs = 265.108 + 5.103 x1 + 22.39 x2 + 10.931 x3 ET (days) = -10.85 + 0.031 x1 + 2.11 x2 x1 = stone density (Hounsfield unit [HUs]), x2 = stone diameter (mm), and x3 = SSD (mm). Receiver operating characteristic curves demonstrated a cutoff value of ≤ 934 HUs with 94.4% sensitivity and 66.7% specificity and P = .0211. The SSD curve showed that a distance ≤ 99 mm was 85.7% sensitive, 87.5% specific, P <.0001. Stone disintegration is not recommended if MSD is >934 HUs and SSD >99 mm. The required number of SWs and the expected ET can be anticipated. Copyright © 2013 Elsevier Inc. All rights reserved.

SU-E-T-370: Measurement of Conical Cone Output Factors for the Varian Edge Linear Accelerator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, H; Kim, J; Gordon, J

Purpose: To quantify the impact of detector type, SSD/depth, and intermediate reference on conical cone output factor (OF) measurements for the Varian Edge linac. Methods: OF's for 4, 5, 7.5, 10, 12.5, 15, and 17.5 mm diameter cones relative to 10cmx10cm field were measured for the 6X FFF and 10X FFF energies, with jaws set to 5cmx5cm. Measurements were performed with an Edge diode (0.8mmx0.8mmx0.03mm WxLxT), stereotatic diode SFD, photon diode, CC01 and pinpoint chambers (2mm diameter for both). 95cm SSD/5cm depth were used in a water tank. For the measurement with diodes, OF's were cross-referred to CC13 ion chambermore » measurements with 3cmx3cm field, as recommended, to help mitigate the energy variation in diode response with field size. Results were compared to the representative data from Varian measured with Edge detector. With SFD, OF's at 98.5cm SSD/1.5cm depth and 90cm SSD/10cm depth were also measured. Results: OF's measured with the Edge detector matched within 1.3% (max diff) with the representative data from Varian. For the SFD, OF's matched within 1.3% for the 4, 5 and 17.5 mm cones and within 3.7% for the other cones. OF's with photon diode were within 1.3% except for the 4 and 5 mm cones where they were 8.1% and 3.7%, respectively. OF's for the CC01 and pinpoint chamber deviated up to 36% and 44%, respectively for the 4 mm cone. OF's after intermediate reference with 3cmx3cm field changed by 3.7% for SFD, 0.8% for photon diode, and 0.6% for Edge detector. OF's at 98.5cm SSD/1.5cm depth were 10.8% higher than that at 95cm SSD/5cm depth, and OF's at 90cm SSD/1.5cm depth were 7.5% lower. Conclusion: OF's measured with the Edge detector appear to be reliable. CC01 and pinpoint chambers do not appear suitable for measuring the small cone OF's. SSD/depth affects OF measurements significantly.« less

Initialize and Weak-Program Erasing Scheme for High-Performance and High-Reliability Ferroelectric NAND Flash Solid-State Drive

NASA Astrophysics Data System (ADS)

Miyaji, Kousuke; Yajima, Ryoji; Hatanaka, Teruyoshi; Takahashi, Mitsue; Sakai, Shigeki; Takeuchi, Ken

Initialize and weak-program erasing scheme is proposed to achieve high-performance and high-reliability Ferroelectric (Fe-) NAND flash solid-state drive (SSD). Bit-by-bit erase VTH control is achieved by the proposed erasing scheme and history effects in Fe-NAND is also suppressed. History effects change the future erase VTH shift characteristics by the past program voltage. The proposed erasing scheme decreases VTH shift variation due to history effects from ±40% to ±2% and the erase VTH distribution width is reduced from over 0.4V to 0.045V. As a result, the read and VPASS disturbance decrease by 42% and 37%, respectively. The proposed erasing scheme is immune to VTH variations and voltage stress. The proposed erasing scheme also suppresses the power and bandwidth degradation of SSD.

Alaska Imagery (GOES-WEST) - Satellite Services Division / Office of

Science.gov Websites

-- Dissemination Schedules METEOSAT MTSAT-1R POES -- Satellite Operations -- Satellite Status Pre-Processing Status Pre-Processing -- Dissemination Schedules Original SSD Links SSD Fire Products Precipitation

Hawaii Imagery (GOES-WEST) - Satellite Services Division / Office of

Science.gov Websites

-- Dissemination Schedules METEOSAT MTSAT-1R POES -- Satellite Operations -- Satellite Status Pre-Processing Status Pre-Processing -- Dissemination Schedules Original SSD Links SSD Fire Products Precipitation

Saikosaponin D relieves unpredictable chronic mild stress induced depressive-like behavior in rats: involvement of HPA axis and hippocampal neurogenesis.

PubMed

Li, Hong-Yan; Zhao, Ying-Hua; Zeng, Min-Jie; Fang, Fang; Li, Min; Qin, Ting-Ting; Ye, Lu-Yu; Li, Hong-Wei; Qu, Rong; Ma, Shi-Ping

2017-11-01

Saikosaponin D (SSD), a major bioactive component isolated from Radix Bupleuri, has been reported to exert neuroprotective properties. The present study was designed to investigate the anti-depressant-like effects and the potential mechanisms of SSD. Behavioural tests including sucrose preference test (SPT), open field test (OFT) and forced swim test (FST) were performed to study the antidepressant-like effects of SSD. In addition, we examined corticosterone and glucocorticoid receptor (GR) levels to evaluate hypothalamic-pituitary-adrenal (HPA) axis function. Furthermore, hippocampal neurogenesis was assessed by testing doublecortin (DCX) levels, and neurotrophic molecule levels were also investigated in the hippocampus of rats. We found that unpredictable chronic mild stress (UCMS) rats displayed lost body weight, decreased sucrose consumption in SPT, reduced locomotive activity in OFT, and increased immobility time in FST. Chronic treatment with SSD (0.75, 1.50 mg/kg) remarkably ameliorated the behavioral deficiency induced by UCMS procedure. SSD administration downregulated elevated serum corticosterone levels, as well as alleviated the suppression of GR expression and nuclear translocation caused by UCMS, suggesting that SSD is able to remit the dysfunction of HPA axis. In addition, Western blot and immunohistochemistry analysis showed that SSD treatment significantly increased the generation of neurons in the hippocampus of UCMS rats indicated by elevated DCX levels. Moreover, hippocampal neurotrophic molecule levels of UCMS rats such as phosphorylated cAMP response element binding protein (p-CREB) and brain-derived neurotrophic factor (BDNF) were raised after SSD treatment. Together, Our results suggest that SSD opposed UCMS-induced depressive behaviors in rats, which was mediated, partially, by the enhancement of HPA axis function and consolidation of hippocampal neurogenesis.

Renshaw cell interneuron specialization is controlled by a temporally restricted transcription factor program

PubMed Central

Stam, Floor J.; Hendricks, Timothy J.; Zhang, Jingming; Geiman, Eric J.; Francius, Cedric; Labosky, Patricia A.; Clotman, Frederic; Goulding, Martyn

2012-01-01

The spinal cord contains a diverse array of physiologically distinct interneuron cell types that subserve specialized roles in somatosensory perception and motor control. The mechanisms that generate these specialized interneuronal cell types from multipotential spinal progenitors are not known. In this study, we describe a temporally regulated transcriptional program that controls the differentiation of Renshaw cells (RCs), an anatomically and functionally discrete spinal interneuron subtype. We show that the selective activation of the Onecut transcription factors Oc1 and Oc2 during the first wave of V1 interneuron neurogenesis is a key step in the RC differentiation program. The development of RCs is additionally dependent on the forkhead transcription factor Foxd3, which is more broadly expressed in postmitotic V1 interneurons. Our demonstration that RCs are born, and activate Oc1 and Oc2 expression, in a narrow temporal window leads us to posit that neuronal diversity in the developing spinal cord is established by the composite actions of early spatial and temporal determinants. PMID:22115757

Auditory and Visual Sustained Attention in Children with Speech Sound Disorder

PubMed Central

Murphy, Cristina F. B.; Pagan-Neves, Luciana O.; Wertzner, Haydée F.; Schochat, Eliane

2014-01-01

Although research has demonstrated that children with specific language impairment (SLI) and reading disorder (RD) exhibit sustained attention deficits, no study has investigated sustained attention in children with speech sound disorder (SSD). Given the overlap of symptoms, such as phonological memory deficits, between these different language disorders (i.e., SLI, SSD and RD) and the relationships between working memory, attention and language processing, it is worthwhile to investigate whether deficits in sustained attention also occur in children with SSD. A total of 55 children (18 diagnosed with SSD (8.11±1.231) and 37 typically developing children (8.76±1.461)) were invited to participate in this study. Auditory and visual sustained-attention tasks were applied. Children with SSD performed worse on these tasks; they committed a greater number of auditory false alarms and exhibited a significant decline in performance over the course of the auditory detection task. The extent to which performance is related to auditory perceptual difficulties and probable working memory deficits is discussed. Further studies are needed to better understand the specific nature of these deficits and their clinical implications. PMID:24675815

Ablation of the auditory cortex results in changes in the expression of neurotransmission-related mRNAs in the cochlea.

PubMed

Lamas, Verónica; Juiz, José M; Merchán, Miguel A

2017-03-01

The auditory cortex (AC) dynamically regulates responses of the Organ of Corti to sound through descending connections to both the medial (MOC) and lateral (LOC) olivocochlear efferent systems. We have recently provided evidence that AC has a reinforcement role in the responses to sound of the auditory brainstem nuclei. In a molecular level, we have shown that descending inputs from AC are needed to regulate the expression of molecules involved in outer hair cell (OHC) electromotility control, such as prestin and the α10 nicotinic acetylcholine receptor (nAchR). In this report, we show that descending connections from AC to olivocochlear neurons are necessary to regulate the expression of molecules involved in cochlear afferent signaling. RT-qPCR was performed in rats at 1, 7 and 15 days after unilateral ablation of the AC, and analyzed the time course changes in gene transcripts involved in neurotransmission at the first auditory synapse. This included the glutamate metabolism enzyme glutamate decarboxylase 1 (glud1) and AMPA glutamate receptor subunits GluA2-4. In addition, gene transcripts involved in efferent regulation of type I spiral ganglion neuron (SGN) excitability mediated by LOC, such as the α7 nAchR, the D2 dopamine receptor, and the α1, and γ2 GABAA receptor subunits, were also investigated. Unilateral AC ablation induced up-regulation of GluA3 receptor subunit transcripts, whereas both GluA2 and GluA4 mRNA receptors were down-regulated already at 1 day after the ablation. Unilateral removal of the AC also resulted in up-regulation of the transcripts for α7 nAchR subunit, D2 dopamine receptor, and α1 GABAA receptor subunit at 1 day after the ablation. Fifteen days after the injury, AC ablations induced an up-regulation of glud1 transcripts. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Direct Costs of Very Old Persons with Subsyndromal Depression: A 5-Year Prospective Study.

PubMed

Ludvigsson, Mikael; Bernfort, Lars; Marcusson, Jan; Wressle, Ewa; Milberg, Anna

2018-03-15

This study aimed to compare, over a 5-year period, the prospective direct healthcare costs and service utilization of persons with subsyndromal depression (SSD) and non-depressive persons (ND), in a population of very old persons. A second aim was to develop a model that predicts direct healthcare costs in very old persons with SSD. A prospective population-based study was undertaken on 85-year-old persons in Sweden. Depressiveness was screened with the Geriatric Depression Scale at baseline and at 1-year follow-up, and the results were classified into ND, SSD, and syndromal depression. Data on individual healthcare costs and service use from a 5-year period were derived from national database registers. Direct costs were compared between categories using Mann-Whitney U tests, and a prediction model was identified with linear regression. For persons with SSD, the direct healthcare costs per month of survival exceeded those of persons with ND by a ratio 1.45 (€634 versus €436), a difference that was significant even after controlling for somatic multimorbidity. The final regression model consisted of five independent variables predicting direct healthcare costs: male sex, activities of daily living functions, loneliness, presence of SSD, and somatic multimorbidity. SSD among very old persons is associated with increased direct healthcare costs independently of somatic multimorbidity. The associations between SSD, somatic multimorbidity, and healthcare costs in the very old need to be analyzed further in order to better guide allocation of resources in health policy. Copyright © 2018 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators

PubMed Central

Jers, Carsten; Ravikumar, Vaishnavi; Lezyk, Mateusz; Sultan, Abida; Sjöling, Åsa; Wai, Sun N.; Mijakovic, Ivan

2018-01-01

Protein lysine acetylation is recognized as an important reversible post translational modification in all domains of life. While its primary roles appear to reside in metabolic processes, lysine acetylation has also been implicated in regulating pathogenesis in bacteria. Several global lysine acetylome analyses have been carried out in various bacteria, but thus far there have been no reports of lysine acetylation taking place in the important human pathogen Vibrio cholerae. In this study, we analyzed the lysine acetylproteome of the human pathogen V. cholerae V52. By applying a combination of immuno-enrichment of acetylated peptides and high resolution mass spectrometry, we identified 3,402 acetylation sites on 1,240 proteins. Of the acetylated proteins, more than half were acetylated on two or more sites. As reported for other bacteria, we observed that many of the acetylated proteins were involved in metabolic and cellular processes and there was an over-representation of acetylated proteins involved in protein synthesis. Of interest, we demonstrated that many global transcription factors such as CRP, H-NS, IHF, Lrp and RpoN as well as transcription factors AphB, TcpP, and PhoB involved in direct regulation of virulence in V. cholerae were acetylated. In conclusion, this is the first global protein lysine acetylome analysis of V. cholerae and should constitute a valuable resource for in-depth studies of the impact of lysine acetylation in pathogenesis and other cellular processes. PMID:29376036

Subsurface damage and microstructure development in precision microground hard ceramics using magnetorheological finishing spots.

PubMed

Shafrir, Shai N; Lambropoulos, John C; Jacobs, Stephen D

2007-08-01

We demonstrate the use of spots taken with magnetorheological finishing (MRF) for estimating subsurface damage (SSD) depth from deterministic microgrinding for three hard ceramics: aluminum oxynitride (Al(23)O(27)N(5)/ALON), polycrystalline alumina (Al(2)O(3)/PCA), and chemical vapor deposited (CVD) silicon carbide (Si(4)C/SiC). Using various microscopy techniques to characterize the surfaces, we find that the evolution of surface microroughness with the amount of material removed shows two stages. In the first, the damaged layer and SSD induced by microgrinding are removed, and the surface microroughness reaches a low value. Peak-to-valley (p-v) surface microroughness induced from grinding gives a measure of the SSD depth in the first stage. With the removal of additional material, a second stage develops, wherein the interaction of MRF and the material's microstructure is revealed. We study the development of this texture for these hard ceramics with the use of power spectral density to characterize surface features.

Subsurface Damage and Microstructure Development in Precision Microground Hard Ceramics Using Magnetorheological Finishing Spots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shafrir, S.N.; Lambropoulos, J.C.; Jacobs, S.D.

2007-08-01

We demonstrate the use of spots taken with magnetorheological finishing (MRF) for estimating subsurface damage (SSD) depth from deterministic microgrinding for three hard ceramics: aluminum oxynitride (Al23O27N5/ALON), polycrystalline alumina (AL2O3/PCA), and chemical vapor deposited (CVD) silicon carbide (Si4C/SiC). Using various microscopy techniques to characterize the surfaces, we find that the evolution of surface microroughness with the amount of material removed shows two stages. In the first, the damaged layer and SSD induced by microgrinding are removed, and the surface roughness reaches a low value. Peak-to-valley (p-v) surface microroughness induced from grinding gives a measure of the SSD depth in themore » first stage. With the removal of additional material, a second stage develops, wherein the interaction of MRF and the material's microstructure is revealed. We study the development of this texture for these har ceramics with the use of power spectral density to characterize surface features.« less

Saikosaponin D disrupts platelet-derived growth factor-β receptor/p38 pathway leading to mitochondrial apoptosis in human LO2 hepatocyte cells: a potential mechanism of hepatotoxicity.

PubMed

Chen, Li; Zhang, Feng; Kong, Desong; Zhu, Xiaojing; Chen, Wenxing; Wang, Aiyun; Zheng, Shizhong

2013-10-25

Herbal hepatotoxicity has been increasingly reported in clinical context, but the underlying mechanisms are poorly understood. Saikosaponin D (SSD) is a major component of saikosaponins isolated from Bupleurum falactum, a herb that has been linked to hepatotoxicity. Our current study was to examine the toxic effect of SSD on human hepatocyte LO2 cells and explore the possible mechanism. The results demonstrated that SSD reduced cell viability and led to dramatic morphological alterations in LO2 cells. Hoechst staining and flow cytometry analyses showed that SSD stimulated hepatocyte apoptosis. SSD-treated cells exhibited apparent nuclear condensation and fragmentation, and the apoptotic cells were increased by SSD dose-dependently. Subsequent experiments showed that SSD decreased mitochondrial membrane potential and downregulated Bcl-2 but upregulated Bax. Moreover, caspase-9 and caspase-3 were activated in SSD-treated LO2 cells. These data consistently indicated that SSD stimulated mitochondrial apoptosis in hepatocytes. Mechanistic investigations showed that SSD disrupted p38 signaling and that p38 specific inhibitor SB203580 mimicked the pro-apoptotic effect of SSD. In addition, platelet-derived growth factor-β receptor (PDGF-βR) blocker imatinib reduced p38 phosphorylation and also mimicked the pro-apoptotic effect of SSD in LO2 cells. These data collectively indicated that SSD induced apoptosis by interrupting PDGF-βR/p38 pathway in LO2 hepatocytes. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Efficiency of broadband terahertz rectennas based on self-switching nanodiodes

NASA Astrophysics Data System (ADS)

Briones, Edgar; Cortes-Mestizo, Irving E.; Briones, Joel; Droopad, Ravindranath; Espinosa-Vega, Leticia I.; Vilchis, Heber; Mendez-Garcia, Victor H.

2017-04-01

The authors investigate the efficiency of a series of broadband rectennas designed to harvest the free-propagating electromagnetic energy at terahertz frequencies. We analyze by simulations the case of self-complementary square- and Archimedean-spiral antennas coupled to L-shaped self-switching diodes (L-SSDs). First, the geometry (i.e., the width and length of the channel) of the L-SSD was optimized to obtain a remarkable diode-like I-V response. Subsequently, the optimized L-SSD geometry was coupled to both types of spiral antennas and their characteristic impedance was studied. Finally, the energy conversion efficiency was evaluated for both rectenna architectures.

Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues

PubMed Central

Peyer, Suzanne M.; Pankey, M. Sabrina; Oakley, Todd H.; McFall-Ngai, Margaret J.

2014-01-01

The squid Euprymna scolopes has evolved independent sets of tissues capable of light detection, including a complex eye and a photophore or ‘light organ’, which houses the luminous bacterial symbiont Vibrio fischeri. As the eye and light organ originate from different embryonic tissues, we examined whether the eye-specification genes, pax6, eya, six, and dac, are shared by these two organs, and if so, whether they are regulated in the light organ by symbiosis. We obtained sequences of the four genes with PCR, confirmed orthology with phylogenetic analysis, and determined that each was expressed in the eye and light organ. With in situ hybridization (ISH), we localized the gene transcripts in developing embryos, comparing the patterns of expression in the two organs. The four transcripts localized to similar tissues, including those associated with the visual system ~1/4 into embryogenesis (Naef stage 18) and the light organ ~3/4 into embryogenesis (Naef stage 26). We used ISH and quantitative real-time PCR to examine transcript expression and differential regulation in postembryonic light organs in response to the following colonization conditions: wild-type, luminescent V. fischeri; a mutant strain defective in light production; and as a control, no symbiont. In ISH experiments light organs showed down regulation of the pax6, eya, and six transcripts in response to wild-type V. fischeri. Mutant strains also induced down regulation of the pax6 and eya transcripts, but not of the six transcript. Thus, luminescence was required for down regulation of the six transcript. We discuss these results in the context of symbiont-induced light-organ development. Our study indicates that the eye-specification genes are expressed in light-interacting tissues independent of their embryonic origin and are capable of responding to bacterial cues. These results offer evidence for evolutionary tinkering or the recruitment of eye development genes for use in a light-sensing photophore. PMID:24157521

Eukaryotic and prokaryotic promoter databases as valuable tools in exploring the regulation of gene transcription: a comprehensive overview.

PubMed

Majewska, Małgorzata; Wysokińska, Halina; Kuźma, Łukasz; Szymczyk, Piotr

2018-02-20

The complete exploration of the regulation of gene expression remains one of the top-priority goals for researchers. As the regulation is mainly controlled at the level of transcription by promoters, study on promoters and findings are of great importance. This review summarizes forty selected databases that centralize experimental and theoretical knowledge regarding the organization of promoters, interacting transcription factors (TFs) and microRNAs (miRNAs) in many eukaryotic and prokaryotic species. The presented databases offer researchers valuable support in elucidating the regulation of gene transcription. Copyright © 2017 Elsevier B.V. All rights reserved.

Efficacy of continuous versus intermittent subglottic secretion drainage in preventing ventilator-associated pneumonia in patients requiring mechanical ventilation: A single-center randomized controlled trial.

PubMed

Fujimoto, Hiroko; Yamaguchi, Osamu; Hayami, Hajime; Shimosaka, Mika; Tsuboi, Sayaka; Sato, Mitsunori; Takebayashi, Shigeo; Morita, Satoshi; Saito, Mari; Goto, Takahisa; Kurahashi, Kiyoyasu

2018-03-23

Aspiration of subglottic secretion is a widely used intervention to prevent ventilator-associated pneumonia (VAP). This study aimed to compare the efficacy of continuous and intermittent subglottic secretion drainage (SSD) in preventing VAP. A single-center randomized controlled trial was conducted on adult postoperative patients who were expected to undergo mechanical ventilation for more than 48 hours. Primary outcome measure was incidence of VAP and secondary outcome measures were length of mechanical ventilation and intensive-care unit (ICU) stay. Fifty-nine patients received continuous SSD, while 60 patients received intermittent SSD. Of these 119 patients, 88 (74%) were excluded and 15 and 16 patients were allocated to receive continuous and intermittent SSD, respectively. VAP was detected in 4 (26.7%) and 7 (43.8%) patients in the continuous and intermittent groups, respectively, (p=0.320). The length of mechanical ventilation was significantly shorter (p=0.034) in the continuous group (99.5±47.1 h) than in the intermittent group (159.9±94.5 h). The length of ICU stay was also shorter (p=0.0097) in the continuous group (6.3±2.1 days) than the intermittent group (9.8±4.8 days). Although continuous SSD did not reduce the incidence of VAP, it reduced the length of mechanical ventilation and ICU stay when compared to intermittent SSD.

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels.

PubMed

Miles, Anna L; Burr, Stephen P; Grice, Guinevere L; Nathan, James A

2017-03-15

Hypoxia Inducible transcription Factors (HIFs) are principally regulated by the 2-oxoglutarate and Iron(II) prolyl hydroxylase (PHD) enzymes, which hydroxylate the HIFα subunit, facilitating its proteasome-mediated degradation. Observations that HIFα hydroxylation can be impaired even when oxygen is sufficient emphasise the importance of understanding the complex nature of PHD regulation. Here, we use an unbiased genome-wide genetic screen in near-haploid human cells to uncover cellular processes that regulate HIF1α. We identify that genetic disruption of the Vacuolar H+ ATPase (V-ATPase), the key proton pump for endo-lysosomal acidification, and two previously uncharacterised V-ATPase assembly factors, TMEM199 and CCDC115, stabilise HIF1α in aerobic conditions. Rather than preventing the lysosomal degradation of HIF1α, disrupting the V-ATPase results in intracellular iron depletion, thereby impairing PHD activity and leading to HIF activation. Iron supplementation directly restores PHD catalytic activity following V-ATPase inhibition, revealing important links between the V-ATPase, iron metabolism and HIFs.

SU-E-T-276: Dose Calculation Accuracy with a Standard Beam Model for Extended SSD Treatments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kisling, K; Court, L; Kirsner, S

2015-06-15

Purpose: While most photon treatments are delivered near 100cm SSD or less, a subset of patients may benefit from treatment at SSDs greater than 100cm. A proposed rotating chair for upright treatments would enable isocentric treatments at extended SSDs. The purpose of this study was to assess the accuracy of the Pinnacle{sup 3} treatment planning system dose calculation for standard beam geometries delivered at extended SSDs with a beam model commissioned at 100cm SSD. Methods: Dose to a water phantom at 100, 110, and 120cm SSD was calculated with the Pinnacle {sup 3} CC convolve algorithm for 6x beams formore » 5×5, 10×10, 20×20, and 30×30cm{sup 2} field sizes (defined at the water surface for each SSD). PDDs and profiles (depths of 1.5, 12.5, and 22cm) were compared to measurements in water with an ionization chamber. Point-by-point agreement was analyzed, as well as agreement in field size defined by the 50% isodose. Results: The deviations of the calculated PDDs from measurement, analyzed from depth of maximum dose to 23cm, were all within 1.3% for all beam geometries. In particular, the calculated PDDs at 10cm depth were all within 0.7% of measurement. For profiles, the deviations within the central 80% of the field were within 2.2% for all geometries. The field sizes all agreed within 2mm. Conclusion: The agreement of the PDDs and profiles calculated by Pinnacle3 for extended SSD geometries were within the acceptability criteria defined by Van Dyk (±2% for PDDs and ±3% for profiles). The accuracy of the calculation of more complex beam geometries at extended SSDs will be investigated to further assess the feasibility of using a standard beam model commissioned at 100cm SSD in Pinnacle3 for extended SSD treatments.« less

High conductivity a-C:N thin films prepared by electron gun evaporation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rebollo-Plata, B.; Lozada-Morales, R.; Palomino-Merino, R.

2007-08-15

By employing electron beam evaporation, amorphous carbon nitride (a-C:N) thin films, with a low nitrogen content ({approx} 1%), were prepared on Si(110) and glass substrates at about 150 deg. C. The source was a graphite target and an ambient of N{sub 2} was introduced into the growing chamber. The source-substrate distance (SSD) was the main parameter that was intentionally varied. Electron dispersion spectroscopy measurements indicate the nitrogen concentration in the layer as {approx} 1%. The dark electrical conductivity ({sigma}) of layers was very sensitive to SSD variation, changing up to six orders of magnitude when this parameter was varied frommore » 10.5 to 23.5 cm. A maximum value of {sigma} = 1 x 10{sup 3} {omega}{sup -1} cm{sup -1} at room temperature was obtained when the SSD was equal to 15.5 cm. We have deduced that, in accordance with the Ferrari-Robertson model (FRM), our samples are localized in the second stage of the amorphization trajectory of FRM. When the SSD increases the C atoms have more probability to collide with N{sub 2} molecules, and the content of nitrogen in the a-C film increases. The amorphization trajectory followed by the films with an SSD increase is from nanocrystalline graphite to amorphous carbon. The changes in the amorphization are due to the nitrogen content in the layers.« less

The Jupiter Energetic Particle Detector Instrument (JEDI) Investigation for the Juno Mission

NASA Astrophysics Data System (ADS)

Mauk, B. H.; Haggerty, D. K.; Jaskulek, S. E.; Schlemm, C. E.; Brown, L. E.; Cooper, S. A.; Gurnee, R. S.; Hammock, C. M.; Hayes, J. R.; Ho, G. C.; Hutcheson, J. C.; Jacques, A. D.; Kerem, S.; Kim, C. K.; Mitchell, D. G.; Nelson, K. S.; Paranicas, C. P.; Paschalidis, N.; Rossano, E.; Stokes, M. R.

2017-11-01

The Jupiter Energetic Particle Detector Instruments (JEDI) on the Juno Jupiter polar-orbiting, atmosphere-skimming, mission to Jupiter will coordinate with the several other space physics instruments on the Juno spacecraft to characterize and understand the space environment of Jupiter's polar regions, and specifically to understand the generation of Jupiter's powerful aurora. JEDI comprises 3 nearly-identical instruments and measures at minimum the energy, angle, and ion composition distributions of ions with energies from H:20 keV and O: 50 keV to >1 MeV, and the energy and angle distribution of electrons from <40 to >500 keV. Each JEDI instrument uses microchannel plates (MCP) and thin foils to measure the times of flight (TOF) of incoming ions and the pulse height associated with the interaction of ions with the foils, and it uses solid state detectors (SSD's) to measure the total energy ( E) of both the ions and the electrons. The MCP anodes and the SSD arrays are configured to determine the directions of arrivals of the incoming charged particles. The instruments also use fast triple coincidence and optimum shielding to suppress penetrating background radiation and incoming UV foreground. Here we describe the science objectives of JEDI, the science and measurement requirements, the challenges that the JEDI team had in meeting these requirements, the design and operation of the JEDI instruments, their calibrated performances, the JEDI inflight and ground operations, and the initial measurements of the JEDI instruments in interplanetary space following the Juno launch on 5 August 2011. Juno will begin its prime science operations, comprising 32 orbits with dimensions 1.1×40 RJ, in mid-2016.

The WRKY transcription factor family in Brachypodium distachyon.

PubMed

Tripathi, Prateek; Rabara, Roel C; Langum, Tanner J; Boken, Ashley K; Rushton, Deena L; Boomsma, Darius D; Rinerson, Charles I; Rabara, Jennifer; Reese, R Neil; Chen, Xianfeng; Rohila, Jai S; Rushton, Paul J

2012-06-22

A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.

The WRKY transcription factor family in Brachypodium distachyon

PubMed Central

2012-01-01

Background A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. Results We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. Conclusions The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors. PMID:22726208

Macroecological patterns of sexual size dimorphism in turtles of the world

USGS Publications Warehouse

Agha, Mickey; Ennen, Joshua R.; Nowakowski, A. Justin; Lovich, Jeffrey E.; Sweat, Sarah C.; Todd, Brian D.

2018-01-01

Sexual size dimorphism (SSD) is a well-documented phenomenon in both plants and animals; however, the ecological and evolutionary mechanisms that drive and maintain SSD patterns across geographic space at regional and global scales are understudied, especially for reptiles. Our goal was to examine geographic variation of turtle SSD and to explore ecological and environmental correlates using phylogenetic comparative methods. We use published body size data on 135 species from nine turtle families to examine how geographic patterns and the evolution of SSD are influenced by habitat specialization, climate (annual mean temperature and annual precipitation) and climate variability, latitude, or a combination of these predictor variables. We found that geographic variation, magnitude and direction of turtle SSD are best explained by habitat association, annual temperature variance and annual precipitation. Use of semi-aquatic and terrestrial habitats was associated with male-biased SSD, whereas use of aquatic habitat was associated with female-biased SSD. Our results also suggest that greater temperature variability is associated with female-biased SSD. In contrast, wetter climates are associated with male-biased SSD compared with arid climates that are associated with female-biased SSD. We also show support for a global latitudinal trend in SSD, with females being larger than males towards the poles, especially in the families Emydidae and Geoemydidae. Estimates of phylogenetic signal for both SSD and habitat type indicate that closely related species occupy similar habitats and exhibit similar direction and magnitude of SSD. These global patterns of SSD may arise from sex-specific reproductive behaviour, fecundity and sex-specific responses to environmental factors that differ among habitats and vary systematically across latitude. Thus, this study adds to our current understanding that while SSD can vary dramatically across and within turtle species under phylogenetic constraints, it may be driven, maintained and exaggerated by habitat type, climate and geographic location.

Environmental signals modulate ToxT-dependent virulence factor expression in Vibrio cholerae.

PubMed

Schuhmacher, D A; Klose, K E

1999-03-01

The regulatory protein ToxT directly activates the transcription of virulence factors in Vibrio cholerae, including cholera toxin (CT) and the toxin-coregulated pilus (TCP). Specific environmental signals stimulate virulence factor expression by inducing the transcription of toxT. We demonstrate that transcriptional activation by the ToxT protein is also modulated by environmental signals. ToxT expressed from an inducible promoter activated high-level expression of CT and TCP in V. cholerae at 30 degrees C, but expression of CT and TCP was significantly decreased or abolished by the addition of 0.4% bile to the medium and/or an increase of the temperature to 37 degrees C. Also, expression of six ToxT-dependent TnphoA fusions was modulated by temperature and bile. Measurement of ToxT-dependent transcription of genes encoding CT and TCP by ctxAp- and tcpAp-luciferase fusions confirmed that negative regulation by 37 degrees C or bile occurs at the transcriptional level in V. cholerae. Interestingly, ToxT-dependent transcription of these same promoters in Salmonella typhimurium was relatively insensitive to regulation by temperature or bile. These data are consistent with ToxT transcriptional activity being modulated by environmental signals in V. cholerae and demonstrate an additional level of complexity governing the expression of virulence factors in this pathogen. We propose that negative regulation of ToxT-dependent transcription by environmental signals prevents the incorrect temporal and spatial expression of virulence factors during cholera pathogenesis.

Dosimetric effects of weight loss or gain during volumetric modulated arc therapy and intensity-modulated radiation therapy for prostate cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pair, Matthew L.; Du, Weiliang; Rojas, Hector D.

Weight loss or gain during the course of radiation therapy for prostate cancer can alter the planned dose to the target volumes and critical organs. Typically, source-to-surface distance (SSD) measurements are documented by therapists on a weekly basis to ensure that patients' exterior surface and isocenter-to-skin surface distances remain stable. The radiation oncology team then determines whether the patient has undergone a physical change sufficient to require a new treatment plan. The effect of weight change (SSD increase or decrease) on intensity-modulated radiation therapy (IMRT) or volumetric modulated arc therapy (VMAT) dosimetry is not well known, and it is unclearmore » when rescanning or replanning is needed. The purpose of this study was to determine the effects of weight change (SSD increase or decrease) on IMRT or VMAT dose delivery in patients with prostate cancer and to determine the SSD change threshold for replanning. Whether IMRT or VMAT provides better dose stability under weight change conditions was also determined. We generated clinical IMRT and VMAT prostate and seminal vesicle treatment plans for varying SSDs for 10 randomly selected patients with prostate cancer. The differences due to SSD change were quantified by a specific dose change for a specified volume of interest. The target mean dose, decreased or increased by 2.9% per 1-cm SSD decrease or increase in IMRT and by 3.6% in VMAT. If the SSD deviation is more than 1 cm, the radiation oncology team should determine whether to continue treatment without modifications, to adjust monitor units, or to resimulate and replan.« less

The Persian version of auditory word discrimination test (P-AWDT) for children: Development, validity, and reliability.

PubMed

Hashemi, Nassim; Ghorbani, Ali; Soleymani, Zahra; Kamali, Mohmmad; Ahmadi, Zohreh Ziatabar; Mahmoudian, Saeid

2018-07-01

Auditory discrimination of speech sounds is an important perceptual ability and a precursor to the acquisition of language. Auditory information is at least partially necessary for the acquisition and organization of phonological rules. There are few standardized behavioral tests to evaluate phonemic distinctive features in children with or without speech and language disorders. The main objective of the present study was the development, validity, and reliability of the Persian version of auditory word discrimination test (P-AWDT) for 4-8-year-old children. A total of 120 typical children and 40 children with speech sound disorder (SSD) participated in the present study. The test comprised of 160 monosyllabic paired-words distributed in the Forms A-1 and the Form A-2 for the initial consonants (80 words) and the Forms B-1 and the Form B-2 for the final consonants (80 words). Moreover, the discrimination of vowels was randomly included in all forms. Content validity was calculated and 50 children repeated the test twice with two weeks of interval (test-retest reliability). Further analysis was also implemented including validity, intraclass correlation coefficient (ICC), Cronbach's alpha (internal consistency), age groups, and gender. The content validity index (CVI) and the test-retest reliability of the P-AWDT were achieved 63%-86% and 81%-96%, respectively. Moreover, the total Cronbach's alpha for the internal consistency was estimated relatively high (0.93). Comparison of the mean scores of the P-AWDT in the typical children and the children with SSD revealed a significant difference. The results revealed that the group with SSD had greater severity of deficit than the typical group in auditory word discrimination. In addition, the difference between the age groups was statistically significant, especially in 4-4.11-year-old children. The performance of the two gender groups was relatively same. The comparison of the P-AWDT scores between the typical children and the children with SSD demonstrated differences in the capabilities of auditory phonological discrimination in both initial and final positions. It supposed that the P-AWDT meets the appropriate validity and reliability criteria. The P-AWDT test can be utilized to measure the distinctive features of phonemes, the auditory discrimination of initial and final consonants and middle vowels of words in 4-8-year-old typical children and children with SSD. Copyright © 2018. Published by Elsevier B.V.

Speech abilities in preschool children with speech sound disorder with and without co-occurring language impairment.

PubMed

Macrae, Toby; Tyler, Ann A

2014-10-01

The authors compared preschool children with co-occurring speech sound disorder (SSD) and language impairment (LI) to children with SSD only in their numbers and types of speech sound errors. In this post hoc quasi-experimental study, independent samples t tests were used to compare the groups in the standard score from different tests of articulation/phonology, percent consonants correct, and the number of omission, substitution, distortion, typical, and atypical error patterns used in the production of different wordlists that had similar levels of phonetic and structural complexity. In comparison with children with SSD only, children with SSD and LI used similar numbers but different types of errors, including more omission patterns ( p < .001, d = 1.55) and fewer distortion patterns ( p = .022, d = 1.03). There were no significant differences in substitution, typical, and atypical error pattern use. Frequent omission error pattern use may reflect a more compromised linguistic system characterized by absent phonological representations for target sounds (see Shriberg et al., 2005). Research is required to examine the diagnostic potential of early frequent omission error pattern use in predicting later diagnoses of co-occurring SSD and LI and/or reading problems.

Identification of novel non-coding RNA-based negative feedback regulating the expression of the oncogenic transcription factor GLI1.

PubMed

Villegas, Victoria E; Rahman, Mohammed Ferdous-Ur; Fernandez-Barrena, Maite G; Diao, Yumei; Liapi, Eleni; Sonkoly, Enikö; Ståhle, Mona; Pivarcsi, Andor; Annaratone, Laura; Sapino, Anna; Ramírez Clavijo, Sandra; Bürglin, Thomas R; Shimokawa, Takashi; Ramachandran, Saraswathi; Kapranov, Philipp; Fernandez-Zapico, Martin E; Zaphiropoulos, Peter G

2014-07-01

Non-coding RNAs are a complex class of nucleic acids, with growing evidence supporting regulatory roles in gene expression. Here we identify a non-coding RNA located head-to-head with the gene encoding the Glioma-associated oncogene 1 (GLI1), a transcriptional effector of multiple cancer-associated signaling pathways. The expression of this three-exon GLI1 antisense (GLI1AS) RNA in cancer cells was concordant with GLI1 levels. siRNAs knockdown of GLI1AS up-regulated GLI1 and increased cellular proliferation and tumor growth in a xenograft model system. Conversely, GLI1AS overexpression decreased the levels of GLI1, its target genes PTCH1 and PTCH2, and cellular proliferation. Additionally, we demonstrate that GLI1 knockdown reduced GLI1AS, while GLI1 overexpression increased GLI1AS, supporting the role of GLI1AS as a target gene of the GLI1 transcription factor. Activation of TGFβ and Hedgehog signaling, two known regulators of GLI1 expression, conferred a concordant up-regulation of GLI1 and GLI1AS in cancer cells. Finally, analysis of the mechanism underlying the interplay between GLI1 and GLI1AS indicates that the non-coding RNA elicits a local alteration of chromatin structure by increasing the silencing mark H3K27me3 and decreasing the recruitment of RNA polymerase II to this locus. Taken together, the data demonstrate the existence of a novel non-coding RNA-based negative feedback loop controlling GLI1 levels, thus expanding the repertoire of mechanisms regulating the expression of this oncogenic transcription factor. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Cdk-related kinase 9 regulates RNA polymerase II mediated transcription in Toxoplasma gondii.

PubMed

Deshmukh, Abhijit S; Mitra, Pallabi; Kolagani, Ashok; Gurupwar, Rajkumar

2018-06-01

Cyclin-dependent kinases are an essential part of eukaryotic transcriptional machinery. In Apicomplexan parasites, the role and relevance of the kinases in the multistep process of transcription seeks more attention given the absence of full repertoire of canonical Cdks and cognate cyclin partners. In this study, we functionally characterize T. gondii Cdk-related kinase 9 (TgCrk9) showing maximal homology to eukaryotic Cdk9. An uncanonical cyclin, TgCyclin L, colocalizes with TgCrk9 in the parasite nucleus and co-immunoprecipitate, could activate the kinase in-vitro. We identify two threonines in conserved T-loop domain of TgCrk9 that are important for its activity. The activated TgCrk9 phosphorylates C-terminal domain (CTD) of TgRpb1, the largest subunit of RNA polymerase II highlighting its role in transcription. Selective chemical inhibition of TgCrk9 affected serine 2 phosphorylation in the heptapeptide repeats of TgRpb1-CTD towards 3' end of genes consistent with a possible role in transcription elongation. Interestingly, TgCrk9 kinase activity is regulated by the upstream TgCrk7 based CAK complex. TgCrk9 was found to functionally complement the role of its yeast counterpart Bur1 establishing its role as an important transcriptional kinase. In this study, we provide robust evidence that TgCrk9 is an important part of transcription machinery regulating gene expression in T. gondii. Copyright © 2018 Elsevier B.V. All rights reserved.

Transcription Mapping of the Kaposi’s Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Genome in a Body Cavity-Based Lymphoma Cell Line (BC-1)

PubMed Central

Sarid, Ronit; Flore, Ornella; Bohenzky, Roy A.; Chang, Yuan; Moore, Patrick S.

1998-01-01

Kaposi’s sarcoma-associated herpesvirus (KSHV) gene transcription in the BC-1 cell line (KSHV and Epstein-Barr virus coinfected) was examined by using Northern analysis with DNA probes extending across the viral genome except for a 3-kb unclonable rightmost region. Three broad classes of viral gene transcription have been identified. Class I genes, such as those encoding the v-cyclin, latency-associated nuclear antigen, and v-FLIP, are constitutively transcribed under standard growth conditions, are unaffected by tetradecanoylphorbol acetate (TPA) induction, and presumably represent latent viral transcripts. Class II genes are primarily clustered in nonconserved regions of the genome and include small polyadenylated RNAs (T0.7 and T1.1) as well as most of the virus-encoded cytokines and signal transduction genes. Class II genes are transcribed without TPA treatment but are induced to higher transcription levels by TPA treatment. Class III genes are primarily structural and replication genes that are transcribed only following TPA treatment and are presumably responsible for lytic virion production. These results indicate that BC-1 cells have detectable transcription of a number of KSHV genes, particularly nonconserved genes involved in cellular signal transduction and regulation, during noninduced (latent) virus culture. PMID:9444993

Molecular Etiology of Hereditary Single-Side Deafness: Its Association With Pigmentary Disorders and Waardenburg Syndrome.

PubMed

Kim, Shin Hye; Kim, Ah Reum; Choi, Hyun Seok; Kim, Min Young; Chun, Eun Hi; Oh, Seung-Ha; Choi, Byung Yoon

2015-10-01

Unilateral sensorineural hearing loss (USNHL)/single-side deafness (SSD) is a frequently encountered disability in children. The etiology of a substantial portion of USNHL/SSD still remains unknown, and genetic causes have not been clearly elucidated. In this study, the authors evaluated the heritability of USNHL/SSD.The authors sequentially recruited 50 unrelated children with SSD. For an etiologic diagnosis, we performed a rigorous review on the phenotypes of family members of all children and conducted, if necessary, molecular genetic tests including targeted exome sequencing of 129 deafness genes.Among the 50 SSD children cohort, the authors identify 4 (8%) unrelated SSD probands from 4 families (SH136, SB173, SB177, and SB199) with another hearing impaired family members. Notably, all 4 probands in our cohort with a familial history of SSD also have pigmentary abnormalities such as brown freckles or premature gray hair within first degree relatives, which may indicate that genes whose products are involved with pigmentary disorder could be candidates for heritable SSD. Indeed, SH136 and SB199 turned out to segregate a mutation in MITF and PAX3, respectively, leading to a molecular diagnosis of Waardenburg syndrome (WS).We report, for the first time in the literature, a significant heritability of pediatric SSD. There is a strong association between the heritability of USNHL/SSD and the pigmentary abnormality, shedding a new light on the understanding of the molecular basis of heritable USNHL/SSD. In case of children with congenital SSD, it would be mandatory to rigorously screen pigmentary abnormalities. WS should also be included in the differential diagnosis of children with USNHL/SSD, especially in a familial form.

Molecular Etiology of Hereditary Single-Side Deafness

PubMed Central

Kim, Shin Hye; Kim, Ah Reum; Choi, Hyun Seok; Kim, Min Young; Chun, Eun Hi; Oh, Seung-Ha; Choi, Byung Yoon

2015-01-01

Abstract Unilateral sensorineural hearing loss (USNHL)/single-side deafness (SSD) is a frequently encountered disability in children. The etiology of a substantial portion of USNHL/SSD still remains unknown, and genetic causes have not been clearly elucidated. In this study, the authors evaluated the heritability of USNHL/SSD. The authors sequentially recruited 50 unrelated children with SSD. For an etiologic diagnosis, we performed a rigorous review on the phenotypes of family members of all children and conducted, if necessary, molecular genetic tests including targeted exome sequencing of 129 deafness genes. Among the 50 SSD children cohort, the authors identify 4 (8%) unrelated SSD probands from 4 families (SH136, SB173, SB177, and SB199) with another hearing impaired family members. Notably, all 4 probands in our cohort with a familial history of SSD also have pigmentary abnormalities such as brown freckles or premature gray hair within first degree relatives, which may indicate that genes whose products are involved with pigmentary disorder could be candidates for heritable SSD. Indeed, SH136 and SB199 turned out to segregate a mutation in MITF and PAX3, respectively, leading to a molecular diagnosis of Waardenburg syndrome (WS). We report, for the first time in the literature, a significant heritability of pediatric SSD. There is a strong association between the heritability of USNHL/SSD and the pigmentary abnormality, shedding a new light on the understanding of the molecular basis of heritable USNHL/SSD. In case of children with congenital SSD, it would be mandatory to rigorously screen pigmentary abnormalities. WS should also be included in the differential diagnosis of children with USNHL/SSD, especially in a familial form. PMID:26512583

Cognitive reserve as a predictor of two year neuropsychological performance in early onset first-episode schizophrenia.

PubMed

de la Serna, Elena; Andrés-Perpiñá, Susana; Puig, Olga; Baeza, Inmaculada; Bombin, Igor; Bartrés-Faz, David; Arango, Celso; Gonzalez-Pinto, Ana; Parellada, Mara; Mayoral, María; Graell, Montserrat; Otero, Soraya; Guardia, Joan; Castro-Fornieles, Josefina

2013-01-01

The concept of cognitive reserve (CR) has been defined as individual differences in the efficient utilization of brain networks which allow some people to cope better than others with brain pathology. CR has been developed mainly in the field of aging and dementia after it was observed that there appears to be no direct relationship between the degree of brain pathology and the severity of clinical manifestations of this damage. The present study applies the concept of CR to a sample of children and adolescents with a first episode of schizophrenia, aiming to assess the possible influence of CR on neuropsychological performance after two year follow-up, controlling for the influence of clinical psychopathology. 35 patients meeting DSM-IV criteria for schizophrenia or schizoaffective disorder (SSD) and 98 healthy controls (HC) matched for age and gender were included. CR was assessed at baseline, taking into account premorbid IQ, educational-occupational level and leisure activities. Clinical and neuropsychological assessments were completed by all patients at two year follow-up. The CR proxy was able to predict working memory and attention at two year follow-up. Verbal memory and cognitive flexibility were not predicted by any of the variables included in the regression model. The SSD group obtained lower scores than HC on CR. CR measures correctly classified 79.8% of the sample as being SSD or HC. Lower scores on CR were observed in SSD than in HC and the CR measure correctly classified a high percentage of the sample into the two groups. CR may predict SSD performance on working memory and attention tasks. Copyright © 2012 Elsevier B.V. All rights reserved.

Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability

PubMed Central

Miller, Christopher B.; Bartlett, Delwyn J.; Mullins, Anna E.; Dodds, Kirsty L.; Gordon, Christopher J.; Kyle, Simon D.; Kim, Jong Won; D'Rozario, Angela L.; Lee, Rico S.C.; Comas, Maria; Marshall, Nathaniel S.; Yee, Brendon J.; Espie, Colin A.; Grunstein, Ronald R.

2016-01-01

Study Objectives: To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative (q)-EEG and heart rate variability (HRV). Methods: Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. Results: From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P < 0.05). Preliminary work suggested three clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q-EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Conclusions: Two insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q-EEG. Clinical Trial Registration: Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. Citation: Miller CB, Bartlett DJ, Mullins AE, Dodds KL, Gordon CJ, Kyle SD, Kim JW, D'Rozario AL, Lee RS, Comas M, Marshall NS, Yee BJ, Espie CA, Grunstein RR. Clusters of Insomnia Disorder: an exploratory cluster analysis of objective sleep parameters reveals differences in neurocognitive functioning, quantitative EEG, and heart rate variability. SLEEP 2016;39(11):1993–2004. PMID:27568796

Dominance of high-energy (>150 keV) heavy ion intensities in Earth's middle to outer magnetosphere

NASA Astrophysics Data System (ADS)

Cohen, Ian J.; Mitchell, Donald G.; Kistler, Lynn M.; Mauk, Barry H.; Anderson, Brian J.; Westlake, Joseph H.; Ohtani, Shinichi; Hamilton, Douglas C.; Turner, Drew L.; Blake, J. Bernard; Fennell, Joseph F.; Jaynes, Allison N.; Leonard, Trevor W.; Gerrard, Andrew J.; Lanzerotti, Louis J.; Allen, Robert C.; Burch, James L.

2017-09-01

Previous observations have driven the prevailing assumption in the field that energetic ions measured by an instrument using a bare solid state detector (SSD) are predominantly protons. However, new near-equatorial energetic particle observations obtained between 7 and 12 RE during Phase 1 of the Magnetospheric Multiscale mission challenge the validity of this assumption. In particular, measurements by the Energetic Ion Spectrometer (EIS) instruments have revealed that the intensities of heavy ion species (specifically oxygen and helium) dominate those of protons at energies ≳150-220 keV in the middle to outer (>7 RE) magnetosphere. Given that relative composition measurements can drift as sensors degrade in gain, quality cross-calibration agreement between EIS observations and those from the SSD-based Fly's Eye Energetic Particle Spectrometer (FEEPS) sensors provides critical support to the veracity of the measurement. Similar observations from the Radiation Belt Storm Probes Ion Composition Experiment (RBSPICE) instruments aboard the Van Allen Probes spacecraft extend the ion composition measurements into the middle magnetosphere and reveal a strongly proton-dominated environment at L≲6 but decreasing proton intensities at L≳6. It is concluded that the intensity dominance of the heavy ions at higher energies (>150 keV) arises from the existence of significant populations of multiply-charged heavy ions, presumably of solar wind origin.

Does life history shape sexual size dimorphism in anurans? A comparative analysis

PubMed Central

2013-01-01

Background The evolution of sexual size dimorphism (SSD) is likely constrained by life history. Using phylogenetic comparative methods, we examined correlations between SSD among anurans and their life history traits, including egg size, clutch size, mating combat, and parental care behaviour. We used sexual dimorphism index (SDI = Body-sizefemale /Body-sizemale –1) as the measurement for SSD. Body size, life history and phylogenetic data were collected from published literature. Data were analysed at two levels: all anuran species and within individual families. Results Female-biased SSD is the predominant form in anurans. SSD decreases along with the body size increase, following the prediction of Rensch’s rule, but the magnitude of decrease is very small. More importantly, female body size is positively correlated with both fecundity related traits, egg size and clutch size, and SDI is also positively correlated with clutch size, suggesting fecundity advantage may have driven the evolution of female body size and consequently leads to the evolution of female-biased SSD. Furthermore, the presence of parental care, male parental care in particular, is negatively correlated with SDI, indicating that species with parental care tend to have a smaller SDI. A negative correlation between clutch size and parental care further suggests that parental care likely reduces the fecundity selection pressure on female body size. On the other hand, there is a general lack of significant correlation between SDI and the presence of male combat behaviour, which is surprising and contradictory to previous studies. Conclusions We find clear evidence to support the ‘fecundity advantage hypothesis’ and the ‘parental care hypothesis’ in shaping SSD in anurans. Nevertheless, the relationships of both parental care and combat behaviour to the evolution of SSD are complex in anurans and the extreme diversity of life history traits may have masked some potential interesting relationships. Our study represents the most comprehensive study of SSD in anurans to date. PMID:23368708

Suspended-sediment trapping in the tidal reach of an estuarine tributary channel

USGS Publications Warehouse

Downing-Kunz, Maureen; Schoellhamer, David H.

2015-01-01

Evidence of decreasing sediment supply to estuaries and coastal oceans worldwide illustrates the need for accurate and updated estimates. In the San Francisco Estuary (Estuary), recent research suggests a decrease in supply from its largest tributaries, implying the increasing role of smaller, local tributaries in sediment supply to this estuary. Common techniques for estimating supply from tributaries are based on gages located above head of tide, which do not account for trapping processes within the tidal reach. We investigated the effect of a tidal reach on suspended-sediment discharge for Corte Madera Creek, a small tributary of the Estuary. Discharge of water (Q) and suspended-sediment (SSD) were observed for 3 years at two locations along the creek: upstream of tidal influence and at the mouth. Comparison of upstream and mouth gages showed nearly 50 % trapping of upstream SSD input within the tidal reach over this period. At the storm time scale, suspended-sediment trapping efficiency varied greatly (range −31 to 93 %); storms were classified as low- or high-yield based on upstream SSD. As upstream peak Q increased, high-yield storms exhibited significantly decreased trapping. Tidal conditions at the mouth—ebb duration and peak ebb velocity—during storms had a minor effect on sediment trapping, suggesting fluvial processes dominate. Comparison of characteristic fluvial and tidal discharges at the storm time scale demonstrated longitudinal differences in the regulating process for SSD. These results suggest that SSD from gages situated above head of tide overestimate sediment supply to the open waters beyond tributary mouths and thus trapping processes within the tidal reach should be considered.

PPARγ regulates exocrine pancreas lipase.

PubMed

Danino, Hila; Naor, Ronny Peri-; Fogel, Chen; Ben-Harosh, Yael; Kadir, Rotem; Salem, Hagit; Birk, Ruth

2016-12-01

Pancreatic lipase (triacylglycerol lipase EC 3.1.1.3) is an essential enzyme in hydrolysis of dietary fat. Dietary fat, especially polyunsaturated fatty acids (PUFA), regulate pancreatic lipase (PNLIP); however, the molecular mechanism underlying this regulation is mostly unknown. As PUFA are known to regulate expression of proliferator-activated receptor gamma (PPARγ), and as we identified in-silico putative PPARγ binding sites within the putative PNLIP promoter sequence, we hypothesized that PUFA regulation of PNLIP might be mediated by PPARγ. We used in silico bioinformatics tools, reporter luciferase assay, PPARγ agonists and antagonists, PPARγ overexpression in exocrine pancreas AR42J and primary cells to study PPARγ regulation of PNLIP. Using in silico bioinformatics tools we mapped PPARγ binding sites (PPRE) to the putative promoter region of PNLIP. Reporter luciferase assay in AR42J rat exocrine pancreas acinar cells transfected with various constructs of the putative PNLIP promoter showed that PNLIP transcription is significantly enhanced by PPARγ dose-dependently, reaching maximal levels with multi PPRE sites. This effect was significantly augmented in the presence of PPARγ agonists and reduced by PPARγ antagonists or mutagenesis abrogating PPRE sites. Over-expression of PPARγ significantly elevated PNLIP transcript and protein levels in AR42J cells and in primary pancreas cells. Moreover, PNLIP expression was up-regulated by PPARγ agonists (pioglitazone and 15dPGJ2) and significantly down-regulated by PPARγ antagonists in non-transfected rat exocrine pancreas AR42J cell line cells. PPARγ transcriptionally regulates PNLIP gene expression. This transcript regulation resolves part of the missing link between dietary PUFA direct regulation of PNLIP. Copyright © 2016 Elsevier B.V. All rights reserved.

Operationalization of diagnostic criteria of DSM-5 somatic symptom disorders.

PubMed

Xiong, Nana; Zhang, Yaoyin; Wei, Jing; Leonhart, Rainer; Fritzsche, Kurt; Mewes, Ricarda; Hong, Xia; Cao, Jinya; Li, Tao; Jiang, Jing; Zhao, Xudong; Zhang, Lan; Schaefert, Rainer

2017-11-07

The aim of this study was to test the operationalization of DSM-5 somatic symptom disorder (SSD) psychological criteria among Chinese general hospital outpatients. This multicenter, cross-sectional study enrolled 491 patients from 10 general hospital outpatient departments. The structured clinical "interview about cognitive, affective, and behavioral features associated with somatic complaints" was used to operationalize the SSD criteria B. For comparison, DSM-IV somatoform disorders were assessed with the Mini International Neuropsychiatric Interview plus. Cohen's к scores were given to illustrate the agreement of the diagnoses. A three-structure model of the interview, within which items were classified as respectively assessing the cognitive (B1), affective (B2), and behavioral (B3) features, was examined. According to percentages of screening-positive persons and the receiver operator characteristic (ROC) analysis, a cut-off point of 2 was recommended for each subscale of the interview. With the operationalization, the frequency of DSM-5 SSD was estimated as 36.5% in our sample, and that of DSM-IV somatoform disorders was 8.2%. The agreement between them was small (Cohen's к = 0.152). Comparisons of sociodemographic features of SSD patients with different severity levels (mild, moderate, severe) showed that mild SSD patients were better-off in terms of financial and employment status, and that the severity subtypes were congruent with the level of depression, anxiety, quality of life impairment, and the frequency of doctor visits. The operationalization of the diagnosis and severity specifications of SSD was valid, but the diagnostic agreement between DSM-5 SSD and DSM-IV somatoform disorders was small. The interpretation the SSD criteria should be made cautiously, so that the diagnosis would not became over-inclusive.

Clinical value of DSM IV and DSM 5 criteria for diagnosing the most prevalent somatoform disorders in patients with medically unexplained physical symptoms (MUPS).

PubMed

van Dessel, Nikki Claassen-; van der Wouden, Johannes C; Dekker, Joost; van der Horst, Henriette E

2016-03-01

This study aimed (1) to describe frequencies of DSM IV somatisation disorder, undifferentiated somatoform disorder and pain disorder versus DSM 5 somatic symptom disorder (SSD) in a multi-setting population of patients with medically unexplained physical symptoms (MUPS), (2) to investigate differences in sociodemographic and (psycho)pathological characteristics between these diagnostic groups and (3) to explore the clinical relevance of the distinction between mild and moderate DSM 5 SSD. We used baseline data of a cohort of 325 MUPS patients. Measurements included questionnaires about symptom severity, physical functioning, anxiety, depression, health anxiety and illness perceptions. These questionnaires were used as proxy measures for operationalization of DSM IV and DSM 5 diagnostic criteria. 92.9% of participants fulfilled criteria of a DSM IV somatoform disorder, while 45.5% fulfilled criteria of DSM 5 SSD. Participants fulfilling criteria of DSM 5 SSD suffered from more severe symptoms than those only fulfilling criteria of a DSM IV somatoform disorder(mean PHQ-15 score of 13.98 (SD 5.17) versus 11.23 (SD 4.71), P-value<0.001). Furthermore their level of physical functioning was significantly lower. Compared to patients with mild SSD, patients with moderate SSD suffered from significantly lower physical functioning and higher levels of depression. Within a population of MUPS patients DSM 5 SSD criteria are more restrictive than DSM IV criteria for somatoform disorders. They are associated with higher symptom severity and lower physical functioning. However, further specification of the positive psychological criteria of DSM 5 SSD may improve utility in research and practice. Copyright © 2016 Elsevier Inc. All rights reserved.

Effects of glucose, ethanol and acetic acid on regulation of ADH2 gene from Lachancea fermentati.

PubMed

Yaacob, Norhayati; Mohamad Ali, Mohd Shukuri; Salleh, Abu Bakar; Abdul Rahman, Nor Aini

2016-01-01

Background. Not all yeast alcohol dehydrogenase 2 (ADH2) are repressed by glucose, as reported in Saccharomyces cerevisiae. Pichia stipitis ADH2 is regulated by oxygen instead of glucose, whereas Kluyveromyces marxianus ADH2 is regulated by neither glucose nor ethanol. For this reason, ADH2 regulation of yeasts may be species dependent, leading to a different type of expression and fermentation efficiency. Lachancea fermentati is a highly efficient ethanol producer, fast-growing cells and adapted to fermentation-related stresses such as ethanol and organic acid, but the metabolic information regarding the regulation of glucose and ethanol production is still lacking. Methods. Our investigation started with the stimulation of ADH2 activity from S. cerevisiae and L. fermentati by glucose and ethanol induction in a glucose-repressed medium. The study also embarked on the retrospective analysis of ADH2 genomic and protein level through direct sequencing and sites identification. Based on the sequence generated, we demonstrated ADH2 gene expression highlighting the conserved NAD(P)-binding domain in the context of glucose fermentation and ethanol production. Results. An increase of ADH2 activity was observed in starved L. fermentati (LfeADH2) and S. cerevisiae (SceADH2) in response to 2% (w/v) glucose induction. These suggest that in the presence of glucose, ADH2 activity was activated instead of being repressed. An induction of 0.5% (v/v) ethanol also increased LfeADH2 activity, promoting ethanol resistance, whereas accumulating acetic acid at a later stage of fermentation stimulated ADH2 activity and enhanced glucose consumption rates. The lack in upper stream activating sequence (UAS) and TATA elements hindered the possibility of Adr1 binding to LfeADH2. Transcription factors such as SP1 and RAP1 observed in LfeADH2 sequence have been implicated in the regulation of many genes including ADH2. In glucose fermentation, L. fermentati exhibited a bell-shaped ADH2 expression, showing the highest expression when glucose was depleted and ethanol-acetic acid was increased. Meanwhile, S. cerevisiae showed a constitutive ADH2 expression throughout the fermentation process. Discussion. ADH2 expression in L. fermentati may be subjected to changes in the presence of non-fermentative carbon source. The nucleotide sequence showed that ADH2 transcription could be influenced by other transcription genes of glycolysis oriented due to the lack of specific activation sites for Adr1. Our study suggests that if Adr1 is not capable of promoting LfeADH2 activation, the transcription can be controlled by Rap1 and Sp1 due to their inherent roles. Therefore in future, it is interesting to observe ADH2 gene being highly regulated by these potential transcription factors and functioned as a promoter for yeast under high volume of ethanol and organic acids.

Evaluation of testicular dose and associated risk from common pelvis radiation therapy in Iran.

PubMed

Shanei, Ahmad; Baradaran-Ghahfarokhi, Milad

2014-12-01

This study aimed to investigate testicular dose (TD) and the associated risk of heritable disease from common pelvis radiotherapy of male patients in Iran. In this work, the relation between TD and changes in beam energy, pelvis size, source to skin distance (SSD) and beam directions (anterior or posterior) was also evaluated. The values of TDs were measured on 67 randomly selected male patients during common pelvis radiotherapy using 1.17 and 1.33 MeV, Theratron Cobalt-60 unit at SSD of 80 cm and 9 MV, Neptun 10 PC and 18 MV, GE Saturne 20 at SSD of 100 cm at Seyed-Al Shohada Hospital, Isfahan, Iran. Results showed that, the maximum TD was up to 12% of the tumor dose. Considering the risk factor for radiation-induced heritable disorders of 0.1% per Sv, an excess risk of hereditary disorders of 72 per 10,000 births was conservatively calculated. There was a significant difference in the measured TD using different treatment machines and energies (P < 0.001). The Pearson Correlation test showed that, as expected, there was a correlation between TD and patient's pelvis size (r = 0.275, P < 0.001). Using the student's t-tests, it was found that, there was not a significant difference between TD and beam direction (P = 0.231). Iranian male patients undergoing pelvic radiotherapy have the potential of receiving a TD of more than 1 Gy which might result in temporary azoospermia. The risk for induction of hereditary disorders in future generations should be considered as low but not negligible in comparison with the correspondent nominal risk. Copyright © 2014 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

RNA Pol IV and V in Gene Silencing: Rebel Polymerases Evolving Away From Pol II’s Rules

PubMed Central

Zhou, Ming; Law, Julie A.

2015-01-01

Noncoding RNAs regulate gene expression at both the transcriptional and post-transcriptional levels, and play critical roles in development, imprinting and the maintenance of genome integrity in eukaryotic organisms [1–3]. Therefore, it is important to understand how the production of such RNAs are controlled. In addition to the three canonical DNA dependent RNA polymerases (Pol) Pol I, II and III, two non-redundant plant-specific RNA polymerases, Pol IV and Pol V, have been identified and shown to generate noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway. Thus, somewhat paradoxically, transcription is required for gene silencing. This paradox extends beyond plants, as silencing pathways in yeast, fungi, flies, worms, and mammals also require transcriptional machinery [4,5]. As plants have evolved specialized RNA polymerases to carry out gene silencing in a manner that is separate from the essential roles of Pol II, their characterization offers unique insight into how RNA polymerases facilitate gene silencing. In this review, we focus on the mechanisms of Pol IV and Pol V function, including their compositions, their transcripts, and their modes of recruitment to chromatin. PMID:26344361

Ecotoxicologically based marine acute water quality criteria for metals intended for protection of coastal areas.

PubMed

Durán, I; Beiras, R

2013-10-01

Acute water quality criteria (WQC) for the protection of coastal ecosystems are developed on the basis of short-term ecotoxicological data using the most sensitive life stages of representative species from the main taxa of marine water column organisms. A probabilistic approach based on species sensitivity distribution (SSD) curves has been chosen and compared to the WQC obtained applying an assessment factor to the critical toxicity values, i.e. the 'deterministic' approach. The criteria obtained from HC5 values (5th percentile of the SSD) were 1.01 μg/l for Hg, 1.39 μg/l for Cu, 3.83 μg/l for Cd, 25.3 μg/l for Pb and 8.24 μg/l for Zn. Using sensitive early life stages and very sensitive endpoints allowed calculation of WQC for marine coastal ecosystems. These probabilistic WQC, intended to protect 95% of the species in 95% of the cases, were calculated on the basis of a limited ecotoxicological dataset, avoiding the use of large and uncertain assessment factors. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular characterization of estrogen receptor genes in Gobiocypris rarus and their expression upon endocrine disrupting chemicals exposure in juveniles.

PubMed

Wang, Houpeng; Wang, Jingjing; Wu, Tingting; Qin, Fang; Hu, Xiaoqi; Wang, Lihong; Wang, Zaizhao

2011-01-17

Estrogens play an important role in many physiological processes of vertebrates, mediated by estrogen receptors (ERs). The full length of the cDNAs for ERα, ERβ1, and ERβ2 were isolated and characterized from Gobiocypris rarus. G. rarus ERs shared the highest amino acid identities with counterparts of three cyprinidae species (Pimephales promelas ERα: 91.1%, Rutilus rutilus ERβ1: 92.9%, Tanichthy albonubes ERβ2: 93.5%). The phylogenic tree of vertebrate ERs indicates G. rarus ER isoforms are more related to counterparts of cyprinidae species. The expression of ERα mRNA was high in gonad and liver. The ERβ1 transcript was the highest in the liver of female fish and was evenly high in the liver, testis and intestine in male. The ERβ2 transcript was high in liver, gonad, and intestine. G. rarus juvenile at 34 days post fertilization were exposed for 3 days to endocrine disrupting chemicals including 17α-ethynylestradiol (EE2), 4-nonylphenol (NP) and bisphenol A (BPA). ER mRNA expression following the xenoestrogens' exposure was analyzed by quantitative real-time PCR. EE2 exposure at 0.01, 0.1 and 1 nM significantly up-regulated ERα transcript. ERβ1 mRNA expression was suppressed by EE2 at all concentrations. However ERβ2 transcript had opposite response to EE2 at low and high concentrations (up-regulation at 0.1 nM, down-regulation at 1 nM). Except a weak increase of ERα at 10 nM EE2, varying decrease of three ER transcripts was resulted in by NP at 10, 100 and 1000 nM. ERα transcript was significantly up-regulated by BPA at 10 nM. A non-significant weak increase in ERβ1 mRNA expression was caused by 1 nM BPA. However 1 nM and 10 nM BPA exposures resulted in significant and non-significant decrease of ERβ2 transcript, respectively. The BPA exposures at other concentrations almost had no effect on the ER transcripts. Vitellogenin (Vtg) mRNA expression profiling following exposure to three xenoestrogens indicated that Vtg transcript is a sensitive biomarker of the juvenile G. rarus at 34 dpf to the EDCs, especially to EE2. These results combined suggest that the ER genes are not modulated in the same manner by EE2, NP, and BPA and that ERs may not contribute equally to the transcriptional regulation of genes involved in fish development and reproduction. Copyright © 2010 Elsevier B.V. All rights reserved.

Ethanol induced astaxanthin accumulation and transcriptional expression of carotenogenic genes in Haematococcus pluvialis.

PubMed

Wen, Zewen; Liu, Zhiyong; Hou, Yuyong; Liu, Chenfeng; Gao, Feng; Zheng, Yubin; Chen, Fangjian

2015-10-01

Haematococcus pluvialis is one of the most promising natural sources of astaxanthin. However, inducing the accumulation process has become one of the primary obstacles in astaxanthin production. In this study, the effect of ethanol on astaxanthin accumulation was investigated. The results demonstrated that astaxanthin accumulation occurred with ethanol addition even under low-light conditions. The astaxanthin productivity could reach 11.26 mg L(-1) d(-1) at 3% (v/v) ethanol, which was 2.03 times of that of the control. The transcriptional expression patterns of eight carotenogenic genes were evaluated using real-time PCR. The results showed that ethanol greatly enhanced transcription of the isopentenyl diphosphate (IPP) isomerase genes (ipi-1 and ipi-2), which were responsible for isomerization reaction of IPP and dimethylallyl diphosphate (DMAPP). This finding suggests that ethanol induced astaxanthin biosynthesis was up-regulated mainly by ipi-1 and ipi-2 at transcriptional level, promoting isoprenoid synthesis and substrate supply to carotenoid formation. Thus ethanol has the potential to be used as an effective reagent to induce astaxanthin accumulation in H. pluvialis. Copyright © 2015 Elsevier Inc. All rights reserved.

A Prospective Evaluation of High-Resolution CT Parameters in Predicting Extracorporeal Shockwave Lithotripsy Success for Upper Urinary Tract Calculi.

PubMed

Abdelhamid, Mahmoud; Mosharafa, Ashraf A; Ibrahim, Hamdy; Selim, Hany M; Hamed, Mohamed; Elghoneimy, Mohamed N; Salem, Hosny K; Abdelazim, Mohamed S; Badawy, Hesham

2016-11-01

To evaluate the ability of noncontrast CT parameters (stone size, stone attenuation, and skin-to-stone distance [SSD]) to predict the outcome of extracorporeal shockwave lithotripsy (SWL) in a prospective cohort of patients with renal and upper ureteric stones. Patients with stones 5 to 20 mm were prospectively enrolled from 2011 to 2014. Patients had NCCT with recording of stone size, stone mean attenuation, and SSD, as well as various stone and patient parameters. The numbers of needed sessions as well as the final outcome were determined, with SWL failure defined as residual fragments >3 mm. Predictors of SWL failure were assessed by multiple regression analysis. Two hundred twenty patients (mean ± standard deviation [SD] age 41.5 ± 12.4 years) underwent SWL. Mean ± SD stone size was 11.3 ± 4.1 mm, while mean ± SD stone attenuation was 795.1 ± 340.4 HU. Mean ± SD SSD was 9.4 ± 2.1 cm. The average number of sessions was 1.64. SWL was effective in 186 (84.5%) patients (group A), while 34 (15.5%) patients had significant residual fragments (>3 mm). On univariate analysis, predictors of SWL failure included stone attenuation >1000 HU, older age, higher body mass index, higher attenuation value, larger stone size, and longer SSD. Increased SSD and higher stone attenuation retained their significance as independent predictors of SWL failure (p < 0.05) on multiple regression analysis both after first session and as final SWL outcome. A positive correlation was found between number of SWL sessions and mean stone attenuation (r = 0.6, p < 0.001) and SSD (r = 4, p < 0.001). Stone mean attenuation and SSD on noncontrast CT are significant independent predictors of SWL outcome in patients with renal and ureteric stones. These parameters should be included in clinical decision algorithms for patients with urolithiasis. For patients with stones having mean attenuation of >1000 HU and/or large SSDs, alternatives to SWL should be considered.

Hypoxia as a target for tissue specific gene therapy.

PubMed

Rhim, Taiyoun; Lee, Dong Yun; Lee, Minhyung

2013-12-10

Hypoxia is a hallmark of various ischemic diseases such as ischemic heart disease, ischemic limb, ischemic stroke, and solid tumors. Gene therapies for these diseases have been developed with various therapeutic genes including growth factors, anti-apoptotic genes, and toxins. However, non-specific expression of these therapeutic genes may induce dangerous side effects in the normal tissues. To avoid the side effects, gene expression should be tightly regulated in an oxygen concentration dependent manner. The hypoxia inducible promoters and enhancers have been evaluated as a transcriptional regulation tool for hypoxia inducible gene therapy. The hypoxia inducible UTRs were also used in gene therapy for spinal cord injury as a translational regulation strategy. In addition to transcriptional and translational regulations, post-translational regulation strategies have been developed using the HIF-1α ODD domain. Hypoxia inducible transcriptional, translational, and post-translational regulations are useful for tissue specific gene therapy of ischemic diseases. In this review, hypoxia inducible gene expression systems are discussed and their applications are introduced. Copyright © 2013 Elsevier B.V. All rights reserved.

Regulation of yeast fatty acid desaturase in response to iron deficiency.

PubMed

Romero, Antonia María; Jordá, Tania; Rozès, Nicolas; Martínez-Pastor, María Teresa; Puig, Sergi

2018-06-01

Unsaturated fatty acids (UFA) are essential components of phospholipids that greatly contribute to the biophysical properties of cellular membranes. Biosynthesis of UFAs relies on a conserved family of iron-dependent fatty acid desaturases, whose representative in the model yeast Saccharomyces cerevisiae is Ole1. OLE1 expression is tightly regulated to adapt UFA biosynthesis and lipid bilayer properties to changes in temperature, and in UFA or oxygen availability. Despite iron deficiency being the most extended nutritional disorder worldwide, very little is known about the mechanisms and the biological relevance of fatty acid desaturases regulation in response to iron starvation. In this report, we show that endoplasmic reticulum-anchored transcription factor Mga2 activates OLE1 transcription in response to nutritional and genetic iron deficiencies. Cells lacking MGA2 display low UFA levels and do not grow under iron-limited conditions, unless UFAs are supplemented or OLE1 is overexpressed. The proteasome, E3 ubiquitin ligase Rsp5 and the Cdc48 Npl4/Ufd1 complex are required for OLE1 activation during iron depletion. Interestingly, Mga2 also activates the transcription of its own mRNA in response to iron deficiency, hypoxia, low temperature and low UFAs. MGA2 up-regulation contributes to increase OLE1 expression in these situations. These results reveal the mechanism of OLE1 regulation when iron is scarce and identify the MGA2 auto-regulation as a potential activation strategy in multiple stresses. Copyright © 2018 Elsevier B.V. All rights reserved.

Determination of the soil hazardous concentrations of bisphenol A using the species sensitivity approach.

PubMed

Kwak, Jin Il; Moon, Jongmin; Kim, Dokyung; Cui, Rongxue; An, Youn-Joo

2018-02-15

This study describes the determination of the species sensitivity distribution (SSD)-based soil hazardous contamination of bisphenol A for environmental risk assessment. We conducted a battery of bioassays, including acute assays using eight species from six different taxonomic groups and chronic assays using five species from four different taxonomic groups. We determined that our dataset satisfied Australia & New Zealand's guidelines for applying the SSD methodology. Finally, the chronic soil HC 5 and HC 50 values for bisphenol A were estimated to be 13.7 and 74.7mg/kg soil, respectively, for soil ecosystem protection against chronic exposure using the data generated from this and previous studies. Because the soil standard values of bisphenol A for protection of the soil ecosystem are not currently available, the HC values of bisphenol A that we suggested based on the SSD approach would be applied as fundamental data to establish soil standards of bisphenol A for soil ecosystem protection. To our knowledge, this is the first study reporting the soil hazardous concentration of bisphenol A for environmental risk assessment. Copyright © 2017 Elsevier B.V. All rights reserved.

Three-Dimensional Computed Tomography (3–D CT) for Evaluation and Management of Children with Complex Chest Wall Anomalies: Useful Information or Just Pretty Pictures?

PubMed Central

Calloway, E. Hollin; Chhotani, Ali N.; Lee, Yueh Z.; Phillips, J. Duncan

2013-01-01

Purpose Shaded Surface Display (SSD) technology, with 3-D CT reconstruction, has been reported in a few small series of patients with congenital or acquired chest wall deformities. SSD images are visually attractive and educational, but many institutions are hesitant to utilize these secondary to cost and image data storage concerns. This study was designed to assess the true value of SSD to the patient, family, and operating surgeon, in the evaluation and management of these children. Methods Following IRB approval, we performed a retrospective review of records of 82 patients with chest wall deformities, evaluated with SSD, from 2002 to 2009. SSD usefulness, when compared with routine 2-D CT, was graded on a strict numerical scale from 0 (added no value besides education for the patient/family) to 3 (critical for surgical planning and patient management). Results There were 56 males and 26 females. Median age was 15.3 years (range: 0.6–41.1). Deformities included 56 pectus excavatum, 19 pectus carinatum, and 8 other/mixed deformities. 6 patients also had acquired asphyxiating thoracic dystrophy (AATD). Eleven (13%) had previous chest wall reconstructive surgery. In 25 (30%) patients, SSD was useful or critical. Findings underappreciated on 2-D images included: sternal abnormalities (29), rib abnormalities (28), and heterotopic calcifications (7). SSD changed or influenced operation choice (4), clarified bone versus soft tissue (3), helped clarify AATD (3), and aided in rib graft evaluation (2). Point biserial correlation coefficient analysis (Rpb) displayed significance for SSD usefulness in patients with previous chest repair surgery (Rpb=0.48, p≤0.001), AATD (Rpb=0.34, p=0.001), pectus carinatum (Rpb=0.27, p=0.008), and females (Rpb=0.19, p=0.044). Conclusions Shaded Surface Display, when used to evaluate children and young adults with congenital or acquired chest wall deformities, provides useful or critical information for surgical planning and patient management in almost 1/3 of patients, especially those requiring a second operation, with acquired asphyxiating thoracic dystrophy, pectus carinatum, and females. PMID:21496531

Black Carbon Emissions from In-use Ships: Results from CalNex 2010

NASA Astrophysics Data System (ADS)

Buffaloe, Gina Marise

Black carbon (BC) mass emission factors (EFBC; g-BC (kg-fuel)--1) from a variety of ocean going vessels have been determined from measurements of BC and CO2 concentrations in ship plumes intercepted by the R/V Atlantis during the 2010 California Nexus (CalNex) campaign. The ships encountered were all operating within 24 nautical miles of the California coast and were utilizing relatively low sulphur fuels. Black carbon concentrations within the plumes, from which EFBC values are determined, were measured using four independent instruments: a photoacoustic spectrometer and a particle soot absorption photometer, which measure light absorption, and a single particle soot photometer and soot particle aerosol mass spectrometer, which measure the mass concentration of refractory BC directly. The measured EFBC have been divided into vessel type categories and engine type categories, from which averages have been determined. The geometric average EFBC, determined from over 71 vessels and 135 plumes encountered, was 0.31 g-BC (kg-fuel)--1. The most frequent engine type encountered was the slow speed diesel (SSD), and the most frequent SSD vessel type was the cargo ship sub-category. Average and median EF BC values from these two categories are compared to previous observations from the Texas Air Quality Study (TexAQS) in 2006, in which the ships encountered were predominately operating high sulphur fuels. There is some indication that the EFBC values for SSD vessels during CalNex were lower than during TexAQS, although ship-to-ship variability in these data sets makes it difficult to draw firm conclusions about the influence of fuel quality on EFBC.

Optical smoothing of laser imprinting in planar-target experiments on OMEGA EP using multi-FM 1-D smoothing by spectral dispersion

DOE PAGES

Hohenberger, M.; Shvydky, A.; Marozas, J. A.; ...

2016-09-07

Direct-drive ignition on the National Ignition Facility (NIF) requires single-beam smoothing to minimize imprinting of laser nonuniformities that can negatively affect implosion performance. One-dimensional, multi-FM smoothing by spectral dispersion (SSD) has been proposed to provide the required smoothing [J. A. Marozas, J. D. Zuegel, and T. J. B. Collins, Bull. Am. Phys. Soc. 55, 294 (2010)]. A prototype multi-FM SSD system has been integrated into the NIF-like beamline of the OMEGA EP Laser System. Experiments have been performed to verify the smoothing performance by measuring Rayleigh–Taylor growth rates in planar targets of laser-imprinted and preimposed surface modulations. Multi-FM 1-D SSDmore » has been observed to reduce imprint levels by ~50% compared to the nominal OMEGA EP SSD system. In conclusion, the experimental results are in agreement with 2-D DRACO simulations using realistic, time-dependent far-field spot-intensity calculations that emulate the effect of SSD.« less

Optical smoothing of laser imprinting in planar-target experiments on OMEGA EP using multi-FM 1-D smoothing by spectral dispersion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hohenberger, M.; Shvydky, A.; Marozas, J. A.

Direct-drive ignition on the National Ignition Facility (NIF) requires single-beam smoothing to minimize imprinting of laser nonuniformities that can negatively affect implosion performance. One-dimensional, multi-FM smoothing by spectral dispersion (SSD) has been proposed to provide the required smoothing [J. A. Marozas, J. D. Zuegel, and T. J. B. Collins, Bull. Am. Phys. Soc. 55, 294 (2010)]. A prototype multi-FM SSD system has been integrated into the NIF-like beamline of the OMEGA EP Laser System. Experiments have been performed to verify the smoothing performance by measuring Rayleigh–Taylor growth rates in planar targets of laser-imprinted and preimposed surface modulations. Multi-FM 1-D SSDmore » has been observed to reduce imprint levels by ~50% compared to the nominal OMEGA EP SSD system. In conclusion, the experimental results are in agreement with 2-D DRACO simulations using realistic, time-dependent far-field spot-intensity calculations that emulate the effect of SSD.« less

Resveratrol stimulates c-Fos gene transcription via activation of ERK1/2 involving multiple genetic elements.

PubMed

Thiel, Gerald; Rössler, Oliver G

2018-06-05

The polyphenol resveratrol is found in many plant and fruits and is a constituent of our diet. Resveratrol has been proposed to have chemopreventive and anti-inflammatory activities. On the cellular level, resveratrol activates stimulus-regulated transcription factors. To identify resveratrol-responsive elements within a natural gene promoter, the molecular pathway leading to c-Fos gene expression by resveratrol was dissected. The c-Fos gene encodes a basic region leucine zipper transcription factor and is a prototype of an immediate-early gene that is regulated by a wide range of signaling molecules. We analyzed chromatin-integrated c-Fos promoter-luciferase reporter genes where transcription factor binding sites were destroyed by point mutations or deletion mutagenesis. The results show that mutation of the binding sites for serum response factor (SRF), activator protein-1 (AP-1) and cAMP response element binding protein (CREB) significantly reduced reporter gene transcription following stimulation of the cells with resveratrol. Inactivation of the binding sites for signal transducer and activator of transcription (STAT) or ternary complex factors did not influence resveratrol-regulated c-Fos promoter activity. Thus, the c-Fos promoter contains three resveratrol-responsive elements, the cAMP response element (CRE), and the binding sites for SRF and AP-1. Moreover, we show that the transcriptional activation potential of the c-Fos protein is increased in resveratrol-stimulated cells, indicating that the biological activity of c-Fos is elevated by resveratrol stimulation. Pharmacological and genetic experiments revealed that the protein kinase ERK1/2 is the signal transducer that connects resveratrol treatment with the c-Fos gene. Copyright © 2018 Elsevier B.V. All rights reserved.

Sexual selection on male size drives the evolution of male-biased sexual size dimorphism via the prolongation of male development.

PubMed

Rohner, Patrick T; Blanckenhorn, Wolf U; Puniamoorthy, Nalini

2016-06-01

Sexual size dimorphism (SSD) arises when the net effects of natural and sexual selection on body size differ between the sexes. Quantitative SSD variation between taxa is common, but directional intraspecific SSD reversals are rare. We combined micro- and macroevolutionary approaches to study geographic SSD variation in closely related black scavenger flies. Common garden experiments revealed stark intra- and interspecific variation: Sepsis biflexuosa is monomorphic across the Holarctic, while S. cynipsea (only in Europe) consistently exhibits female-biased SSD. Interestingly, S. neocynipsea displays contrasting SSD in Europe (females larger) and North America (males larger), a pattern opposite to the geographic reversal in SSD of S. punctum documented in a previous study. In accordance with the differential equilibrium model for the evolution of SSD, the intensity of sexual selection on male size varied between continents (weaker in Europe), whereas fecundity selection on female body size did not. Subsequent comparative analyses of 49 taxa documented at least six independent origins of male-biased SSD in Sepsidae, which is likely caused by sexual selection on male size and mediated by bimaturism. Therefore, reversals in SSD and the associated changes in larval development might be much more common and rapid and less constrained than currently assumed. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Patterns of sexual size dimorphism in horseshoe bats: Testing Rensch's rule and potential causes.

PubMed

Wu, Hui; Jiang, Tinglei; Huang, Xiaobin; Feng, Jiang

2018-02-08

Rensch's rule, stating that sexual size dimorphism (SSD) becomes more evident and male-biased with increasing body size, has been well supported for taxa that exhibit male-biased SSD. Bats, primarily having female-biased SSD, have so far been tested for whether SSD allometry conforms to Rensch's rule in only three studies. However, these studies did not consider phylogeny, and thus the mechanisms underlying SSD variations in bats remain unclear. Thus, the present study reviewed published and original data, including body size, baculum size, and habitat types in 45 bats of the family Rhinolophidae to determine whether horseshoe bats follow Rensch's rule using a phylogenetic comparative framework. We also investigated the potential effect of postcopulatory sexual selection and habitat type on SSD. Our findings indicated that Rensch's rule did not apply to Rhinolophidae, suggesting that SSD did not significantly vary with increasing size. This pattern may be attributable interactions between weak sexual selection to male body size and strong fecundity selection for on female body size. The degree of SSD among horseshoe bats may be attributed to a phylogenetic effect rather than to the intersexual competition for food or to baculum length. Interestingly, we observed that species in open habitats exhibited greater SSD than those in dense forests, suggesting that habitat types may be associated with variations in SSD in horseshoe bats.

Effect of grinding parameters on surface roughness and subsurface damage and their evaluation in fused silica.

PubMed

Xiao, Huapan; Chen, Zhi; Wang, Hairong; Wang, Jiuhong; Zhu, Nan

2018-02-19

Based on micro-indentation mechanics and kinematics of grinding processes, theoretical formulas are deduced to calculate surface roughness (SR) and subsurface damage (SSD) depth. The SRs and SSD depths of a series of fused silica samples, which are prepared under different grinding parameters, are measured. By experimental and theoretical analysis, the relationship between SR and SSD depth is discussed. The effect of grinding parameters on SR and SSD depth is investigated quantitatively. The results show that SR and SSD depth decrease with the increase of wheel speed or the decrease of feed speed as well as cutting depth. The interaction effect between wheel speed and feed speed should be emphasized greatly. Furthermore, a relationship model between SSD depth and grinding parameters is established, which could be employed to evaluate SSD depth efficiently.

Risk of schizophrenia and minority status: a comparison of the Swedish-speaking minority and the Finnish-speaking majority in Finland

PubMed Central

Suvisaari, Jaana; Opler, Mark; Lindbohm, Marja-Liisa; Sallmén, Markku

2014-01-01

Approximately five percent of the Finnish population are Swedish-speaking and have higher socioeconomic position and longer life expectancy than the Finnish-speaking majority. Previous studies have not investigated whether Swedish-speaking Finns have lower risk of schizophrenia spectrum disorders (SSD) than Finnish-speaking Finns. We investigated this in a representative sample of 47 445 Finns born in 1972–1984. Hazard ratios of SSD between language groups were assessed with conditional proportional hazards regression. Sex, parental ages at birth, paternal employment around conception, parental psychosis and place and residence in the capital area were used as other explanatory variables. The prevalence of SSD was 0.7% in the Swedish-speaking minority and 1.5% in the Finnish-speaking majority. In the adjusted regression model, belonging to the Swedish-speaking minority was associated with lower risk of SSD (hazard ratio (HR) 0.41, 95% confidence interval (CI) 0.24–0.69). In a subset analysis by gender, the protective effect was evident among Swedish-speaking males (HR 0.32, 95% CI 0.15–0.68) but marginal in females (HR 0.75, 95% CI 0.41–1.37). Parental psychosis and place of birth in the capital area were associated with higher risk of SSD, whereas paternal employment at the time of conception was associated with lower risk of SSD. Our results support the role of social factors in the etiology of schizophrenia. Belonging to a minority with high socioeconomic status and social capital may be protective against schizophrenia, especially for males. PMID:25263996

Partial agonism at the α7 nicotinic acetylcholine receptor improves attention, impulsive action and vigilance in low attentive rats.

PubMed

Hayward, Andrew; Adamson, Lisa; Neill, Joanna C

2017-04-01

Inattention is a disabling symptom in conditions such as schizophrenia and attention deficit/hyperactivity disorder. Nicotine can improve attention and vigilance, but is unsuitable for clinical use due to abuse liability. Genetic knockout of the α7 nicotinic acetylcholine receptor (nAChR) induces attention deficits therefore selective agonism may improve attention, without the abuse liability associated with nicotine. The α7 nAChR partial agonist encenicline (formerly EVP-6124) enhances memory in rodents and humans. Here we investigate, for the first time, efficacy of encenicline to improve attention and vigilance in animals behaviourally grouped for low attentive traits in the 5 choice-continuous performance task (5C-CPT). Female Lister Hooded rats were trained to perform the 5C-CPT with a variable stimulus duration (SD). Animals were then grouped based on performance into upper and lower quartiles of d' (vigilance) and accuracy (selective attention), producing high-attentive (HA) and low-attentive (LA) groups. LA animals showed an increase in selective attention and vigilance at 0.3mg/kg encenicline, a reduction in impulsive action (probability of false alarms) and increase in vigilance following 1mg/kg at 0.75sSD. At 1mg/kg, HA animals had reduced selective attention at 0.75sSD and reduced vigilance at 0.75 and 1.25sSD. Improvement of attention, vigilance and impulsive action in LA animals demonstrates that encenicline has pro-attentive properties dependent on baseline levels of performance. Our work suggests that α7 nAChR partial agonism may improve attention particularly in conditions with low attention. Copyright © 2017 Elsevier B.V. and ECNP. All rights reserved.

DSM-5 illness anxiety disorder and somatic symptom disorder: Comorbidity, correlates, and overlap with DSM-IV hypochondriasis.

PubMed

Newby, Jill M; Hobbs, Megan J; Mahoney, Alison E J; Wong, Shiu Kelvin; Andrews, Gavin

2017-10-01

To investigate the reliability, validity and utility of DSM-5 illness anxiety disorder (IAD) and somatic symptom disorder (SSD), and explore their overlap with DSM-IV Hypochondriasis in a health anxious sample. Treatment-seeking patients with health anxiety (N=118) completed structured diagnostic interviews to assess DSM-IV Hypochondriasis, DSM-5 IAD, SSD, and comorbid mental disorders, and completed self-report measures of health anxiety, comorbid symptoms, cognitions and behaviours, and service utilization. IAD and SSD were more reliable diagnoses than Hypochondriasis (kappa estimates: IAD: 0.80, SSD: 0.92, Hypochondriasis: 0.60). 45% of patients were diagnosed with SSD, 47% with IAD, and 8% with comorbid IAD/SSD. Most patients with IAD fluctuated between seeking and avoiding care (61%), whereas care-seeking (25%) and care-avoidant subtypes were less common (14%). Half the sample met criteria for DSM-IV Hypochondriasis; of those, 56% met criteria for SSD criteria, 36% for IAD, and 8% for comorbid IAD/SSD. Compared to IAD, SSD was characterized by more severe health anxiety, somatic symptoms, depression, and higher health service use, and higher rates of major depressive disorder, panic disorder and agoraphobia. DSM-5 IAD and SSD classifications reliably detect more cases of clinically significant health anxiety than DSM-IV Hypochondriasis. The differences between IAD and SSD appear to be due to severity. Future research should explore the generalizability of these findings to other samples, and whether diagnostic status predicts treatment response and long-term outcome. Copyright © 2017 Elsevier Inc. All rights reserved.

VpRFP1, a novel C4C4-type RING finger protein gene from Chinese wild Vitis pseudoreticulata, functions as a transcriptional activator in defence response of grapevine

PubMed Central

Yu, Yihe; Xu, Weirong; Wang, Shengyi; Xu, Yan; Li, Hui'e; Wang, Yuejin; Li, Shuxiu

2011-01-01

RING finger proteins comprise a large family and play important roles in regulation of growth and development, hormone signalling, and responses to biotic and abiotic stresses in plants. In this study, the identification and functional characterization of a C4C4-type RING finger protein gene from the Chinese wild grapevine Vitis pseudoreticulata (designated VpRFP1) are reported. VpRFP1 was initially identified as an expressed sequence tag (EST) from a cDNA library constructed from leaves of V. pseudoreticulata inoculated with the grapevine powdery mildew Uncinula necator. Sequence analysis of the deduced VpRFP1 protein based on the full-length cDNA revealed an N-terminal nuclear localization signal (NLS) and a C-terminal C4C4-type RING finger motif with the consensus sequence Cys-X2-Cys-X13-Cys-X1-Cys-X4-Cys-X2-Cys-X10-Cys-X2-Cys. Upon inoculation with U. necator, expression of VpRFP1 was rapidly induced to higher levels in mildew-resistant V. pseudoreticulata plants. In contrast, expression of VpRFP1 was down-regulated in mildew-susceptible V. vinifera plants. Western blotting using an antibody raised against VpRFP1 showed that VpRFP1 was also induced to higher levels in V. pseudoreticulata plants at 12–48 hours post-inoculation (hpi). However, there was only slight increase in VpRFP in V. vinifera plants in the same time frame, even though a more significant increase was observed at 96–144 hpi in these plants. Results from transactivation assays in yeast showed that the RING finger motif of VpRFP1 exhibited some activity of transcriptional activation; however, no activity was seen with the full-length VpRFP1. Overexpression of VpRFP1 in Arabidopsis plants was found to enhance resistance to Arabidopsis powdery mildew Golovinomyces cichoracearum, which seemed to be correlated with increased transcript levels of AtPR1 and AtPR2 in the pathogen-infected tissues. In addition, the Arabidopsis transgenic lines showed enhanced resistance to a virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Taken together, the results suggested that VpRFP1 may be a transcriptional activator of defence-related genes in grapevines. PMID:21862480

Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues.

PubMed

Peyer, Suzanne M; Pankey, M Sabrina; Oakley, Todd H; McFall-Ngai, Margaret J

2014-02-01

The squid Euprymna scolopes has evolved independent sets of tissues capable of light detection, including a complex eye and a photophore or 'light organ', which houses the luminous bacterial symbiont Vibrio fischeri. As the eye and light organ originate from different embryonic tissues, we examined whether the eye-specification genes, pax6, eya, six, and dac, are shared by these two organs, and if so, whether they are regulated in the light organ by symbiosis. We obtained sequences of the four genes with PCR, confirmed orthology with phylogenetic analysis, and determined that each was expressed in the eye and light organ. With in situ hybridization (ISH), we localized the gene transcripts in developing embryos, comparing the patterns of expression in the two organs. The four transcripts localized to similar tissues, including those associated with the visual system ∼1/4 into embryogenesis (Naef stage 18) and the light organ ∼3/4 into embryogenesis (Naef stage 26). We used ISH and quantitative real-time PCR to examine transcript expression and differential regulation in postembryonic light organs in response to the following colonization conditions: wild-type, luminescent V. fischeri; a mutant strain defective in light production; and as a control, no symbiont. In ISH experiments light organs showed down regulation of the pax6, eya, and six transcripts in response to wild-type V. fischeri. Mutant strains also induced down regulation of the pax6 and eya transcripts, but not of the six transcript. Thus, luminescence was required for down regulation of the six transcript. We discuss these results in the context of symbiont-induced light-organ development. Our study indicates that the eye-specification genes are expressed in light-interacting tissues independent of their embryonic origin and are capable of responding to bacterial cues. These results offer evidence for evolutionary tinkering or the recruitment of eye development genes for use in a light-sensing photophore. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

The FOX transcription factor Hcm1 regulates oxidative metabolism in response to early nutrient limitation in yeast. Role of Snf1 and Tor1/Sch9 kinases.

PubMed

Rodríguez-Colman, María José; Sorolla, M Alba; Vall-Llaura, Núria; Tamarit, Jordi; Ros, Joaquim; Cabiscol, Elisa

2013-08-01

Within Saccharomyces cerevisiae, Hcm1is a member of the forkhead transcription factor family with a role in chromosome organization. Our group recently described its involvement in mitochondrial biogenesis and stress resistance, and reports here that Hcm1 played a role in adaptation to respiratory metabolism when glucose or nitrogen was decreased. Regulation of Hcm1 activity occurs in at least three ways: i) protein quantity, ii) subcellular localization, and iii) transcriptional activity. Transcriptional activity was measured using a reporter gene fused to a promoter that contains a binding site for Hcm1. We also analyzed the levels of several genes whose expression is known to be regulated by Hcm1 levels and the role of the main kinases known to respond to nutrients. Lack of sucrose-nonfermenting (Snf1) kinase increases cytoplasmic localization of Hcm1, whereas Δtor1 cells showed a mild increase in nuclear Hcm1. In vitro experiments showed that Snf1 clearly phosphorylates Hcm1 while Sch9 exerts a milder phosphorylation. Although in vitroTor1 does not directly phosphorylate Hcm1, in vivo rapamycin treatment increases nuclear Hcm1. We conclude that Hcm1 participates in the adaptation of cells from fermentation to respiratory metabolism during nutrient scarcity. According to our hypothesis, when nutrient levels decrease, Snf1 phosphorylates Hcm1. This results in a shift from the cytoplasm to the nucleus and increased transcriptional activity of genes involved in respiration, use of alternative energy sources, NAD synthesis and oxidative stress resistance. Copyright © 2013 Elsevier B.V. All rights reserved.

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data.

PubMed

Zhou, Ke-Ren; Liu, Shun; Sun, Wen-Ju; Zheng, Ling-Ling; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

2017-01-04

The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version. We identified thousands of binding motif matrices and their binding sites from ChIP-seq data of DNA-binding proteins and predicted millions of transcriptional regulatory relationships between transcription factors (TFs) and genes. We constructed 'Regulator' module to predict hundreds of TFs and histone modifications that were involved in or affected transcription of ncRNAs and PCGs. Moreover, we built a web-based tool, Co-Expression, to explore the co-expression patterns between DNA-binding proteins and various types of genes by integrating the gene expression profiles of ∼10 000 tumor samples and ∼9100 normal tissues and cell lines. ChIPBase also provides a ChIP-Function tool and a genome browser to predict functions of diverse genes and visualize various ChIP-seq data. This study will greatly expand our understanding of the transcriptional regulations of ncRNAs and PCGs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DCGL v2.0: an R package for unveiling differential regulation from differential co-expression.

PubMed

Yang, Jing; Yu, Hui; Liu, Bao-Hong; Zhao, Zhongming; Liu, Lei; Ma, Liang-Xiao; Li, Yi-Xue; Li, Yuan-Yuan

2013-01-01

Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner. To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp.

A Comparison of the Metalinguistic Performance and Spelling Development of Children With Inconsistent Speech Sound Disorder and Their Age-Matched and Reading-Matched Peers.

PubMed

McNeill, Brigid C; Wolter, Julie; Gillon, Gail T

2017-05-17

This study explored the specific nature of a spelling impairment in children with speech sound disorder (SSD) in relation to metalinguistic predictors of spelling development. The metalinguistic (phoneme, morphological, and orthographic awareness) and spelling development of 28 children ages 6-8 years with a history of inconsistent SSD were compared to those of their age-matched (n = 28) and reading-matched (n = 28) peers. Analysis of the literacy outcomes of children within the cohort with persistent (n = 18) versus resolved (n = 10) SSD was also conducted. The age-matched peers outperformed the SSD group on all measures. Children with SSD performed comparably to their reading-matched peers on metalinguistic measures but exhibited lower spelling scores. Children with persistent SSD generally had less favorable outcomes than children with resolved SSD; however, even children with resolved SSD performed poorly on normative spelling measures. Children with SSD have a specific difficulty with spelling that is not commensurate with their metalinguistic and reading ability. Although low metalinguistic awareness appears to inhibit these children's spelling development, other factors should be considered, such as nonverbal rehearsal during spelling attempts and motoric ability. Integration of speech-production and spelling-intervention goals is important to enhance literacy outcomes for this group.

Size-dependent selective mechanisms on males and females and the evolution of sexual size dimorphism in frogs.

PubMed

Nali, Renato C; Zamudio, Kelly R; Haddad, Célio F B; Prado, Cynthia P A

2014-12-01

Sexual size dimorphism (SSD) varies in animals from male biased to female biased. The evolution of SSD is potentially influenced by a number of factors, such as territoriality, fecundity, and temporal breeding patterns (explosive vs. prolonged). In general, frogs show female-biased SSD with broad variance among species. Using comparative methods, we examine how different selective forces affect male and female sizes, and we test hypotheses about size-dependent mechanisms shaping SSD in frogs. Male size was weakly associated with SSD in all size classes, and we found no significant association among SSD, male size, temporal breeding pattern, and male territoriality. In contrast, female size best explained SSD variation across all size classes but especially for small-bodied species. We found a stronger evolutionary association between female body size and fecundity, and this fecundity advantage was highest in explosively breeding species. Our data indicate that the fecundity advantage associated with female body size may not be linear, such that intermediate and large females benefit less with body size increases. Therefore, size-dependent selection in females associated with fecundity and breeding patterns is an important mechanism driving SSD evolution in frogs. Our study underscores the fact that lineage-specific ecology and behavior should be incorporated in comparative analyses of animal SSD.

Topical silver sulfadiazine vs collagenase ointment for the treatment of partial thickness burns in children: a prospective randomized trial.

PubMed

Ostlie, Daniel J; Juang, David; Aguayo, Pablo; Pettiford-Cunningham, Janine P; Erkmann, Erin A; Rash, Diane E; Sharp, Susan W; Sharp, Ronald J; St Peter, Shawn D

2012-06-01

The 2 most commonly used topical agents for partial thickness burns are silver sulfadiazine (SSD) and collagenase ointment (CO). Silver sulfadiazine holds antibacterial properties, and eschar separation occurs naturally. Collagenase ointment is an enzyme that cleaves denatured collagen facilitating separation but has no antibacterial properties. Currently, there are no prospective comparative data in children for these 2 agents. Therefore, we conducted a prospective randomized trial. After institutional review board approval, patients were randomized to daily debridement with SSD or CO. Primary outcome was the need for skin grafting. Patients were treated for 2 days with SSD with subsequent randomization. Polymyxin was mixed with CO for antibacterial coverage. Debridements were performed daily for 10 days or until the burn healed. Grafting was performed after 10 days if not healed. From January 2008 to January 2011, 100 patients were enrolled, with no differences in patient characteristics. There were no differences in clinical course, outcome, or need for skin grafting. Wound infections occurred in 7 patients treated with CO and 1 patient treated with SSD (P = .06). Collagenase ointment was more expensive than SSD (P < .001). However, total hospital charges did not differ. There are no differences in outcomes between topical SSD or CO in the management of childhood burns results. Copyright © 2012 Elsevier Inc. All rights reserved.

Fricative Contrast and Coarticulation in Children With and Without Speech Sound Disorders

PubMed Central

Mailend, Marja-Liisa

2017-01-01

Purpose The purpose of this study was, first, to expand our understanding of typical speech development regarding segmental contrast and anticipatory coarticulation, and second, to explore the potential diagnostic utility of acoustic measures of fricative contrast and anticipatory coarticulation in children with speech sound disorders (SSD). Method In a cross-sectional design, 10 adults, 17 typically developing children, and 11 children with SSD repeated carrier phrases with novel words with fricatives (/s/, /ʃ/). Dependent measures were 2 ratios derived from spectral mean, obtained from perceptually accurate tokens. Group analyses compared adults and typically developing children; individual children with SSD were compared to their respective typically developing peers. Results Typically developing children demonstrated smaller fricative acoustic contrast than adults but similar coarticulatory patterns. Three children with SSD showed smaller fricative acoustic contrast than their typically developing peers, and 2 children showed abnormal coarticulation. The 2 children with abnormal coarticulation both had a clinical diagnosis of childhood apraxia of speech; no clear pattern was evident regarding SSD subtype for smaller fricative contrast. Conclusions Children have not reached adult-like speech motor control for fricative production by age 10 even when fricatives are perceptually accurate. Present findings also suggest that abnormal coarticulation but not reduced fricative contrast is SSD-subtype–specific. Supplemental Materials S1: https://doi.org/10.23641/asha.5103070. S2 and S3: https://doi.org/10.23641/asha.5106508 PMID:28654946

Sensory substitution information informs locomotor adjustments when walking through apertures.

PubMed

Kolarik, Andrew J; Timmis, Matthew A; Cirstea, Silvia; Pardhan, Shahina

2014-03-01

The study assessed the ability of the central nervous system (CNS) to use echoic information from sensory substitution devices (SSDs) to rotate the shoulders and safely pass through apertures of different width. Ten visually normal participants performed this task with full vision, or blindfolded using an SSD to obtain information regarding the width of an aperture created by two parallel panels. Two SSDs were tested. Participants passed through apertures of +0, +18, +35 and +70 % of measured body width. Kinematic indices recorded movement time, shoulder rotation, average walking velocity across the trial, peak walking velocities before crossing, after crossing and throughout a whole trial. Analyses showed participants used SSD information to regulate shoulder rotation, with greater rotation associated with narrower apertures. Rotations made using an SSD were greater compared to vision, movement times were longer, average walking velocity lower and peak velocities before crossing, after crossing and throughout the whole trial were smaller, suggesting greater caution. Collisions sometimes occurred using an SSD but not using vision, indicating that substituted information did not always result in accurate shoulder rotation judgements. No differences were found between the two SSDs. The data suggest that spatial information, provided by sensory substitution, allows the relative position of aperture panels to be internally represented, enabling the CNS to modify shoulder rotation according to aperture width. Increased buffer space indicated by greater rotations (up to approximately 35 % for apertures of +18 % of body width) suggests that spatial representations are not as accurate as offered by full vision.

The influence of schizotypal traits on attention under high perceptual load.

PubMed

Stotesbury, Hanne; Gaigg, Sebastian B; Kirhan, Saim; Haenschel, Corinna

2018-03-01

Schizophrenia Spectrum Disorders (SSD) are known to be characterised by abnormalities in attentional processes, but there are inconsistencies in the literature that remain unresolved. This article considers whether perceptual resource limitations play a role in moderating attentional abnormalities in SSD. According to perceptual load theory, perceptual resource limitations can lead to attenuated or superior performance on dual-task paradigms depending on whether participants are required to process, or attempt to ignore, secondary stimuli. If SSD is associated with perceptual resource limitations, and if it represents the extreme end of an otherwise normally distributed neuropsychological phenotype, schizotypal traits in the general population should lead to disproportionate performance costs on dual-task paradigms as a function of the perceptual task demands. To test this prediction, schizotypal traits were quantified via the Schizotypal Personality Questionnaire (SPQ) in 74 healthy volunteers, who also completed a dual-task signal detection paradigm that required participants to detect central and peripheral stimuli across conditions that varied in the overall number of stimuli presented. The results confirmed decreasing performance as the perceptual load of the task increased. More importantly, significant correlations between SPQ scores and task performance confirmed that increased schizotypal traits, particularly in the cognitive-perceptual domain, are associated with greater performance decrements under increasing perceptual load. These results confirm that attentional difficulties associated with SSD extend sub-clinically into the general population and suggest that cognitive-perceptual schizotypal traits may represent a risk factor for difficulties in the regulation of attention under increasing perceptual load.

Enhancing E. coli isobutanol tolerance through engineering its global transcription factor cAMP receptor protein (CRP).

PubMed

Chong, Huiqing; Geng, Hefang; Zhang, Hongfang; Song, Hao; Huang, Lei; Jiang, Rongrong

2014-04-01

The limited isobutanol tolerance of Escherichia coli is a major drawback during fermentative isobutanol production. Different from classical strain engineering approaches, this work was initiated to improve E. coli isobutanol tolerance from its transcriptional level by engineering its global transcription factor cAMP receptor protein (CRP). Random mutagenesis libraries were generated by error-prone PCR of crp, and the libraries were subjected to isobutanol stress for selection. Variant IB2 (S179P, H199R) was isolated and exhibited much better growth (0.18 h(-1) ) than the control (0.05 h(-1) ) in 1.2% (v/v) isobutanol (9.6 g/L). Genome-wide DNA microarray analysis revealed that 58 and 308 genes in IB2 had differential expression (>2-fold, p < 0.05) in the absence and presence of 1% (v/v) isobutanol, respectively. When challenged with isobutanol, genes related to acid resistance (gadABCE, hdeABD), nitrate reduction (narUZYWV), flagella and fimbrial activity (lfhA, yehB, ycgR, fimCDF), and sulfate reduction and transportation (cysIJH, cysC, cysN) were the major functional groups that were up-regulated, whereas most of the down-regulated genes were enzyme (tnaA) and transporters (proVWX, manXYZ). As demonstrated by single-gene knockout experiments, gadX, nirB, rhaS, hdeB, and ybaS were found associated with strain isobutanol resistance. The intracellular reactive oxygen species (ROS) level in IB2 was only half of that of the control when facing stress, indicating that IB2 can withstand toxic isobutanol much better than the control. © 2013 Wiley Periodicals, Inc.

FlrA, a σ54-Dependent Transcriptional Activator in Vibrio fischeri, Is Required for Motility and Symbiotic Light-Organ Colonization

PubMed Central

Millikan, Deborah S.; Ruby, Edward G.

2003-01-01

Flagellum-mediated motility of Vibrio fischeri is an essential factor in the bacterium's ability to colonize its host, the Hawaiian squid Euprymna scolopes. To begin characterizing the nature of the flagellar regulon, we have cloned a gene, designated flrA, from V. fischeri that encodes a putative σ54-dependent transcriptional activator. Genetic arrangement of the flrA locus in V. fischeri is similar to motility master-regulator operons of Vibrio cholerae and Vibrio parahaemolyticus. In addition, examination of regulatory regions of a number of flagellar operons in V. fischeri revealed apparent σ54 recognition motifs, suggesting that the flagellar regulatory hierarchy is controlled by a similar mechanism to that described in V. cholerae. However, in contrast to its closest known relatives, flrA mutant strains of V. fischeri ES114 were completely abolished in swimming capability. Although flrA provided in trans restored motility to the flrA mutant, the complemented strain was unable to reach wild-type levels of symbiotic colonization in juvenile squid, suggesting a possible role for the proper expression of FlrA in regulating symbiotic colonization factors in addition to those required for motility. Comparative RNA arbitrarily primed PCR analysis of the flrA mutant and its wild-type parent revealed several differentially expressed transcripts. These results define a regulon that includes both flagellar structural genes and other genes apparently not involved in flagellum elaboration or function. Thus, the transcriptional activator FlrA plays an essential role in regulating motility, and apparently in modulating other symbiotic functions, in V. fischeri. PMID:12775692

The role of silver sulphadiazine in the conservative treatment of partial thickness burn wounds: A systematic review.

PubMed

Heyneman, A; Hoeksema, H; Vandekerckhove, D; Pirayesh, A; Monstrey, S

2016-11-01

For more than 40 years, silver sulphadiazine 1% (SSD) is considered as standard therapy for the conservative treatment of burn wounds. However, in the last 10 years, substantial disadvantages of SSD have been reported in the literature and probably as a result of this, several new dressings for burn wounds have been developed and put on the market. The objective of this systematic review is to evaluate the available evidence on SSD in the conservative treatment of burns, specifically in comparison with the newer burn dressings that are increasingly being used nowadays. A search filter was composed to select randomized controlled trials (RCTs) from the MEDLINE database. Only RCTs studying the effect of conservative treatment on burns were selected. At least one of the two comparative groups was treated with SSD. Each included article was analysed and relevant data (baseline parameters, interventions, outcomes and methodological parameters) were registered using Microsoft Office Excel 2007. Many dressings showed superior healing properties compared to SSD, but no dressing was able to show a clear benefit over SSD regarding infection. The number of dressing changes, pain and patient's satisfaction are more favourable in the newer dressings, especially with solid and biological dressings. The results of this systematic review clearly demonstrate that a faster wound healing is obtained with the newly developed burn dressings. Additionally, these new dressings tend to be more comfortable for the patients and easier to use for care givers. The minor differences in antibacterial activity between SSD and the new products did not seem to have any influence on the rate of wound healing. Since rapid wound closure is essential to obtain an optimal functional and aesthetic outcome, it can be concluded from the results of this systemic review that the standard use of SSD in the conservative treatment of burn wounds can no longer be supported. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

NRL SSD Research Achievements: 19701980. Volume 2

DTIC Science & Technology

2015-10-30

Astronomy Observatory (HEAO-1) was launched, which carried the very large NRL SSD Large Area Sky Survey (LASS) experiment (HEAO-1 A1). These X-ray...overview of this research. High energy space environment research was fundamentally advanced in the 1970’s. The first High Energy Astronomy ...larger than any previously flown X-ray astronomy spacecraft, and the X-ray detectors provided the most comprehensive X-ray catalogue of astrophysical

Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs.

PubMed

Imamura, Katsutoshi; Takaya, Akiko; Ishida, Yo-Ichi; Fukuoka, Yayoi; Taya, Toshiki; Nakaki, Ryo; Kakeda, Miho; Imamachi, Naoto; Sato, Aiko; Yamada, Toshimichi; Onoguchi-Mizutani, Rena; Akizuki, Gen; Tanu, Tanzina; Tao, Kazuyuki; Miyao, Sotaro; Suzuki, Yutaka; Nagahama, Masami; Yamamoto, Tomoko; Jensen, Torben Heick; Akimitsu, Nobuyoshi

2018-06-07

Cytoplasmic mRNA degradation controls gene expression to help eliminate pathogens during infection. However, it has remained unclear whether such regulation also extends to nuclear RNA decay. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection. © 2018 The Authors.

Leptin attenuates BACE1 expression and amyloid-β genesis via the activation of SIRT1 signaling pathway.

PubMed

Marwarha, Gurdeep; Raza, Shaneabbas; Meiers, Craig; Ghribi, Othman

2014-09-01

The aspartyl protease β-site AβPP-cleaving enzyme 1 (BACE1) catalyzes the rate-limiting step in Aβ production, a peptide at the nexus of neurodegenerative cascades in Alzheimer Disease (AD). The adipocytokine leptin has been demonstrated to reduce Aβ production and decrease BACE1 activity and expression levels. However, the signaling cascades involved in the leptin-induced mitigation in Aβ levels and BACE1 expression levels have not been elucidated. We have demonstrated that the transcription factor nuclear factor - kappa B (NF-κB) positively regulates BACE1 transcription. NF-κB activity is tightly regulated by the mammalian sirtuin SIRT1. Multiple studies have cogently evinced that leptin activates the metabolic master regulator SIRT1. In this study, we determined the extent to which SIRT1 expression and activity regulate the leptin-induced attenuation in BACE1 expression and Aβ levels in cultured human neuroblastoma SH-SY5Y cells. This study also elucidated and delineated the signal transduction pathways involved in the leptin induced mitigation in BACE1 expression. Our results demonstrate for the first time that leptin attenuates the activation and transcriptional activity of NF-κB by reducing the acetylation of the p65 subunit in a SIRT1-dependent manner. Furthermore, our data shows that leptin reduces the NF-κB-mediated transcription of BACE1 and consequently reduces Amyloid-β genesis. Our study provides a valuable insight and a novel mechanism by which leptin reduces BACE1 expression and Amyloid-β production and may help design potential therapeutic interventions. Copyright © 2014 Elsevier B.V. All rights reserved.

Speech-Sound Disorders and Attention-Deficit/Hyperactivity Disorder Symptoms

ERIC Educational Resources Information Center

Lewis, Barbara A.; Short, Elizabeth J.; Iyengar, Sudha K.; Taylor, H. Gerry; Freebairn, Lisa; Tag, Jessica; Avrich, Allison A.; Stein, Catherine M.

2012-01-01

Purpose: The purpose of this study was to examine the association of speech-sound disorders (SSD) with symptoms of attention-deficit/hyperactivity disorder (ADHD) by the severity of the SSD and the mode of transmission of SSD within the pedigrees of children with SSD. Participants and Methods: The participants were 412 children who were enrolled…

The Healing Effect of Arnebia Euchroma Ointment versus Silver Sulfadiazine on Burn Wounds in Rat

PubMed Central

Nasiri, Ebrahim; Hosseinimehr, Seyed Jalal; Azadbakht, Mohammad; Akbari, Jafar; Enayati-Fard, Reza; Azizi, Sohail; Azadbakht, Masoud

2015-01-01

BACKGROUND Burn is still a majordevastating condition in emergency medicine departments among both genders and all age groups in all developed and developing countries, leading to physical, psychological scars and economical burden. The present study aimed to determine the healing effect of topical treatment with Arnebia euchroma on second-degree burn wound in rats. METHODS Fifty rats were divided into 4 equal groups receiving the ointment base, normal saline (NS), standard 1% silver sulfadiazine (SSD), and 5% and 10% Arnebia euchroma ointments (AEO). The mean of burn area, percentage of wound contraction, histopathological and bacteriological assessments in the injured area were dtermined during the study. RESULTS Average area of wound on the 10th day was 10.2±2.3, 8.4±2.6, 12.4±2.5, 5.9±2.2 and 5.7±2 cm2 for ointment base, NS, 1% SSD, and 5% and 10% AEO, respectively. Wound size was significantly lower in 10% AEO than 1% SSD and control groups on the 10th day post-burn injury. On day 11, the percentage of wound contraction in 5% and 10% AEO was 53.9%±14.7% and 55.9±10.5% which was more than 1% SSD (15.3±10.8%). The collagen fibers were well formed and horizontally-oriented in 5% and 10% AEO groups when compared with other groups. CONCLUSION Arnebia euchroma ointment was an effective treatment for healing of burn wounds in comparison with SSD and can be regarded as an alternative topical treatment for burn wounds. PMID:26284182

The Wilms tumor protein WT1 stimulates transcription of the gene encoding insulin-like growth factor binding protein 5 (IGFBP5).

PubMed

Müller, Miriam; Persson, Anja Bondke; Krueger, Katharina; Kirschner, Karin M; Scholz, Holger

2017-07-01

Insulin-like growth factor (IGF) binding proteins (IGFBPs) constitute a family of six secreted proteins that regulate the signaling of insulin-like growth factors (IGFs). IGFBP5 is the most conserved family member in vertebrates and the major IGF binding protein in bone. IGFBP5 is required for normal development of the musculoskeletal system, and various types of cancer frequently express high levels of IGFP5. Here we identify the gene encoding IGFBP5 as a novel downstream target of the Wilms tumor protein WT1. IGFBP5 and WT1 are expressed in an overlapping pattern in the condensing metanephric mesenchyme of embryonic murine kidneys. Down-regulation of WT1 by transfection with antisense vivo-morpholino significantly decreased Igfbp5 transcripts in murine embryonic kidney explants. Likewise, silencing of Wt1 in a mouse mesonephros-derived cell line reduced Igfbp5 mRNA levels by approximately 80%. Conversely, induction of the WT1(-KTS) isoform, whose role as transcriptional regulator has been firmly established, significantly increased IGFBP5 mRNA and protein levels in osteosarcoma cells. IGFBP5 expression was not significantly changed by WT1(+KTS) protein, which exhibits lower DNA binding affinity than the WT1(-KTS) isoform and has a presumed role in post-transcriptional gene regulation. Luciferase reporter constructs harboring 0.8 and 1.6 kilobases of the murine Igfbp5 promoter, respectively, were stimulated approximately 5-fold by co-transfection of WT1(-KTS). The WT1(+KTS) variant had no significant effect on IGFBP5 promoter activity. Binding of WT1(-KTS), but not of WT1(+KTS) protein, to the IGFBP5 promoter in human osteosarcoma cells was proven by chromatin immunoprecipitation (ChIP) and confirmed by electrophoretic mobility shift assay. These findings demonstrate that WT1 activates transcription of the IGFBP5 gene with possible implications for kidney development and bone (patho)physiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Epigenetic regulation of the NR4A orphan nuclear receptor NOR1 by histone acetylation.

PubMed

Zhao, Yue; Nomiyama, Takashi; Findeisen, Hannes M; Qing, Hua; Aono, Jun; Jones, Karrie L; Heywood, Elizabeth B; Bruemmer, Dennis

2014-12-20

The nuclear receptor NOR1 is an immediate-early response gene implicated in the transcriptional control of proliferation. Since the expression level of NOR1 is rapidly induced through cAMP response element binding (CREB) protein-dependent promoter activation, we investigated the contribution of histone acetylation to this transient induction. We demonstrate that NOR1 transcription is induced by histone deacetylase (HDAC) inhibition and by depletion of HDAC1 and HDAC3. HDAC inhibition activated the NOR1 promoter, increased histone acetylation and augmented the recruitment of phosphorylated CREB to the promoter. Furthermore, HDAC inhibition increased Ser133 phosphorylation of CREB and augmented NOR1 protein stability. These data outline previously unrecognized mechanisms of NOR1 regulation and illustrate a key role for histone acetylation in the rapid induction of NOR1. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Healing of burn wounds by topical treatment: A randomized controlled comparison between silver sulfadiazine and nano-crystalline silver

PubMed Central

Adhya, Abhishek; Bain, Jayanta; Ray, Oindri; Hazra, Avijit; Adhikari, Souvik; Dutta, Gouranga; Ray, Sudhin; Majumdar, Bijay Kumar

2014-01-01

Background: Silver sulfadiazine (SSD) has been the standard topical antimicrobial for burn wounds for decades. Recently, nanometer-sized silver particles are available which have high surface to volume ratio and remain effective even at a very low concentration and minimizes the chance for tissue toxicity due to silver. Hence, we conducted a randomized controlled trial to compare the effectiveness of topical SSD and nano-crystalline silver (AgNP) hydrogel in burn wounds management. Materials and Methods: Study was conducted in the Burn Unit of IPGME&R & SSKM Hospital Calcutta, from January 2011 to August 2012. Patients with 2° burn injury were randomly allocated to SSD and AgNP treatment group. Clinical assessments of burn wound were done on every week till 4th week and on completion of treatment. Results: Data for evaluation were obtained for 54 patients on SSD (2° deep-dermal cases 27) and 52 (2° deep-dermal cases 31) on AgNP treatment. Healing status of 2° deep-dermal burns was more satisfactory for AgNP group than SSD treatment at 4 weeks. Among patients receiving AgNP, 80.6% showed at least 50% healing of 2° deep-dermal wounds compared to 48.1% on SSD at 4 weeks (P = 0.001). The figures for complete healing at 4 weeks were, respectively, 4% and 0% (P = 0.116). Conclusions: AgNP can be an effective and superior alternative to SSD for burn wounds, particularly 2° deep-dermal burns. Healing can be expected, in general, in 6 to 8 weeks time, depending upon the extent of body surface involvement. PMID:25538469

FTO promotes SREBP1c maturation and enhances CIDEC transcription during lipid accumulation in HepG2 cells.

PubMed

Chen, Ao; Chen, Xiaodong; Cheng, Shiqiang; Shu, Le; Yan, Meiping; Yao, Lun; Wang, Binyu; Huang, Shuguang; Zhou, Lei; Yang, Zaiqing; Liu, Guoquan

2018-05-01

The fat mass and obesity-associated (FTO) gene is tightly related to body weight and fat mass, and plays a pivotal role in regulating lipid accumulation in hepatocytes. However, the mechanisms underlying its function are poorly understood. Sterol regulatory element binding protein-1c (SREBP1c) is a transcription factor that regulates lipogenesis. Cell death-inducing DFFA (DNA fragmentation factor-α)-like effector c (CIDEC) plays a crucial role in lipid droplets (LDs) size controlling and lipid accumulation. In this report, we first observed that FTO overexpression in HepG2 cells resulted in an increase of lipogenesis and up-regulation of SREBP1c and CIDEC, two key regulatory factors in lipogenesis. In contrast, FTO knockdown in HepG2 cells resulted in a decrease of lipogenesis and down-regulation of SREBP1c and CIDEC expression. Moreover, SREBP1c knockdown resulted in a decrease of lipogenesis in HepG2 cells with FTO overexpression. In addition, FTO demethylation defect mutant presented less transcription of the key genes, and less nuclear translocation and maturation of SREBP1c. Further investigation demonstrated that overexpression of SREBP1c in HepG2 cells also promoted high CIDEC expression. Luciferase reporter assays showed that SREBP1c significantly stimulated CIDEC gene promoter activity. Finally, CIDEC knockdown reduced SREBP1c-induced lipogenesis. In conclusion, our studies suggest that FTO increased the lipid accumulation in hepatocytes by increasing nuclear translocation of SREBP1c and SREBP1c maturation, thus improving the transcriptional activity of LD-associated protein CIDEC. Our studies may provide new mechanistic insight into nonalcoholic fatty liver disease (NAFLD) mediated by FTO. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

The association between MR T1ρ and T2 of cartilage and patient-reported outcomes after ACL injury and reconstruction.

PubMed

Su, F; Pedoia, V; Teng, H-L; Kretzschmar, M; Lau, B C; McCulloch, C E; Link, T M; Ma, C B; Li, X

2016-07-01

To determine if cartilage T1ρ and T2 relaxation time measures after ACL injury and prior to reconstruction (baseline) are associated with patient-reported outcomes at baseline, 6-months, and 1-year after surgery. Fifty-four ACL-injured participants were scanned in both knees at baseline using 3T MR T1ρ and T2 mapping. Participants also completed Knee-injury and Osteoarthritis Outcome Score (KOOS) and Marx activity level questionnaires at baseline, 6-months, and 1-year after reconstruction. The difference between cartilage T1ρ or T2 of the injured and contralateral knee (side-to-side difference, SSD) was calculated to account for physiological variations among patients. Linear regression models were built to evaluate the association between the baseline SSD T1ρ or T2 and KOOS or Marx at all time points. Higher baseline SSD T1ρ posterolateral tibia (pLT) was associated with worse KOOS in all subscales except symptoms at baseline, worse KOOS pain at 6-months, and worse KOOS in all subscales except sports function at 1-year. Higher baseline SSD T2 femoral trochlea (TrF) was associated with worse KOOS activities of daily living (ADL) at 1-year. Higher baseline SSD T1ρ pLT was associated with lower Marx activity level at 1-year. More severe cartilage lesions, as assessed by Whole-Organ MRI Scoring (WORMS), was significantly associated with worse KOOS pain at 6-months and 1-year. T1ρ and T2 of cartilage after ACL injury were associated with KOOS after injury and both KOOS and Marx after reconstruction. Such associations may help clinicians stratify outcomes post-injury, and thus, improve patient management. Copyright © 2016 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Multiple functions of p21 in cell cycle, apoptosis and transcriptional regulation after DNA damage.

PubMed

Karimian, Ansar; Ahmadi, Yasin; Yousefi, Bahman

2016-06-01

An appropriate control over cell cycle progression depends on many factors. Cyclin-dependent kinase (CDK) inhibitor p21 (also known as p21(WAF1/Cip1)) is one of these factors that promote cell cycle arrest in response to a variety of stimuli. The inhibitory effect of P21 on cell cycle progression correlates with its nuclear localization. P21 can be induced by both p53-dependent and p53-independent mechanisms. Some other important functions attributed to p21 include transcriptional regulation, modulation or inhibition of apoptosis. These functions are largely dependent on direct p21/protein interactions and also on p21 subcellular localizations. In addition, p21 can play a role in DNA repair by interacting with proliferating cell nuclear antigen (PCNA). In this review, we will focus on the multiple functions of p21 in cell cycle regulation, apoptosis and gene transcription after DNA damage and briefly discuss the pathways and factors that have critical roles in p21 expression and activity. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

NASA Astrophysics Data System (ADS)

Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

2018-05-01

Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis.

PubMed

Liu, Wanlu; Duttke, Sascha H; Hetzel, Jonathan; Groth, Martin; Feng, Suhua; Gallego-Bartolome, Javier; Zhong, Zhenhui; Kuo, Hsuan Yu; Wang, Zonghua; Zhai, Jixian; Chory, Joanne; Jacobsen, Steven E

2018-03-01

Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide small interfering RNAs (siRNAs) that bind to ARGONAUTE 4 (AGO4) and target genomic regions for silencing. RdDM also requires non-coding RNAs transcribed by RNA polymerase V (Pol V) that probably serve as scaffolds for binding of AGO4-siRNA complexes. Here, we used a modified global nuclear run-on protocol followed by deep sequencing to capture Pol V nascent transcripts genome-wide. We uncovered unique characteristics of Pol V RNAs, including a uracil (U) common at position 10. This uracil was complementary to the 5' adenine found in many AGO4-bound 24-nucleotide siRNAs and was eliminated in a siRNA-deficient mutant as well as in the ago4/6/9 triple mutant, suggesting that the +10 U signature is due to siRNA-mediated co-transcriptional slicing of Pol V transcripts. Expression of wild-type AGO4 in ago4/6/9 mutants was able to restore slicing of Pol V transcripts, but a catalytically inactive AGO4 mutant did not correct the slicing defect. We also found that Pol V transcript slicing required SUPPRESSOR OF TY INSERTION 5-LIKE (SPT5L), an elongation factor whose function is not well understood. These results highlight the importance of Pol V transcript slicing in RNA-mediated transcriptional gene silencing, which is a conserved process in many eukaryotes.

Feature-fused SSD: fast detection for small objects

NASA Astrophysics Data System (ADS)

Cao, Guimei; Xie, Xuemei; Yang, Wenzhe; Liao, Quan; Shi, Guangming; Wu, Jinjian

2018-04-01

Small objects detection is a challenging task in computer vision due to its limited resolution and information. In order to solve this problem, the majority of existing methods sacrifice speed for improvement in accuracy. In this paper, we aim to detect small objects at a fast speed, using the best object detector Single Shot Multibox Detector (SSD) with respect to accuracy-vs-speed trade-off as base architecture. We propose a multi-level feature fusion method for introducing contextual information in SSD, in order to improve the accuracy for small objects. In detailed fusion operation, we design two feature fusion modules, concatenation module and element-sum module, different in the way of adding contextual information. Experimental results show that these two fusion modules obtain higher mAP on PASCAL VOC2007 than baseline SSD by 1.6 and 1.7 points respectively, especially with 2-3 points improvement on some small objects categories. The testing speed of them is 43 and 40 FPS respectively, superior to the state of the art Deconvolutional single shot detector (DSSD) by 29.4 and 26.4 FPS.

Literacy outcomes of children with early childhood speech sound disorders: impact of endophenotypes.

PubMed

Lewis, Barbara A; Avrich, Allison A; Freebairn, Lisa A; Hansen, Amy J; Sucheston, Lara E; Kuo, Iris; Taylor, H Gerry; Iyengar, Sudha K; Stein, Catherine M

2011-12-01

To demonstrate that early childhood speech sound disorders (SSD) and later school-age reading, written expression, and spelling skills are influenced by shared endophenotypes that may be in part genetic. Children with SSD and their siblings were assessed at early childhood (ages 4-6 years) and followed at school age (7-12 years). The relationship of shared endophenotypes with early childhood SSD and school-age outcomes and the shared genetic influences on these outcomes were examined. Structural equation modeling demonstrated that oral motor skills, phonological awareness, phonological memory, vocabulary, and speeded naming have varying influences on reading decoding, spelling, spoken language, and written expression at school age. Genetic linkage studies demonstrated linkage for reading, spelling, and written expression measures to regions on chromosomes 1, 3, 6, and 15 that were previously linked to oral motor skills, articulation, phonological memory, and vocabulary at early childhood testing. Endophenotypes predict school-age literacy outcomes over and above that predicted by clinical diagnoses of SSD or language impairment. Findings suggest that these shared endophenotypes and common genetic influences affect early childhood SSD and later school-age reading, spelling, spoken language, and written expression skills.

Literacy Outcomes of Children With Early Childhood Speech Sound Disorders: Impact of Endophenotypes

PubMed Central

Lewis, Barbara A.; Avrich, Allison A.; Freebairn, Lisa A.; Hansen, Amy J.; Sucheston, Lara E.; Kuo, Iris; Taylor, H. Gerry; Iyengar, Sudha K.; Stein, Catherine M.

2012-01-01

Purpose To demonstrate that early childhood speech sound disorders (SSD) and later school-age reading, written expression, and spelling skills are influenced by shared endophenotypes that may be in part genetic. Method Children with SSD and their siblings were assessed at early childhood (ages 4–6 years) and followed at school age (7–12 years). The relationship of shared endophenotypes with early childhood SSD and school-age outcomes and the shared genetic influences on these outcomes were examined. Results Structural equation modeling demonstrated that oral motor skills, phonological awareness, phonological memory, vocabulary, and speeded naming have varying influences on reading decoding, spelling, spoken language, and written expression at school age. Genetic linkage studies demonstrated linkage for reading, spelling, and written expression measures to regions on chromosomes 1, 3, 6, and 15 that were previously linked to oral motor skills, articulation, phonological memory, and vocabulary at early childhood testing. Conclusions Endophenotypes predict school-age literacy outcomes over and above that predicted by clinical diagnoses of SSD or language impairment. Findings suggest that these shared endophenotypes and common genetic influences affect early childhood SSD and later school-age reading, spelling, spoken language, and written expression skills. PMID:21930616

ReHypar: A Recursive Hybrid Chunk Partitioning Method Using NAND-Flash Memory SSD

PubMed Central

Park, Sung-Soon; Lim, Cheol-Su

2014-01-01

Due to the rapid development of flash memory, SSD is considered to be the replacement of HDD in the storage market. Although SSD retains several promising characteristics, such as high random I/O performance and nonvolatility, its high expense per capacity is the main obstacle in replacing HDD in all storage solutions. An alternative is to provide a hybrid structure where a small portion of SSD address space is combined with the much larger HDD address space. In such a structure, maximizing the space utilization of SSD in a cost-effective way is extremely important to generate high I/O performance. We developed ReHypar (recursive hybrid chunk partitioning) that enables improving the space utilization of SSD in the hybrid structure. The first objective of ReHypar is to mitigate the fragmentation overhead of SSD address space, by reusing the remaining free space of I/O units as much as possible. Furthermore, ReHypar allows defining several, logical data sections in SSD address space, with each of those sections being configured with the different I/O unit. We integrated ReHypar with ext2 and ext4 and evaluated it using two public benchmarks including IOzone and Postmark. PMID:24987741

Impact of fasting followed by short-term exposure to interleukin-6 on cytochrome P450 mRNA in mice.

PubMed

Rasmussen, Martin Krøyer; Bertholdt, Lærke; Gudiksen, Anders; Pilegaard, Henriette; Knudsen, Jakob G

2018-01-05

The gene expression of the cytochrome P450 (CYP) enzyme family is regulated by numerous factors. Fasting has been shown to induce increased hepatic CYP mRNA in both humans and animals. However, the coordinated regulation of CYP, CYP-regulating transcription factors, and transcriptional co-factors in the liver linking energy metabolism to detoxification has never been investigated. Interleukin-6 (IL-6) has been suggested to be released during fasting and has been shown to regulate CYP expression. The present study investigated the hepatic mRNA content of selected CYP, AhR, CAR, PXR and PPARα in mice fasted for 18h and subsequently exposed to IL-6. Furthermore, the impact of fasting on PGC-1α, HNF-4α, SIRT1 and SIRT3 mRNA was examined. Fasting induced a marked increase in Cyp2b10, Cyp2e1 and Cyp4a10 mRNA, while CYP1a1, Cyp1a2, Cyp2a4 and Cyp3a11 mRNA levels remained unchanged. In accordance, the mRNA levels of CAR and PPARα were also increased with fasting. The PGC-1α, SIRT1 and SIRT3 mRNA levels were also increased after fasting, while the HNF-4α mRNA levels remained unchanged. In mice subjected to IL-6 injection, the fasting-induced PXR, PPARα and PGC-1α mRNA responses were lower than after saline injection. In conclusion, fasting was demonstrated to be a strong inducer of hepatic CYP mRNA as well as selected transcription factors controlling the expression of the investigated CYP. Moreover, the mRNA levels of transcriptional co-factors acting as energy sensors and co-factors for CYP regulation was also increased in the liver, suggesting crosstalk at the molecular level between regulation of energy metabolism and detoxification. Copyright © 2017 Elsevier B.V. All rights reserved.

Nuclear factor erythroid-2-related factor regulates LRWD1 expression and cellular adaptation to oxidative stress in human embryonal carcinoma cells.

PubMed

Hung, Jui-Hsiang; Wee, Shi-Kae; Omar, Hany A; Su, Chia-Hui; Chen, Hsing-Yi; Chen, Pin-Shern; Chiu, Chien-Chih; Wu, Ming-Syuan; Teng, Yen-Ni

2018-05-01

Leucine-rich repeats and WD repeat domain-containing protein 1 (LRWD1) is implicated in the regulation of signal transduction, transcription, RNA processing and tumor development. However, LRWD1 transcriptional regulation is not fully understood. This study aimed to investigate the relationship between LRWD1 expression and reactive oxygen species (ROS) level in human embryonal carcinoma cell line, NT2/D1 cells, which will help in understanding the transcriptional regulatory role of ROS in cells. Results showed that the exposure of NT2/D1 cells to various concentrations of hydrogen peroxide (H 2 O 2 ) and the nitric oxide (NO) donor sodium nitroprusside (SNP) caused a significant increase in the mRNA and protein expression of LRWD1. In addition, LRWD1 promoter luciferase reporter assay, and Chromatin Immunoprecipitation assay (CHIP assay) showed that nuclear factor erythroid-2-related factor (Nrf2) was involved in the regulation of LRWD1 expression in response to oxidative stress. The involvement of Nrf2 was confirmed by shRNA-mediated knockdown of Nrf2 in NT2/D1 cells, which caused a significant decrease in LRWD1 expression in response to oxidative stress. Similarly, LRWD1 knockdown resulted in the accumulation of H 2 O 2 and superoxide anion radical (O2-). Blocking ROS production by N-acetyl cysteine (NAC) protected NT2/D1 shLRWD1cells from H 2 O 2 -induced cell death. Collectively, oxidative stress increased LRWD1 expression through a Nrf2-dependent mechanism, which plays an important role in cellular adaptation to oxidative stress. These results highlight an evidence, on the molecular level, about LRWD1 transcriptional regulation under oxidative stress. Copyright © 2018 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

SARS coronavirus papain-like protease induces Egr-1-dependent up-regulation of TGF-β1 via ROS/p38 MAPK/STAT3 pathway

PubMed Central

Li, Shih-Wein; Wang, Ching-Ying; Jou, Yu-Jen; Yang, Tsuey-Ching; Huang, Su-Hua; Wan, Lei; Lin, Ying-Ju; Lin, Cheng-Wen

2016-01-01

SARS coronavirus (SARS-CoV) papain-like protease (PLpro) has been identified in TGF-β1 up-regulation in human promonocytes (Proteomics 2012, 12: 3193-205). This study investigates the mechanisms of SARS-CoV PLpro-induced TGF-β1 promoter activation in human lung epithelial cells and mouse models. SARS-CoV PLpro dose- and time-dependently up-regulates TGF-β1 and vimentin in A549 cells. Dual luciferase reporter assays with TGF-β1 promoter plasmids indicated that TGF-β1 promoter region between −175 to −60, the Egr-1 binding site, was responsible for TGF-β1 promoter activation induced by SARS-CoV PLpro. Subcellular localization analysis of transcription factors showed PLpro triggering nuclear translocation of Egr-1, but not NF-κB and Sp-1. Meanwhile, Egr-1 silencing by siRNA significantly reduced PLpro-induced up-regulation of TGF-β1, TSP-1 and pro-fibrotic genes. Furthermore, the inhibitors for ROS (YCG063), p38 MAPK (SB203580), and STAT3 (Stattic) revealed ROS/p38 MAPK/STAT3 pathway involving in Egr-1 dependent activation of TGF-β1 promoter induced by PLpro. In a mouse model with a direct pulmonary injection, PLpro stimulated macrophage infiltration into lung, up-regulating Egr-1, TSP-1, TGF-β1 and vimentin expression in lung tissues. The results revealed that SARS-CoV PLpro significantly triggered Egr-1 dependent activation of TGF-β1 promoter via ROS/p38 MAPK/STAT3 pathway, correlating with up-regulation of pro-fibrotic responses in vitro and in vivo. PMID:27173006

SARS coronavirus papain-like protease induces Egr-1-dependent up-regulation of TGF-β1 via ROS/p38 MAPK/STAT3 pathway.

PubMed

Li, Shih-Wein; Wang, Ching-Ying; Jou, Yu-Jen; Yang, Tsuey-Ching; Huang, Su-Hua; Wan, Lei; Lin, Ying-Ju; Lin, Cheng-Wen

2016-05-13

SARS coronavirus (SARS-CoV) papain-like protease (PLpro) has been identified in TGF-β1 up-regulation in human promonocytes (Proteomics 2012, 12: 3193-205). This study investigates the mechanisms of SARS-CoV PLpro-induced TGF-β1 promoter activation in human lung epithelial cells and mouse models. SARS-CoV PLpro dose- and time-dependently up-regulates TGF-β1 and vimentin in A549 cells. Dual luciferase reporter assays with TGF-β1 promoter plasmids indicated that TGF-β1 promoter region between -175 to -60, the Egr-1 binding site, was responsible for TGF-β1 promoter activation induced by SARS-CoV PLpro. Subcellular localization analysis of transcription factors showed PLpro triggering nuclear translocation of Egr-1, but not NF-κB and Sp-1. Meanwhile, Egr-1 silencing by siRNA significantly reduced PLpro-induced up-regulation of TGF-β1, TSP-1 and pro-fibrotic genes. Furthermore, the inhibitors for ROS (YCG063), p38 MAPK (SB203580), and STAT3 (Stattic) revealed ROS/p38 MAPK/STAT3 pathway involving in Egr-1 dependent activation of TGF-β1 promoter induced by PLpro. In a mouse model with a direct pulmonary injection, PLpro stimulated macrophage infiltration into lung, up-regulating Egr-1, TSP-1, TGF-β1 and vimentin expression in lung tissues. The results revealed that SARS-CoV PLpro significantly triggered Egr-1 dependent activation of TGF-β1 promoter via ROS/p38 MAPK/STAT3 pathway, correlating with up-regulation of pro-fibrotic responses in vitro and in vivo.

Regulation of an H-ras-related transcript by parathyroid hormone in rat osteosarcoma cells

NASA Technical Reports Server (NTRS)

Scott, D. K.; Weaver, W. R.; Clohisy, J. C.; Brakenhoff, K. D.; Kahn, A. J.; Partridge, N. C.

1992-01-01

The rat osteosarcoma cell line UMR 106-01 is a commonly used model system for the study of osteoblast function. However, it also expresses a phenotype characteristic of transformed cells. To test whether the latter could be accounted for by aberrant oncogene expression, we probed Northern blots of UMR and other osteoblastic cells with a panel of oncogene probes. These blots, when probed with a cDNA specific for v-H-ras, revealed a 7.0-kilobase (kb) H-ras-related transcript (designated HRRT) in UMR 106-01 cells that was not expressed in other osteoblastic cells. Osteoblast-enriched calvarial cells expressed the typical 1.1-kb H-ras mRNA, which was absent in UMR cells. Additionally, Western blots of lysates of UMR cells documented the presence of three proteins immunologically related to H-rasp21. To determine whether HRRT represented a recombinant retrovirus product, Northern blots were probed with a cDNA specific for the highly conserved gag-pol region of Moloney murine leukemia virus. These blots showed parallel cross-reactivity with an apparently identical transcript of 7.0 kb. The 7.0-kb transcripts detected by both v-H-ras and gag-pol probes declined to the same extent after treatment with concentrations of PTH known to inhibit proliferation of these cells. PTH regulated the abundance of HRRT in a time- and dose-dependent manner, with greatest repression of the transcript after 8 h of treatment with 10(-8) M PTH. The decrease in HRRT could not be completely accounted for by changes in transcriptional activity, as determined by nuclear run-on assays.(ABSTRACT TRUNCATED AT 250 WORDS).

Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies.

PubMed

Mukherjee, Debadrita; Pal, Aritrika; Chakravarty, Devlina; Chakrabarti, Pinak

2015-02-18

HlyU, a transcriptional regulator common in many Vibrio species, activates the hemolysin gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus and the genes of plp-vah1 and rtxACHBDE gene clusters in Vibrio anguillarum. The protein is also proposed to be a potential global virulence regulator for V. cholerae and V. vulnificus. Mechanisms of gene control by HlyU in V. vulnificus and V. anguillarum are reported. However, detailed elucidation of the interaction of HlyU in V. cholerae with its target DNA at the molecular level is not available. Here we report a 17-bp imperfect palindrome sequence, 5'-TAATTCAGACTAAATTA-3', 173 bp upstream of hlyA promoter, as the binding site of HlyU. This winged helix-turn-helix protein binds necessarily as a dimer with the recognition helices contacting the major grooves and the β-sheet wings, the minor grooves. Such interactions enhance hlyA promoter activity in vivo. Mutations affecting dimerization as well as those in the DNA-protein interface hamper DNA binding and transcription regulation. Molecular dynamic simulations show hydrogen bonding patterns involving residues at the mutation sites and confirmed their importance in DNA binding. On binding to HlyU, DNA deviates by ∼68º from linearity. Dynamics also suggest a possible redox control in HlyU. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Turbidostat Culture of Saccharomyces cerevisiae W303-1A under Selective Pressure Elicited by Ethanol Selects for Mutations in SSD1 and UTH1

PubMed Central

Avrahami-Moyal, Liat; Engelberg, David; Wenger, Jared. W.; Sherlock, Gavin; Braun, Sergei

2012-01-01

We investigated the genetic causes of ethanol tolerance by characterizing mutations selected in Saccharomyces cerevisiae W303-1A under the selective pressure of ethanol. W303-1A was subjected to three rounds of turbidostat, in medium supplemented with increasing amounts of ethanol. By the end of selection, the growth rate of the culture has increased from 0.029 h-1 to 0.32 h-1. Unlike the progenitor strain, all yeast cells isolated from this population were able to form colonies on medium supplemented with 7% ethanol within six days, our definition of ethanol tolerance. Several clones selected from all three stages of selection were able to form dense colonies within two days on solid medium supplemented with 9% ethanol. We sequenced the whole genomes of 6 clones and identified mutations responsible for ethanol tolerance. Thirteen additional clones were tested for the presence of similar mutations. In 15 out of 19 tolerant clones the stop-codon in ssd1-d was replaced with an aminoacid-encoding codon. Three other clones contained one of two mutations in UTH1, and one clone did not contain mutations in either SSD1 or UTH1. We showed that the mutations in SSD1 and UTH1 increased tolerance of the cell wall to zymolyase and conclude that stability of the cell wall is a major factor in increased tolerance to ethanol. PMID:22443114

Potassium Channel Interacting Protein 2 (KChIP2) is not a transcriptional regulator of cardiac electrical remodeling

PubMed Central

Winther, Sine V.; Tuomainen, Tomi; Borup, Rehannah; Tavi, Pasi; Antoons, Gudrun; Thomsen, Morten B.

2016-01-01

The heart-failure relevant Potassium Channel Interacting Protein 2 (KChIP2) augments CaV1.2 and KV4.3. KChIP3 represses CaV1.2 transcription in cardiomyocytes via interaction with regulatory DNA elements. Hence, we tested nuclear presence of KChIP2 and if KChIP2 translocates into the nucleus in a Ca2+ dependent manner. Cardiac biopsies from human heart-failure patients and healthy donor controls showed that nuclear KChIP2 abundance was significantly increased in heart failure; however, this was secondary to a large variation of total KChIP2 content. Administration of ouabain did not increase KChIP2 content in nuclear protein fractions in anesthetized mice. KChIP2 was expressed in cell lines, and Ca2+ ionophores were applied in a concentration- and time-dependent manner. The cell lines had KChIP2-immunoreactive protein in the nucleus in the absence of treatments to modulate intracellular Ca2+ concentration. Neither increasing nor decreasing intracellular Ca2+ concentrations caused translocation of KChIP2. Microarray analysis did not identify relief of transcriptional repression in murine KChIP2−/− heart samples. We conclude that although there is a baseline presence of KChIP2 in the nucleus both in vivo and in vitro, KChIP2 does not directly regulate transcriptional activity. Moreover, the nuclear transport of KChIP2 is not dependent on Ca2+. Thus, KChIP2 does not function as a conventional transcription factor in the heart. PMID:27349185

The prognostic significance of subsyndromal delirium in elderly medical inpatients.

PubMed

Cole, Martin; McCusker, Jane; Dendukuri, Nandini; Han, Ling

2003-06-01

To determine the prognostic significance of subsyndromal delirium (SSD) presentations. Cohort study. University-affiliated primary acute care hospital. One hundred sixty-four elderly medical inpatients who did not meet Diagnostic and Statistical Manual of Mental Disorders, Third Edition, Revised (DSM-III-R) criteria for delirium during the first week after admission were classified into three mutually exclusive groups. The first group, prevalent SSD, included those who had two or more of four core symptoms of delirium (clouding of consciousness, inattention, disorientation, perceptual disturbances) at admission. The second group, incident SSD, included those who did not meet criteria for prevalent SSD but displayed one or more new core symptoms during the week after admission. The third group had no prevalent or incident SSD. The three groups were followed up at 2, 6, and 12 months. Outcomes (length of stay, symptoms of delirium (Delirium index), cognitive (Mini-Mental State Examination) and functional status (instrumental activities of daily living), and mortality) were compared using univariate techniques and multivariate regression models that adjusted for age, sex, marital status, living arrangements before admission, comorbidity, clinical and physiological severity of illness, and dementia status and severity. Patients with prevalent SSD had longer acute care hospital stay, increased postdischarge mortality, more symptoms of delirium, and a lower cognitive and functional level at follow-up than patients with no SSD. Most of the findings for incident SSD were similar but not statistically significant. Patients with prevalent or incident SSD had risk factors for DSM-defined delirium. SSD in elderly medical inpatients appears to be a clinically important syndrome that falls on a continuum between no symptoms and DSM-defined delirium.

Blood-Based Gene Expression Profiles Models for Classification of Subsyndromal Symptomatic Depression and Major Depressive Disorder

PubMed Central

Yu, Shunying; Yuan, Chengmei; Hong, Wu; Wang, Zuowei; Cui, Jian; Shi, Tieliu; Fang, Yiru

2012-01-01

Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and also lead to significant psychosocial functional impairment as same as major depressive disorder (MDD). Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step. Firstly, we identified 63 differentially expressed SSD signatures in contrast to control (P< = 5.0E-4) and 30 differentially expressed MDD signatures in contrast to control, respectively. Then, 123 gene signatures were identified with significantly differential expression level between SSD and MDD. Secondly, in order to conduct priority selection for biomarkers for SSD and MDD together, we selected top gene signatures from each group of pair-wise comparison results, and merged the signatures together to generate better profiles used for clearly classify SSD and MDD sets in the same time. In details, we tried different combination of signatures from the three pair-wise compartmental results and finally determined 48 gene expression signatures with 100% accuracy. Our finding suggested that SSD and MDD did not exhibit the same expressed genome signature with peripheral blood leukocyte, and blood cell–derived RNA of these 48 gene models may have significant value for performing diagnostic functions and classifying SSD, MDD, and healthy controls. PMID:22348066

Parental Beliefs and Experiences Regarding Involvement in Intervention for Their Child with Speech Sound Disorder

ERIC Educational Resources Information Center

Watts Pappas, Nicole; McAllister, Lindy; McLeod, Sharynne

2016-01-01

Parental beliefs and experiences regarding involvement in speech intervention for their child with mild to moderate speech sound disorder (SSD) were explored using multiple, sequential interviews conducted during a course of treatment. Twenty-one interviews were conducted with seven parents of six children with SSD: (1) after their child's initial…

The effects of spinal support device on pain and extensibility of the hamstrings in patients with non-specific low back pain.

PubMed

Jeon, Eun Tae; Jung, Jin-Hwa; Moon, Jong Hoon; Jung, Kyoung-Sim; Won, Young Sik; Kim, Sung-Jin; Hahm, Suk-Chan; Cho, Hwi-Young

2017-08-01

[Purpose] The objective of this study was to investigate the effects of spinal support device (SSD) on pain and hamstring extensibility in patients with non-specific low back pain (NSLBP). [Subjects and Methods] 20 patients with NSLBP were recruited and randomly assigned to either the SSD group or the control group. In the SSD group, SSD was applied; in the control group, bed rest in supine position was performed. Both groups underwent treatment 20 min/day, 3 times a week, for a duration of 4 weeks. To assess the hamstring extensibility, sit and reach test (SRT) was performed. To assess pain pressure threshold (PPT) of the sacroiliac joint, a pressure algometer was used. Visual analog scale (VAS) was used to quantify pain. [Results] The SSD group showed a significant improvement in sacroiliac joint pain with increased VAS, and the control group showed a significantly increased VAS after intervention. In the SSD group, VAS was significantly increased, but SRT was not changed compared with the control group. [Conclusion] These results demonstrated that an application of SSD effectively attenuates low back pain. Therefore, SSD may be a suitable intervention for pain control in patients with NSLBP.

Detection of the pedogenic magnetic fraction in volcanic soils developed on basalts using frequency-dependent magnetic susceptibility: comparison of two instruments

NASA Astrophysics Data System (ADS)

Grison, Hana; Petrovsky, Eduard; Kapicka, Ales; Hanzlikova, Hana

2017-05-01

In studies of the magnetic properties of soils, the frequency-dependent magnetic susceptibility percentage (χFD%) is often used for the identification of ultrafine magnetically superparamagnetic/stable single-domain (SP/SSD) particles. This parameter is commonly used as an indicator for increased pedogenesis. In strongly magnetic soils, the SP/SSD magnetic signal (mostly bio-pedogenic) may be masked by lithological signals; making pedogenesis hard to detect. In this study, we compare results for the detection of ultrafine SP/SSD magnetic particles in andic soils using two instruments: a Bartington MS2B dual-frequency meter and an AGICO Kappabridge MFK1-FA. In particular, the study focuses on the effect of pedogenesis by investigating the relationship between specific soil magnetic and chemical properties (soil organic carbon and pHH2O). The values of χFD% obtained with the MS2B varied from 2.4 to 5.9 per cent, and mass-specific magnetic susceptibility (χLF) from 283 to 1688 × 10-8 m3 kg-1, while values of χFD% and χLF obtained with the MFK1-FA varied from 2.7 to 8.2 per cent and from 299 to 1859 × 10-8 m3 kg-1, respectively. Our results suggest that the detection of the SP/SSD magnetic fraction can be accomplished by comparing relative trends of χFD% along the soil profile. Moreover, the discrimination between bio-pedogenic and lithogenic magnetic contributions in the SP/SSD fraction is possible by comparing the χFD% and χLF data determined in the fine earth (<2 mm) and the coarse fraction (4-10 mm) samples down the soil profile.

Comparative study of the failure rates among 3 implantable defibrillator leads.

PubMed

van Malderen, Sophie C H; Szili-Torok, Tamas; Yap, Sing C; Hoeks, Sanne E; Zijlstra, Felix; Theuns, Dominic A M J

2016-12-01

After the introduction of the Biotronik Linox S/SD high-voltage lead, several cases of early failure have been observed. The purpose of this article was to assess the performance of the Linox S/SD lead in comparison to 2 other contemporary leads. We used the prospective Erasmus MC ICD registry to identify all implanted Linox S/SD (n = 408), Durata (St. Jude Medical, model 7122) (n = 340), and Endotak Reliance (Boston Scientific, models 0155, 0138, and 0158) (n = 343) leads. Lead failure was defined by low- or high-voltage impedance, failure to capture, sense or defibrillate, or the presence of nonphysiological signals not due to external interference. During a median follow-up of 5.1 years, 24 Linox (5.9%), 5 Endotak (1.5%), and 5 Durata (1.5%) leads failed. At 5-year follow-up, the cumulative failure rate of Linox leads (6.4%) was higher than that of Endotak (0.4%; P < .0001) and Durata (2.0%; P = .003) leads. The incidence rate was higher in Linox leads (1.3 per 100 patient-years) than in Endotak and Durata leads (0.2 and 0.3 per 100 patient-years, respectively; P < .001). A log-log analysis of the cumulative hazard for Linox leads functioning at 3-year follow-up revealed a stable failure rate of 3% per year. The majority of failures consisted of noise (62.5%) and abnormal impedance (33.3%). This study demonstrates a higher failure rate of Linox S/SD high-voltage leads compared to contemporary leads. Although the mechanism of lead failure is unclear, the majority presents with abnormal electrical parameters. Comprehensive monitoring of Linox S/SD high-voltage leads includes remote monitoring to facilitate early detection of lead failure. Copyright © 2016. Published by Elsevier Inc.

Structure of human Niemann–Pick C1 protein

PubMed Central

Li, Xiaochun; Wang, Jiawei; Coutavas, Elias; Shi, Hang; Hao, Qi; Blobel, Günter

2016-01-01

Niemann–Pick C1 protein (NPC1) is a late-endosomal membrane protein involved in trafficking of LDL-derived cholesterol, Niemann–Pick disease type C, and Ebola virus infection. NPC1 contains 13 transmembrane segments (TMs), five of which are thought to represent a “sterol-sensing domain” (SSD). Although present also in other key regulatory proteins of cholesterol biosynthesis, uptake, and signaling, the structure and mechanism of action of the SSD are unknown. Here we report a crystal structure of a large fragment of human NPC1 at 3.6 Å resolution, which reveals internal twofold pseudosymmetry along TM 2–13 and two structurally homologous domains that protrude 60 Å into the endosomal lumen. Strikingly, NPC1's SSD forms a cavity that is accessible from both the luminal bilayer leaflet and the endosomal lumen; computational modeling suggests that this cavity is large enough to accommodate one cholesterol molecule. We propose a model for NPC1 function in cholesterol sensing and transport. PMID:27307437

[Correlation between long time systolic blood pressure variability and short time systolic blood pressure in aged population].

PubMed

An, Shasha; Zheng, Xiaoming; Li, Zhifang; Wang, Yang; Wu, Yuntao; Zhang, Wenyan; Zhao, Haiyan; Wu, Aiping; Wang, Ruixia; Tao, Jie; Gao, Xinying; Wu, Shouling

2015-11-01

To investigate the correlation between long time systolic blood pressure variability(SBPV)and short time SBPV in aged population. A total of 752 subjects aged ≥60 years of Kailuan Group who took part in 2006-2007, 2008-2009, 2010-2011 and 2012-2013 health examination were included by cluster sampling method.Long time SBPV was calculated by standard deviation of mean systolic blood pressure measured in 2006-2007, 2008-2009, 2010-2011 and 2012-2013, standard deviation represents short time systolic blood pressure which is derived from 24 hour ambulatory blood pressure monitoring. The observation population was divided into three groups according to the third tertiles of the time systolic blood pressure variability: the first point(<9.09 mmHg (1 mmHg=0.133 kPa)), second point (≥9.09 mmHg, and <14.29 mmHg), and third point (≥14.29 mmHg). Multivariate logistic regression analysis was used to analyze the correlation between long time systolic blood pressure variability and short time systolic blood pressure. (1) The participants' age were (67.0±5.7) years old (284 women). (2) The 24 hours and daytime SSD were (14.7±4.0) mmHg, (14.7±3.5) mmHg, (15.7±4.4) mmHg (P=0.010) and (14.1±4.4) mmHg, (14.2±3.5) mmHg and (15.4±4.6) mmHg (P<0.001) according to the tertiles of long time systolic blood pressure variability, respectively, nighttime SSD were (12.0±4.4) mmHg, (11.8±4.8) mmHg and (11.9±4.9) mmHg (P=0.900). (3) Multiple logistic regression analysis showed that the tertiles of long time SSD was the risk factor for increasing daytime SSD>14.00 mmHg (OR=1.51, 95%CI: 1.03-2.23, P=0.037), but not a risk factor for increasing 24 hours SSD>14.41 mmHg (OR=1.10, 95%CI: 0.75-1.61, P=0.639) and nighttime SSD>11.11 mmHg (OR=0.98, 95%CI: 0.67-1.42, P=0.899). Increased long time SBPV is a risk factor for increasing daytime SBPV.

Nuclear respiratory factor 2 regulates the expression of the same NMDA receptor subunit genes as NRF-1: both factors act by a concurrent and parallel mechanism to couple energy metabolism and synaptic transmission.

PubMed

Priya, Anusha; Johar, Kaid; Wong-Riley, Margaret T T

2013-01-01

Neuronal activity and energy metabolism are tightly coupled processes. Previously, we found that nuclear respiratory factor 1 (NRF-1) transcriptionally co-regulates energy metabolism and neuronal activity by regulating all 13 subunits of the critical energy generating enzyme, cytochrome c oxidase (COX), as well as N-methyl-d-aspartate (NMDA) receptor subunits 1 and 2B, GluN1 (Grin1) and GluN2B (Grin2b). We also found that another transcription factor, nuclear respiratory factor 2 (NRF-2 or GA-binding protein) regulates all subunits of COX as well. The goal of the present study was to test our hypothesis that NRF-2 also regulates specific subunits of NMDA receptors, and that it functions with NRF-1 via one of three mechanisms: complementary, concurrent and parallel, or a combination of complementary and concurrent/parallel. By means of multiple approaches, including in silico analysis, electrophoretic mobility shift and supershift assays, in vivo chromatin immunoprecipitation of mouse neuroblastoma cells and rat visual cortical tissue, promoter mutations, real-time quantitative PCR, and western blot analysis, NRF-2 was found to functionally regulate Grin1 and Grin2b genes, but not any other NMDA subunit genes. Grin1 and Grin2b transcripts were up-regulated by depolarizing KCl, but silencing of NRF-2 prevented this up-regulation. On the other hand, over-expression of NRF-2 rescued the down-regulation of these subunits by the impulse blocker TTX. NRF-2 binding sites on Grin1 and Grin2b are conserved among species. Our data indicate that NRF-2 and NRF-1 operate in a concurrent and parallel manner in mediating the tight coupling between energy metabolism and neuronal activity at the molecular level. Copyright © 2012 Elsevier B.V. All rights reserved.

Drosophila Mitf regulates the V-ATPase and the lysosomal-autophagic pathway.

PubMed

Bouché, Valentina; Espinosa, Alma Perez; Leone, Luigi; Sardiello, Marco; Ballabio, Andrea; Botas, Juan

2016-01-01

An evolutionarily conserved gene network regulates the expression of genes involved in lysosome biogenesis, autophagy, and lipid metabolism. In mammals, TFEB and other members of the MiTF-TFE family of transcription factors control this network. Here we report that the lysosomal-autophagy pathway is controlled by Mitf gene in Drosophila melanogaster. Mitf is the single MiTF-TFE family member in Drosophila and prior to this work was known only for its function in eye development. We show that Mitf regulates the expression of genes encoding V-ATPase subunits as well as many additional genes involved in the lysosomal-autophagy pathway. Reduction of Mitf function leads to abnormal lysosomes and impairs autophagosome fusion and lipid breakdown during the response to starvation. In contrast, elevated Mitf levels increase the number of lysosomes, autophagosomes and autolysosomes, and decrease the size of lipid droplets. Inhibition of Drosophila MTORC1 induces Mitf translocation to the nucleus, underscoring conserved regulatory mechanisms between Drosophila and mammalian systems. Furthermore, we show Mitf-mediated clearance of cytosolic and nuclear expanded ATXN1 (ataxin 1) in a cellular model of spinocerebellar ataxia type 1 (SCA1). This remarkable observation illustrates the potential of the lysosomal-autophagy system to prevent toxic protein aggregation in both the cytoplasmic and nuclear compartments. We anticipate that the genetics of the Drosophila model and the absence of redundant MIT transcription factors will be exploited to investigate the regulation and function of the lysosomal-autophagy gene network.

Spots of Seismic Danger Extracted by Properties of Low-Frequency Seismic Noise

NASA Astrophysics Data System (ADS)

Lyubushin, Alexey

2013-04-01

A new method of seismic danger estimate is presented which is based on using properties of low-frequency seismic noise from broadband networks. Two statistics of noise waveforms are considered: multi-fractal singularity spectrum support width D and minimum normalized entropy En of squared orthogonal wavelet coefficients. The maps of D and En are plotted in the moving time window. Let us call the regions extracted by low values of D and high values of En as "spots of seismic danger" - SSD. Mean values of D and En are strongly anti-correlated - that is why statistics D and En extract the same SSD. Nevertheless their mutual considering is expedient because these parameters are based on different approaches. The physical mechanism which underlies the method is consolidation of small blocks of the Earth's crust into the large one before the strong earthquake. This effect has a consequence that seismic noise does not include spikes which are connected with mutual movements of small blocks. The absence of irregular spikes in the noise follows the decreasing of D and increasing of entropy En. The stability in space and size of the SSD provides estimates of the place and energy of the probable future earthquake. The increasing or decreasing of SSD size and minimum or maximum values of D and En within SSD allows estimate the trend of seismic danger. The method is illustrating by the analysis of seismic noise from broadband seismic network F-net in Japan [1-5]. Statistically significant decreasing of D allowed a hypothesis about approaching Japan to a future seismic catastrophe to be formulated at the middle of 2008. The peculiarities of correlation coefficient estimate within 1 year time window between median values of D and generalized Hurst exponent allowed to make a decision that starting from July of 2010 Japan come to the state of waiting strong earthquake [3]. The method extracted a huge SSD near Japan which includes the region of future Tohoku mega-earthquake and the region of Nankai Trough. The analysis of seismic noise after March 2011 indicates increasing of probability of the 2nd mega-earthquake starting from the middle of 2013 within the region of Nankai Trough which remains to be SSD. References 1. Lyubushin A. Multifractal Parameters of Low-Frequency Microseisms // V. de Rubeis et al. (eds.), Synchronization and Triggering: from Fracture to Earthquake Processes, GeoPlanet: Earth and Planetary Sciences 1, DOI 10.1007/978-3-642-12300-9_15, Springer-Verlag Berlin Heidelberg, 2010, 388p., Chapter 15, pp.253-272. http://www.springerlink.com/content/hj2l211577533261/ 2. Lyubushin A.A. Synchronization of multifractal parameters of regional and global low-frequency microseisms - European Geosciences Union General Assembly 2010, Vienna, 02-07 of May, 2010, Geophysical Research Abstracts, Vol. 12, EGU2010-696, 2010. http://meetingorganizer.copernicus.org/EGU2010/EGU2010-696.pdf 3. Lyubushin A.A. Synchronization phenomena of low-frequency microseisms. European Seismological Commission, 32nd General Assembly, September 06-10, 2010, Montpelier, France. Book of abstracts, p.124, session ES6. http://alexeylyubushin.narod.ru/ESC-2010_Book_of_abstracts.pdf 4. Lyubushin A.A. Seismic Catastrophe in Japan on March 11, 2011: Long-Term Prediction on the Basis of Low-Frequency Microseisms - Izvestiya, Atmospheric and Oceanic Physics, 2011, Vol. 46, No. 8, pp. 904-921. http://www.springerlink.com/content/kq53j2667024w715/ 5. Lyubushin, A. Prognostic properties of low-frequency seismic noise. Natural Science, 4, 659-666.doi: 10.4236/ns.2012.428087. http://www.scirp.org/journal/PaperInformation.aspx?paperID=21656

Leukocyte susceptibility and immune response against Vibrio parahaemolyticus in Totoaba macdonaldi.

PubMed

Reyes-Becerril, Martha; Alamillo, Erika; Sánchez-Torres, Luvia; Ascencio-Valle, Felipe; Perez-Urbiola, Juan C; Angulo, Carlos

2016-12-01

Vibrio parahaemolyticus is a serious pathogen that affects aquaculture. Nonetheless, to the best of our knowledge, no studies have focused on its immunological implications in Totoaba macdonaldi. Thus, the early immune response to V. parahaemolyticus in juveniles of totoaba was studied at 24 h post-infection with an in vivo study. In addition, changes in cellular innate immune parameters - phagocytosis, respiratory burst activity and viability (annexin V/propidium iodide) - were evaluated in vitro in head-kidney, spleen and thymus leukocytes at 6 and 24 h after bacterial stimulation by flow cytometry. Simultaneously, the expression levels of two immune-relevant genes (IL-1β and IL-8) were measured by using real time PCR. During in vivo study, mRNA transcripts of IL-1β were highly expressed in spleen, thymus and intestine and down-regulated in liver after 24 h post-infection. IL-8 gene expression was upregulated in spleen, intestine and liver compared to that of non-infected fish and down-regulated in thymus after 24 h post-infection. Generally, the results showed a significant decrease in cellular immune responses during the infection, principally in phagocytic ability and respiratory burst. The survival or viability of stimulated leukocytes was significantly reduced causing necrosis and apoptosis, indicating a robust killing response by V. parahaemolyticus. Finally the in vitro analysis showed that transcript levels of IL-1β and IL-8 were up-regulated during stimulation with V. parahaemolyticus in head-kidney, spleen and intestine and down-regulated in thymus at any time of the experiment. Although V. parahaemolyticus has been reported to be an important pathogen for many aquatic organisms, to our knowledge this might be the first report of early-immune response in juvenile totoaba and these immune parameters may be reliable indicators and can be useful in the health control of this species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2-independent mechanism.

PubMed

Juárez-Morales, José L; Schulte, Claus J; Pezoa, Sofia A; Vallejo, Grace K; Hilinski, William C; England, Samantha J; de Jager, Sarah; Lewis, Katharine E

2016-02-19

For neurons to function correctly in neuronal circuitry they must utilize appropriate neurotransmitters. However, even though neurotransmitter specificity is one of the most important and defining properties of a neuron we still do not fully understand how neurotransmitter fates are specified during development. Most neuronal properties are determined by the transcription factors that neurons express as they start to differentiate. While we know a few transcription factors that specify the neurotransmitter fates of particular neurons, there are still many spinal neurons for which the transcription factors specifying this critical phenotype are unknown. Strikingly, all of the transcription factors that have been identified so far as specifying inhibitory fates in the spinal cord act through Pax2. Even Tlx1 and Tlx3, which specify the excitatory fates of dI3 and dI5 spinal neurons work at least in part by down-regulating Pax2. In this paper we use single and double mutant zebrafish embryos to identify the spinal cord functions of Evx1 and Evx2. We demonstrate that Evx1 and Evx2 are expressed by spinal cord V0v cells and we show that these cells develop into excitatory (glutamatergic) Commissural Ascending (CoSA) interneurons. In the absence of both Evx1 and Evx2, V0v cells still form and develop a CoSA morphology. However, they lose their excitatory fate and instead express markers of a glycinergic fate. Interestingly, they do not express Pax2, suggesting that they are acquiring their inhibitory fate through a novel Pax2-independent mechanism. Evx1 and Evx2 are required, partially redundantly, for spinal cord V0v cells to become excitatory (glutamatergic) interneurons. These results significantly increase our understanding of the mechanisms of neuronal specification and the genetic networks involved in these processes.

Traditional test administration and proactive interference undermine visual-spatial working memory performance in schizophrenia-spectrum disorders.

PubMed

Girard, Todd A; Wilkins, Leanne K; Lyons, Kathleen M; Yang, Lixia; Christensen, Bruce K

2018-05-31

Introduction Working-memory (WM) is a core cognitive deficit among individuals with Schizophrenia Spectrum Disorders (SSD). However, the underlying cognitive mechanisms of this deficit are less known. This study applies a modified version of the Corsi Block Test to investigate the role of proactive interference in visuospatial WM (VSWM) impairment in SSD. Methods Healthy and SSD participants completed a modified version of the Corsi Block Test involving both high (typical ascending set size from 4 to 7 items) and low (descending set size from 7 to 4 items) proactive interference conditions. Results The results confirmed that the SSD group performed worse overall relative to a healthy comparison group. More importantly, the SSD group demonstrated greater VSWM scores under low (Descending) versus high (Ascending) proactive interference; this pattern is opposite to that of healthy participants. Conclusions This differential pattern of performance supports that proactive interference associated with the traditional administration format contributes to VSWM impairment in SSD. Further research investigating associated neurocognitive mechanisms and the contribution of proactive interference across other domains of cognition in SSD is warranted.

Development and application of a species sensitivity distribution for temperature-induced mortality in the aquatic environment.

PubMed

de Vries, Pepijn; Tamis, Jacqueline E; Murk, Albertinka J; Smit, Mathijs G D

2008-12-01

Current European legislation has static water quality objectives for temperature effects, based on the most sensitive species. In the present study a species sensitivity distribution (SSD) for elevated temperatures is developed on the basis of temperature sensitivity data (mortality) of 50 aquatic species. The SSD applies to risk assessment of heat discharges that are localized in space or time. As collected median lethal temperatures (LT50 values) for different species depend on the acclimation temperature, the SSD is also a function of the acclimation temperature. Data from a thermal discharge in The Netherlands are used to show the applicability of the developed SSD in environmental risk assessment. Although restrictions exist in the application of the developed SSD, it is concluded that the SSD approach can be applied to assess the effects of elevated temperature. Application of the concept of SSD to temperature changes allows harmonization of environmental risk assessment for stressors in the aquatic environment. When a synchronization of the assessment methods is achieved, the steps to integration of risks from toxic and nontoxic stressors can be made.

Parameters Comparsion of Leads Detection in Arctic Sea Ice Using CRYOSAT-2 Waveform Data

NASA Astrophysics Data System (ADS)

Li, J.; Zhang, S.; Xiao, F.; Zhu, C.; Zhang, Y.; Zhu, T.; Yuan, L.

2018-04-01

Leads are only a small part of the polar sea ice structure, but they play a dominant role on the turbulence exchange between the ocean and the atmosphere, they are also important factors about sea ice thickness inversion. Since the early 2000s, Satellite altimetry has been applied to monitor the Arctic sea ice thickness, Satellite altimetry data can be used to distinguish leads and sea ice. In this paper, four parameters including Pulse peakiness (PP), stack standard deviation (SSD), stack kurtosis (SKU) and stack skewness (SSK) are extracted from CryoSat-2 satellite altimetry waveform data. The four parameters are combined into five combinations (PP, PP&SSD, PP&SSD&SKU, PP&SSD&SSK, PP&SSD&SSK&SKU) with constrain conditions to detect the leads. The results of the five methods are compared with MODIS (moderate-resolution imagining spectroradiometer) images and show that, the combination of PP&SSD is better than the single PP, the rest of combinations are the same as the combination of PP&SSD. It turns out, there is no promotion when we add SSK and SKU, successively or simultaneously.

SARS-CoV Regulates Immune Function-Related Gene Expression in Human Monocytic Cells

PubMed Central

Hu, Wanchung; Yen, Yu-Ting; Singh, Sher; Kao, Chuan-Liang

2012-01-01

Abstract Severe acute respiratory syndrome (SARS) is characterized by acute respiratory distress syndrome (ARDS) and pulmonary fibrosis, and monocytes/macrophages are the key players in the pathogenesis of SARS. In this study, we compared the transcriptional profiles of SARS coronavirus (SARS-CoV)-infected monocytic cells against that infected by coronavirus 229E (CoV-229E). Total RNA was extracted from infected DC-SIGN-transfected monocytes (THP-1-DC-SIGN) at 6 and 24 h after infection, and the gene expression was profiled in oligonucleotide-based microarrays. Analysis of immune-related gene expression profiles showed that at 24 h after SARS-CoV infection: (1) IFN-α/β-inducible and cathepsin/proteasome genes were downregulated; (2) hypoxia/hyperoxia-related genes were upregulated; and (3) TLR/TLR-signaling, cytokine/cytokine receptor-related, chemokine/chemokine receptor-related, lysosome-related, MHC/chaperon-related, and fibrosis-related genes were differentially regulated. These results elucidate that SARS-CoV infection regulates immune-related genes in monocytes/macrophages, which may be important to the pathogenesis of SARS. PMID:22876772

SARS-CoV regulates immune function-related gene expression in human monocytic cells.

PubMed

Hu, Wanchung; Yen, Yu-Ting; Singh, Sher; Kao, Chuan-Liang; Wu-Hsieh, Betty A

2012-08-01

Severe acute respiratory syndrome (SARS) is characterized by acute respiratory distress syndrome (ARDS) and pulmonary fibrosis, and monocytes/macrophages are the key players in the pathogenesis of SARS. In this study, we compared the transcriptional profiles of SARS coronavirus (SARS-CoV)-infected monocytic cells against that infected by coronavirus 229E (CoV-229E). Total RNA was extracted from infected DC-SIGN-transfected monocytes (THP-1-DC-SIGN) at 6 and 24 h after infection, and the gene expression was profiled in oligonucleotide-based microarrays. Analysis of immune-related gene expression profiles showed that at 24 h after SARS-CoV infection: (1) IFN-α/β-inducible and cathepsin/proteasome genes were downregulated; (2) hypoxia/hyperoxia-related genes were upregulated; and (3) TLR/TLR-signaling, cytokine/cytokine receptor-related, chemokine/chemokine receptor-related, lysosome-related, MHC/chaperon-related, and fibrosis-related genes were differentially regulated. These results elucidate that SARS-CoV infection regulates immune-related genes in monocytes/macrophages, which may be important to the pathogenesis of SARS.

The glucose sensor Snf1 and the transcription factors Msn2 and Msn4 regulate transcription of the vacuolar iron importer gene CCC1 and iron resistance in yeast.

PubMed

Li, Liangtao; Kaplan, Jerry; Ward, Diane M

2017-09-15

The budding yeast Saccharomyces cerevisiae stores iron in the vacuole, which is a major resistance mechanism against iron toxicity. One key protein involved in vacuolar iron storage is the iron importer Ccc1, which facilitates iron entry into the vacuole. Transcription of the CCC1 gene is largely regulated by the binding of iron-sulfur clusters to the activator domain of the transcriptional activator Yap5. Additional evidence, however, suggests that Yap5-independent transcriptional activation of CCC1 also contributes to iron resistance. Here, we demonstrate that components of the signaling pathway involving the low-glucose sensor Snf1 regulate CCC1 transcription and iron resistance. We found that SNF1 deletion acts synergistically with YAP5 deletion to regulate CCC1 transcription and iron resistance. A kinase-dead mutation of Snf1 lowered iron resistance as did deletion of SNF4 , which encodes a partner protein of Snf1. Deletion of all three alternative partners of Snf1 encoded by SIT1 , SIT2 , and GAL83 decreased both CCC1 transcription and iron resistance. The Snf1 complex is known to activate the general stress transcription factors Msn2 and Msn4. We show that Msn2 and Msn4 contribute to Snf1-mediated CCC1 transcription. Of note, SNF1 deletion in combination with MSN2 and MSN4 deletion resulted in additive effects on CCC1 transcription, suggesting that other activators contribute to the regulation of CCC1 transcription. In conclusion, we show that yeast have developed multiple transcriptional mechanisms to regulate Ccc1 expression and to protect against high cytosolic iron toxicity. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

ACK1/TNK2 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration-Resistant Prostate Cancer.

PubMed

Mahajan, Kiran; Malla, Pavani; Lawrence, Harshani R; Chen, Zhihua; Kumar-Sinha, Chandan; Malik, Rohit; Shukla, Sudhanshu; Kim, Jongphil; Coppola, Domenico; Lawrence, Nicholas J; Mahajan, Nupam P

2017-06-12

The androgen receptor (AR) is critical for the progression of prostate cancer to a castration-resistant (CRPC) state. AR antagonists are ineffective due to their inability to repress the expression of AR or its splice variant, AR-V7. Here, we report that the tyrosine kinase ACK1 (TNK2) phosphorylates histone H4 at tyrosine 88 upstream of the AR transcription start site. The WDR5/MLL2 complex reads the H4-Y88-phosphorylation marks and deposits the transcriptionally activating H3K4-trimethyl marks promoting AR transcription. Reversal of the pY88-H4 epigenetic marks by the ACK1 inhibitor (R)-9bMS-sensitized naive and enzalutamide-resistant prostate cancer cells and reduced AR and AR-V7 levels to mitigate CRPC tumor growth. Thus, a feedforward ACK1/pY88-H4/WDR5/MLL2/AR epigenetic circuit drives CRPC and is necessary for maintenance of the malignant state. Copyright © 2017 Elsevier Inc. All rights reserved.

Interaction between HIV-1 Tat and DNA-PKcs modulates HIV transcription and class switch recombination.

PubMed

Zhang, Shi-Meng; Zhang, He; Yang, Tian-Yi; Ying, Tian-Yi; Yang, Pei-Xiang; Liu, Xiao-Dan; Tang, Sheng-Jian; Zhou, Ping-Kun

2014-01-01

HIV-1 tat targets a variety of host cell proteins to facilitate viral transcription and disrupts host cellular immunity by inducing lymphocyte apoptosis, but whether it influences humoral immunity remains unclear. Previously, our group demonstrated that tat depresses expression of DNA-PKcs, a critical component of the non-homologous end joining pathway (NHEJ) of DNA double-strand breaks repair, immunoglobulin class switch recombination (CSR) and V(D)J recombination, and sensitizes cells to ionizing radiation. In this study, we demonstrated that HIV-1 Tat down-regulates DNA-PKcs expression by directly binding to the core promoter sequence. In addition, Tat interacts with and activates the kinase activity of DNA-PKcs in a dose-dependent and DNA independent manner. Furthermore, Tat inhibits class switch recombination (CSR) at low concentrations (≤ 4 µg/ml) and stimulates CSR at high concentrations (≥ 8 µg/ml). On the other hand, low protein level and high kinase activity of DNA-PKcs promotes HIV-1 transcription, while high protein level and low kinase activity inhibit HIV-1 transcription. Co-immunoprecipitation results revealed that DNA-PKcs forms a large complex comprised of Cyclin T1, CDK9 and Tat via direct interacting with CDK9 and Tat but not Cyclin T1. Taken together, our results provide new clues that Tat regulates host humoral immunity via both transcriptional depression and kinase activation of DNA-PKcs. We also raise the possibility that inhibitors and interventions directed towards DNA-PKcs may inhibit HIV-1 transcription in AIDS patients.

Introducing the refined gravity hypothesis of extreme sexual size dimorphism

PubMed Central

2010-01-01

Background Explanations for the evolution of female-biased, extreme Sexual Size Dimorphism (SSD), which has puzzled researchers since Darwin, are still controversial. Here we propose an extension of the Gravity Hypothesis (i.e., the GH, which postulates a climbing advantage for small males) that in conjunction with the fecundity hypothesis appears to have the most general power to explain the evolution of SSD in spiders so far. In this "Bridging GH" we propose that bridging locomotion (i.e., walking upside-down under own-made silk bridges) may be behind the evolution of extreme SSD. A biomechanical model shows that there is a physical constraint for large spiders to bridge. This should lead to a trade-off between other traits and dispersal in which bridging would favor smaller sizes and other selective forces (e.g. fecundity selection in females) would favor larger sizes. If bridging allows faster dispersal, small males would have a selective advantage by enjoying more mating opportunities. We predicted that both large males and females would show a lower propensity to bridge, and that SSD would be negatively correlated with sexual dimorphism in bridging propensity. To test these hypotheses we experimentally induced bridging in males and females of 13 species of spiders belonging to the two clades in which bridging locomotion has evolved independently and in which most of the cases of extreme SSD in spiders are found. Results We found that 1) as the degree of SSD increased and females became larger, females tended to bridge less relative to males, and that 2) smaller males and females show a higher propensity to bridge. Conclusions Physical constraints make bridging inefficient for large spiders. Thus, in species where bridging is a very common mode of locomotion, small males, by being more efficient at bridging, will be competitively superior and enjoy more mating opportunities. This "Bridging GH" helps to solve the controversial question of what keeps males small and also contributes to explain the wide range of SSD in spiders, as those spider species in which extreme SSD has not evolved but still live in tall vegetation, do not use bridging locomotion to disperse. PMID:20682029

Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform

PubMed Central

Pervaiz, Tariq; Haifeng, Jia; Salman Haider, Muhammad; Cheng, Zhang; Cui, Mengjie; Wang, Mengqi; Cui, Liwen; Wang, Xicheng; Fang, Jinggui

2016-01-01

Proceeding to illumina sequencing, determining RNA integrity numbers for poly RNA were separated from each of the four developmental stages of cv. Summer Black leaves by using Illumina HiSeq™ 2000. The sums of 272,941,656 reads were generated from vitis vinifera leaf at four different developmental stages, with more than 27 billion nucleotides of the sequence data. At each growth stage, RNA samples were indexed through unique nucleic acid identifiers and sequenced. KEGG annotation results depicted that the highest number of transcripts in 2,963 (2Avs4A) followed by 1Avs4A (2,920), and 3Avs4A (2,294) out of 15,614 (71%) transcripts were recorded. In comparison, a total of 1,532 transcripts were annotated in GOs, including Cellular component, with the highest number in “Cell part” 251 out of 353 transcripts (71.1%), followed by intracellular organelle 163 out of 353 transcripts (46.2%), while in molecular function and metabolic process 375 out of 525 (71.4%) transcripts, multicellular organism process 40 out of 525 (7.6%) transcripts in biological process were most common in 1Avs2A. While in case of 1Avs3A, cell part 476 out of 662 transcripts (71.9%), and membrane-bounded organelle 263 out of 662 transcripts (39.7%) were recorded in Cellular component. In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down-regulated and none of them were up-regulated. While in comparison of 1A to 3A showed one up-regulated (photosystem II reaction center protein C) and one down regulated (conserved gene of unknown function) transcripts, during the hormone regulating pathway namely SAUR-like auxin-responsive protein family having 2 up-regulated and 7 down-regulated transcripts, phytochrome-associated protein showed 1 up-regulated and 9 down-regulated transcripts, whereas genes associated with the Leucine-rich repeat protein kinase family protein showed 7 up-regulated and 1 down-regulated transcript, meanwhile Auxin Resistant 2 has single up-regulated transcript in second developmental stage, although 3 were down-regulated at lateral growth stages (3A and 4A). In the present study, 489 secondary metabolic pathways related genes were identified during leaf growth, which mainly includes alkaloid (40), anthocyanins (21), Diterpenoid (144), Monoterpenoid (90) and Flavonoids (93). Quantitative real-time PCR was applied to validate 10 differentially expressed transcripts patterns from flower, leaf and fruit metabolic pathways at different growth stages. PMID:26824474

Early growth response 1 (EGR-1) is a transcriptional regulator of mitochondrial carrier homolog 1 (MTCH 1)/presenilin 1-associated protein (PSAP).

PubMed

Nelo-Bazán, María Alejandra; Latorre, Pedro; Bolado-Carrancio, Alfonso; Pérez-Campo, Flor M; Echenique-Robba, Pablo; Rodríguez-Rey, José Carlos; Carrodeguas, José Alberto

2016-03-01

Attempts to elucidate the cellular function of MTCH1 (mitochondrial carrier homolog 1) have not yet rendered a clear insight into the function of this outer mitochondrial membrane protein. Classical biochemical and cell biology approaches have not produced the expected outcome. In vitro experiments have indicated a likely role in the regulation of cell death by apoptosis, and its reported interaction with presenilin 1 suggests a role in the cellular pathways in which this membrane protease participates, nevertheless in vivo data are missing. In an attempt to identify cellular pathways in which this protein might participate, we have studied its promoter looking for transcriptional regulators. We have identified several putative binding sites for EGR-1 (Early growth response 1; a protein involved in growth, proliferation and differentiation), in the proximal region of the MTCH1 promoter. Chromatin immunoprecipitation showed an enrichment of these sequences in genomic DNA bound to EGR-1 and transient overexpression of EGR-1 in cultured HEK293T cells induces an increase of endogenous MTCH1 levels. We also show that MTCH1 levels increase in response to treatment of cells with doxorubicin, an apoptosis inducer through DNA damage. The endogenous levels of MTCH1 decrease when EGR-1 levels are lowered by RNA interference. Our results indicate that EGR-1 is a transcriptional regulator of MTCH1 and give some clues about the cellular processes in which MTCH1 might participate. Copyright © 2015 Elsevier B.V. All rights reserved.

Source to Skin Distance (SSD) Characteristics from Varian CX Linear Accelerator

NASA Astrophysics Data System (ADS)

Bahari Nurdin, Wira; Purnomo, Aji; Dewang, Syamsir

2018-03-01

This study aims to describe the characteristics of the source to skin distance (SSD) of Varian CX linear accelerator (LINAC) using the X-ray beam of 6 MV and 10 MV. The variation of the source to the SSD are 90, 100 and 110 cms; the depth of the water phantom used are 5, 10, 15, 20, and 25 cms, respectively. The depth of the water phantom was created for analysis of percentage depth dose (PDD) and profile dose. It can be concluded from the tests that from the measured SSD, SSD of 110 cm with the depth water phantom of 20-25 cm for energy beam of 6 MV and at all levels of depth for 10 MV energy corresponding tolerance limits to be used in clinical radiotherapy. For the SSD 90 and 100, the values beam symmetry and flatness obtained slightly beyond the limits of tolerance.

Surface Solid Dispersion and Solid Dispersion of Meloxicam: Comparison and Product Development.

PubMed

Chaturvedi, Mayank; Kumar, Manish; Pathak, Kamla; Bhatt, Shailendra; Saini, Vipin

2017-12-01

Purpose: A comparative study was carried out between surface solid dispersion (SSD) and solid dispersion (SD) of meloxicam (MLX) to assess the solubility and dissolution enhancement approach and thereafter develop as patient friendly orodispersible tablet. Methods: Crospovidone (CPV), a hydrophilic carrier was selected for SSD preparation on the basis of 89% in- vitro MLX adsorption, 19% hydration capacity and high swelling index. SD on the other hand was made with PEG4000. Both were prepared by co-grinding and solvent evaporation method using drug: carrier ratios of 1:1, 1:4, and 1:8. Formulation SSDS3 (MLX: CPV in 1:8 ratio) made by solvent evaporation method showed t 50% of 28 min and 80.9% DE 50min which was higher in comparison to the corresponding solid dispersion, SDS3 (t 50% of 35min and 76.4% DE 50min ). Both SSDS3 and SDS3 were developed as orodispersible tablets and evaluated. Results: Tablet formulation F3 made with SSD3 with a disintegration time of 11 secs, by wetting time= 6 sec, high water absorption of 78%by wt and cumulative drug release of 97% proved to be superior than the tablet made with SD3. Conclusion: Conclusively, the SSD of meloxicam has the potential to be developed as fast acing formulation that can ensure almost complete release of drug.

Oral administration of Lactobacillus plantarum 299v modulates gene expression in the ileum of pigs: prediction of crosstalk between intestinal immune cells and sub-mucosal adipocytes.

PubMed

Hulst, Marcel; Gross, Gabriele; Liu, Yaping; Hoekman, Arjan; Niewold, Theo; van der Meulen, Jan; Smits, Mari

2015-05-01

To study host-probiotic interactions in parts of the intestine only accessible in humans by surgery (jejunum, ileum and colon), pigs were used as model for humans. Groups of eight 6-week-old pigs were repeatedly orally administered with 5 × 10(12) CFU Lactobacillus plantarum 299v (L. plantarum 299v) or PBS, starting with a single dose followed by three consecutive daily dosings 10 days later. Gene expression was assessed with pooled RNA samples isolated from jejunum, ileum and colon scrapings of the eight pigs per group using Affymetrix porcine microarrays. Comparison of gene expression profiles recorded from L. plantarum 299v-treated pigs with PBS-treated pigs indicated that L. plantarum 299v affected metabolic and immunological processes, particularly in the ileum. A higher expression level of several B cell-specific transcription factors/regulators was observed, suggesting that an influx of B cells from the periphery to the ileum and/or the proliferation of progenitor B cells to IgA-committed plasma cells in the Peyer's patches of the ileum was stimulated. Genes coding for enzymes that metabolize leukotriene B4, 1,25-dihydroxyvitamin D3 and steroids were regulated in the ileum. Bioinformatics analysis predicted that these metabolites may play a role in the crosstalk between intestinal immune cells and sub-mucosal adipocytes. Together with regulation of genes that repress NFKB- and PPARG-mediated transcription, this crosstalk may contribute to tempering of inflammatory reactions. Furthermore, the enzyme adenosine deaminase, responsible for the breakdown of the anti-inflammatory mediator adenosine, was strongly down-regulated in response to L. plantarum 299v. This suggested that L. plantarum 299v-regulated production of adenosine by immune cells like regulatory T cells may also be a mechanism that tempers inflammation in the ileum, and perhaps also in other parts of the pig's body.

Nursing preference of topical silver sulfadiazine versus collagenase ointment for treatment of partial thickness burns in children: survey follow-up of a prospective randomized trial.

PubMed

Sharp, Nicole E; Aguayo, Pablo; Marx, Daniel J; Polak, Erin E; Rash, Diane E; Peter, Shawn D; Ostlie, Daniel J; Juang, David

2014-01-01

We performed a nursing survey to inquire about nursing preferences toward the use of silver sulfadiazine (SSD) and collagenase (CO). We performed a survey between September 2012 and December 2012 asking nurses to rate the application/removal of both products and provide a description of their preferences. Ten study nurses (83%) preferred CO over SSD (P < .001). Two nurses (17%) had no preference. Negative comments on SSD were pseudoeschar (50%), difficult application burns (25%), messiness (67%), and increased number of dressing changes (25%). Negative comments on CO were the need for an additional antimicrobial agent (58%), although 1 nurse noted the higher expense with CO. Nurses preferred CO because of cleanliness of dressing (17%), lack of pseudoeschar (25%), and less pain with dressing changes (8%). Despite no difference in outcomes between SSD and CO, experienced burn nurses prefer CO because of perceptions of decreased trauma and frequency of dressing changes.

The DNA Replication Checkpoint Directly Regulates MBF-Dependent G1/S Transcription▿

PubMed Central

Dutta, Chaitali; Patel, Prasanta K.; Rosebrock, Adam; Oliva, Anna; Leatherwood, Janet; Rhind, Nicholas

2008-01-01

The DNA replication checkpoint transcriptionally upregulates genes that allow cells to adapt to and survive replication stress. Our results show that, in the fission yeast Schizosaccharomyces pombe, the replication checkpoint regulates the entire G1/S transcriptional program by directly regulating MBF, the G1/S transcription factor. Instead of initiating a checkpoint-specific transcriptional program, the replication checkpoint targets MBF to maintain the normal G1/S transcriptional program during replication stress. We propose a mechanism for this regulation, based on in vitro phosphorylation of the Cdc10 subunit of MBF by the Cds1 replication-checkpoint kinase. Replacement of two potential phosphorylation sites with phosphomimetic amino acids suffices to promote the checkpoint transcriptional program, suggesting that Cds1 phosphorylation directly regulates MBF-dependent transcription. The conservation of MBF between fission and budding yeast, and recent results implicating MBF as a target of the budding yeast replication checkpoint, suggests that checkpoint regulation of the MBF transcription factor is a conserved strategy for coping with replication stress. Furthermore, the structural and regulatory similarity between MBF and E2F, the metazoan G1/S transcription factor, suggests that this checkpoint mechanism may be broadly conserved among eukaryotes. PMID:18662996

Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions.

PubMed

Li, Ping; Shi, Ming-Lei; Shen, Wen-Long; Zhang, Zhang; Xie, De-Jian; Zhang, Xiang-Yuan; He, Chao; Zhang, Yan; Zhao, Zhi-Hu

2017-08-01

Interferon-induced transmembrane protein (IFITM) 1, 2 and 3 genes encode a family of interferon (IFN)-induced transmembrane proteins that block entry of a broad spectrum of pathogens. However, the transcriptional regulation of these genes, especially whether there exist any enhancers and their roles during the IFN induction process remain elusive. Here, through public data mining, episomal luciferase reporter assay and in vivo CRISPR-Cas9 genome editing, we identified an IFN-responsive enhancer located 35kb upstream of IFITM3 gene promoter upregulating the IFN-induced expression of IFITM1, 2 and 3 genes. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA) and luciferase reporter assay demonstrated that signal transducers and activators of transcription (STAT) 1 bound to the enhancer with the treatment of IFN and was indispensable for the enhancer activity. Furthermore, using chromosome conformation capture technique, we revealed that the IFITM1, 2 and 3 genes physically clustered together and constitutively looped to the distal enhancer through long-range interactions in both HEK293 and A549 cells, providing structural basis for coordinated regulation of IFITM1, 2 and 3 by the enhancer. Finally, we showed that in vivo truncation of the enhancer impaired IFN-induced resistance to influenza A virus (IAV) infection. These findings expand our understanding of the mechanisms underlying the transcriptional regulation of IFITM1, 2 and 3 expression and its ability to mediate IFN signaling. Copyright © 2017 Elsevier B.V. All rights reserved.

Sensitivity to Structure in the Speech Signal by Children with Speech Sound Disorder and Reading Disability

PubMed Central

Johnson, Erin Phinney; Pennington, Bruce F.; Lowenstein, Joanna H.; Nittrouer, Susan

2011-01-01

Purpose Children with speech sound disorder (SSD) and reading disability (RD) have poor phonological awareness, a problem believed to arise largely from deficits in processing the sensory information in speech, specifically individual acoustic cues. However, such cues are details of acoustic structure. Recent theories suggest that listeners also need to be able to integrate those details to perceive linguistically relevant form. This study examined abilities of children with SSD, RD, and SSD+RD not only to process acoustic cues but also to recover linguistically relevant form from the speech signal. Method Ten- to 11-year-olds with SSD (n = 17), RD (n = 16), SSD+RD (n = 17), and Controls (n = 16) were tested to examine their sensitivity to (1) voice onset times (VOT); (2) spectral structure in fricative-vowel syllables; and (3) vocoded sentences. Results Children in all groups performed similarly with VOT stimuli, but children with disorders showed delays on other tasks, although the specifics of their performance varied. Conclusion Children with poor phonemic awareness not only lack sensitivity to acoustic details, but are also less able to recover linguistically relevant forms. This is contrary to one of the main current theories of the relation between spoken and written language development. PMID:21329941

Automatic verification of SSD and generation of respiratory signal with lasers in radiotherapy: a preliminary study.

PubMed

Prabhakar, Ramachandran

2012-01-01

Source to surface distance (SSD) plays a very important role in external beam radiotherapy treatment verification. In this study, a simple technique has been developed to verify the SSD automatically with lasers. The study also suggests a methodology for determining the respiratory signal with lasers. Two lasers, red and green are mounted on the collimator head of a Clinac 2300 C/D linac along with a camera to determine the SSD. A software (SSDLas) was developed to estimate the SSD automatically from the images captured by a 12-megapixel camera. To determine the SSD to a patient surface, the external body contour of the central axis transverse computed tomography (CT) cut is imported into the software. Another important aspect in radiotherapy is the generation of respiratory signal. The changes in the lasers separation as the patient breathes are converted to produce a respiratory signal. Multiple frames of laser images were acquired from the camera mounted on the collimator head and each frame was analyzed with SSDLas to generate the respiratory signal. The SSD as observed with the ODI on the machine and SSD measured by the SSDlas software was found to be within the tolerance limit. The methodology described for generating the respiratory signals will be useful for the treatment of mobile tumors such as lung, liver, breast, pancreas etc. The technique described for determining the SSD and the generation of respiratory signals using lasers is cost effective and simple to implement. Copyright © 2011 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Evolution of sexual dimorphism and Rensch’s rule in the beetle genus Limnebius (Hydraenidae): is sexual selection opportunistic?

PubMed Central

Rudoy, Andrey

2017-01-01

Sexual size dimorphism (SSD) is widespread among animals, with larger females usually attributed to an optimization of resources in reproduction and larger males to sexual selection. A general pattern in the evolution of SSD is Rensch’s rule, which states that SSD increases with body size in species with larger males but decreases when females are larger. We studied the evolution of SSD in the genus Limnebius (Coleoptera, Hydraenidae), measuring SSD and male genital size and complexity of ca. 80% of its 150 species and reconstructing its evolution in a molecular phylogeny with 71 species. We found strong support for a higher evolutionary lability of male body size, which had an overall positive allometry with respect to females and higher evolutionary rates measured over the individual branches of the phylogeny. Increases in SSD were associated to increases in body size, but there were some exceptions with an increase associated to changes in only one sex. Secondary sexual characters (SSC) in the external morphology of males appeared several times independently, generally on species that had already increased their size. There was an overall significant correlation between SSD, male body size and male genital size and complexity, although some lineages with complex genitalia had low SSD, and some small species with complex genitalia had no SSD. Our results suggest that the origin of the higher evolutionary variance of male body size may be due to lack of constraints rather than to sexual selection, that may start to act in species with already larger males due to random variation. PMID:28286715

Evolution of sexual dimorphism and Rensch's rule in the beetle genus Limnebius (Hydraenidae): is sexual selection opportunistic?

PubMed

Rudoy, Andrey; Ribera, Ignacio

2017-01-01

Sexual size dimorphism (SSD) is widespread among animals, with larger females usually attributed to an optimization of resources in reproduction and larger males to sexual selection. A general pattern in the evolution of SSD is Rensch's rule, which states that SSD increases with body size in species with larger males but decreases when females are larger. We studied the evolution of SSD in the genus Limnebius (Coleoptera, Hydraenidae), measuring SSD and male genital size and complexity of ca. 80% of its 150 species and reconstructing its evolution in a molecular phylogeny with 71 species. We found strong support for a higher evolutionary lability of male body size, which had an overall positive allometry with respect to females and higher evolutionary rates measured over the individual branches of the phylogeny. Increases in SSD were associated to increases in body size, but there were some exceptions with an increase associated to changes in only one sex. Secondary sexual characters (SSC) in the external morphology of males appeared several times independently, generally on species that had already increased their size. There was an overall significant correlation between SSD, male body size and male genital size and complexity, although some lineages with complex genitalia had low SSD, and some small species with complex genitalia had no SSD. Our results suggest that the origin of the higher evolutionary variance of male body size may be due to lack of constraints rather than to sexual selection, that may start to act in species with already larger males due to random variation.

Domestic chickens defy Rensch's rule: sexual size dimorphism in chicken breeds.

PubMed

Remeš, V; Székely, T

2010-12-01

Sexual size dimorphism (SSD), i.e. the difference in sizes of males and females, is a key evolutionary feature that is related to ecology, behaviour and life histories of organisms. Although the basic patterns of SSD are well documented for several major taxa, the processes generating SSD are poorly understood. Domesticated animals offer excellent opportunities for testing predictions of functional explanations of SSD theory because domestic stocks were often selected by humans for particular desirable traits. Here, we analyse SSD in 139 breeds of domestic chickens Gallus gallus domesticus and compare them to their wild relatives (pheasants, partridges and grouse; Phasianidae, 53 species). SSD was male-biased in all chicken breeds, because males were 21.5 ± 0.55% (mean ± SE) heavier than females. The extent of SSD did not differ among breed categories (cock fighting, ornamental and breeds selected for egg and meat production). SSD of chicken breeds was not different from wild pheasants and allies (23.5 ± 3.43%), although the wild ancestor of chickens, the red jungle fowl G. gallus, had more extreme SSD (male 68.8% heavier) than any domesticated breed. Male mass and female mass exhibited positive allometry among pheasants and allies, consistently with the Rensch's rule reported from various taxa. However, body mass scaled isometrically across chicken breeds. The latter results suggest that sex-specific selection on males vs. females is necessary to generate positive allometry, i.e. the Rensch's rule, in wild populations. © 2010 The Authors. Journal Compilation © 2010 European Society For Evolutionary Biology.

Genome-wide transcriptome profiling of nitrogen fixation in Paenibacillus sp. WLY78.

PubMed

Shi, Hao-wen; Wang, Li-ying; Li, Xin-xin; Liu, Xiao-meng; Hao, Tian-yi; He, Xiao-juan; Chen, San-feng

2016-03-01

Diazotrophic (nitrogen-fixing) Gram-positive and endospore-formed Paenibacillus spp. have potential uses as a bacterial fertilizer in agriculture. The transcriptional analysis of nitrogen fixation in Paenibacillus is lacking, although regulation mechanisms of nitrogen fixation have been well studied in Gram-negative diazotrophs. Here we report a global transcriptional profiling analysis of nitrogen fixation in Paenibacillus sp. WLY78 cultured under N2-fixing condition (without O2 and NH4(+)) and non-N2-fixing condition (air and 100 mM NH4(+)). The nif (nitrogen fixation) gene operon composed of 9 genes (nifBHDKENXhesAnifV) in this bacterium was significantly up-regulated in N2-fixing condition compared to non-N2-fixing condition, indicating that nif gene transcription is strictly controlled by NH4(+) and O2. qRT-PCR confirmed that these nif genes were differently expressed. Non-nif genes specifically required in nitrogen fixation, such as mod, feoAB and cys encoding transporters of Mo, Fe and S atoms, were coordinately transcribed with nif genes in N2-fixing condition. The transcript abundance of suf operon specific for synthesis of Fe-S cluster was up-regulated in N2-fixing condition, suggesting that Sul system, which takes place of nifS and nifU, plays important role in the synthesis of nitrogenase. We discover potential specific electron transporters which might provide electron from Fe protein to MoFe protein of nitrogenase. The glnR whose predicted protein might mediate nif transcription regulation by NH4(+) is significantly up-regulated in N2-fixing condition. The transcription levels of nitrogen metabolism and anaerobic respiration were also analyzed. The nif gene operon (nifBHDKENXhesAnifV) in Paenibacillus sp. WLY78 is significantly up-regulated in N2-fixing condition compared to non-N2-fixing condition. Non-nif genes specifically required in nitrogen fixation were also significantly up-regulated in N2-fixing condition. Fur and Fnr which are involved in anaerobic regulation and GlnR which might mediate nif gene transcription regulation by NH4(+) were significantly up-regulated in N2-fixing condition. This study provides valuable insights into nitrogen fixation process and regulation in Gram-positive firmicutes.

SiC As An Energetic Particle Detector

NASA Technical Reports Server (NTRS)

Yan, F.; Hicks, J.; Shappirio, Mark D.; Brown, S.; Smith, C.; Xin, X.; Zhao, J. H.

2005-01-01

Several new technologies have been introduced recently in the region of semiconductor material for solid state detectors (SSD). Of particular interest is silicon carbide (SIC) since its band gap is larger than that of pure silicon, reducing its dark current and making SIC capable of operating at high temperatures and more tolerant of radiation damage. But the trade off is that a higher band gap also means fewer electron hole pairs generated, and thus a smaller signal, for detecting incident radiation. To determine what the lower limit of SiC detectors to energetic particles is, we irradiated a SiC diode with particles ranging in energy from 50 keV to 1.6 MeV and masses from 1 to 16 amu. We found that the SiC detectors sensitivity was comparable to that of pure silicon, with the SiC detector being able to measure particles down to 50 keV/amu and possibly lower.

Identification of insulin as a novel retinoic acid receptor-related orphan receptor α target gene.

PubMed

Kuang, Jiangying; Hou, Xiaoming; Zhang, Jinlong; Chen, Yulong; Su, Zhiguang

2014-03-18

Insulin plays an important role in regulation of lipid and glucose metabolism. Retinoic acid receptor-related orphan receptor α (RORα) modulates physiopathological processes such as dyslipidemia and diabetes. In this study, we found overexpression of RORα in INS1 cells resulted in increased expression and secretion of insulin. Suppression of endogenous RORα caused a decrease of insulin expression. Luciferase and electrophoretic mobility shift assay (EMSA) assays demonstrated that RORα activated insulin transcription via direct binding to its promoter. RORα was also observed to regulate BETA2 expression, which is one of the insulin active transfactors. In vivo analyses showed that the insulin transcription is increased by the synthetic RORα agonist SR1078. These findings identify RORα as a transcriptional activator of insulin and suggest novel therapeutic opportunities for management of the disease. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Strong support for Rensch's rule in an American clade of lizards (Teiidae and Gymnophtalmidae) and a paradox of the largest tejus

NASA Astrophysics Data System (ADS)

Frýdlová, Petra; Frynta, Daniel

2015-06-01

Rensch's rule predicts an allometric relationship between male and female body size stating that the sexual size dimorphism (SSD) increases with body size in male-larger taxa and decreases in female-larger taxa in groups of related species. It means that the relationship between the male and female body size is hyperallometric, i.e., the allometric exponent of this relationship exceeds the unity. We explored the relationship between the male and female body size in a New World clade of lizards consisting of sister families Teiidae and Gymnophthalmidae, which exhibit a great variation in both their adult body sizes and SSD. All our estimates of the reduced major axis regression slopes ranged from 1.067 to 1.229 and clearly followed a pattern consistent with the Rensch's rule. Despite a clear general trend, giant species from the subfamily Tupinambinae show paradoxically only poor SSD. The cases of extreme male-larger SSD were found in species of moderate body size belonging to the genera Ameiva and Cnemidophorus. The abovementioned deviations from the hyperallometric relationship between the male and female body size are surprising and require further examination.

Strong support for Rensch's rule in an American clade of lizards (Teiidae and Gymnophtalmidae) and a paradox of the largest tejus.

PubMed

Frýdlová, Petra; Frynta, Daniel

2015-06-01

Rensch's rule predicts an allometric relationship between male and female body size stating that the sexual size dimorphism (SSD) increases with body size in male-larger taxa and decreases in female-larger taxa in groups of related species. It means that the relationship between the male and female body size is hyperallometric, i.e., the allometric exponent of this relationship exceeds the unity. We explored the relationship between the male and female body size in a New World clade of lizards consisting of sister families Teiidae and Gymnophthalmidae, which exhibit a great variation in both their adult body sizes and SSD. All our estimates of the reduced major axis regression slopes ranged from 1.067 to 1.229 and clearly followed a pattern consistent with the Rensch's rule. Despite a clear general trend, giant species from the subfamily Tupinambinae show paradoxically only poor SSD. The cases of extreme male-larger SSD were found in species of moderate body size belonging to the genera Ameiva and Cnemidophorus. The abovementioned deviations from the hyperallometric relationship between the male and female body size are surprising and require further examination.

The fission yeast CENP-B protein Abp1 prevents pervasive transcription of repetitive DNA elements.

PubMed

Daulny, Anne; Mejía-Ramírez, Eva; Reina, Oscar; Rosado-Lugo, Jesus; Aguilar-Arnal, Lorena; Auer, Herbert; Zaratiegui, Mikel; Azorin, Fernando

2016-10-01

It is well established that eukaryotic genomes are pervasively transcribed producing cryptic unstable transcripts (CUTs). However, the mechanisms regulating pervasive transcription are not well understood. Here, we report that the fission yeast CENP-B homolog Abp1 plays an important role in preventing pervasive transcription. We show that loss of abp1 results in the accumulation of CUTs, which are targeted for degradation by the exosome pathway. These CUTs originate from different types of genomic features, but the highest increase corresponds to Tf2 retrotransposons and rDNA repeats, where they map along the entire elements. In the absence of abp1, increased RNAPII-Ser5P occupancy is observed throughout the Tf2 coding region and, unexpectedly, RNAPII-Ser5P is enriched at rDNA repeats. Loss of abp1 also results in Tf2 derepression and increased nucleolus size. Altogether these results suggest that Abp1 prevents pervasive RNAPII transcription of repetitive DNA elements (i.e., Tf2 and rDNA repeats) from internal cryptic sites. Copyright © 2016 Elsevier B.V. All rights reserved.

Research of beam conditioning technologies on SG-III laser facility

NASA Astrophysics Data System (ADS)

Zhang, Rui; Su, Jingqin; Yuan, Haoyu; Li, Ping; Tian, Xiaocheng; Wang, Jianjun; Dong, Jun; Zhang, Ying; Yuan, Qiang; Wang, Yuancheng; Zhou, Wei; Peng, Zhitao; Wang, Fang; Hu, Dongxia; Zhu, Qihua; Zheng, Wanguo; Zhang, Xiaomin

2014-12-01

Multi-FM SSD and CPP was experimentally studied in high fluence and will be equipped on all the beams of SG-III laser facility. The output spectrum of the cascade phase modulators are stable and the residual amplitude modulation is small. FM-to-AM effect caused by free-space propagation after using smoothing by spectral dispersion is theoretically analyzed. Results indicate inserting a dispersion grating in places with larger beam aperture could alleviate the FM-to- AM effect, suggesting minimizing free-space propagation and adopting image relay. Experiments taken on SG-III laser facility indicate when the number of color cycles (Nc) adopts 1, imposing of SSD with 3.3 times diffraction limit (TDL) did not lead to pinhole closure in the spatial filters of the preamplifier and main amplifier with 30-TDL pinhole size. The nonuniformity of the focal spot using Multi-FM SSD and CPP drops to 0.26, comparing to 0.84 only using CPP. The experiments solve some key technical problems using SSD and CPP on SG-III laser facility, and provide a flexible platform for laser-plasma interaction experiments. Combined beam smoothing and polarization smoothing are also analyzed. Simulation results indicate through adjusting dispersion directions of one-dimensional SSD beams in a quad, two-dimensional SSD could be obtained. The near field and far field properties of beams using polarization smoothing were also studied, including birefringent wedge and polarization control plate (PCP). By using PCP, cylindrical vector beams could be obtained. New solutions will be provided to solve the LPI problem encountered in indirect drive laser fusion.

Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence.

PubMed

Davies, Bryan W; Bogard, Ryan W; Young, Travis S; Mekalanos, John J

2012-04-13

The function of the Vibrio 7(th) pandemic island-1 (VSP-1) in cholera pathogenesis has remained obscure. Utilizing chromatin immunoprecipitation sequencing and RNA sequencing to map the regulon of the master virulence regulator ToxT, we identify a TCP island-encoded small RNA that reduces the expression of a previously unrecognized VSP-1-encoded transcription factor termed VspR. VspR modulates the expression of several VSP-1 genes including one that encodes a novel class of di-nucleotide cyclase (DncV), which preferentially synthesizes a previously undescribed hybrid cyclic AMP-GMP molecule. We show that DncV is required for efficient intestinal colonization and downregulates V. cholerae chemotaxis, a phenotype previously associated with hyperinfectivity. This pathway couples the actions of previously disparate genomic islands, defines VSP-1 as a pathogenicity island in V. cholerae, and implicates its occurrence in 7(th) pandemic strains as a benefit for host adaptation through the production of a regulatory cyclic di-nucleotide. Copyright © 2012 Elsevier Inc. All rights reserved.

A reticle retrofit and dosimetric consideration for a linear accelerator.

PubMed

Krithivas, V

1996-01-01

An imperfect reticle system in an accelerator causes uncertainties in source-skin distance (SSD), off-axis distance (OAD), isocenter, and so forth. A reticle was designed and fabricated, and its implications on x-ray and electron beam dosimetry were investigated. A new reticle frame was dimensioned to fit snugly in the accelerator. The frame was fabricated to carry a pair of adjustable cross wires and to allow the machine operation in the photon and electron modes. The impact of the cross wires on 6 MV photon and 5-10 MeV electron beam parameters such as dose rate (Gy/monitor unit), beam uniformity, surface dose, and so forth, were studied using suitable ion chambers and phantoms. The retrofitted system offered long-term mechanical stability leading to precise SSD, OAD, and isocenter measurements. Changes introduced by the cross wires on the 6 MV photon and 5-10 MeV electron beams are presented. Long-term stability of a reticle in an accelerator is important for an accurate patient setup and for making reliable dosimetric measurements. Beam characteristrics have to be studied whenever modifications on a reticle system are made.

Increasing the treatment motivation of patients with somatic symptom disorder: applying the URICA-S scale.

PubMed

Mander, Johannes; Schaller, Georg; Bents, Hinrich; Dinger, Ulrike; Zipfel, Stephan; Junne, Florian

2017-07-03

Therapeutic intervention programs for somatic symptom disorder (SSD) show only small-to-moderate effect sizes. These effects are partly explained by the motivational problems of SSD patients. Hence, fostering treatment motivation could increase treatment success. One central aspect in SSD patients might be damage to motivation because of symptomatic relapses. Consequently, the aim of the present study was to investigate associations between motivational relapse struggle and therapeutic outcome in SSD patients. We assessed 84 inpatients diagnosed with SSD in the early, middle and late stages of their inpatient treatment. The maintenance subscale of the University of Rhode Island Change Assessment-Short (URICA-S) was applied as a measure to assess motivational relapse struggle. Additionally, patients completed measures of treatment outcome that focus on clinical symptoms, stress levels and interpersonal functioning. The results from multiple regression analyses indicate that higher URICA-S maintenance scores assessed in early stages of inpatient treatment were related to more negative treatment outcomes in SSD patients. SSD patients with ambivalent treatment motivation may fail in their struggle against relapse over the course of therapy. The URICA-S maintenance score assessed at therapy admission facilitated early identification of SSD patients who are at greater risk of relapse. Future studies should incorporate randomized controlled trials to investigate whether this subgroup could benefit from motivational interventions that address relapse.

Selective deficit in spatial memory strategies contrast to intact response strategies in patients with schizophrenia spectrum disorders tested in a virtual navigation task.

PubMed

Wilkins, Leanne K; Girard, Todd A; Konishi, Kyoko; King, Matthew; Herdman, Katherine A; King, Jelena; Christensen, Bruce; Bohbot, Veronique D

2013-11-01

Spatial memory is impaired among persons with schizophrenia (SCZ). However, different strategies may be used to solve most spatial memory and navigation tasks. This study investigated the hypothesis that participants with schizophrenia-spectrum disorders (SSD) would demonstrate differential impairment during acquisition and retrieval of target locations when using a hippocampal-dependent spatial strategy, but not a response strategy, which is more associated with caudate function. Healthy control (CON) and SSD participants were tested using the 4-on-8 virtual maze (4/8VM), a virtual navigation task designed to differentiate between participants' use of spatial and response strategies. Consistent with our predictions, SSD participants demonstrated a differential deficit such that those who navigated using a spatial strategy made more errors and took longer to locate targets. In contrast, SSD participants who spontaneously used a response strategy performed as well as CON participants. The differential pattern of spatial-memory impairment in SSD provides only indirect support for underlying hippocampal dysfunction. These findings emphasize the importance of considering individual strategies when investigating SSD-related memory and navigation performance. Future cognitive intervention protocols may harness SSD participants' intact ability to navigate using a response strategy and/or train the deficient ability to navigate using a spatial strategy to improve navigation and memory abilities in participants with SSD. Copyright © 2013 Wiley Periodicals, Inc.

The transcriptional regulatory network of Corynebacterium jeikeium K411 and its interaction with metabolic routes contributing to human body odor formation.

PubMed

Barzantny, Helena; Schröder, Jasmin; Strotmeier, Jasmin; Fredrich, Eugenie; Brune, Iris; Tauch, Andreas

2012-06-15

Lipophilic corynebacteria are involved in the generation of volatile odorous products in the process of human body odor formation by degrading skin lipids and specific odor precursors. Therefore, these bacteria represent appropriate model systems for the cosmetic industry to examine axillary malodor formation on the molecular level. To understand the transcriptional control of metabolic pathways involved in this process, the transcriptional regulatory network of the lipophilic axilla isolate Corynebacterium jeikeium K411 was reconstructed from the complete genome sequence. This bioinformatic approach detected a gene-regulatory repertoire of 83 candidate proteins, including 56 DNA-binding transcriptional regulators, nine two-component systems, nine sigma factors, and nine regulators with diverse physiological functions. Furthermore, a cross-genome comparison among selected corynebacterial species of the taxonomic cluster 3 revealed a common gene-regulatory repertoire of 44 transcriptional regulators, including the MarR-like regulator Jk0257, which is exclusively encoded in the genomes of this taxonomical subline. The current network reconstruction comprises 48 transcriptional regulators and 674 gene-regulatory interactions that were assigned to five interconnected functional modules. Most genes involved in lipid degradation are under the combined control of the global cAMP-sensing transcriptional regulator GlxR and the LuxR-family regulator RamA, probably reflecting the essential role of lipid degradation in C. jeikeium. This study provides the first genome-scale in silico analysis of the transcriptional regulation of metabolism in a lipophilic bacterium involved in the formation of human body odor. Copyright © 2012 Elsevier B.V. All rights reserved.

CalR is required for the expression of T6SS2 and the adhesion of Vibrio parahaemolyticus to HeLa cells.

PubMed

Zhang, Lingyu; Osei-Adjei, George; Zhang, Ying; Gao, He; Yang, Wenhui; Zhou, Dongsheng; Huang, Xinxiang; Yang, Huiying; Zhang, Yiquan

2017-08-01

Vibrio parahaemolyticus expresses one major virulence determinant T6SS2, which is constituted into three putative operons, i.e., VPA1027-1024, VPA1043-1028, and VPA1044-1046. CalR, a LysR-type transcriptional regulator, was originally identified as a repressor of the swarming motility and T3SS1 gene expression. As shown in this study, CalR binds to the promoter-proximal region of each of the three operons to activate their transcription, and moreover, CalR activates the adhesion of V. parahaemolyticus to HeLa cells. In addition, competitive EMSAs demonstrated that CalR acts as an antagonist of H-NS in V. parahaemolyticus. Collectively, these studies confirmed a new physiological role for CalR in V. parahaemolyticus.

An Objective Short Sleep Insomnia Disorder Subtype Is Associated With Reduced Brain Metabolite Concentrations In Vivo: A Preliminary Magnetic Resonance Spectroscopy Assessment.

PubMed

Miller, Christopher B; Rae, Caroline D; Green, Michael A; Yee, Brendon J; Gordon, Christopher J; D'Rozario, Angela L; Kyle, Simon D; Espie, Colin A; Grunstein, Ronald R; Bartlett, Delwyn J

2017-11-01

To evaluate brain metabolites in objective insomnia subtypes defined from polysomnography (PSG): insomnia with short sleep duration (I-SSD) and insomnia with normal sleep duration (I-NSD), relative to good sleeping controls (GSCs). PSG empirically grouped insomnia patients into I-SSD (n = 12: mean [SD] total sleep time [TST] = 294.7 minutes [30.5]) or I-NSD (n = 19: TST = 394.4 minutes [34.9]). 1H magnetic resonance spectroscopy (MRS) acquired in the left occipital cortex (LOCC), left prefrontal cortex, and anterior cingulate cortex was used to determine levels of creatine, aspartate, glutamate, and glutamine (referenced to water). Glutathione, glycerophosphocholine, lactate, myoinositol, and N-acetylaspartate measurements were also obtained. Sixteen GSCs were included for comparison. Multivariate analysis of variance was used to evaluate differences in creatine, aspartate, glutamate, and glutamine. Aspartate and glutamine concentrations were reduced in the LOCC in I-SSD compared with I-NSD (both p < .05, d = .80-.99). Creatine displayed a nonsignificant mean reduction in I-SSD compared with I-NSD (p = .05, d = .58). Glutamine was reduced in I-SSD compared with controls (p < .05, d = .93). There were no differences in metabolites between all (I-SSD and I-NSD) insomnia patients and controls. In patients with insomnia, LOCC glutamine concentrations were found to be positively correlated with TST (r = .43, p < .05) and negatively correlated with wake-time after sleep onset (r = -.40, p < .05). Results indicate that I-SSD is associated with reduced brain metabolites in the LOCC compared with I-NSD and control concentrations of aspartate, glutamine, and creatine. Insomnia MRS imaging sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR): https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=12612000050853. 12612000050853. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

Characterization of two homeodomain transcription factors with critical but distinct roles in virulence in the vascular pathogen Verticillium dahliae.

PubMed

Sarmiento-Villamil, Jorge L; Prieto, Pilar; Klosterman, Steven J; García-Pedrajas, María D

2018-04-01

Vascular wilt caused by Verticillium dahliae is a destructive disease that represents a chronic economic problem for crop production worldwide. In this work, we characterized two new regulators of pathogenicity in this species. Vph1 (VDAG_06555) was identified in a candidate gene approach as a putative homologue of the transcription factor Ste12. Vhb1 (VDAG_08786), identified in a forward genetics approach, is similar to the homeobox transcription factor Htf1, reported as a regulator of conidiogenesis in several fungi. Deletion of vph1 did not affect vegetative growth, whereas deletion of vhb1 greatly reduced sporulation rates in liquid medium. Both mutants failed to induce Verticillium wilt symptoms. However, unlike Δvph1, Δvhb1 could be re-isolated from the vascular system of some asymptomatic plants. Confocal microscopy further indicated that Δvph1 and Δvhb1 differed in their behaviour in planta; Δvph1 could not penetrate the root cortex, whereas Δvhb1 was impaired in its ability to colonize the xylem. In agreement with these observations, only Δvhb1 could penetrate cellophane paper. On cellophane, wild-type and Δvhb1 strains produced numerous short branches with swollen tips, resembling the hyphopodia formed on root surfaces, contrasting with Δvph1, which generated unbranched long filaments without swollen tips. A microarray analysis showed that these differences in growth were associated with differences in global transcription patterns, and allowed us to identify a large set of novel genes potentially involved in virulence in V. dahliae. Ste12 homologues are known regulators of invasive growth, but Vhb1 is the first putative Htf1 homologue identified with a critical role in virulence. © 2017 BSPP AND JOHN WILEY & SONS LTD.

The seed dormancy defect of Arabidopsis mutants lacking the transcript elongation factor TFIIS is caused by reduced expression of the DOG1 gene.

PubMed

Mortensen, Simon A; Grasser, Klaus D

2014-01-03

TFIIS is a transcript elongation factor that facilitates transcription by RNA polymerase II, as it assists the enzyme to bypass blocks to mRNA synthesis. Previously, we have reported that Arabidopsis plants lacking TFIIS exhibit reduced seed dormancy. Among the genes differentially expressed in tfIIs seeds, the DOG1 gene was identified that is a known QTL for seed dormancy. Here we have analysed plants that overexpress TFIIS in wild type background, or that harbour an additional copy of DOG1 in tfIIs mutant background. These experiments demonstrate that the down-regulation of DOG1 expression causes the seed dormancy phenotype of tfIIs mutants. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Hybrid RAID With Dual Control Architecture for SSD Reliability

NASA Astrophysics Data System (ADS)

Chatterjee, Santanu

2010-10-01

The Solid State Devices (SSD) which are increasingly being adopted in today's data storage Systems, have higher capacity and performance but lower reliability, which leads to more frequent rebuilds and to a higher risk. Although SSD is very energy efficient compared to Hard Disk Drives but Bit Error Rate (BER) of an SSD require expensive erase operations between successive writes. Parity based RAID (for Example RAID4,5,6)provides data integrity using parity information and supports losing of any one (RAID4, 5)or two drives(RAID6), but the parity blocks are updated more often than the data blocks due to random access pattern so SSD devices holding more parity receive more writes and consequently age faster. To address this problem, in this paper we propose a Model based System of hybrid disk array architecture in which we plan to use RAID 4(Stripping with Parity) technique and SSD drives as Data drives while any fastest Hard disk drives of same capacity can be used as dedicated parity drives. By this proposed architecture we can open the door to using commodity SSD's past their erasure limit and it can also reduce the need for expensive hardware Error Correction Code (ECC) in the devices.

Speech sound disorder influenced by a locus in 15q14 region.

PubMed

Stein, Catherine M; Millard, Christopher; Kluge, Amy; Miscimarra, Lara E; Cartier, Kevin C; Freebairn, Lisa A; Hansen, Amy J; Shriberg, Lawrence D; Taylor, H Gerry; Lewis, Barbara A; Iyengar, Sudha K

2006-11-01

Despite a growing body of evidence indicating that speech sound disorder (SSD) has an underlying genetic etiology, researchers have not yet identified specific genes predisposing to this condition. The speech and language deficits associated with SSD are shared with several other disorders, including dyslexia, autism, Prader-Willi Syndrome (PWS), and Angelman's Syndrome (AS), raising the possibility of gene sharing. Furthermore, we previously demonstrated that dyslexia and SSD share genetic susceptibility loci. The present study assesses the hypothesis that SSD also shares susceptibility loci with autism and PWS. To test this hypothesis, we examined linkage between SSD phenotypes and microsatellite markers on the chromosome 15q14-21 region, which has been associated with autism, PWS/AS, and dyslexia. Using SSD as the phenotype, we replicated linkage to the 15q14 region (P=0.004). Further modeling revealed that this locus influenced oral-motor function, articulation and phonological memory, and that linkage at D15S118 was potentially influenced by a parent-of-origin effect (LOD score increase from 0.97 to 2.17, P=0.0633). These results suggest shared genetic determinants in this chromosomal region for SSD, autism, and PWS/AS.

Antioxidant response elements: Discovery, classes, regulation and potential applications.

PubMed

Raghunath, Azhwar; Sundarraj, Kiruthika; Nagarajan, Raju; Arfuso, Frank; Bian, Jinsong; Kumar, Alan P; Sethi, Gautam; Perumal, Ekambaram

2018-07-01

Exposure to antioxidants and xenobiotics triggers the expression of a myriad of genes encoding antioxidant proteins, detoxifying enzymes, and xenobiotic transporters to offer protection against oxidative stress. This articulated universal mechanism is regulated through the cis-acting elements in an array of Nrf2 target genes called antioxidant response elements (AREs), which play a critical role in redox homeostasis. Though the Keap1/Nrf2/ARE system involves many players, AREs hold the key in transcriptional regulation of cytoprotective genes. ARE-mediated reporter constructs have been widely used, including xenobiotics profiling and Nrf2 activator screening. The complexity of AREs is brought by the presence of other regulatory elements within the AREs. The diversity in the ARE sequences not only bring regulatory selectivity of diverse transcription factors, but also confer functional complexity in the Keap1/Nrf2/ARE pathway. The different transcription factors either homodimerize or heterodimerize to bind the AREs. Depending on the nature of partners, they may activate or suppress the transcription. Attention is required for deeper mechanistic understanding of ARE-mediated gene regulation. The computational methods of identification and analysis of AREs are still in their infancy. Investigations are required to know whether epigenetics mechanism plays a role in the regulation of genes mediated through AREs. The polymorphisms in the AREs leading to oxidative stress related diseases are warranted. A thorough understanding of AREs will pave the way for the development of therapeutic agents against cancer, neurodegenerative, cardiovascular, metabolic and other diseases with oxidative stress. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Subsurface damage distribution in the lapping process.

PubMed

Wang, Zhuo; Wu, Yulie; Dai, Yifan; Li, Shengyi

2008-04-01

To systematically investigate the influence of lapping parameters on subsurface damage (SSD) depth and characterize the damage feature comprehensively, maximum depth and distribution of SSD generated in the optical lapping process were measured with the magnetorheological finishing wedge technique. Then, an interaction of adjacent indentations was applied to interpret the generation of maximum depth of SSD. Eventually, the lapping procedure based on the influence of lapping parameters on the material removal rate and SSD depth was proposed to improve the lapping efficiency.

Somatic symptom disorder treated with electroconvulsive therapy.

PubMed

Borisovskaya, Anna; Augsburger, Jay Alan

2017-05-01

Somatic symptom disorder (SSD) is a challenging condition to treat with chronic pain, a common and disabling symptom. We present a patient who received electroconvulsive therapy (ECT) for SSD with significant improvement in pain and gastrointestinal symptoms. We also present a brief literature review of similar cases treated with ECT. Preliminary evidence suggests that ECT should be considered for treatment of SSD comorbid with major depressive disorder, when standard treatments fail. Further research is needed to clarify whether ECT can be used for SSD without associated depression.

SUMOylated MAFB promotes colorectal cancer tumorigenesis

PubMed Central

Xie, Yin-Yin; Sun, Xiao-Jian; Zhao, Ren; Huang, Qiu-Hua

2016-01-01

The transcription factor, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB), promotes tumorigenesis in some cancers. In this study, we found that MAFB levels were increased in clinical colorectal cancer (CRC) samples, and higher expression correlated with more advanced TNM stage. We identified MAFB amplifications in a majority of tumor types in an assessment of The Cancer Genome Atlas database. Altered MAFB levels due to gene amplification, deletion, mutation, or transcription upregulation occurred in 9% of CRC cases within the database. shRNA knockdown experiments demonstrated that MAFB deficiency blocked CRC cell proliferation by arresting the cell cycle at G0/G1 phase in vitro. We found that MAFB could be SUMOylated by SUMO1 at lysine 32, and this modification was critical for cell cycle regulation by MAFB in CRC cells. SUMOylated MAFB directly regulated cyclin-dependent kinase 6 transcription by binding to its promoter. MAFB knockdown CRC cell xenograft tumors in mice grew more slowly than controls, and wild-type MAFB-overexpressing tumors grew more quickly than tumors overexpressing MAFB mutated at lysine 32. These data suggest that SUMOylated MAFB promotes CRC tumorigenesis through cell cycle regulation. MAFB and its SUMOylation process may serve as novel therapeutic targets for CRC treatment. PMID:27829226

Development and Validation of the Somatic Symptom Disorder-B Criteria Scale (SSD-12).

PubMed

Toussaint, Anne; Murray, Alexandra M; Voigt, Katharina; Herzog, Annabel; Gierk, Benjamin; Kroenke, Kurt; Rief, Winfried; Henningsen, Peter; Löwe, Bernd

2016-01-01

To develop and validate a new self-report questionnaire for the assessment of the psychological features of Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition somatic symptom disorder. The Somatic Symptom Disorder-B Criteria Scale (SSD-12) was developed in several steps from an initial pool of 98 items. The SSD-12 is composed of 12 items; each of the three psychological subcriteria is measured by four items. In a cross-sectional study, the SSD-12 was administered to 698 patients (65.8% female, mean [standard deviation] age = 38.79 [14.15] years) from a psychosomatic outpatient clinic. Item and scale characteristics as well as measures of reliability and validity were determined. The SSD-12 has good item characteristics and excellent reliability (Cronbach α = .95). Confirmatory factor analyses suggested that a three-factorial structure that reflects the three psychological criteria interpreted as cognitive, affective, and behavioral aspects (n = 663, Comparative Fit Index > 0.99, Tucker-Lewis Index > 0.99, Root Mean Square Error of Approximation = 0.06, 90% confidence interval = 0.01-0.08). SSD-12 total sum score was significantly associated with somatic symptom burden (r = 0.47, p < .001) and health anxiety (r = 0.71, p < .001), and moderately associated with general anxiety (r = 0.35, p < .001) and depressive symptoms (r = 0.22, p < .001). Patients with a higher SSD-12 psychological symptom burden reported higher general physical and mental health impairment and significantly higher health care use. The SSD-12 is the first self-report questionnaire that operationalizes the new psychological characteristics of Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition somatic symptom disorder. Initial assessment indicates that the SSD-12 has sufficient reliability and validity to warrant further testing in both research and clinical settings.

Available sight distance on existing highways: Meeting stopping sight distance requirements of an aging population.

PubMed

Gargoum, Suliman A; Tawfeek, Mostafa H; El-Basyouny, Karim; Koch, James C

2018-03-01

An important element of highway design is ensuring that the available sight distance (ASD) on a highway meets driver needs. For instance, if the ASD at any point on a highway is less than the distance required to come to a complete stop after seeing a hazard (i.e. Stopping Sight Distance (SSD)), the driver will not be able to stop in time to avoid a collision. SSD is function of a number of variables which vary depending on the driver, the vehicle driven and surface conditions; examples of such variables include a driver's perception reaction time or PRT (i.e. the time required by the driver to perceive and react to a hazard) and the deceleration rate of the vehicle. Most design guides recommend deterministic values for PRT and deceleration rates. Although these values may serve the needs of the average driver, they may not satisfy the needs of drivers with limited abilities. In other words, even if the ASD exceeds required SSD defined in the design guide, it might not always satisfy the needs of all drivers. While it is impossible to design roads that satisfy the needs of all drivers, the fact that most developed countries suffer from an aging population, means that the number of old drivers on our roads is expected to increase. Since a large proportion of old drivers often have limited abilities, it is expected that the general population of drivers with limited abilities on our roads will increase with time. Accordingly, more efforts are required to ensure that existing road infrastructure is prepared to handle such a change. This paper aims to explore the extent to which ASD on highways satisfies the needs of drivers with limited abilities. The paper first develops MATLAB and Python codes to automatically estimate the ASD on highway point cloud data collected using Light Detection and Ranging (LiDAR) remote sensing technology. The developed algorithms are then used to estimate ASD on seven different crash prone segments in the Province of Alberta, Canada and the ASD is compared to the required SSD on each highway. Three different levels of SSD are defined (SSD for drivers with limited ability, AASHTOs SSD requirements and SSD for drivers with high skill). The results show that, when compared to SSD requirements which integrate limitations in cognitive abilities, a substantial portion of the analyzed segments do not meet the requirements (up to 20%). Similarly, when compared to AASHTO's SSD requirements, up to 6% of the analyzed segments do not meet the requirements. In an attempt to explore the effects of such design limitations on safety, the paper also explores crash rates in noncompliant regions (i.e. regions that do not provide sufficient SSD) and compares them to crash rates in compliant regions. On average, it was found that noncompliant regions experience crash rates that are 2.15 and 1.25 times higher than compliant regions for AASHTO's SSD requirements and those integrating driver limitations, respectively. Furthermore, the study found that a significantly higher proportion of drivers involved in collisions in the noncompliant regions were old drivers. Copyright © 2018 Elsevier Ltd. All rights reserved.

Establishing a design for passive vertical flow constructed wetlands treating small sewage discharges to meet British Standard EN 12566.

PubMed

Weedon, Christopher Michael; Murphy, Clodagh; Sweaney, Geoff

2017-01-01

Owing to legislation change (which made General Binding Rules effective from 1 January 2015) unless discharge is to specified environmentally sensitive sites, small sewage discharges (SSDs) in England - that is, <2 m 3  d -1 to ground; <5 m 3  d -1 to surface waters - no longer require an Environmental Permit (EP) and need not be registered for exemption, provided discharge to surface waters is preceded by treatment using equipment complying with BS EN 12566. This effectively excludes the use of treatment wetlands, unless covered by an EP, because the cost of certification to EN 12566 for bespoke designs is prohibitive. EPs take up to four months to obtain. Therefore, the new legislation has created a commercial disadvantage for constructed wetlands treating SSDs, compared with mass-produced sewage treatment plants. However, the UK statutory pollution regulators have maintained a dialogue with the Constructed Wetland Association (CWA), with a view to assessing whether treatment of SSD using constructed wetlands might be allowable, without requiring EPs. This paper presents treatment performance data obtained over 15 years, from a variety of full-scale operational treatment wetlands, as supporting evidence for design guidelines, proposed by the CWA to the UK regulators, for the implementation of constructed wetlands continuously passively treating SSD to 20:30:20 mg l -1 BOD/SS/NH4-N under a wide range of loading rates. Relevant experience of UK designers, installers and operators since the early 1990s is included, resulting in recommended physical design criteria and loading rates for compact vertical flow reed beds, presented here as key elements of the draft guidelines.

5-HT1A receptor gene silencers Freud-1 and Freud-2 are differently expressed in the brain of rats with genetically determined high level of fear-induced aggression or its absence.

PubMed

Kondaurova, Elena M; Ilchibaeva, Tatiana V; Tsybko, Anton S; Kozhemyakina, Rimma V; Popova, Nina K; Naumenko, Vladimir S

2016-09-01

Serotonin 5-HT1A receptor is known to play a crucial role in the mechanisms of genetically defined aggression. In its turn, 5-HT1A receptor functional state is under control of multiple factors. Among others, transcriptional factors Freud-1 and Freud-2 are known to be involved in the repression of 5-HT1A receptor gene expression. However, implication of these factors in the regulation of behavior is unclear. Here, we investigated the expression of 5-HT1A receptor and silencers Freud-1 and Freud-2 in the brain of rats selectively bred for 85 generations for either high level of fear-induced aggression or its absence. It was shown that Freud-1 and Freud-2 levels were different in aggressive and nonaggressive animals. Freud-1 protein level was decreased in the hippocampus, whereas Freud-2 protein level was increased in the frontal cortex of highly aggressive rats. There no differences in 5-HT1A receptor gene expression were found in the brains of highly aggressive and nonaggressive rats. However, 5-HT1A receptor protein level was decreased in the midbrain and increased in the hippocampus of highly aggressive rats. These data showed the involvement of Freud-1 and Freud-2 in the regulation of genetically defined fear-induced aggression. However, these silencers do not affect transcription of the 5-HT1A receptor gene in the investigated rats. Our data indicate the implication of posttranscriptional rather than transcriptional regulation of 5-HT1A receptor functional state in the mechanisms of genetically determined aggressive behavior. On the other hand, the implication of other transcriptional regulators for 5-HT1A receptor gene in the mechanisms of genetically defined aggression could be suggested. Copyright © 2016 Elsevier B.V. All rights reserved.

Identification of Candidate Transcriptional Regulators of Epidermal Transfer Cell Development in Vicia faba Cotyledons

PubMed Central

Arun-Chinnappa, Kiruba S.; McCurdy, David W.

2016-01-01

Transfer cells (TCs) are anatomically-specialized cells formed at apoplasmic-symplasmic bottlenecks in nutrient transport pathways in plants. TCs form invaginated wall ingrowths which provide a scaffold to amplify plasma membrane surface area and thus increase the density of nutrient transporters required to achieve enhanced nutrient flow across these bottlenecks. Despite their importance to nutrient transport in plants, little is known of the transcriptional regulation of wall ingrowth formation. Here, we used RNA-Seq to identify transcription factors putatively involved in regulating epidermal TC development in cotyledons of Vicia faba. Comparing cotyledons cultured for 0, 3, 9, and 24 h to induce trans-differentiation of epidermal TCs identified 43 transcription factors that showed either epidermal-specific or epidermal–enhanced expression, and 10 that showed epidermal-specific down regulation. Members of the WRKY and ethylene-responsive families were prominent in the cohort of transcription factors showing epidermal-specific or epidermal–enhanced expression, consistent with the initiation of TC development often representing a response to stress. Members of the MYB family were also prominent in these categories, including orthologs of MYB genes involved in localized secondary wall deposition in Arabidopsis thaliana. Among the group of transcription factors showing down regulation were various homeobox genes and members of the MADs-box and zinc-finger families of poorly defined functions. Collectively, this study identified several transcription factors showing expression characteristics and orthologous functions that indicate likely participation in transcriptional regulation of epidermal TC development in V. faba cotyledons. PMID:27252730

Method and apparatus for offloading compute resources to a flash co-processing appliance

DOEpatents

Tzelnic, Percy; Faibish, Sorin; Gupta, Uday K.; Bent, John; Grider, Gary Alan; Chen, Hsing -bung

2015-10-13

Solid-State Drive (SSD) burst buffer nodes are interposed into a parallel supercomputing cluster to enable fast burst checkpoint of cluster memory to or from nearby interconnected solid-state storage with asynchronous migration between the burst buffer nodes and slower more distant disk storage. The SSD nodes also perform tasks offloaded from the compute nodes or associated with the checkpoint data. For example, the data for the next job is preloaded in the SSD node and very fast uploaded to the respective compute node just before the next job starts. During a job, the SSD nodes perform fast visualization and statistical analysis upon the checkpoint data. The SSD nodes can also perform data reduction and encryption of the checkpoint data.

Expression of NF-kappaB dependent genes in human cells in response to heavy ion beams

NASA Astrophysics Data System (ADS)

Hellweg, Christine; Baumstark-Khan, Christa; Ruland, Rebecca; Schmitz, Claudia; Lau, Patrick; Testard, Isabelle; Reitz, Guenther

Space radiation is a primary concern for manned spaceflight and is a potentially limiting factor for long term orbital and interplanetary missions. Understanding of the cellular and molecular processes underlying cell death and transformation related events by space radiation may allow better risk estimation and development of appropriate countermeasures. The pathway leading to activation of the transcription factor nuclear factor κB (NF-κB) and increased transcription of its target gene might modulate cellular radiation response. Previous studies suggest a linear energy transfer (LET) dependency of transcription factor nuclear factor κB (NF-κB) activation: high LET radiation activates NF-κB more efficiently than low LET radiation. In this work, the relative expressions of several NF-κB regulated genes (Gadd45β, NFKBIA encoding the NF-κB inhibitor IκBα, and the anti-apoptotic genes XIAP, bcl-2, and bcl-xL) were examined by quantitative real-time Reverse Transcriptase Polymerase Chain Reaction (qRT-PCR). Human embryonic cells with neuronal differentiation potential (HEK/293) were exposed to accelerated heavy ions or to X-rays (200 kV) or incubated in presence of the strong NF-κB activator tumor necrosis factor α (TNF-α). Target gene expression data were normalized to the expression index of several unregulated reference genes (B2M, GAPDH, PBGD, HPRT). NFKBIA expression is enhanced for 24 h after TNF-α treatment, while Gadd45β expression was only temporarily up-regulated. High doses of X-rays (8 and 16 Gy) and of 13 C ions (75 MeV/n, LET 33 keV/µm, 4.7 Gy) up-regulate NFKBIA and Gadd45β expression temporarily. 13 C ion with higher LET (35 MeV/n, 73 keV/µm) enhance NFKBIA expression already after 1 Gy, and a passing up-regulation of Bcl-2, bcl-xL and XIAP expression was observed 2 h after 0.5 Gy. 20 Ne (95 MeV/A, 80 keV/µm) and 36 Ar ions (95 MeV/A, 271 keV/µm) were the strongest inducers of Gadd45β, NFKBIA, and XIAP with doses from 0.5 to 3.8 Gy. 58 Ni (75 MeV/A, 906 keV/µm) and 208 Pb ion exposure (29 MeV/A, 9764 keV/µm) reduced the expression of Gadd45β. NFKBIA expression was enhanced after 58 Ni ion exposure, but down-regulated after 208 Pb ion exposure. Bcl-2 and Bcl-xL were mostly unaffected by the tested irradiation conditions or only transitorily up-regulated. In conclusion, genes involved in cell cycle regulation (Gadd45β), in inhibition of apoptosis (XIAP, bcl-2, and bcl-xL) and in control of the NF-κB pathway (NFKBIA) show a differentiated expression profile after exposure of human cells to heavy ions of different LET. This might be a step towards understanding of the previously observed LET dependency of cell survival and cell cycle arrest.

[Isolation and function of genes regulating aphB expression in Vibrio cholerae].

PubMed

Chen, Haili; Zhu, Zhaoqin; Zhong, Zengtao; Zhu, Jun; Kan, Biao

2012-02-04

We identified genes that regulate the expression of aphB, the gene encoding a key virulence regulator in Vibrio cholerae O1 E1 Tor C6706(-). We constructed a transposon library in V. cholerae C6706 strain containing a P(aphB)-luxCDABE and P(aphB)-lacZ transcriptional reporter plasmids. Using a chemiluminescence imager system, we rapidly detected aphB promoter expression level at a large scale. We then sequenced the transposon insertion sites by arbitrary PCR and sequencing analysis. We obtained two candidate mutants T1 and T2 which displayed reduced aphB expression from approximately 40,000 transposon insertion mutants. Sequencing analysis shows that Tn inserted in vc1585 reading frame in the T1 mutant and Tn inserted in the end of coding sequence of vc1602 in the T2 mutant. By using a genetic screen, we identified two potential genes that may involve in regulation of the expression of the key virulence regulator AphB. This study sheds light on our further investigation to fully understand V. cholerae virulence gene regulatory cascades.

Research on subsurface defects of potassium dihydrogen phosphate crystals fabricated by single point diamond turning technique

NASA Astrophysics Data System (ADS)

Tie, Guipeng; Dai, Yifan; Guan, Chaoliang; Chen, Shaoshan; Song, Bing

2013-03-01

Potassium dihydrogen phosphate (KDP) crystals, which are widely used in high-power laser systems, are required to be free of defects on fabricated subsurfaces. The depth of subsurface defects (SSD) of KDP crystals is significantly influenced by the parameters used in the single point diamond turning technique. In this paper, based on the deliquescent magnetorheological finishing technique, the SSD of KDP crystals is observed and the depths under various cutting parameters are detected and discussed. The results indicate that no SSD is generated under small parameters and with the increase of cutting parameters, SSD appears and the depth rises almost linearly. Although the ascending trends of SSD depths caused by cutting depth and feed rate are much alike, the two parameters make different contributions. Taking the same material removal efficiency as a criterion, a large cutting depth generates shallower SSD depth than a large feed rate. Based on the experiment results, an optimized cutting procedure is obtained to generate defect-free surfaces.

Extended bidirectional reflectance distribution function for polarized light scattering from subsurface defects under a smooth surface.

PubMed

Shen, Jian; Deng, Degang; Kong, Weijin; Liu, Shijie; Shen, Zicai; Wei, Chaoyang; He, Hongbo; Shao, Jianda; Fan, Zhengxiu

2006-11-01

By introducing the scattering probability of a subsurface defect (SSD) and statistical distribution functions of SSD radius, refractive index, and position, we derive an extended bidirectional reflectance distribution function (BRDF) from the Jones scattering matrix. This function is applicable to the calculation for comparison with measurement of polarized light-scattering resulting from a SSD. A numerical calculation of the extended BRDF for the case of p-polarized incident light was performed by means of the Monte Carlo method. Our numerical results indicate that the extended BRDF strongly depends on the light incidence angle, the light scattering angle, and the out-of-plane azimuth angle. We observe a 180 degrees symmetry with respect to the azimuth angle. We further investigate the influence of the SSD density, the substrate refractive index, and the statistical distributions of the SSD radius and refractive index on the extended BRDF. For transparent substrates, we also find the dependence of the extended BRDF on the SSD positions.

Nuclear Lamins

PubMed Central

Dechat, Thomas; Adam, Stephen A.; Taimen, Pekka; Shimi, Takeshi; Goldman, Robert D.

2010-01-01

The nuclear lamins are type V intermediate filament proteins that are critically important for the structural properties of the nucleus. In addition, they are involved in the regulation of numerous nuclear processes, including DNA replication, transcription and chromatin organization. The developmentally regulated expression of lamins suggests that they are involved in cellular differentiation. Their assembly dynamic properties throughout the cell cycle, particularly in mitosis, are influenced by posttranslational modifications. Lamins may regulate nuclear functions by direct interactions with chromatin and determining the spatial organization of chromosomes within the nuclear space. They may also regulate chromatin functions by interacting with factors that epigenetically modify the chromatin or directly regulate replication or transcription. PMID:20826548

Towards a Quantitative Understanding of Single-Gene Transcription

NASA Astrophysics Data System (ADS)

O'Maoiléidigh, Dáibhid

2008-03-01

The transcription of the genetic information in DNA into RNA is the first step in protein synthesis. This process is highly regulated and is carried out by RNA polymerase (RNAP), a complex molecular motor. Here we discuss some of the consequences of a Brownian ratchet model of transcription, which incorporates internal structural degrees of freedom of RNAP and kinetic barriers to backtracking of RNAP resulting from steric clashes with co-transcriptionally folded RNA. This approach was previously used (a) to successfully predict sequence dependent positions of pauses during the elongation process [1,2]; (b) to study the behavior of a number of mutants of RNAP, with different elongation behaviors, believed to involve different internal motions of the enzyme [3]; and (c) to gain insight into the interpretation of single-molecule transcription elongation experiments [2]. The same model can be used to characterize the stability of the elongation complex at specific termination sequences, places along DNA where, with high probability, RNAP releases the RNA transcript and disengages from the template. Recent experimental results on termination reinforce a picture of the elongation complex as a flexible structure, not a rigid body [4]. In more general terms, some of the modeling to be presented raises fundamental issues related to ``model comparison'' and ``model selection,'' the problem of identifying and characterizing quantitative models on the basis of limited sets of experimental data [5]. [1] Tadigotla V. R., 'O Maoil'eidigh D., Sengupta A. M., Epshtein V., Ebright R. H., Nudler E., Ruckenstein A. E., Thermodynamic and Kinetic Modeling of Transcriptional Pausing. Proc Natl Acad Sci U S A,03:4439-4444 (2006). [2] D. 'O Maoil'eidigh, Ph.D. Thesis, Rutgers University, 2006 [3] Bar-Nahum, G., Epshtein, V., Ruckenstein, A. E., Rafikov, R., Mustaev, A. and Nudler E., A Ratchet Mechanism of Transcription Elongation and its Control. Cell, 120:183-193 (2005). [4] Epshtein, V., Cardinale, C.J., Ruckenstein, A.E., Borukhov, S., and Nudler, E., An Allosteric Path to Transcription Termination. Mol. Cell,28; 991-1001 (2007). [5] Vasisht R. Tadigotla, Ph.D. Thesis, Rutgers University, 2006

Genome Wide Transcriptional Profile Analysis of Vitis amurensis and Vitis vinifera in Response to Cold Stress

PubMed Central

Xin, Haiping; Zhu, Wei; Wang, Lina; Xiang, Yue; Fang, Linchuan; Li, Jitao; Sun, Xiaoming; Wang, Nian; Londo, Jason P.; Li, Shaohua

2013-01-01

Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of V. amurensis remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of V. amurensis under cold treatment. Vitis vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amruensis in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT) and cold treatment (CT) cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into V. vinifera cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in V. amruensis and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that V. amurensis has fewer differential expressed genes (DEGs, 1314 transcripts) than Muscat of Hamburg (2307 transcripts) when exposed to cold stress. Common DEGs (408 transcripts) suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change) also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in V. amurensis. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis are discussed in detail. This subset of unique candidate transcripts may contribute to the excellent cold-hardiness of V. amurensis. PMID:23516547

Acute stress blocks the caffeine-induced enhancement of contextual memory retrieval in mice.

PubMed

Pierard, Chistophe; Krazem, Ali; Henkous, Nadia; Decorte, Laurence; Béracochéa, Daniel

2015-08-15

This study investigated in mice the dose-effect of caffeine on memory retrieval in non-stress and stress conditions. C57 Bl/6 Jico mice learned two consecutive discriminations (D1 and D2) in a four-hole board which involved either distinct contextual (CSD) or similar contextual (SSD) cues. All mice received an i.p. injection of vehicle or caffeine (8, 16 or 32mg/kg) 30min before the test session. Results showed that in non-stress conditions, the 16mg/kg caffeine dose induced a significant enhancement of D1 performance in CSD but not in SSD. Hence, we studied the effect of an acute stress (electric footshocks) administered 15min before the test session on D1 performance in caffeine-treated mice. Results showed that stress significantly decreased D1 performance in vehicle-treated controls and the memory-enhancing effect induced by the 16mg/kg caffeine dose in non-stress condition is no longer observed. Interestingly, whereas caffeine-treated mice exhibited weaker concentrations of plasma corticosterone as compared to vehicles in non-stress condition, stress significantly increased plasma corticosterone concentrations in caffeine-treated mice which reached similar level to that of controls. Overall, the acute stress blocked both the endocrinological and memory retrieval enhancing effects of caffeine. Copyright © 2015 Elsevier B.V. All rights reserved.

kdgREcc Negatively Regulates Genes for Pectinases, Cellulase, Protease, HarpinEcc, and a Global RNA Regulator in Erwinia carotovora subsp. carotovora†

PubMed Central

Liu, Yang; Jiang, Guoqiao; Cui, Yaya; Mukherjee, Asita; Ma, Wei Lei; Chatterjee, Arun K.

1999-01-01

Erwinia carotovora subsp. carotovora produces extracellular pectate lyase (Pel), polygalacturonase (Peh), cellulase (Cel), and protease (Prt). The concerted actions of these enzymes largely determine the virulence of this plant-pathogenic bacterium. E. carotovora subsp. carotovora also produces HarpinEcc, the elicitor of the hypersensitive reaction. We document here that KdgREcc (Kdg, 2-keto-3-deoxygluconate; KdgR, general repressor of genes involved in pectin and galacturonate catabolism), a homolog of the E. chrysanthemi repressor, KdgREch and the Escherichia coli repressor, KdgREco, negatively controls not only the pectinases, Pel and Peh, but also Cel, Prt, and HarpinEcc production in E. carotovora subsp. carotovora. The levels of pel-1, peh-1, celV, and hrpNEcc transcripts are markedly affected by KdgREcc. The KdgREcc− mutant is more virulent than the KdgREcc+ parent. Thus, our data for the first time establish a global regulatory role for KdgREcc in E. carotovora subsp. carotovora. Another novel observation is the negative effect of KdgREcc on the transcription of rsmB (previously aepH), which specifies an RNA regulator controlling exoenzyme and HarpinEcc production. The levels of rsmB RNA are higher in the KdgREcc− mutant than in the KdgREcc+ parent. Moreover, by DNase I protection assays we determined that purified KdgREcc protected three 25-bp regions within the transcriptional unit of rsmB. Alignment of the protected sequences revealed the 21-mer consensus sequence of the KdgREcc-binding site as 5′-G/AA/TA/TGAAA[N6]TTTCAG/TG/TA-3′. Two such KdgREcc-binding sites occur in rsmB DNA in a close proximity to each other within nucleotides +79 and +139 and the third KdgREcc-binding site within nucleotides +207 and +231. Analysis of lacZ transcriptional fusions shows that the KdgR-binding sites negatively affect the expression of rsmB. KdgREcc also binds the operator DNAs of pel-1 and peh-1 genes and represses expression of a pel1-lacZ and a peh1-lacZ transcriptional fusions. We conclude that KdgREcc affects extracellular enzyme production by two ways: (i) directly, by inhibiting the transcription of exoenzyme genes; and (ii) indirectly, by preventing the production of a global RNA regulator. Our findings support the idea that KdgREcc affects transcription by promoter occlusion, i.e., preventing the initiation of transcription, and by a roadblock mechanism, i.e., by affecting the elongation of transcription. PMID:10198003

Genetic regulation of adipose tissue transcript expression is involved in modulating serum triglyceride and HDL-cholesterol.

PubMed

Sajuthi, Satria P; Sharma, Neeraj K; Comeau, Mary E; Chou, Jeff W; Bowden, Donald W; Freedman, Barry I; Langefeld, Carl D; Parks, John S; Das, Swapan K

2017-10-20

Dyslipidemia is a major contributor to the increased cardiovascular disease and mortality associated with obesity and type 2 diabetes. We hypothesized that variation in expression of adipose tissue transcripts is associated with serum lipid concentrations in African Americans (AAs), and common genetic variants regulate expression levels of these transcripts. Fasting serum lipid levels, genome-wide transcript expression profiles of subcutaneous adipose tissue, and genome-wide SNP genotypes were analyzed in a cohort of non-diabetic AAs (N=250). Serum triglyceride (TRIG) and high density lipoprotein-cholesterol (HDL-C) levels were associated (FDR<0.01) with expression level of 1021 and 1875 adipose tissue transcripts, respectively, but none associated with total cholesterol or LDL-C levels. Serum HDL-C-associated transcripts were enriched for salient biological pathways, including branched-chain amino acid degradation, and oxidative phosphorylation. Genes in immuno-inflammatory pathways were activated among individuals with higher serum TRIG levels. We identified significant cis-regulatory SNPs (cis-eSNPs) for 449 serum lipid-associated transcripts in adipose tissue. The cis-eSNPs of 12 genes were nominally associated (p<0.001) with serum lipid level in genome wide association studies in Global Lipids Genetics Consortium (GLGC) cohorts. Allelic effect direction of cis-eSNPs on expression of MARCH2, BEST1 and TMEM258 matched with effect direction of these SNP alleles on serum TRIG or HDL-C levels in GLGC cohorts. These data suggest that expressions of serum lipid-associated transcripts in adipose tissue are dependent on common cis-eSNPs in African Americans. Thus, genetically-mediated transcriptional regulation in adipose tissue may play a role in reducing HDL-C and increasing TRIG in serum. Copyright © 2017 Elsevier B.V. All rights reserved.

Phylogeny suggests nondirectional and isometric evolution of sexual size dimorphism in argiopine spiders.

PubMed

Cheng, Ren-Chung; Kuntner, Matjaž

2014-10-01

Sexual dimorphism describes substantial differences between male and female phenotypes. In spiders, sexual dimorphism research almost exclusively focuses on size, and recent studies have recovered steady evolutionary size increases in females, and independent evolutionary size changes in males. Their discordance is due to negative allometric size patterns caused by different selection pressures on male and female sizes (converse Rensch's rule). Here, we investigated macroevolutionary patterns of sexual size dimorphism (SSD) in Argiopinae, a global lineage of orb-weaving spiders with varying degrees of SSD. We devised a Bayesian and maximum-likelihood molecular species-level phylogeny, and then used it to reconstruct sex-specific size evolution, to examine general hypotheses and different models of size evolution, to test for sexual size coevolution, and to examine allometric patterns of SSD. Our results, revealing ancestral moderate sizes and SSD, failed to reject the Brownian motion model, which suggests a nondirectional size evolution. Contrary to predictions, male and female sizes were phylogenetically correlated, and SSD evolution was isometric. We interpret these results to question the classical explanations of female-biased SSD via fecundity, gravity, and differential mortality. In argiopines, SSD evolution may be driven by these or additional selection mechanisms, but perhaps at different phylogenetic scales. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Subsyndromal delirium compared with delirium, dementia, and subjects without delirium or dementia in elderly general hospital admissions and nursing home residents.

PubMed

Sepulveda, Esteban; Leonard, Maeve; Franco, Jose G; Adamis, Dimitrios; McCarthy, Geraldine; Dunne, Colum; Trzepacz, Paula T; Gaviria, Ana M; de Pablo, Joan; Vilella, Elisabet; Meagher, David J

2017-01-01

Subsyndromal delirium (SSD) complicates diagnosis of delirium and dementia, although there is little research comparing their symptom profiles. Cross-sectional study of 400 elderly patients' admission to a general hospital or nursing home diagnosed with delirium, SSD, dementia, or no-delirium/no-dementia (NDND). Symptom profiles were assessed using the Delirium Rating Scale-Revised-98 (DRS-R98). Twenty percent patients had delirium, 19.3% had SSD, 29.8% had dementia-only, and 31% had NDND. Eighty-one percent of subsyndromal and 76% of delirium groups had comorbid dementia. DRS-R98 scores showed ascending severity from NDND < dementia-only < SSD < delirium. DRS-R98 scores for items evaluating the three core symptom domains (cognitive, higher-order thinking, and circadian) distinguished SSD from delirium and both from nondelirium groups. DRS-R98 profiles were essentially the same in delirium and SSD subgroups with or without dementia, although total scale scores were generally higher when in comorbid subgroups. SSD shared characteristic core domain symptoms with delirium, which distinguished each from nondelirium groups, although severity was intermediate in the subsyndromal group. Delirium core symptoms overshadowed the dementia phenotype when comorbid. Milder disturbances of delirium core domain symptoms are highly suggestive of SSD.

Impacts of pesticide mixtures in European rivers as predicted by the Species Sensitivity Distribution (SSD) models and SPEAR bioindication

NASA Astrophysics Data System (ADS)

Jesenska, Sona; Liess, Mathias; Schäfer, Ralf; Beketov, Mikhail; Blaha, Ludek

2013-04-01

Species sensitivity distribution (SSD) is statistical method broadly used in the ecotoxicological risk assessment of chemicals. Originally it has been used for prospective risk assessment of single substances but nowadays it is becoming more important also in the retrospective risk assessment of mixtures, including the catchment scale. In the present work, SSD predictions (impacts of mixtures consisting of 25 pesticides; data from several catchments in Germany, France and Finland) were compared with SPEAR-pesticides, which a bioindicator index based on biological traits responsive to the effects of pesticides and post-contamination recovery. The results showed statistically significant correlations (Pearson's R, p<0.01) between SSD (predicted msPAF values) and values of SPEAR-pesticides (based on field biomonitoring observations). Comparisons of the thresholds established for the SSD and SPEAR approaches (SPEAR-pesticides=45%, i.e. LOEC level, and msPAF = 0.05 for SSD, i.e. HC5) showed that use of chronic toxicity data significantly improved the agreement between the two methods but the SPEAR-pesticides index was still more sensitive. Taken together, the validation study shows good potential of SSD models in predicting the real impacts of micropollutant mixtures on natural communities of aquatic biota.

p53 mediated transcriptional regulation of long non-coding RNA by 1-hydroxy-1-norresistomycin triggers intrinsic apoptosis in adenocarcinoma lung cancer.

PubMed

Ramalingam, Vaikundamoorthy; Varunkumar, Krishnamoorthy; Ravikumar, Vilwanathan; Rajaram, Rajendran

2018-05-01

Over a few decades, systemic chemotherapy and surgery are the only treatment options for lung cancer. Due to limited efficacy and overall poor survival of patients, it is necessary to develop a newer therapeutic strategy which specifically targets cancer cell proliferation pathway. Deciphering the role of long non-coding RNAs (lncRNAs) in tumorigenesis and pathogenesis of cancer cells has recently emerged. In the present study, marine actinomycetes derived 1-hydroxy-1-norresistomycin (HNM) was used to enhance the expression of lncRNAs through p53 transcriptional regulation and induced intrinsic apoptosis in non-small cell lung cancer cells. Initially, concentration dependent treatment with HNM has increased the ROS generation in mitochondria and sensitizes the mitochondrial membrane potential. Further, HNM downregulates the numerous oncogenes which regulate cancer cell proliferation, metastasis and invasion and tumor suppressor genes which are involved in intrinsic apoptosis confirmed with adopting techniques such as RT-PCR and western blot analysis. Moreover, ChIP assay results showed that HNM upregulates the p53 mediated transcriptional regulation of lncRNAs lead to apoptosis of cancer cells through cell cycle arrest and inhibition of proliferation. In conclusion, HNM found to be a potential therapeutic agent for treatment of lung cancer via suppression of oncogenes and expression of wide range of tumor suppressor genes are might have significant implications in cancer treatment and drug development. Copyright © 2018 Elsevier B.V. All rights reserved.

What's the FOX Got to Do with the KITten? Regulating the Lineage-Specific Transcriptional Landscape in GIST.

PubMed

Lee, Donna M; Duensing, Anette

2018-02-01

Transcriptional regulation of the KIT receptor tyrosine kinase, a master regulator in gastrointestinal stromal tumors (GIST) and their precursors, the interstitial cells of Cajal (ICC), is part of a positive feedback loop involving the transcription factor ETV1. A new study now shows that the forkhead box (FOX) family transcription factor FOXF1 not only is an upstream regulator of ETV1 and hence ICC/GIST lineage-specific gene transcription, but also functions as lineage-specific pioneer factor with an active role in chromatin rearrangement to facilitate ETV1 binding and transcriptional activity. Cancer Discov; 8(2); 146-9. ©2018 AACR See related article by Ran et al., p. 234 . ©2018 American Association for Cancer Research.

Transcription factor PU.1 is expressed in white adipose and inhibits adipocyte differentiation

USDA-ARS?s Scientific Manuscript database

PU.1 transcription factor is a critical regulator of hematopoiesis and leukemogenesis. Because PU.1 interacts with transcription factors GATA-2 and C/EBPa, both of which are involved in the regulation of adipogenesis, we investigated whether PU.1 also plays a role in the regulation of adipocyte diff...

NF-Y and the immune response: Dissecting the complex regulation of MHC genes.

PubMed

Sachini, Nikoleta; Papamatheakis, Joseph

2017-05-01

Nuclear Factor Y (NF-Y) was first described as one of the CCAAT binding factors. Although CCAAT motifs were found to be present in various genes, NF-Y attracted a lot of interest early on, due to its role in Major Histocompatibility Complex (MHC) gene regulation. MHC genes are crucial in immune response and show peculiar expression patterns. Among other conserved elements on MHC promoters, an NF-Y binding CCAAT box was found to contribute to MHC transcriptional regulation. NF-Y along with other DNA binding factors assembles in a stereospecific manner to form a multiprotein scaffold, the MHC enhanceosome, which is necessary but not sufficient to drive transcription. Transcriptional activation is achieved by the recruitment of yet another factor, the class II transcriptional activator (CIITA). In this review, we briefly discuss basic findings on MHCII transcription regulation and we highlight NF-Y different modes of function in MHCII gene activation. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of maltreatment and parental schizophrenia spectrum disorders on early childhood social-emotional functioning: a population record linkage study.

PubMed

Matheson, S L; Kariuki, M; Green, M J; Dean, K; Harris, F; Tzoumakis, S; Tarren-Sweeney, M; Brinkman, S; Chilvers, M; Sprague, T; Carr, V J; Laurens, K R

2017-12-01

Childhood maltreatment and a family history of a schizophrenia spectrum disorder (SSD) are each associated with social-emotional dysfunction in childhood. Both are also strong risk factors for adult SSDs, and social-emotional dysfunction in childhood may be an antecedent of these disorders. We used data from a large Australian population cohort to determine the independent and moderating effects of maltreatment and parental SSDs on early childhood social-emotional functioning. The New South Wales Child Development Study combines intergenerational multi-agency data using record linkage methods. Multiple measures of social-emotional functioning (social competency, prosocial/helping behaviour, anxious/fearful behaviour; aggressive behaviour, and hyperactivity/inattention) on 69 116 kindergarten children (age ~5 years) were linked with government records of child maltreatment and parental presentations to health services for SSD. Multivariable analyses investigated the association between maltreatment and social-emotional functioning, adjusting for demographic variables and parental SSD history, in the population sample and in sub-cohorts exposed and not exposed to parental SSD history. We also examined the association of parental SSD history and social-emotional functioning, adjusting for demographic variables and maltreatment. Medium-sized associations were identified between maltreatment and poor social competency, aggressive behaviour and hyperactivity/inattention; small associations were revealed between maltreatment and poor prosocial/helping and anxious/fearful behaviours. These associations did not differ greatly when adjusted for parental SSD, and were greater in magnitude among children with no history of parental SSD. Small associations between parental SSD and poor social-emotional functioning remained after adjusting for demographic variables and maltreatment. Childhood maltreatment and history of parental SSD are associated independently with poor early childhood social-emotional functioning, with the impact of exposure to maltreatment on social-emotional functioning in early childhood of greater magnitude than that observed for parental SSDs. The impact of maltreatment was reduced in the context of parental SSDs. The influence of parental SSDs on later outcomes of maltreated children may become more apparent during adolescence and young adulthood when overt symptoms of SSD are likely to emerge. Early intervention to strengthen childhood social-emotional functioning might mitigate the impact of maltreatment, and potentially also avert future psychopathology.

Superoxide dismutase 1 expression is modulated by the core pluripotency transcription factors Oct4, Sox2 and Nanog in embryonic stem cells.

PubMed

Solari, Claudia; Petrone, María Victoria; Echegaray, Camila Vázquez; Cosentino, María Soledad; Waisman, Ariel; Francia, Marcos; Barañao, Lino; Miriuka, Santiago; Guberman, Alejandra

2018-06-19

Redox homeostasis is vital for cellular functions and to prevent the detrimental consequences of oxidative stress. Pluripotent stem cells (PSCs) have an enhanced antioxidant system which supports the preservation of their genome. Besides, reactive oxygen species (ROS) are proposed to be involved in both self-renewal maintenance and in differentiation in embryonic stem cells (ESCs). Increasing evidence shows that cellular systems related to the oxidative stress defense decline along differentiation of PSCs. Although redox homeostasis has been extensively studied for many years, the knowledge about the transcriptional regulation of the genes involved in these systems is still limited. In this work, we studied Sod1 gene modulation by the PSCs fundamental transcription factors Oct4, Sox2 and Nanog. We found that this gene, which is expressed in mouse ESCs (mESCs), was repressed when they were induced to differentiate. Accordingly, these factors induced Sod1 promoter activity in a trans-activation assay. Finally, Sod1 mRNA levels were reduced when Oct4, Sox2 and Nanog were down-regulated by a shRNA approach in mESCs. Taken together, we found that PSCs' key transcription factors are involved in the modulation of Sod1 gene, suggesting a relationship between the pluripotency core and redox homeostasis in these cells. Copyright © 2018. Published by Elsevier B.V.

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

PubMed

Borirak, Orawan; Rolfe, Matthew D; de Koning, Leo J; Hoefsloot, Huub C J; Bekker, Martijn; Dekker, Henk L; Roseboom, Winfried; Green, Jeffrey; de Koster, Chris G; Hellingwerf, Klaas J

2015-10-01

Time-series transcript- and protein-profiles were measured upon initiation of carbon catabolite repression in Escherichia coli, in order to investigate the extent of post-transcriptional control in this prototypical response. A glucose-limited chemostat culture was used as the CCR-free reference condition. Stopping the pump and simultaneously adding a pulse of glucose, that saturated the cells for at least 1h, was used to initiate the glucose response. Samples were collected and subjected to quantitative time-series analysis of both the transcriptome (using microarray analysis) and the proteome (through a combination of 15N-metabolic labeling and mass spectrometry). Changes in the transcriptome and corresponding proteome were analyzed using statistical procedures designed specifically for time-series data. By comparison of the two sets of data, a total of 96 genes were identified that are post-transcriptionally regulated. This gene list provides candidates for future in-depth investigation of the molecular mechanisms involved in post-transcriptional regulation during carbon catabolite repression in E. coli, like the involvement of small RNAs. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Predictors of aggression in 3.322 patients with affective disorders and schizophrenia spectrum disorders evaluated in an emergency department setting.

PubMed

Blanco, Emily A; Duque, Laura M; Rachamallu, Vivekananda; Yuen, Eunice; Kane, John M; Gallego, Juan A

2018-05-01

The aim of this study is to determine odds of aggression and associated factors in patients with schizophrenia-spectrum disorders (SSD) and affective disorders who were evaluated in an emergency department setting. A retrospective study was conducted using de-identified data from electronic medical records from 3.322 patients who were evaluated at emergency psychiatric settings. Data extracted included demographic information, variables related to aggression towards people or property in the past 6months, and other factors that could potentially impact the risk of aggression, such as comorbid diagnoses, physical abuse and sexual abuse. Bivariate analyses and multivariate regression analyses were conducted to determine the variables significantly associated with aggression. An initial multivariate regression analysis showed that SSD had 3.1 times the odds of aggression, while bipolar disorder had 2.2 times the odds of aggression compared to unipolar depression. A second regression analysis including bipolar subtypes showed, using unipolar depression as the reference group, that bipolar disorder with a recent mixed episode had an odds ratio (OR) of 4.3, schizophrenia had an OR of 2.6 and bipolar disorder with a recent manic episode had an OR of 2.2. Generalized anxiety disorder was associated with lower odds in both regression analyses. As a whole, the SSD group had higher odds of aggression than the bipolar disorder group. However, after subdividing the groups, schizophrenia had higher odds of aggression than bipolar disorder with a recent manic episode and lower odds of aggression than bipolar disorder with a recent mixed episode. Copyright © 2017 Elsevier B.V. All rights reserved.

[Characterization of a diode system for in vivo dosimetry with electron beams].

PubMed

Ragona, R; Rossetti, V; Lucio, F; Anglesio, S; Giglioli, F R

2001-10-01

Current quality assurance regulation stresses the basic role of in vivo dosimetry. Our study evaluates the usefulness and reliability of semiconductor diodes in determining the electron absorbed dose. P-type EDE semiconductor detectors were irradiated with electron beams of different energies produced by a CGR Saturn Therac 20. The diode and ionization chamber response were compared, and effect of energy value, collimator opening, source skin distance and gantry angle on diode response was studied. Measurements show a maximum increment of about 20% in diode response increasing the beam energy (6-20 MeV). The response also increases with: collimator opening, reaching 5% with field sizes larger than 10x10 cm2 (with the exception of 20 MeV energy); SSD increase (with a maximum of 8% for 20 MeV); transversal gantry incidence, compared with the diode longitudinal axis; it does not affect the response in the interval of +/- 45 degrees. Absorbed dose attenuation at dmax, due to the presence of diode on the axis of the beam as a function of electron energy was also determined : the maximum attenuation value is 15% in 6 MeV electron beams. A dose calculation algorithm, taking into account diode response dependence was outlined. In vivo dosimetry was performed in 92 fields for 80 patients, with an agreement of +/-4 % (1 SD) between prescribed and measured dose. It is possible to use the EDE semiconductor detectors on a quality control program of dose delivery for electron beam therapy, but particular attention should be paid to the beam incidence angle and diode dose attenuation.

Stage-specific regulation of four HD-ZIP III transcription factors during polar pattern formation in Larix leptolepis somatic embryos.

PubMed

Li, Shui-gen; Li, Wan-feng; Han, Su-ying; Yang, Wen-hua; Qi, Li-wang

2013-06-15

Polar auxin transport provides a developmental signal for cell fate specification during somatic embryogenesis. Some members of the HD-ZIP III transcription factors participate in regulation of auxin transport, but little is known about this regulation in somatic embryogenesis. Here, four HD-ZIP III homologues from Larix leptolepis were identified and designated LaHDZ31, 32, 33 and 34. The occurrence of a miR165/166 target sequence in all four cDNA sequences indicated that they might be targets of miR165/166. Identification of the cleavage products of LaHDZ31 and LaHDZ32 in vivo confirmed that they were regulated by miRNA. Their mRNA accumulation patterns during somatic embryogenesis and the effects of 1-N-naphthylphthalamic acid (NPA) on their transcript levels and somatic embryo maturation were investigated. The results showed that the four genes had higher transcript levels at mature stages than at the proliferation stage, and that NPA treatment down-regulated the mRNA abundance of LaHDZ31, 32 and 33 at cotyledonary embryo stages, but had no effect on the mRNA abundance of LaHDZ34. We concluded that these four members of Larix HD-ZIP III family might participate in polar auxin transport and the development of somatic embryos, providing new insights into the regulatory mechanisms of somatic embryogenesis. Copyright © 2013 Elsevier B.V. All rights reserved.

Pou1f1, the key transcription factor related to somatic growth in tilapia (Orechromis niloticus), is regulated by two independent post-transcriptional regulation mechanisms.

PubMed

Wang, Dongfang; Qin, Jingkai; Jia, Jirong; Yan, Peipei; Li, Wensheng

2017-01-29

This study aims to determine the post-transcriptional regulation mechanism of the transcription factor pou1f1 (pou class 1 homeobox 1), which is the key gene for pituitary development, somatic growth in vertebrates, and transcription of several hormone genes in teleost fish. MicroRNA miR-223-3p was identified as a bona fide target of pou1f; overexpression of miR-223-3p in primary pituitary cells led to the down-regulation of pou1f1 and downstream genes, and inhibition of miR-223-3p led to the up-regulation of pou1f1 in Nile tilapia dispersed primary pituitary cells. An adenylate-uridylate-rich element (AU-Rich element) was found in the 3'UTR of pou1f1 mRNA, and deletion of the AU-Rich element led to slower mRNA decay and therefore more protein output. A potential mutual relationship between miR-223-3p and the AU-rich element was also investigated, and the results demonstrated that with or without the AU-Rich element, miR-223-3p induced the up-regulation of a reporter system under serum starvation conditions, indicating that miR-223-3p and the AU-Rich element function independent of each other. This study is the first to investigate the post-transcriptional mechanism of pou1f1, which revealed that miR-223-3p down-regulated pou1f1 and downstream gene expressions, and the AU-Rich element led to rapid decay of pou1f1 mRNA. MicroRNA miR-223-3p and the AU-Rich element co-regulated the post-transcriptional expression of pou1f1 independently in Nile tilapia, demonstrating that pou1f1 is under the control of a dual post-transcription regulation mechanism. Copyright © 2016 Elsevier Inc. All rights reserved.

Management of the Acute Partial-thickness Burned Hand; Moist Exposed Burn Ointment or Silver Sulphadiazine Cream both Combined with a Polyethylene Bag.

PubMed

Allam, A M; Mostafa, W; Zayed, E; El-Gamaly, J

2007-09-30

Hand burns predominantly affect young adults, and therefore have serious social and financial implications. In the present work, 106 patients with less than 25% body surface area burns and acute partial-thickness burned hands were managed using polyethylene bags and 1% local silver sulphadiazine (SSD) cream or moist exposed burn ointment (MEBO). Females made up 61.3% of the cases and flame burn was the majority cause (54.7%). There were no significant differences between the two groups regarding either the analgesic effect after local ointment application or hand movement inside the polyethylene bag. Local agent crustation over the wound was very evident in the hands managed by local 1% SSD cream (69.81%). On follow-up, the burned hands healed faster using local MEBO (10.48 versus 14.53 days), with fewer post-burn hand deformities and better active hand movements; however, the total cost until complete hand burn wound healing was higher with MEBO than with 1% SSD, although the final results were superior, with early return to work, when MEBO was used. We concluded that the use of MEBO as a topical agent and of polyethylene bags for the dressing of the acute partial-thickness burned hand accelerated healing; daily wound evaluation was easy as there was no crustation over it of the agent. It was more expensive than 1% SSD cream but presented fewer post-burn complications and more rapid healing, with shorter hospital stay.

Pre-Literacy Skills of Subgroups of Children with Speech Sound Disorders

ERIC Educational Resources Information Center

Raitano, Nancy A.; Pennington, Bruce F.; Tunick, Rachel A.; Boada, Richard; Shriberg, Lawrence D.

2004-01-01

Background: The existing literature has conflicting findings about the literacy outcome of children with speech sound disorders (SSD), which may be due to the heterogeneity within SSD. Previous studies have documented that two important dimensions of heterogeneity are the presence of a comorbid language impairment (LI) and the persistence of SSD,…

p21 Activated kinase 1: Nuclear activity and its role during DNA damage repair.

PubMed

Pérez-Yépez, Eloy Andrés; Saldívar-Cerón, Héctor Iván; Villamar-Cruz, Olga; Pérez-Plasencia, Carlos; Arias-Romero, Luis Enrique

2018-05-01

p21-activated kinase 1 (PAK1) is a serine/threonine kinase activated by the small GTPases Rac1 and Cdc42. It is located in the chromosome 11q13 and is amplified and/or overexpressed in several human cancer types including 25-30% of breast tumors. This enzyme plays a pivotal role in the control of a number of fundamental cellular processes by phosphorylating its downstream substrates. In addition to its role in the cytoplasm, it is well documented that PAK1 also plays crucial roles in the nucleus participating in mitotic events and gene expression through its association and/or phosphorylation of several transcription factors, transcriptional co-regulators and cell cycle-related proteins, including Aurora kinase A (AURKA), polo-like kinase 1 (PLK1), the forkhead transcription factor (FKHR), estrogen receptor α (ERα), and Snail. More recently, PAK signaling has emerged as a component of the DNA damage response (DDR) as PAK1 activity influences the cellular sensitivity to ionizing radiation and promotes the expression of several genes involved in the Fanconi Anemia/BRCA pathway. This review will focus on the nuclear functions of PAK1 and its role in the regulation of DNA damage repair. Copyright © 2018 Elsevier B.V. All rights reserved.

Subsurface Damage in Polishing Process of Silicon Carbide Ceramic

PubMed Central

Gu, Yan; Zhu, Wenhui; Lin, Jieqiong; Lu, Mingming; Kang, Mingshuo

2018-01-01

Subsurface damage (SSD) in the polishing process of silicon carbide (SiC) ceramic presents one of the most significant challenges for practical applications. In this study, the theoretical models of SSD depth are established on the basis of the material removal mechanism and indentation fracture mechanics in the SiC ceramic polishing process. In addition, the three-dimensional (3D) models of single grit polishing are also developed by using the finite element simulation; thereby, the dynamic effects of different process parameters on SSD depth are analyzed. The results demonstrate that the material removal was mainly in brittle mode when the cutting depth was larger than the critical depth of the brittle material. The SSD depth increased as the polishing depth and abrasive grain size increased, and decreased with respect to the increase in polishing speed. The experimental results suggested a good agreement with the theoretical simulation results in terms of SSD depth as a function of polishing depth, spindle speed, and abrasive grain size. This study provides a mechanistic insight into the dependence of SSD on key operational parameters in the polishing process of SiC ceramic. PMID:29584694

Zero-bias microwave detectors based on array of nanorectifiers coupled with a dipole antenna

NASA Astrophysics Data System (ADS)

Kasjoo, Shahrir R.; Singh, Arun K.; Mat Isa, Siti S.; Ramli, Muhammad M.; Mohamad Isa, Muammar; Ahmad, Norhawati; Mohd Nor, Nurul I.; Khalid, Nazuhusna; Song, Ai Min

2016-04-01

We report on zero-bias microwave detection using a large array of unipolar nanodevices, known as the self-switching diodes (SSDs). The large array was realized in a single lithography step without the need of interconnection layers, hence allowing for a simple and low-cost fabrication process. The SSD array was coupled with a narrowband dipole antenna with a resonant frequency of 890 MHz, to form a simple rectenna (rectifying antenna). The extrinsic voltage responsivity and noise-equivalent-power (NEP) of the rectenna were ∼70 V/W and ∼0.18 nW/Hz1/2, respectively, measured in the far-field region at unbiased condition. Nevertheless, the estimated intrinsic voltage responsivity can achieve up to ∼5 kV/W with NEP of ∼2.6 pW/Hz1/2.

Estradiol Membrane-Initiated Signaling and Female Reproduction.

PubMed

Micevych, Paul E; Wong, Angela May; Mittelman-Smith, Melinda Anne

2015-07-01

The discoveries of rapid, membrane-initiated steroid actions and central nervous system steroidogenesis have changed our understanding of the neuroendocrinology of reproduction. Classical nuclear actions of estradiol and progesterone steroids affecting transcription are essential. However, with the discoveries of membrane-associated steroid receptors, it is becoming clear that estradiol and progesterone have neurotransmitter-like actions activating intracellular events. Ultimately, membrane-initiated actions can influence transcription. Estradiol membrane-initiated signaling (EMS) modulates female sexual receptivity and estrogen feedback regulating the luteinizing hormone (LH) surge. In the arcuate nucleus, EMS activates a lordosis-regulating circuit that extends to the medial preoptic nucleus and subsequently to the ventromedial nucleus (VMH)--the output from the limbic and hypothalamic regions. Here, we discuss how EMS leads to an active inhibition of lordosis behavior. To stimulate ovulation, EMS facilitates astrocyte synthesis of progesterone (neuroP) in the hypothalamus. Regulation of GnRH release driving the LH surge is dependent on estradiol-sensitive kisspeptin (Kiss1) expression in the rostral periventricular nucleus of the third ventricle (RP3V). NeuroP activation of the LH surge depends on Kiss1, but the specifics of signaling have not been well elucidated. RP3V Kiss1 neurons appear to integrate estradiol and progesterone information which feeds back onto GnRH neurons to stimulate the LH surge. In a second population of Kiss1 neurons, estradiol suppresses the surge but maintains tonic LH release, another critical component of the estrous cycle. Together, evidence suggests that regulation of reproduction involves membrane action of steroids, some of which are synthesized in the brain. © 2015 American Physiological Society.

(Un)healthy relationships: African labourers, profits and health services in Angola's colonial-era diamond mines, 1917-75.

PubMed

Varanda, Jorge; Cleveland, Todd

2014-01-01

The Companhia de Diamantes de Angola, or Diamang, mined for diamonds in colonial Angola from 1917 until independence in 1975. The enterprise's Health Services Division (SSD) was responsible for supplying mine managers with an African labour force comprised of healthy, and therefore productive, employees. In practice, though, this otherwise 'healthy' system did not always work. While SSD personnel attempted to fulfil their charge by implementing a series of screening measures, production targets and a scarcely-populated regional labour pool regularly prompted senior officials to compel the SSD to clear recruits who were otherwise unfit for mine service. Drawing upon interviews with former SSD staff and African labourers, as well as company and colonial archival sources, this article focuses on the interplay over time between the SSD, the company's production demands and these labourers.

FOXK2 transcription factor suppresses ERα-positive breast cancer cell growth through down-regulating the stability of ERα via mechanism involving BRCA1/BARD1.

PubMed

Liu, Ying; Ao, Xiang; Jia, Zhaojun; Bai, Xiao-Yan; Xu, Zhaowei; Hu, Gaolei; Jiang, Xiao; Chen, Min; Wu, Huijian

2015-03-05

Estrogen receptors (ERs) are critical regulators of breast cancer development. Identification of molecules that regulate the function of ERs may facilitate the development of more effective breast cancer treatment strategies. In this study, we showed that the forkhead transcription factor FOXK2 interacted with ERα, and inhibited ERα-regulated transcriptional activities by enhancing the ubiquitin-mediated degradation of ERα. This process involved the interaction between FOXK2 and BRCA1/BARD1, the E3 ubiquitin ligase of ERα. FOXK2 interacted with BARD1 and acted as a scaffold protein for BRCA1/BARD1 and ERα, leading to enhanced degradation of ERα, which eventually accounted for its decreased transcriptional activity. Consistent with these observations, overexpression of FOXK2 inhibited the transcriptional activity of ERα, decreased the transcription of ERα target genes, and suppressed the proliferation of ERα-positive breast cancer cells. In contract, knockdown of FOXK2 in MCF-7 cells promoted cell proliferation. However, when ERα was also knocked down, knockdown of FOXK2 had no effect on cell proliferation. These findings suggested that FOXK2 might act as a negative regulator of ERα, and its association with both ERα and BRCA1/BARD1 could lead to the down-regulation of ERα transcriptional activity, effectively regulating the function of ERα.

Transcriptional activation of human mu-opioid receptor gene by insulin-like growth factor-I in neuronal cells is modulated by the transcription factor REST.

PubMed

Bedini, Andrea; Baiula, Monica; Spampinato, Santi

2008-06-01

The human mu-opioid receptor gene (OPRM1) promoter contains a DNA sequence binding the repressor element 1 silencing transcription factor (REST) that is implicated in transcriptional repression. We investigated whether insulin-like growth factor I (IGF-I), which affects various aspects of neuronal induction and maturation, regulates OPRM1 transcription in neuronal cells in the context of the potential influence of REST. A series of OPRM1-luciferase promoter/reporter constructs were transfected into two neuronal cell models, neuroblastoma-derived SH-SY5Y cells and PC12 cells. In the former, endogenous levels of human mu-opioid receptor (hMOPr) mRNA were evaluated by real-time PCR. IGF-I up-regulated OPRM1 transcription in: PC12 cells lacking REST, in SH-SY5Y cells transfected with constructs deficient in the REST DNA binding element, or when REST was down-regulated in retinoic acid-differentiated cells. IGF-I activates the signal transducer and activator of transcription-3 signaling pathway and this transcription factor, binding to the signal transducer and activator of transcription-1/3 DNA element located in the promoter, increases OPRM1 transcription. We propose that a reduction in REST is a critical switch enabling IGF-I to up-regulate hMOPr. These findings help clarify how hMOPr expression is regulated in neuronal cells.

BRD4 is associated with raccoon polyomavirus genome and mediates viral gene transcription and maintenance of a stem cell state in neuroglial tumour cells.

PubMed

Church, Molly E; Estrada, Marko; Leutenegger, Christian M; Dela Cruz, Florante N; Pesavento, Patricia A; Woolard, Kevin D

2016-11-01

Polyomavirus infection often results in persistence of the viral genome with little or no virion production. However, infection of certain cell types can result in high viral gene transcription and either cytolysis or neoplastic transformation. While infection by polyomavirus is common in humans and many animals, major questions regarding viral persistence of most polyomaviruses remain unanswered. Specifically, identification of target cells for viral infection and the mechanisms polyomaviruses employ to maintain viral genomes within cells are important not only in ascribing causality to polyomaviruses in disease, but in understanding specific mechanisms by which they cause disease. Here, we characterize the cell of origin in raccoon polyomavirus (RacPyV)-associated neuroglial brain tumours as a neural stem cell. Moreover, we identify an association between the viral genome and the host cell bromodomain protein, BRD4, which is involved in numerous cellular functions, including cell cycle progression, differentiation of stem cells, tethering of persistent DNA viruses, and regulation of viral and host-cell gene transcription. We demonstrate that inhibition of BRD4 by the small molecule inhibitors (+)-JQ1 and IBET-151 (GSK1210151A) results in reduced RacPyV genome within cells in vitro, as well as significant reduction of viral gene transcripts LT and VP1, highlighting its importance in both maintenance of the viral genome and in driving oncogenic transformation by RacPyV. This work implicates BRD4 as a central protein involved in RacPyV neuroglial tumour cell proliferation and in the maintenance of a stem cell state.

Antitumorigenic effect of atmospheric-pressure dielectric barrier discharge on human colorectal cancer cells via regulation of Sp1 transcription factor

NASA Astrophysics Data System (ADS)

Han, Duksun; Cho, Jin Hyoung; Lee, Ra Ham; Bang, Woong; Park, Kyungho; Kim, Minseok S.; Shim, Jung-Hyun; Chae, Jung-Il; Moon, Se Youn

2017-02-01

Human colorectal cancer cell lines (HT29 and HCT116) were exposed to dielectric barrier discharge (DBD) plasma at atmospheric pressure to investigate the anticancer capacity of the plasma. The dose- and time-dependent effects of DBDP on cell viability, regulation of transcription factor Sp1, cell-cycle analysis, and colony formation were investigated by means of MTS assay, DAPI staining, propidium iodide staining, annexin V-FITC staining, Western blot analysis, RT-PCR analysis, fluorescence microscopy, and anchorage-independent cell transformation assay. By increasing the duration of plasma dose times, significant reductions in the levels of both Sp1 protein and Sp1 mRNA were observed in both cell lines. Also, expression of negative regulators related to the cell cycle (such as p53, p21, and p27) was increased and of the positive regulator cyclin D1 was decreased, indicating that the plasma treatment led to apoptosis and cell-cycle arrest. In addition, the sizes and quantities of colony formation were significantly suppressed even though two cancer promoters, such as TPA and epidermal growth factor, accompanied the plasma treatment. Thus, plasma treatment inhibited cell viability and colony formation by suppressing Sp1, which induced apoptosis and cell-cycle arrest in these two human colorectal cancer cell lines.

Characterization of a Vibrio vulnificus LysR homologue, HupR, which regulates expression of the haem uptake outer membrane protein, HupA.

PubMed

Litwin, C M; Quackenbush, J

2001-12-01

In Vibrio vulnificus, the ability to acquire iron from the host has been shown to correlate with virulence. Here, we show that the DNA upstream of hupA (haem uptake receptor) in V. vulnificus encodes a protein in the inverse orientation to hupA (named hupR). HupR shares homology with the LysR family of positive transcriptional activators. A hupA-lacZ fusion contained on a plasmid was transformed into Fur(-), Fur(+)and HupR(-)strains of V. vulnificus. The beta-galactosidase assays and Northern blot analysis showed that transcription of hupA is negatively regulated by iron and the Fur repressor in V. vulnificus. Under low-iron conditions with added haemin, the expression of hupA in the hupR mutant was significantly lower than in the wild-type. This diminished response to haem was detected by both Northern blot and hupA-lacZ fusion analysis. The haem response of hupA in the hupR mutant was restored to wild-type levels when complemented with hupR in trans. These studies suggest that HupR may act as a positive regulator of hupA transcription under low-iron conditions in the presence of haemin. Copyright 2001 Academic Press.

A novel luciferase knock-in reporter system for studying transcriptional regulation of the human Sox2 gene.

PubMed

Xiao, Dan; Zhang, Weifeng; Li, Yan; Liu, Kuan; Zhao, Junli; Sun, Xiaohong; Shan, Linlin; Mao, Qinwen; Xia, Haibin

2016-02-10

Sox2 is an important transcriptional factor that has multiple functions in stem cell maintenance and tumorigenesis. To investigate the transcriptional regulation of the Sox2 gene, a luciferase knock-in reporter system was established in HEK293 cells by placing the luciferase gene in the genome under the control of the Sox2 gene promoter using a transcription activator-like effector nuclease (TALEN)-mediated genome editing technique. PCR and Southern blot results confirmed the site-specific integration of a single copy of the exogenous luciferase gene into the genome. To prove the reliability and sensitivity of this novel luciferase knock-in system, a CRISPR/Cas transcription activation system for the Sox2 gene was constructed and applied to the knock-in system. The results indicated that luciferase activity was directly correlated with the activity of the Sox2 endogenous promoter. This novel system will be a useful tool to study the transcriptional regulation of Sox2, and has great potential in medical and industrial applications. Copyright © 2015 Elsevier B.V. All rights reserved.

The Effect of Pycnogenol on Wound Healing in Diabetic Rats.

PubMed

Dogan, Elif; Yanmaz, Latif; Gedikli, Semin; Ersoz, Ugur; Okumus, Zafer

2017-04-01

Pycnogenol (PYC), an extract of pine bark, is known to have photoprotective, antimicrobial, antioxidant, and anti-inflammatory properties. An in vivo study was conducted to evaluate the effects of PYC treatment on wound healing in 48 adult male Sprague-Dawley rats, of which 24 were injected with a single dose of alloxan to induce diabetes. Three (3) excisional skin wounds (1.3 cm x 1.3 cm x 2 mm) were created in each healthy and diabetic animal. One (1) wound in each animal was left untreated, 1 was treated daily with a cleanser (ethacridine lactate) and covered with silver sulfadiazine (SSD), and 1 was treated with PYC powder (30 mg). After measuring wound size, 6 animals from both groups were sacrificed on days 3, 7, 14, and 21 and tissue samples were taken for histopathological evaluation of acute and chronic inflammation, granulation tissue, fibroblast maturation, collagen deposition, epithelialization, and neovascularization using a scoring system of 0 = none, 1 = mild, 2 = moderate, and 3 = abundant. Because the wounds created were not uniform in size within and among the animals, healing was expressed as a percentage of the initial wound size for each animal. Data were compared using 2-way analysis of variance; histopathological lesion scores were reported in median values in univariate analysis, with P <.05 denoting statistical significance. The mean initial wound surface area was 1.69 ± 0.44 cm². On day 21, the average reduction in wound size was lower in diabetic than in healthy rats (47.42% versus 50.91%, P <.0001) and, in both groups combined, the average reduction was 45.73% in untreated, 48.73% in cleanser/SSD-treated, and 58.03% in PYC-treated wounds (P <.0001). Wound size reduction was also significantly different between PYC and the cleanser/SSD treatment depending on the rats' health status (P <.0001): 49.68% and 47.84% using cleanser/SSD and 56.17% and 49.84% using PYC in healthy and diabetic rats, respectively. After 3 weeks, wound size for the healthy rats had decreased more than in the diabetic rats (mean 50.91% versus 47.42%). Although reepithelialization was complete in both groups by day 21, complete neovascularization was evident in the healthy rats but not in the diabetic rats. Overall, compared to the untreated control wounds, treatments with cleanser/SSD and PYC were equally effective in lowering acute and chronic inflammation scores on days 7 and 21. In diabetic rat wounds, collagen deposition and neovascularization scores were higher in wounds treated with PYC than cleanser/SSD-treated wounds (1.5 versus 1.0 and 2.0 versus 1.5, respectively). PYC appears to be a viable option to accelerate wound healing. Further in vivo and human research is warranted.

Transcriptional response of dermal fibroblasts in direct current electric fields.

PubMed

Jennings, Jessica; Chen, Dongquan; Feldman, Dale

2008-07-01

During the course of normal wound healing, fibroblasts at the wound edge are exposed to electric fields (EFs) ranging from 40 to 200 mV/mm. Various forms of EFs influence fibroblast migration, proliferation, and protein synthesis. Thus, EFs may contribute to fibroblast activation during wound repair. To elucidate the role of EFs during the normal progression of healing, this study compares gene expression in normal adult dermal fibroblasts exposed to a 100 mV/mm EF for 1 h to non-stimulated controls. Significantly increased expression of 162 transcripts and decreased expression of 302 transcripts was detected using microarrays, with 126 transcripts above the level of 1.4-fold increases or decreases compared to the controls. Above the level of twofold, only 11 genes were significantly increased or decreased compared to controls. Many of these significantly regulated genes are associated with wound repair through the processes of matrix production, cellular signaling, and growth. Activity within specific cellular signaling pathways is noted, including TGF-beta, G-proteins, and inhibition of apoptosis. In addition, RT-PCR analysis of the expression of KLF6, FN1, RGS2, and JMJD1C over continued stimulation and at different field strengths suggests that there are specific windows of field characteristics for maximum induction of these genes. EFs thus appear to have an important role in controlling fibroblast activity in the process of wound healing.

Berry Flesh and Skin Ripening Features in Vitis vinifera as Assessed by Transcriptional Profiling

PubMed Central

Grimplet, Jérôme; Bravo, Gema; Flores, Pilar; Fenoll, José; Hellín, Pilar; Oliveros, Juan Carlos; Martínez-Zapater, José M.

2012-01-01

Background Ripening of fleshy fruit is a complex developmental process involving the differentiation of tissues with separate functions. During grapevine berry ripening important processes contributing to table and wine grape quality take place, some of them flesh- or skin-specific. In this study, transcriptional profiles throughout flesh and skin ripening were followed during two different seasons in a table grape cultivar ‘Muscat Hamburg’ to determine tissue-specific as well as common developmental programs. Methodology/Principal Findings Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Transcriptional profiles were dominated by changes at the beginning of veraison which affect both pericarp tissues, although frequently delayed or with lower intensity in the skin than in the flesh. Functional enrichment analysis identified the decay on biosynthetic processes, photosynthesis and transport as a major part of the program delayed in the skin. In addition, a higher number of functional categories, including several related to macromolecule transport and phenylpropanoid and lipid biosynthesis, were over-represented in transcripts accumulated to higher levels in the skin. Functional enrichment also indicated auxin, gibberellins and bHLH transcription factors to take part in the regulation of pre-veraison processes in the pericarp, whereas WRKY and C2H2 family transcription factors seems to more specifically participate in the regulation of skin and flesh ripening, respectively. Conclusions/Significance A transcriptomic analysis indicates that a large part of the ripening program is shared by both pericarp tissues despite some components are delayed in the skin. In addition, important tissue differences are present from early stages prior to the ripening onset including tissue-specific regulators. Altogether, these findings provide key elements to understand berry ripening and its differential regulation in flesh and skin. PMID:22768087

Splice variants and promoter methylation status of the Bovine Vasa Homology (Bvh) gene may be involved in bull spermatogenesis

PubMed Central

2013-01-01

Background Vasa is a member of the DEAD-box protein family that plays an indispensable role in mammalian spermatogenesis, particularly during meiosis. Bovine vasa homology (Bvh) of Bos taurus has been reported, however, its function in bovine testicular tissue remains obscure. This study aimed to reveal the functions of Bvh and to determine whether Bvh is a candidate gene in the regulation of spermatogenesis in bovine, and to illustrate whether its transcription is regulated by alternative splicing and DNA methylation. Results Here we report the molecular characterization, alternative splicing pattern, expression and promoter methylation status of Bvh. The full-length coding region of Bvh was 2190 bp, which encodes a 729 amino acid (aa) protein containing nine consensus regions of the DEAD box protein family. Bvh is expressed only in the ovary and testis of adult cattle. Two splice variants were identified and termed Bvh-V4 (2112 bp and 703 aa) and Bvh-V45 (2040 bp and 679 aa). In male cattle, full-length Bvh (Bvh-FL), Bvh-V4 and Bvh-V45 are exclusively expressed in the testes in the ratio of 2.2:1.6:1, respectively. Real-time PCR revealed significantly reduced mRNA expression of Bvh-FL, Bvh-V4 and Bvh-V45 in testes of cattle-yak hybrids, with meiotic arrest compared with cattle and yaks with normal spermatogenesis (P < 0.01). The promoter methylation level of Bvh in the testes of cattle-yak hybrids was significantly greater than in cattle and yaks (P < 0.01). Conclusion In the present study, Bvh was isolated and characterized. These data suggest that Bvh functions in bovine spermatogenesis, and that transcription of the gene in testes were regulated by alternative splice and promoter methylation. PMID:23815438

The regulation of cytochrome P450 2E1 during LPS-induced inflammation in the rat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abdulla, Dalya; Goralski, Kerry B.; College of Pharmacy, Burbidge Building, Dalhousie University, Halifax, Nova Scotia, B3H 3J5

2006-10-01

It is well known that inflammatory and infectious conditions differentially regulate cytochrome P450 (P450)-mediated drug metabolism in the liver. We have previously outlined a potential pathway for the downregulation in hepatic cytochrome P450 following LPS-mediated inflammation in the CNS (Abdulla, D., Goralski, K.B., Garcia Del Busto Cano, E., Renton, K.W., 2005. The signal transduction pathways involved in hepatic cytochrome P450 regulation in the rat during an LPS-induced model of CNS inflammation. Drug Metab. Dispos). The purpose of this study was to outline the effects of LPS-induced peripheral and central nervous system inflammation on hepatic cytochrome P450 2E1 (CYP2E1) in vivo,more » an enzyme that plays an important role in various physiological and pathological states. We report an increase in hepatic mRNA expression of CYP2E1 that occurred as early as 2-3 h following either the intraperitoneal (i.p.) injection of 5 mg/kg LPS or i.c.v. administration of 25 {mu}g of LPS. This increase in CYP2E1 mRNA expression was sustained for 24 h. In sharp contrast to the increase in hepatic CYP2E1 mRNA, we observed a significant reduction in the catalytic activity of this enzyme 24 h following either the i.c.v. or i.p. administration of LPS. Cycloheximide or actinomycin-D did not change the LPS-mediated downregulation in hepatic CYP2E1 catalytic activity. Our results support the idea that LPS acts at two different levels to regulate hepatic CYP2E1: a transcriptional level to increase CYP2E1 mRNA expression and a post-transcriptional level to regulate CYP2E1 protein and activity.« less

Identification and gene-silencing of a putative odorant receptor transcription factor in Varroa destructor: possible role in olfaction.

PubMed

Singh, N K; Eliash, N; Stein, I; Kamer, Y; Ilia, Z; Rafaeli, A; Soroker, V

2016-04-01

The ectoparasitic mite Varroa destructor is one of the major threats to apiculture. Using a behavioural choice bioassay, we determined that phoretic mites were more successful in reaching a bee than reproductive mites, suggesting an energy trade-off between reproduction and host selection. We used both chemo-ecological and molecular strategies to identify the regulation of the olfactory machinery of Varroa and its association with reproduction. We focused on transcription regulation. Using primers designed to the conserved DNA binding region of transcription factors, we identified a gene transcript in V. destructor homologous to the pheromone receptor transcription factor (PRTF) gene of Pediculus humanus corporis. Quantitative PCR (qPCR) revealed that this PRTF-like gene transcript is expressed in the forelegs at higher levels than in the body devoid of forelegs. Subsequent comparative qPCR analysis showed that transcript expression was significantly higher in the phoretic as compared to the reproductive stage. Electrophysiological and behavioural studies revealed a reduction in the sensitivity of PRTF RNA interference-silenced mites to bee headspace, consistent with a reduction in the mites' ability to reach a host. In addition, vitellogenin expression was stimulated in PRTF-silenced mites to similar levels as found in reproductive mites. These data shed light upon the regulatory mechanism of host chemosensing in V. destructor. © 2016 The Royal Entomological Society.

Shaker-related voltage-gated K+ channel expression and vasomotor function in human coronary resistance arteries.

PubMed

Nishijima, Yoshinori; Korishettar, Ankush; Chabowski, Dawid S; Cao, Sheng; Zheng, Xiaodong; Gutterman, David D; Zhang, David X

2018-01-01

K V channels are important regulators of vascular tone, but the identity of specific K V channels involved and their regulation in disease remain less well understood. We determined the expression of K V 1 channel subunits and their role in cAMP-mediated dilation in coronary resistance arteries from subjects with and without CAD. HCAs from patients with and without CAD were assessed for mRNA and protein expression of K V 1 channel subunits with molecular techniques and for vasodilator response with isolated arterial myography. Assays of mRNA transcripts, membrane protein expression, and vascular cell-specific localization revealed abundant expression of K V 1.5 in vascular smooth muscle cells of non-CAD HCAs. Isoproterenol and forskolin, two distinct cAMP-mediated vasodilators, induced potent dilation of non-CAD arterioles, which was inhibited by both the general K V blocker 4-AP and the selective K V 1.5 blocker DPO-1. The cAMP-mediated dilation was reduced in CAD and was accompanied by a loss of or reduced contribution of 4-AP-sensitive K V channels. K V 1.5, as a major 4-AP-sensitive K V 1 channel expressed in coronary VSMCs, mediates cAMP-mediated dilation in non-CAD arterioles. The cAMP-mediated dilation is reduced in CAD coronary arterioles, which is associated with impaired 4-AP-sensitive K V channel function. © 2017 John Wiley & Sons Ltd.

Function-related Drivers of Skull Morphometric Variation and Sexual Size Dimorphism in a Subterranean Rodent, Plateau Zokor (Eospalax baileyi).

PubMed

Su, Junhu; Hegab, Ibrahim M; Ji, Weihong; Nan, Zhibiao

2018-05-01

Sexual dimorphism is prevalent in most living organisms. The difference in size between sexes of a given species is generally known as sexual size dimorphism (SSD). The magnitude of the SSD is determined by Rensch's rule where size dimorphism increases with increasing body size when the male is the larger sex and decreases with increasing average body size when the female is the larger sex. The unique underground environment that zokors ( Eospalax baileyi ) live under in the severe habitat of the Qinghai-Tibetan Plateau (QTP) could create SSD selection pressures that may or may not be supported by Rensch's rule, making this scientific question worthy of investigation. In this study, we investigated the individual variation between sexes in body size and SSD of plateau zokors using measurements of 19 morphological traits. We also investigated the evolutionary mechanisms underlying SSD in plateau zokors. Moreover, we applied Rensch's rule to all extant zokor species. Our results showed male-biased SSD in plateau zokors: The body- and head-related measurements were greater in males than in females. Linear regression analysis between body length, body weight, and carcass weight showed significant relationships with some traits such as skull length, lower incisor length, and tympanic bulla width, which might support our prediction that males have faster growth rates than females. Further, the SSD pattern corroborated the assumption of Rensch's rule in plateau zokors but not in the other zokor species. Our findings suggest that the natural underground habitat and behavioral differences between sexes can generate selection pressures on male traits and contribute to the evolution of SSD in plateau zokors.

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization.

PubMed

True, Jason D; Muldoon, Joseph J; Carver, Melissa N; Poorey, Kunal; Shetty, Savera J; Bekiranov, Stefan; Auble, David T

2016-07-15

Modifier of transcription 1 (Mot1) is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the facilitates chromatin transcription (FACT) histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes. Interestingly, we found that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5' ends of genes. Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Transcription of mouse Sp2 yields alternatively spliced and sub-genomic mRNAs in a tissue- and cell-type-specific fashion.

PubMed

Yin, Haifeng; Nichols, Teresa D; Horowitz, Jonathan M

2010-07-01

The Sp-family of transcription factors is comprised by nine members, Sp1-9, that share a highly conserved DNA-binding domain. Sp2 is a poorly characterized member of this transcription factor family that is widely expressed in murine and human cell lines yet exhibits little DNA-binding or trans-activation activity in these settings. As a prelude to the generation of a "knock-out" mouse strain, we isolated a mouse Sp2 cDNA and performed a detailed analysis of Sp2 transcription in embryonic and adult mouse tissues. We report that (1) the 5' untranslated region of Sp2 is subject to alternative splicing, (2) Sp2 transcription is regulated by at least two promoters that differ in their cell-type specificity, (3) one Sp2 promoter is highly active in nine mammalian cell lines and strains and is regulated by at least five discrete stimulatory and inhibitory elements, (4) a variety of sub-genomic messages are synthesized from the Sp2 locus in a tissue- and cell-type-specific fashion and these transcripts have the capacity to encode a novel partial-Sp2 protein, and (5) RNA in situ hybridization assays indicate that Sp2 is widely expressed during mouse embryogenesis, particularly in the embryonic brain, and robust Sp2 expression occurs in neurogenic regions of the post-natal and adult brain. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Transcriptional regulation of development in heterocyst-forming cyanobacteria.

PubMed

Flores, Enrique; Picossi, Silvia; Valladares, Ana; Herrero, Antonia

2018-04-30

Filamentous, heterocyst-forming cyanobacteria are among the simplest multicellular systems in Nature. In the absence of combined nitrogen, the filaments consist of vegetative cells that fix CO 2 through oxygenic photosynthesis and micro-oxic heterocysts specialized for the fixation of N 2 in a proportion of about 10 to 1. The development of a heterocyst-containing filament involves differentiation of vegetative cells into heterocysts in a process that requires a distinct gene expression program. Two transcription factors are strictly required, NtcA and HetR. The CRP-family protein NtcA directly activates the expression of multiple genes during heterocyst differentiation - in some cases assisted by coactivators including HetR - and in mature heterocysts, whereas HetR is needed to build high NtcA levels in differentiating heterocysts and directly activates some particular genes. A few other regulators of gene expression participate at specific differentiation steps, and a specific transcription factor, CnfR, activates nif gene expression under the micro-oxic conditions of the heterocyst. Copyright © 2018 Elsevier B.V. All rights reserved.

Somatic symptom disorder, a new DSM-5 diagnosis of an old clinical challenge

PubMed Central

Rosic, Tea; Kalra, Sameer; Samaan, Zainab

2016-01-01

Somatic symptom disorder (SSD) is characterised by a dysfunctional preoccupation with one or more physical symptoms. Patients with SSD often pursue excessive and unnecessary investigations, hospitalisations and treatments that significantly affect quality of life and drain healthcare resources. Thus, appropriate diagnosis and careful management are required to mitigate the patient's distress and to reduce the burden to the healthcare system. SSD is a new disorder defined in the Diagnostic and Statistical Manual Fifth Edition (DSM-5), replacing somatoform and related disorders in the DSM-4-Text Revision with diagnostic criteria that are inclusive of a broad array of presentations. This report presents a detailed clinical case of an elderly man with a history of frequent hospital visits presenting with SSD. We discuss diagnostic challenges and evidence-based management in acute inpatient as well as in outpatient settings. We also review data on healthcare utilisation associated with SSD. PMID:26759438

Premorbid intellectual functioning and risk of schizophrenia and spectrum disorders.

PubMed

Reichenberg, Abraham; Weiser, Mark; Caspi, Asaf; Knobler, Haim Y; Lubin, Gad; Harvey, Philip D; Rabinowitz, Jonathan; Davidson, Michael

2006-02-01

Evidence from longitudinal studies indicates that lower IQ score in childhood and early adolescence increases risk of schizophrenia and schizophrenia spectrum disorders (SSD). This study investigated the association between premorbid IQ and risk of SSD in a population-based cohort of 17-year-old conscripts. Fifty four thousand males assessed by the Israeli Draft Board during two consecutive years were followed by means of the Israeli National Psychiatric Hospitalization Case Registry for up to 11 years. Tests of verbal and non-verbal reasoning, mathematical knowledge and instructions comprehension and several psychosocial variables were recorded by the Draft Board. Risk for SSD increased with decreasing IQ score. Only poorer non-verbal reasoning conferred a significant increased risk for SSD after taking into account general intellectual ability. IQ was not associated with age of onset. These results confirm the importance of low intellectual functioning as a risk factor for SSD. This is unlikely to be due to prodrome.

A Trichostatin A (TSA)/Sp1-mediated mechanism for the regulation of SALL2 tumor suppressor in Jurkat T cells.

PubMed

Hepp, Matías I; Escobar, David; Farkas, Carlos; Hermosilla, Viviana; Álvarez, Claudia; Amigo, Roberto; Gutiérrez, José L; Castro, Ariel F; Pincheira, Roxana

2018-05-17

SALL2 is a transcription factor involved in development and disease. Deregulation of SALL2 has been associated with cancer, suggesting that it plays a role in the disease. However, how SALL2 is regulated and why is deregulated in cancer remain poorly understood. We previously showed that the p53 tumor suppressor represses SALL2 under acute genotoxic stress. Here, we investigated the effect of Histone Deacetylase Inhibitor (HDACi) Trichostatin A (TSA), and involvement of Sp1 on expression and function of SALL2 in Jurkat T cells. We show that SALL2 mRNA and protein levels were enhanced under TSA treatment. Both, TSA and ectopic expression of Sp1 transactivated the SALL2 P2 promoter. This transactivation effect was blocked by the Sp1-binding inhibitor mithramycin A. Sp1 bound in vitro and in vivo to the proximal region of the P2 promoter. TSA induced Sp1 binding to the P2 promoter, which correlated with dynamic changes on H4 acetylation and concomitant recruitment of p300 or HDAC1 in a mutually exclusive manner. Our results suggest that TSA-induced Sp1-Lys703 acetylation contributes to the transcriptional activation of the P2 promoter. Finally, using a CRISPR/Cas9 SALL2-KO Jurkat-T cell model and gain of function experiments, we demonstrated that SALL2 upregulation is required for TSA-mediated cell death. Thus, our study identified Sp1 as a novel transcriptional regulator of SALL2, and proposes a novel epigenetic mechanism for SALL2 regulation in Jurkat-T cells. Altogether, our data support SALL2 function as a tumor suppressor, and SALL2 involvement in cell death response to HDACi. Copyright © 2018. Published by Elsevier B.V.

Transcription factor VdCmr1 is required for pigment production, protection from UV irradiation, and regulates expression of melanin biosynthetic genes in Verticillium dahliae

USDA-ARS?s Scientific Manuscript database

Verticillium dahliae is a soilborne fungus that causes vascular wilt diseases on numerous plant species worldwide. The production of darkly melanized microsclerotia is crucial in the disease cycle of V. dahliae, as these structures allow for long-term survival in soil. Previously, transcriptomic and...

FOXM1 promotes the progression of prostate cancer by regulating PSA gene transcription.

PubMed

Liu, Youhong; Liu, Yijun; Yuan, Bowen; Yin, Linglong; Peng, Yuchong; Yu, Xiaohui; Zhou, Weibing; Gong, Zhicheng; Liu, Jianye; He, Leye; Li, Xiong

2017-03-07

Androgen/AR is the primary contributor to prostate cancer (PCa) progression by regulating Prostate Specific Antigen (PSA) gene transcription. The disease inevitably evolves to androgen-independent (AI) status. Other mechanisms by which PSA is regulated and develops to AI have not yet been fully determined. FOXM1 is a cell proliferation-specific transcription factor highly expressed in PCa cells compared to non-malignant prostate epithelial cells, suggesting that the aberrant overexpression of FOXM1 contributes to PCa development. In addition to regulating AR gene transcription and cell cycle-regulatory genes, FOXM1 selectively regulates the gene transcription of KLK2 and PSA, typical androgen responsive genes. Screening the potential FOXM1-binding sites by ChIP-PCR, we found that FOXM1 directly binds to the FHK binding motifs in the PSA promoter/enhancer regions. AI C4-2 cells have more FOXM1 binding sites than androgen dependent LNCaP cells. The depletion of FOXM1 by small molecular inhibitors significantly improves the suppression of PSA gene transcription by the anti-AR agent Cadosax. This is the first report showing that FOXM1 promotes PCa progression by regulating PSA gene transcription, particularly in AI PCa cells. The combination of anti-AR agents and FOXM1 inhibitors has the potential to greatly improve therapy for late-stage PCa patients by suppressing PSA levels.

Identification of a splicing variant that regulates type 2 diabetes risk factor CDKAL1 level by a coding-independent mechanism in human.

PubMed

Zhou, Bo; Wei, Fan-Yan; Kanai, Narumi; Fujimura, Atsushi; Kaitsuka, Taku; Tomizawa, Kazuhito

2014-09-01

Single-nucleotide polymorphisms (SNPs) in CDKAL1 have been associated with the development of type 2 diabetes (T2D). CDKAL1 catalyzes 2-methylthio modification of adenosine at position 37 of tRNA(Lys)(UUU). A deficit of this modification causes aberrant protein synthesis, and is associated with impairment of insulin secretion in both mouse model and human. However, it is unknown whether the T2D-associated SNPs in CDKAL1 are associated with downregulation of CDKAL1 by regulating the gene expression. Here, we report a specific splicing variant of CDKAL1 termed CDKAL1-v1 that is markedly lower in individuals carrying risk SNPs of CDKAL1. Interestingly, CDKAL1-v1 is a non-coding transcript, which regulates the CDKAL1 level by competitive binding to a CDKAL1-targeting miRNA. By direct editing of the genome, we further show that the nucleotides around the SNP regions are critical for the alternative splicing of CDKAL1-v1. These findings reveal that the T2D-associated SNPs in CDKAL1 reduce CDKAL1-v1 levels by impairing splicing, which in turn increases miRNA-mediated suppression of CDKAL1. Our results suggest that CDKAL1-v1-mediated suppression of CDKAL1 might underlie the pathogenesis of T2D in individuals carrying the risk SNPs. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Resveratrol upregulates Egr-1 expression and activity involving extracellular signal-regulated protein kinase and ternary complex factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rössler, Oliver G.; Glatzel, Daniel; Thiel, Gerald, E-mail: gerald.thiel@uks.eu

2015-03-01

Many intracellular functions have been attributed to resveratrol, a polyphenolic phytoalexin found in grapes and in other plants. Here, we show that resveratrol induces the expression of the transcription factor Egr-1 in human embryonic kidney cells. Using a chromosomally embedded Egr-1-responsive reporter gene, we show that the Egr-1 activity was significantly elevated in resveratrol-treated cells, indicating that the newly synthesized Egr-1 protein was biologically active. Stimulus-transcription coupling leading to the resveratrol-induced upregulation of Egr-1 expression and activity requires the protein kinases Raf and extracellular signal-regulated protein kinase ERK, while MAP kinase phosphatase-1 functions as a nuclear shut-off device that interruptsmore » the signaling cascade connecting resveratrol stimulation with enhanced Egr-1 expression. On the transcriptional level, Elk-1, a key transcriptional regulator of serum response element-driven gene transcription, connects the intracellular signaling cascade elicited by resveratrol with transcription of the Egr-1 gene. These data were corroborated by the observation that stimulation of the cells with resveratrol increased the transcriptional activation potential of Elk-1. The SRE as well as the GC-rich DNA binding site of Egr-1 function as resveratrol-responsive elements. Thus, resveratrol regulates gene transcription via activation of the stimulus-regulated protein kinases Raf and ERK and the stimulus-responsive transcription factors TCF and Egr-1. - Highlights: • The plant polyphenol resveratrol upregulates Egr-1 expression and activity. • The stimulation of Egr-1 requires the protein kinases ERK and Raf. • Resveratrol treatment upregulates the transcriptional activation potential of Elk-1. • Resveratrol-induced stimulation of Egr-1 requires ternary complex factors. • Two distinct resveratrol-responsive elements were identified.« less

p65 down-regulates DEPTOR expression in response to LPS stimulation in hepatocytes.

PubMed

Yu, Xiaoling; Jin, Dan; Yu, An; Sun, Jun; Chen, Xiaodong; Yang, Zaiqing

2016-09-01

DEPTOR, a novel endogenous inhibitor of mTOR, plays an important role in regulating the inflammatory response in vascular endothelial cells (ECs) and in mouse skeletal muscle. However, the regulatory mechanism of DEPTOR transcription and its effects on liver inflammation are unknown presently. Here we reported the role of DEPTOR in regulating inflammatory response in mouse liver-derived Hepa1-6 cells and in a mouse model with LPS-induced hepatic inflammation. The results revealed that DEPTOR over-expression in Hepa1-6 liver cells increased the mRNA levels of the pro-inflammatory cytokines interleukin-6 (IL-6) and monocyte chemotactic protein-1 (MCP-1). Contrasting results were observed in Hepa1-6 cells with DEPTOR interference. Treatment Hepa1-6 cells with rapamycin, a specific inhibitor of mTORC1, increased MCP-1 mRNA, but have no significant effect on IL-6 mRNA. DEPTOR expression was down-regulated in Hepa1-6 cells with the treatment of inflammatory stimuli LPS or the over-expression of p65/NF-κB, a key inflammatory transcription factor. NF-κB antagonist (PDTC) and inhibitor (IκBα) blocked the effect of LPS on DEPTOR expression. The study in vivo showed that DEPTOR mRNA and protein were significantly reduced in a mouse model with LPS-induced hepatic inflammation, which was accompanied by a concurrent activation of the mTOR signaling pathway. Further, the transcriptional regulation of DEPTOR was explored, which revealed that DEPTOR promoter activity was significantly down-regulated by NF-κB. The progressive deletions and mutations demonstrated that the NF-κB binding motif situated at -145/-127 region is an essential component required for the DEPTOR promoter activity. Chromatin immunoprecipitation (ChIP) assays determined that p65 can directly interact with the DEPTOR promoter DNA. Those results indicate DEPTOR regulates liver inflammation at least partially via mTORC1 pathway, and is down-regulated by LPS through p65. Copyright © 2016 Elsevier B.V. All rights reserved.

A primer on thermodynamic-based models for deciphering transcriptional regulatory logic.

PubMed

Dresch, Jacqueline M; Richards, Megan; Ay, Ahmet

2013-09-01

A rigorous analysis of transcriptional regulation at the DNA level is crucial to the understanding of many biological systems. Mathematical modeling has offered researchers a new approach to understanding this central process. In particular, thermodynamic-based modeling represents the most biophysically informed approach aimed at connecting DNA level regulatory sequences to the expression of specific genes. The goal of this review is to give biologists a thorough description of the steps involved in building, analyzing, and implementing a thermodynamic-based model of transcriptional regulation. The data requirements for this modeling approach are described, the derivation for a specific regulatory region is shown, and the challenges and future directions for the quantitative modeling of gene regulation are discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

N-Myc Differentially Regulates Expression of MXI1 Isoforms in Neuroblastoma1

PubMed Central

Armstrong, Michael B; Mody, Rajen J; Ellis, D Christian; Hill, Adam B; Erichsen, David A; Wechsler, Daniel S

2013-01-01

Amplification of the MYCN proto-oncogene is associated with a poor prognosis in patients with metastatic neuroblastoma (NB). MYCN encodes the N-Myc protein, a transcriptional regulator that dimerizes with the Max transcription factor, binds to E-box DNA sequences, and regulates genes involved in cell growth and apoptosis. Overexpression of N-Myc leads to transcriptional activation and an increase in NB cell proliferation. Mxi1, a member of the Myc family of transcriptional regulators, also binds to Max. However, Mxi1 is a transcriptional repressor and inhibits proliferation of NB cells, suggesting that Mxi1 functions as an N-Myc antagonist. Our laboratory previously identified Mxi1-0, an alternatively transcribed Mxi1 isoform. Mxi1-0 has properties distinct from those of Mxi1; in contrast to Mxi1, Mxi1-0 is unable to suppress c-Myc-dependent transcription. We now show that Mxi1-0 expression increases in response to MYCN overexpression in NB cells, with a positive correlation between MYCN and MXI1-0 RNA levels. We also show that N-Myc expression differentially regulates the MXI1 and MXI1-0 promoters: Increased MYCN expression suppresses MXI1 promoter activity while enhancing transcription through the MXI1-0 promoter. Finally, induction of Mxi1-0 leads to increased proliferation, whereas expression of Mxi1 inhibits cell growth, indicating differential roles for these two proteins. These data suggest that N-Myc differentially regulates the expression of MXI1 and MXI1-0 and can alter the balance between the two transcription factors. Furthermore, MXI1-0 appears to be a downstream target of MYCN-dependent signaling pathways and may contribute to N-Myc-dependent cell growth and proliferation. PMID:24403858

Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells.

PubMed

Laurette, Patrick; Strub, Thomas; Koludrovic, Dana; Keime, Céline; Le Gras, Stéphanie; Seberg, Hannah; Van Otterloo, Eric; Imrichova, Hana; Siddaway, Robert; Aerts, Stein; Cornell, Robert A; Mengus, Gabrielle; Davidson, Irwin

2015-03-24

Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. To understand how MITF regulates transcription, we used tandem affinity purification and mass spectrometry to define a comprehensive MITF interactome identifying novel cofactors involved in transcription, DNA replication and repair, and chromatin organisation. We show that MITF interacts with a PBAF chromatin remodelling complex comprising BRG1 and CHD7. BRG1 is essential for melanoma cell proliferation in vitro and for normal melanocyte development in vivo. MITF and SOX10 actively recruit BRG1 to a set of MITF-associated regulatory elements (MAREs) at active enhancers. Combinations of MITF, SOX10, TFAP2A, and YY1 bind between two BRG1-occupied nucleosomes thus defining both a signature of transcription factors essential for the melanocyte lineage and a specific chromatin organisation of the regulatory elements they occupy. BRG1 also regulates the dynamics of MITF genomic occupancy. MITF-BRG1 interplay thus plays an essential role in transcription regulation in melanoma.

Transcriptional coupling of synaptic transmission and energy metabolism: role of nuclear respiratory factor 1 in co-regulating neuronal nitric oxide synthase and cytochrome c oxidase genes in neurons.

PubMed

Dhar, Shilpa S; Liang, Huan Ling; Wong-Riley, Margaret T T

2009-10-01

Neuronal activity is highly dependent on energy metabolism; yet, the two processes have traditionally been regarded as independently regulated at the transcriptional level. Recently, we found that the same transcription factor, nuclear respiratory factor 1 (NRF-1) co-regulates an important energy-generating enzyme, cytochrome c oxidase, as well as critical subunits of glutamatergic receptors. The present study tests our hypothesis that the co-regulation extends to the next level of glutamatergic synapses, namely, neuronal nitric oxide synthase, which generates nitric oxide as a downstream signaling molecule. Using in silico analysis, electrophoretic mobility shift assay, chromatin immunoprecipitation, promoter mutations, and NRF-1 silencing, we documented that NRF-1 functionally bound to Nos1, but not Nos2 (inducible) and Nos3 (endothelial) gene promoters. Both COX and Nos1 transcripts were up-regulated by depolarizing KCl treatment and down-regulated by TTX-mediated impulse blockade in neurons. However, NRF-1 silencing blocked the up-regulation of both Nos1 and COX induced by KCl depolarization, and over-expression of NRF-1 rescued both Nos1 and COX transcripts down-regulated by TTX. These findings are consistent with our hypothesis that synaptic neuronal transmission and energy metabolism are tightly coupled at the molecular level.

Subsyndromal symptomatic depression: a new concept.

PubMed

Sadek, N; Bona, J

2000-01-01

Although DSM-IV acknowledged the clinical significance of some subthreshold forms of unipolar depression, such as minor depression (MinD) and recurrent brief depression (RBD), clinicians continued to struggle with the concept of "subthreshold" depression. A substantial number of patients continued to present with depressive symptoms that still did not satisfy any DSM-IV diagnosis. Generally, these patients failed to complain of anhedonia and depressed mood, a criterion that DSM-IV mandates for any diagnosis of depression. Therefore, researchers reexamined the question of whether this cluster of depressive symptoms, in the absence of anhedonia and depressed mood, was clinically significant. Some researchers labeled this cluster of symptoms, "subsyndromal symptomatic depression" (SSD). Specifically, SSD is defined as a depressive state having two or more symptoms of depression of the same quality as in major depression (MD), excluding depressed mood and anhedonia. The symptoms must be present for more than 2 weeks and be associated with social dysfunction. Using Medline Search, the authors reviewed the literature on the epidemiology, demographics, clinical characteristics, and psychosocial impairment of SSD. SSD is found to be comparable in demographics and clinical characteristics to MD, MinD, and dysthymia. SSD is also associated with significant psychosocial dysfunction as compared with healthy subjects. Further; it has significant risk for suicide and future MD. Few studies have been conducted on the treatment of SSD. The high prevalence of SSD, the significant psychosocial impairment associated with it, and the chronicity of its course make subsyndromal symptomatic depression a matter for serious consideration by clinicians and researchers.

Speech sound disorder at 4 years: prevalence, comorbidities, and predictors in a community cohort of children.

PubMed

Eadie, Patricia; Morgan, Angela; Ukoumunne, Obioha C; Ttofari Eecen, Kyriaki; Wake, Melissa; Reilly, Sheena

2015-06-01

The epidemiology of preschool speech sound disorder is poorly understood. Our aims were to determine: the prevalence of idiopathic speech sound disorder; the comorbidity of speech sound disorder with language and pre-literacy difficulties; and the factors contributing to speech outcome at 4 years. One thousand four hundred and ninety-four participants from an Australian longitudinal cohort completed speech, language, and pre-literacy assessments at 4 years. Prevalence of speech sound disorder (SSD) was defined by standard score performance of ≤79 on a speech assessment. Logistic regression examined predictors of SSD within four domains: child and family; parent-reported speech; cognitive-linguistic; and parent-reported motor skills. At 4 years the prevalence of speech disorder in an Australian cohort was 3.4%. Comorbidity with SSD was 40.8% for language disorder and 20.8% for poor pre-literacy skills. Sex, maternal vocabulary, socio-economic status, and family history of speech and language difficulties predicted SSD, as did 2-year speech, language, and motor skills. Together these variables provided good discrimination of SSD (area under the curve=0.78). This is the first epidemiological study to demonstrate prevalence of SSD at 4 years of age that was consistent with previous clinical studies. Early detection of SSD at 4 years should focus on family variables and speech, language, and motor skills measured at 2 years. © 2014 Mac Keith Press.

Amino acid-dependent signaling via S6K1 and MYC is essential for regulation of rDNA transcription

PubMed Central

Kang, Jian; Kusnadi, Eric P.; Ogden, Allison J.; Hicks, Rodney J.; Bammert, Lukas; Kutay, Ulrike; Hung, Sandy; Sanij, Elaine; Hannan, Ross D.; Hannan, Katherine M.; Pearson, Richard B.

2016-01-01

Dysregulation of RNA polymerase I (Pol I)-dependent ribosomal DNA (rDNA) transcription is a consistent feature of malignant transformation that can be targeted to treat cancer. Understanding how rDNA transcription is coupled to the availability of growth factors and nutrients will provide insight into how ribosome biogenesis is maintained in a tumour environment characterised by limiting nutrients. We demonstrate that modulation of rDNA transcription initiation, elongation and rRNA processing is an immediate, co-regulated response to altered amino acid abundance, dependent on both mTORC1 activation of S6K1 and MYC activity. Growth factors regulate rDNA transcription initiation while amino acids modulate growth factor-dependent rDNA transcription by primarily regulating S6K1-dependent rDNA transcription elongation and processing. Thus, we show for the first time amino acids regulate rRNA synthesis by a distinct, post-initiation mechanism, providing a novel model for integrated control of ribosome biogenesis that has implications for understanding how this process is dysregulated in cancer. PMID:27385002

Management of the Acute Partial-thickness Burned Hand; Moist Exposed Burn Ointment or Silver Sulphadiazine Cream both Combined with a Polyethylene Bag

PubMed Central

Allam, A.M.; Mostafa, W.; Zayed, E.; El-Gamaly, J.

2007-01-01

Summary Hand burns predominantly affect young adults, and therefore have serious social and financial implications. In the present work, 106 patients with less than 25% body surface area burns and acute partial-thickness burned hands were managed using polyethylene bags and 1% local silver sulphadiazine (SSD) cream or moist exposed burn ointment (MEBO). Females made up 61.3% of the cases and flame burn was the majority cause (54.7%). There were no significant differences between the two groups regarding either the analgesic effect after local ointment application or hand movement inside the polyethylene bag. Local agent crustation over the wound was very evident in the hands managed by local 1% SSD cream (69.81%). On follow-up, the burned hands healed faster using local MEBO (10.48 versus 14.53 days), with fewer post-burn hand deformities and better active hand movements; however, the total cost until complete hand burn wound healing was higher with MEBO than with 1% SSD, although the final results were superior, with early return to work, when MEBO was used. We concluded that the use of MEBO as a topical agent and of polyethylene bags for the dressing of the acute partial-thickness burned hand accelerated healing; daily wound evaluation was easy as there was no crustation over it of the agent. It was more expensive than 1% SSD cream but presented fewer post-burn complications and more rapid healing, with shorter hospital stay. PMID:21991086

An in vitro study of the anti-microbial efficacy of a 1% silver sulphadiazine and 0.2% chlorhexidine digluconate cream, 1% silver sulphadiazine cream and a silver coated dressing.

PubMed

Fraser, John F; Bodman, Jan; Sturgess, Ruth; Faoagali, Joan; Kimble, Roy M

2004-02-01

Burn sepsis is a leading cause of mortality and morbidity in patients with major burns. The use of topical anti-microbial agents has helped improve the survival in these patients. There are a number of anti-microbials available, one of which, Silvazine (1% silver sulphadiazine (SSD) and 0.2% chlorhexidine digluconate), is used only in Australasia. No study, in vitro or clinical, had compared Silvazine with the new dressing Acticoat. This study compared the anti-microbial activity of Silvazine, Acticoat and 1% silver sulphadiazine (Flamazine) against eight common burn wound pathogens. Each organism was prepared as a suspension. A 10 microl inoculum of the chosen bacterial isolate (representing approximately between 10(4) and 10(5) total bacteria) was added to each of four vials, followed by samples of each dressing and a control. The broths were then incubated and 10 microl loops removed at specified intervals and transferred onto Horse Blood Agar. These plates were then incubated for 18 hours and a colony count was performed. The data demonstrates that the combination of 1% SSD and 0.2% chlorhexidine digluconate (Silvazine) results in the most effective killing of all bacteria. SSD and Acticoat had similar efficacies against a number of isolates, but Acticoat seemed only bacteriostatic against E. faecalis and methicillin-resistant Staphylococcus aureus. Viable quantities of Enterobacter cloacae and Proteus mirabilis remained at 24h. The combination of 1% SSD and 0.2% chlorhexidine digluconate (Silvazine) is a more effective anti-microbial against a number of burn wound pathogens in this in vitro study. A clinical study of its in vivo anti-microbial efficacy is required.

Potential Regulators Driving the Transition in Nonalcoholic Fatty Liver Disease: a Stage-Based View.

PubMed

Lou, Yi; Chen, Yi-Dan; Sun, Fu-Rong; Shi, Jun-Ping; Song, Yu; Yang, Jin

2017-01-01

The incidence of nonalcoholic fatty liver disease (NAFLD), ranging from mild steatosis to hepatocellular injury and inflammation, increases with the rise of obesity. However, the implications of transcription factors network in progressive NAFLD remain to be determined. A co-regulatory network approach by combining gene expression and transcription influence was utilized to dissect transcriptional regulators in different NAFLD stages. In vivo, mice models of NAFLD were used to investigate whether dysregulated expression be undertaken by transcriptional regulators. Through constructing a large-scale co-regulatory network, sample-specific regulator activity was estimated. The combinations of active regulators that drive the progression of NAFLD were identified. Next, top regulators in each stage of NAFLD were determined, and the results were validated using the different experiments and bariatric surgical samples. In particular, Adipocyte enhancer-binding protein 1 (AEBP1) showed increased transcription activity in nonalcoholic steatohepatitis (NASH). Further characterization of the AEBP1 related transcription program defined its co-regulators, targeted genes, and functional organization. The dynamics of AEBP1 and its potential targets were verified in an animal model of NAFLD. This study identifies putative functions for several transcription factors in the pathogenesis of NAFLD and may thus point to potential targets for therapeutic interventions. © 2017 The Author(s) Published by S. Karger AG, Basel.

MicroRNA319-regulated TCPs interact with FBHs and PFT1 to activate CO transcription and control flowering time in Arabidopsis.

PubMed

Liu, Jie; Cheng, Xiliu; Liu, Pan; Li, Dayong; Chen, Tao; Gu, Xiaofeng; Sun, Jiaqiang

2017-05-01

The transcription factor CONSTANS (CO) is a central component that promotes Arabidopsis flowering under long-day conditions (LDs). Here, we show that the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote photoperiodic flowering through binding to the CO promoter and activating its transcription. Meanwhile, these TCPs directly interact with the flowering activators FLOWERING BHLH (FBHs), but not the flowering repressors CYCLING DOF FACTORs (CDFs), to additively activate CO expression. Furthermore, both the TCPs and FBHs physically interact with the flowering time regulator PHYTOCHROME AND FLOWERING TIME 1 (PFT1) to facilitate CO transcription. Our findings provide evidence that a set of transcriptional activators act directly and additively at the CO promoter to promote CO transcription, and establish a molecular mechanism underlying the regulation of photoperiodic flowering time in Arabidopsis.

MicroRNA319-regulated TCPs interact with FBHs and PFT1 to activate CO transcription and control flowering time in Arabidopsis

PubMed Central

Liu, Pan; Li, Dayong; Chen, Tao; Gu, Xiaofeng; Sun, Jiaqiang

2017-01-01

The transcription factor CONSTANS (CO) is a central component that promotes Arabidopsis flowering under long-day conditions (LDs). Here, we show that the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote photoperiodic flowering through binding to the CO promoter and activating its transcription. Meanwhile, these TCPs directly interact with the flowering activators FLOWERING BHLH (FBHs), but not the flowering repressors CYCLING DOF FACTORs (CDFs), to additively activate CO expression. Furthermore, both the TCPs and FBHs physically interact with the flowering time regulator PHYTOCHROME AND FLOWERING TIME 1 (PFT1) to facilitate CO transcription. Our findings provide evidence that a set of transcriptional activators act directly and additively at the CO promoter to promote CO transcription, and establish a molecular mechanism underlying the regulation of photoperiodic flowering time in Arabidopsis. PMID:28558040

Berry skin development in Norton grape: distinct patterns of transcriptional regulation and flavonoid biosynthesis.

PubMed

Ali, Mohammad B; Howard, Susanne; Chen, Shangwu; Wang, Yechun; Yu, Oliver; Kovacs, Laszlo G; Qiu, Wenping

2011-01-10

The complex and dynamic changes during grape berry development have been studied in Vitis vinifera, but little is known about these processes in other Vitis species. The grape variety 'Norton', with a major portion of its genome derived from Vitis aestivalis, maintains high levels of malic acid and phenolic acids in the ripening berries in comparison with V. vinifera varieties such as Cabernet Sauvignon. Furthermore, Norton berries develop a remarkably high level of resistance to most fungal pathogens while Cabernet Sauvignon berries remain susceptible to those pathogens. The distinct characteristics of Norton and Cabernet Sauvignon merit a comprehensive analysis of transcriptional regulation and metabolite pathways. A microarray study was conducted on transcriptome changes of Norton berry skin during the period of 37 to 127 days after bloom, which represents berry developmental phases from herbaceous growth to full ripeness. Samples of six berry developmental stages were collected. Analysis of the microarray data revealed that a total of 3,352 probe sets exhibited significant differences at transcript levels, with two-fold changes between at least two developmental stages. Expression profiles of defense-related genes showed a dynamic modulation of nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes and pathogenesis-related (PR) genes during berry development. Transcript levels of PR-1 in Norton berry skin clearly increased during the ripening phase. As in other grapevines, genes of the phenylpropanoid pathway were up-regulated in Norton as the berry developed. The most noticeable was the steady increase of transcript levels of stilbene synthase genes. Transcriptional patterns of six MYB transcription factors and eleven structural genes of the flavonoid pathway and profiles of anthocyanins and proanthocyanidins (PAs) during berry skin development were analyzed comparatively in Norton and Cabernet Sauvignon. Transcriptional patterns of MYB5A and MYB5B were similar during berry development between the two varieties, but those of MYBPA1 and MYBPA2 were strikingly different, demonstrating that the general flavonoid pathways are regulated under different MYB factors. The data showed that there were higher transcript levels of the genes encoding flavonoid-3'-O-hydroxylase (F3'H), flavonoid-3',5'-hydroxylase (F3'5'H), leucoanthocyanidin dioxygenase (LDOX), UDP-glucose:flavonoid 3'-O-glucosyltransferase (UFGT), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR) 1 and LAR2 in berry skin of Norton than in those of Cabernet Sauvignon. It was also found that the total amount of anthocyanins was markedly higher in Norton than in Cabernet Sauvignon berry skin at harvest, and five anthocyanin derivatives and three PA compounds exhibited distinctive accumulation patterns in Norton berry skin. This study provides an overview of the transcriptome changes and the flavonoid profiles in the berry skin of Norton, an important North American wine grape, during berry development. The steady increase of transcripts of PR-1 and stilbene synthase genes likely contributes to the developmentally regulated resistance during ripening of Norton berries. More studies are required to address the precise role of each stilbene synthase gene in berry development and disease resistance. Transcriptional regulation of MYBA1, MYBA2, MYB5A and MYBPA1 as well as expression levels of their putative targets F3'H, F3'5'H, LDOX, UFGT, ANR, LAR1, and LAR2 are highly correlated with the characteristic anthocyanin and PA profiles in Norton berry skin. These results reveal a unique pattern of the regulation of transcription and biosynthesis pathways underlying the viticultural and enological characteristics of Norton grape, and yield new insights into the understanding of the flavonoid pathway in non-vinifera grape varieties.

Berry skin development in Norton grape: Distinct patterns of transcriptional regulation and flavonoid biosynthesis

PubMed Central

2011-01-01

Background The complex and dynamic changes during grape berry development have been studied in Vitis vinifera, but little is known about these processes in other Vitis species. The grape variety 'Norton', with a major portion of its genome derived from Vitis aestivalis, maintains high levels of malic acid and phenolic acids in the ripening berries in comparison with V. vinifera varieties such as Cabernet Sauvignon. Furthermore, Norton berries develop a remarkably high level of resistance to most fungal pathogens while Cabernet Sauvignon berries remain susceptible to those pathogens. The distinct characteristics of Norton and Cabernet Sauvignon merit a comprehensive analysis of transcriptional regulation and metabolite pathways. Results A microarray study was conducted on transcriptome changes of Norton berry skin during the period of 37 to 127 days after bloom, which represents berry developmental phases from herbaceous growth to full ripeness. Samples of six berry developmental stages were collected. Analysis of the microarray data revealed that a total of 3,352 probe sets exhibited significant differences at transcript levels, with two-fold changes between at least two developmental stages. Expression profiles of defense-related genes showed a dynamic modulation of nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes and pathogenesis-related (PR) genes during berry development. Transcript levels of PR-1 in Norton berry skin clearly increased during the ripening phase. As in other grapevines, genes of the phenylpropanoid pathway were up-regulated in Norton as the berry developed. The most noticeable was the steady increase of transcript levels of stilbene synthase genes. Transcriptional patterns of six MYB transcription factors and eleven structural genes of the flavonoid pathway and profiles of anthocyanins and proanthocyanidins (PAs) during berry skin development were analyzed comparatively in Norton and Cabernet Sauvignon. Transcriptional patterns of MYB5A and MYB5B were similar during berry development between the two varieties, but those of MYBPA1 and MYBPA2 were strikingly different, demonstrating that the general flavonoid pathways are regulated under different MYB factors. The data showed that there were higher transcript levels of the genes encoding flavonoid-3'-O-hydroxylase (F3'H), flavonoid-3',5'-hydroxylase (F3'5'H), leucoanthocyanidin dioxygenase (LDOX), UDP-glucose:flavonoid 3'-O-glucosyltransferase (UFGT), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR) 1 and LAR2 in berry skin of Norton than in those of Cabernet Sauvignon. It was also found that the total amount of anthocyanins was markedly higher in Norton than in Cabernet Sauvignon berry skin at harvest, and five anthocyanin derivatives and three PA compounds exhibited distinctive accumulation patterns in Norton berry skin. Conclusions This study provides an overview of the transcriptome changes and the flavonoid profiles in the berry skin of Norton, an important North American wine grape, during berry development. The steady increase of transcripts of PR-1 and stilbene synthase genes likely contributes to the developmentally regulated resistance during ripening of Norton berries. More studies are required to address the precise role of each stilbene synthase gene in berry development and disease resistance. Transcriptional regulation of MYBA1, MYBA2, MYB5A and MYBPA1 as well as expression levels of their putative targets F3'H, F3'5'H, LDOX, UFGT, ANR, LAR1, and LAR2 are highly correlated with the characteristic anthocyanin and PA profiles in Norton berry skin. These results reveal a unique pattern of the regulation of transcription and biosynthesis pathways underlying the viticultural and enological characteristics of Norton grape, and yield new insights into the understanding of the flavonoid pathway in non-vinifera grape varieties. PMID:21219654

Transcription factor ThWRKY4 binds to a novel WLS motif and a RAV1A element in addition to the W-box to regulate gene expression.

PubMed

Xu, Hongyun; Shi, Xinxin; Wang, Zhibo; Gao, Caiqiu; Wang, Chao; Wang, Yucheng

2017-08-01

WRKY transcription factors play important roles in many biological processes, and mainly bind to the W-box element to regulate gene expression. Previously, we characterized a WRKY gene from Tamarix hispida, ThWRKY4, in response to abiotic stress, and showed that it bound to the W-box motif. However, whether ThWRKY4 could bind to other motifs remains unknown. In this study, we employed a Transcription Factor-Centered Yeast one Hybrid (TF-Centered Y1H) screen to study the motifs recognized by ThWRKY4. In addition to the W-box core cis-element (termed W-box), we identified that ThWRKY4 could bind to two other motifs: the RAV1A element (CAACA) and a novel motif with sequence of GTCTA (W-box like sequence, WLS). The distributions of these motifs were screened in the promoter regions of genes regulated by some WRKYs. The results showed that the W-box, RAV1A, and WLS motifs were all present in high numbers, suggesting that they play key roles in gene expression mediated by WRKYs. Furthermore, five WRKY proteins from different WRKY subfamilies in Arabidopsis thaliana were selected and confirmed to bind to the RAV1A and WLS motifs, indicating that they are recognized commonly by WRKYs. These findings will help to further reveal the functions of WRKY proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

DAG1, no gene for RNA regulation?

PubMed

Brancaccio, Andrea

2012-04-10

DAG1 encodes for a precursor protein that liberates the two subunits featured by the dystroglycan (DG) adhesion complex that are involved in an increasing number of cellular functions in a wide variety of cells and tissues. Aside from the proteolytic events producing the α and β subunits, especially the former undergoes extensive "post-production" modifications taking place within the ER/Golgi where its core protein is both N- and O-decorated with sugars. These post-translational events, that are mainly orchestrated by a plethora of certified, or putative, glycosyltransferases, prelude to the excocytosis-mediated trafficking and targeting of the DG complex to the plasma membrane. Extensive genetic and biochemical evidences have been accumulated so far on α-DG glycosylation, while little is know on possible regulatory events underlying the chromatine activation, transcription or post-transcription (splicing and escape from the nucleus) of DAG1 or of its mRNA. A scenario is envisaged in which cells would use a sort of preferential, and scarcely regulated, route for DAG1 activation, that would imply fast mRNA transcription, maturation and export to the cytosol, and would prelude to the multiple time-consuming enzymatic post-translational activities needed for its glycosylation. Such a provocative view might be helpful to trigger future work aiming at disclosing the complete molecular mechanisms underlying DAG1 activation and at improving our knowledge of any pre-translational step that is involved in dystroglycan regulation. Copyright © 2012 Elsevier B.V. All rights reserved.

Identification of a gene set to evaluate the potential effects of loud sounds from seismic surveys on the ears of fishes: a study with Salmo salar

PubMed Central

Andrews, C D; Payne, J F; Rise, M L

2014-01-01

Functional genomic studies were carried out on the inner ear of Atlantic salmon Salmo salar following exposure to a seismic airgun. Microarray analyses revealed 79 unique transcripts (passing background threshold), with 42 reproducibly up-regulated and 37 reproducibly down-regulated in exposed v. control fish. Regarding the potential effects on cellular energetics and cellular respiration, altered transcripts included those with roles in oxygen transport, the glycolytic pathway, the Krebs cycle and the electron transport chain. Of these, a number of transcripts encoding haemoglobins that are important in oxygen transport were up-regulated and among the most highly expressed. Up-regulation of transcripts encoding nicotinamide riboside kinase 2, which is also important in energy production and linked to nerve cell damage, points to evidence of neuronal damage in the ear following noise exposure. Transcripts related to protein modification or degradation also indicated potential damaging effects of sound on ear tissues. Notable in this regard were transcripts associated with the proteasome–ubiquitin pathway, which is involved in protein degradation, with the transcript encoding ubiquitin family domain-containing protein 1 displaying the highest response to exposure. The differential expression of transcripts observed for some immune responses could potentially be linked to the rupture of cell membranes. Meanwhile, the altered expression of transcripts for cytoskeletal proteins that contribute to the structural integrity of the inner ear could point to repair or regeneration of ear tissues including auditory hair cells. Regarding potential effects on hormones and vitamins, the protein carrier for thyroxine and retinol (vitamin A), namely transthyretin, was altered at the transcript expression level and it has been suggested from studies in mammalian systems that retinoic acid may play a role in the regeneration of damaged hair cells. The microarray experiment identified the transcript encoding growth hormone I as up-regulated by loud sound, supporting previous evidence linking growth hormone to hair cell regeneration in fishes. Quantitative (q) reverse transcription (RT) polymerase chain reaction (qRT-PCR) analyses confirmed dysregulation of some microarray-identified transcripts and in some cases revealed a high level of biological variability in the exposed group. These results support the potential utility of molecular biomarkers to evaluate the effect of seismic surveys on fishes with studies on the ears being placed in a priority category for development of exposure–response relationships. Knowledge of such relationships is necessary for addressing the question of potential size of injury zones. PMID:24814183

The diverse biological roles of mammalian PARPS, a small but powerful family of poly-ADP-ribose polymerases.

PubMed

Hassa, Paul O; Hottiger, Michael O

2008-01-01

Poly-ADP-ribose metabolism plays a mayor role in a wide range of biological processes, such as maintenance of genomic stability, transcriptional regulation, energy metabolism and cell death. Poly-ADP-ribose polymerases (PARPs) are an ancient family of enzymes, as evidenced by the poly-ADP-ribosylating activities reported in dinoflagellates and archaebacteria and by the identification of Parp-like genes in eubacterial and archaeabacterial genomes. Six genes encoding "bona fide" PARP enzymes have been identified in mammalians: PARP1, PARP2, PARP3, PARP4/vPARP, PARP5/Tankyrases-1 and PARP6/Tankyrases-2. The best studied of these enzymes PARP1 plays a primary role in the process of poly-ADP-ribosylation. PARP1-mediated poly-ADP-ribosylation has been implicated in the pathogenesis of cancer, inflammatory and neurodegenerative disorders. This review will summarize the novel findings and concepts for PARP enzymes and their poly-ADP-ribosylation activity in the regulation of physiological and pathophysiological processes. A special focus is placed on the proposed molecular mechanisms involved in these processes, such as signaling, regulation of telomere dynamics, remodeling of chromatin structure and transcriptional regulation. A potential functional cross talk between PARP family members and other NAD+-consuming enzymes is discussed.

APOBEC3G Inhibits HIV-1 RNA Elongation by Inactivating the Viral Trans-Activation Response Element

PubMed Central

Nowarski, Roni; Prabhu, Ponnandy; Kenig, Edan; Smith, Yoav; Britan-Rosich, Elena; Kotler, Moshe

2014-01-01

Deamination of cytidine residues in viral DNA (vDNA) is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient HIV-1 replication. dC to dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here we demonstrate that A3G provides an additional layer of defence against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. Finally, we show that free ssDNA termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3′+5′ ends is sufficient for A3G deamination, identifying A3G as an efficient mutator, and that deamination of (−)SSDNA results in an early block of HIV-1 transcription. PMID:24859335

Repression of myoblast proliferation and fibroblast growth factor receptor 1 promoter activity by KLF10 protein.

PubMed

Parakati, Rajini; DiMario, Joseph X

2013-05-10

FGFR1 gene expression regulates myoblast proliferation and differentiation, and its expression is controlled by Krüppel-like transcription factors. KLF10 interacts with the FGFR1 promoter, repressing its activity and cell proliferation. KLF10 represses FGFR1 promoter activity and thereby myoblast proliferation. A model of transcriptional control of chicken FGFR1 gene regulation during myogenesis is presented. Skeletal muscle development is controlled by regulation of myoblast proliferation and differentiation into muscle fibers. Growth factors such as fibroblast growth factors (FGFs) and their receptors (FGFRs) regulate cell proliferation and differentiation in numerous tissues, including skeletal muscle. Transcriptional regulation of FGFR1 gene expression is developmentally regulated by the Sp1 transcription factor, a member of the Krüppel-like factor (KLF) family of transcriptional regulators. Here, we show that another KLF transcription factor, KLF10, also regulates myoblast proliferation and FGFR1 promoter activity. Expression of KLF10 reduced myoblast proliferation by 86%. KLF10 expression also significantly reduced FGFR1 promoter activity in myoblasts and Sp1-mediated FGFR1 promoter activity in Drosophila SL2 cells. Southwestern blot, electromobility shift, and chromatin immunoprecipitation assays demonstrated that KLF10 bound to the proximal Sp factor binding site of the FGFR1 promoter and reduced Sp1 complex formation with the FGFR1 promoter at that site. These results indicate that KLF10 is an effective repressor of myoblast proliferation and represses FGFR1 promoter activity in these cells via an Sp1 binding site.

Biomaterials for Improved Wound Healing

DTIC Science & Technology

2013-10-01

is silver sulphadiazine (SSD) [6-7]. SSD possesses a broad spectrum of activity against gram- positive and gram-negative bacteria as well as fungi [8... polyethylene glycol-based fibrin gel (PEGylated fibrin gel) induces vasculogenesis both in vitro and in vivo [20]. To exploit the inherent ability of fibrin as...Loaded Chitosan Microspheres Impregnated in Polyethylene Glycol Fibrin Gels (SSD-CSM-PEGylated fibrin gels) and Adipose Derived Stem Cells embedded

Novel signal transducer and activator of transcription 1 mutation disrupts small ubiquitin-related modifier conjugation causing gain of function.

PubMed

Sampaio, Elizabeth P; Ding, Li; Rose, Stacey R; Cruz, Phillip; Hsu, Amy P; Kashyap, Anuj; Rosen, Lindsey B; Smelkinson, Margery; Tavella, Tatyana A; Ferre, Elise M N; Wierman, Meredith K; Zerbe, Christa S; Lionakis, Michail S; Holland, Steven M

2018-05-01

Sumoylation is a posttranslational reversible modification of cellular proteins through the conjugation of small ubiquitin-related modifier (SUMO) and comprises an important regulator of protein function. We sought to characterize the molecular mechanism of a novel mutation at the SUMO motif on signal transducer and activator of transcription 1 (STAT1). STAT1 sequencing and functional characterization were performed in transfection experiments by using immunoblotting and immunoprecipitation in STAT1-deficient cell lines. Transcriptional response and target gene activation were also investigated in PBMCs. We identified a novel STAT1 mutation (c.2114A>T, p.E705V) within the SUMO motif ( 702 IKTE 705 ) in a patient with disseminated Rhodococcus species infection, Norwegian scabies, chronic mucocutaneous candidiasis, hypothyroidism, and esophageal squamous cell carcinoma. The mutation is located in the tail segment and is predicted to disrupt STAT1 sumoylation. Immunoprecipitation experiments performed in transfected cells confirmed absent STAT1 sumoylation for E705V, whereas it was present in wild-type (WT) STAT1 cells, as well as the loss-of-function mutants L706S and Y701C. Furthermore, stimulation with IFN-γ led to enhanced STAT1 phosphorylation, enhanced transcriptional activity, and target gene expression in the E705V-transfected compared with WT-transfected cells. Computer modeling of WT and mutant STAT1 molecules showed variations in the accessibility of the phosphorylation site Y701, which corresponded to the loss-of-function and gain-of-function variants. This is the first report of a mutation in the STAT1 sumoylation motif associated with clinical disease. These data reinforce sumoylation as a key posttranslational regulatory modification of STAT1 and identify a novel mechanism for gain-of-function STAT1 disease in human subjects. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. All rights reserved.

The WRKY Transcription Factor WRKY71/EXB1 Controls Shoot Branching by Transcriptionally Regulating RAX Genes in Arabidopsis.

PubMed

Guo, Dongshu; Zhang, Jinzhe; Wang, Xinlei; Han, Xiang; Wei, Baoye; Wang, Jianqiao; Li, Boxun; Yu, Hao; Huang, Qingpei; Gu, Hongya; Qu, Li-Jia; Qin, Genji

2015-11-01

Plant shoot branching is pivotal for developmental plasticity and crop yield. The formation of branch meristems is regulated by several key transcription factors including REGULATOR OF AXILLARY MERISTEMS1 (RAX1), RAX2, and RAX3. However, the regulatory network of shoot branching is still largely unknown. Here, we report the identification of EXCESSIVE BRANCHES1 (EXB1), which affects axillary meristem (AM) initiation and bud activity. Overexpression of EXB1 in the gain-of-function mutant exb1-D leads to severe bushy and dwarf phenotypes, which result from excessive AM initiation and elevated bud activities. EXB1 encodes the WRKY transcription factor WRKY71, which has demonstrated transactivation activities. Disruption of WRKY71/EXB1 by chimeric repressor silencing technology leads to fewer branches, indicating that EXB1 plays important roles in the control of shoot branching. We demonstrate that EXB1 controls AM initiation by positively regulating the transcription of RAX1, RAX2, and RAX3. Disruption of the RAX genes partially rescues the branching phenotype caused by EXB1 overexpression. We further show that EXB1 also regulates auxin homeostasis in control of shoot branching. Our data demonstrate that EXB1 plays pivotal roles in shoot branching by regulating both transcription of RAX genes and auxin pathways. © 2015 American Society of Plant Biologists. All rights reserved.

The WRKY Transcription Factor WRKY71/EXB1 Controls Shoot Branching by Transcriptionally Regulating RAX Genes in Arabidopsis

PubMed Central

Guo, Dongshu; Zhang, Jinzhe; Wang, Xinlei; Han, Xiang; Wei, Baoye; Yu, Hao; Huang, Qingpei

2015-01-01

Plant shoot branching is pivotal for developmental plasticity and crop yield. The formation of branch meristems is regulated by several key transcription factors including REGULATOR OF AXILLARY MERISTEMS1 (RAX1), RAX2, and RAX3. However, the regulatory network of shoot branching is still largely unknown. Here, we report the identification of EXCESSIVE BRANCHES1 (EXB1), which affects axillary meristem (AM) initiation and bud activity. Overexpression of EXB1 in the gain-of-function mutant exb1-D leads to severe bushy and dwarf phenotypes, which result from excessive AM initiation and elevated bud activities. EXB1 encodes the WRKY transcription factor WRKY71, which has demonstrated transactivation activities. Disruption of WRKY71/EXB1 by chimeric repressor silencing technology leads to fewer branches, indicating that EXB1 plays important roles in the control of shoot branching. We demonstrate that EXB1 controls AM initiation by positively regulating the transcription of RAX1, RAX2, and RAX3. Disruption of the RAX genes partially rescues the branching phenotype caused by EXB1 overexpression. We further show that EXB1 also regulates auxin homeostasis in control of shoot branching. Our data demonstrate that EXB1 plays pivotal roles in shoot branching by regulating both transcription of RAX genes and auxin pathways. PMID:26578700

Regulation of Viral RNA Synthesis by the V Protein of Parainfluenza Virus 5

PubMed Central

Yang, Yang; Zengel, James; Sun, Minghao; Sleeman, Katrina; Timani, Khalid Amine; Aligo, Jason; Rota, Paul

2015-01-01

ABSTRACT Paramyxoviruses include many important animal and human pathogens. The genome of parainfluenza virus 5 (PIV5), a prototypical paramyxovirus, encodes a V protein that inhibits viral RNA synthesis. In this work, the mechanism of inhibition was investigated. Using mutational analysis and a minigenome system, we identified regions in the N and C termini of the V protein that inhibit viral RNA synthesis: one at the very N terminus of V and the second at the C terminus of V. Furthermore, we determined that residues L16 and I17 are critical for the inhibitory function of the N-terminal region of the V protein. Both regions interact with the nucleocapsid protein (NP), an essential component of the viral RNA genome complex (RNP). Mutations at L16 and I17 abolished the interaction between NP and the N-terminal domain of V. This suggests that the interaction between NP and the N-terminal domain plays a critical role in V inhibition of viral RNA synthesis by the N-terminal domain. Both the N- and C-terminal regions inhibited viral RNA replication. The C terminus inhibited viral RNA transcription, while the N-terminal domain enhanced viral RNA transcription, suggesting that the two domains affect viral RNA through different mechanisms. Interestingly, V also inhibited the synthesis of the RNA of other paramyxoviruses, such as Nipah virus (NiV), human parainfluenza virus 3 (HPIV3), measles virus (MeV), mumps virus (MuV), and respiratory syncytial virus (RSV). This suggests that a common host factor may be involved in the replication of these paramyxoviruses. IMPORTANCE We identified two regions of the V protein that interact with NP and determined that one of these regions enhances viral RNA transcription via its interaction with NP. Our data suggest that a common host factor may be involved in the regulation of paramyxovirus replication and could be a target for broad antiviral drug development. Understanding the regulation of paramyxovirus replication will enable the rational design of vaccines and potential antiviral drugs. PMID:26378167

HIF-1α represses the expression of the angiogenesis inhibitor thrombospondin-2.

PubMed

MacLauchlan, Susan C; Calabro, Nicole E; Huang, Yan; Krishna, Meenakshi; Bancroft, Tara; Sharma, Tanuj; Yu, Jun; Sessa, William C; Giordano, Frank; Kyriakides, Themis R

2018-01-01

Thrombospondin-2 (TSP2) is a potent inhibitor of angiogenesis whose expression is dynamically regulated following injury. In the present study, it is shown that HIF-1α represses TSP2 transcription. Specifically, in vitro studies demonstrate that the prolyl hydroxylase inhibitor DMOG or hypoxia decrease TSP2 expression in fibroblasts. This effect is shown to be via a transcriptional mechanism as hypoxia does not alter TSP2 mRNA stability and this effect requires the TSP2 promoter. In addition, the documented repressive effect of nitric oxide (NO) on TSP2 is shown to be non-canonical and involves stabilization of hypoxia inducible factor-1a (HIF-1α). The regulation of TSP2 by hypoxia is supported by the in vivo observation that TSP2 has spatiotemporal expression distinct from regions of hypoxia in gastrocnemius muscle following murine hindlimb ischemia (HLI). A role for TSP2 regulation by HIF-1α is supported by the dysregulation of TSP2 expression in SM22α-cre HIF-1α KO mice following HLI. Indeed, there is a reduction in blood flow recovery in the SM22a-cre HIF-1α KO mice compared to littermate controls following HLI surgery, associated with impaired recovery and increased TSP2 levels. Moreover, SM22α-cre HIF-1α KO smooth muscle cells mice have increased TSP2 mRNA levels that persist in hypoxia. These findings identify a novel, ischemia-induced pro-angiogenic mechanism involving the transcriptional repression of TSP2 by HIF-1α. Copyright © 2017. Published by Elsevier B.V.

Ion channel signaling influences cellular proliferation and phagocyte activity during axolotl tail regeneration.

PubMed

Franklin, Brandon M; Voss, S Randal; Osborn, Jeffrey L

2017-08-01

Little is known about the potential for ion channels to regulate cellular behaviors during tissue regeneration. Here, we utilized an amphibian tail regeneration assay coupled with a chemical genetic screen to identify ion channel antagonists that altered critical cellular processes during regeneration. Inhibition of multiple ion channels either partially (anoctamin1/Tmem16a, anoctamin2/Tmem16b, K V 2.1, K V 2.2, L-type Ca V channels and H/K ATPases) or completely (GlyR, GABA A R, K V 1.5 and SERCA pumps) inhibited tail regeneration. Partial inhibition of tail regeneration by blocking the calcium activated chloride channels, anoctamin1&2, was associated with a reduction of cellular proliferation in tail muscle and mesenchymal regions. Inhibition of anoctamin 1/2 also altered the post-amputation transcriptional response of p44/42 MAPK signaling pathway genes, including decreased expression of erk1/erk2. We also found that complete inhibition via voltage gated K + channel blockade was associated with diminished phagocyte recruitment to the amputation site. The identification of H + pumps as required for axolotl tail regeneration supports findings in Xenopus and Planaria models, and more generally, the conservation of ion channels as regulators of tissue regeneration. This study provides a preliminary framework for an in-depth investigation of the mechanistic role of ion channels and their potential involvement in regulating cellular proliferation and other processes essential to wound healing, appendage regeneration, and tissue repair. Copyright © 2017 Elsevier B.V. All rights reserved.

Resveratrol modulates ATPase activity of liposome-reconstituted ABCG1.

PubMed

de Athayde Moncorvo Collado, Alejandro; Corbalán, Natalia; Homolya, László; Morero, Roberto; Minahk, Carlos

2013-08-02

ABCG1 is a half-sized transporter with an unquestionable importance in cholesterol homeostasis. So far, its expression and thus its activity was suggested to be regulated at transcriptional level by LXR and PPAR agonists including polyphenols. However, it is unknown whether there are other mechanisms of up-regulation of ABCG1 activity. In the present work resveratrol was shown to induce a nearly twofold increase in ATPase activity of reconstituted ABCG1. Evidence is presented for the first time suggesting that resveratrol is able to activate ABCG1 activity by an alternative mechanism that involves an indirect interaction. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Low Temperature Induction of Arabidopsis CBF1, 2, and 3 Is Gated by the Circadian Clock1

PubMed Central

Fowler, Sarah G.; Cook, Daniel; Thomashow, Michael F.

2005-01-01

Exposing Arabidopsis (Arabidopsis thaliana) plants to low temperature results in rapid induction of CBF1, 2, and 3 (CBF1-3; also known as DREB1B, C, and A, respectively), which encode transcriptional activators that induce expression of a battery of genes that increase plant freezing and chilling tolerance. Recently, it has been shown that basal levels of CBF3 transcripts and those of certain CBF-regulated genes exhibit circadian cycling. Here, we further explored the regulation of CBF1-3 by the circadian clock. The results indicated that the extent to which CBF1-3 transcripts accumulated in response to low temperature was dependent on the time of day that the plants were exposed to low temperature and that this was regulated by the circadian clock. The highest and lowest levels of cold-induced CBF1-3 transcript accumulation occurred at 4 and 16 h after subjective dawn, respectively. An analysis of CBF2 promoter-reporter gene fusions indicated that this control included transcriptional regulation. In addition, the cold responsiveness of RAV1 and ZAT12, genes that are cold induced in parallel with CBF1-3, was also subject to circadian regulation. However, whereas the maximum level of cold-induced RAV1 transcript accumulation occurred at the same time of day as did CBF1-3 transcripts, that of ZAT12 was in reverse phase, i.e. the highest level of cold-induced ZAT12 transcript accumulation occurred 16 h after subjective dawn. These results indicate that cold-induced expression of CBF1-3, RAV1, and ZAT12 is gated by the circadian clock and suggest that this regulation likely occurs through at least two nonidentical (though potentially overlapping) signaling pathways. PMID:15728337

Life-time expression of the proteins peroxiredoxin, beta-synuclein, PARK7/DJ-1, and stathmin in the primary visual and primary somatosensory cortices in rats

PubMed Central

Böhm, Michael R. R.; Melkonyan, Harutyun; Thanos, Solon

2015-01-01

Four distinct proteins are regulated in the aging neuroretina and may be regulated in the cerebral cortex, too: peroxiredoxin, beta-synuclein, PARK[Parkinson disease(autosomal recessive, early onset)]7/DJ-1, and Stathmin. Thus, we performed a comparative analysis of these proteins in the the primary somatosensory cortex (S1) and primary visual cortex (V1) in rats, in order to detect putative common development-, maturation- and age-related changes. The expressions of peroxiredoxin, beta-synuclein, PARK[Parkinson disease (autosomal recessive, early onset)]7/DJ-1, and Stathmin were compared in the newborn, juvenile, adult, and aged S1 and V1. Western blot (WB), quantitative reverse-transcription polymerase chain reaction (qRT-PCR), and immunohistochemistry (IHC) analyses were employed to determine whether the changes identified by proteomics were verifiable at the cellular and molecular levels. All of the proteins were detected in both of the investigated cortical areas. Changes in the expressions of the four proteins were found throughout the life-time of the rats. Peroxiredoxin expression remained unchanged over life-time. Beta-Synuclein expression was massively increased up to the adult stage of life in both the S1 and V1. PARK[Parkinson disease (autosomal recessive, early onset)]7/DJ-1 exhibited a massive up-regulation in both the S1 and V1 at all ages. Stathmin expression was massively down regulated after the neonatal period in both the S1 and V1. The detected protein alterations were analogous to their retinal profiles. This study is the first to provide evidence that peroxiredoxin, beta-synuclein, PARK[Parkinson disease (autosomal recessive, early onset)]7/DJ-1, and Stathmin are associated with postnatal maturation and aging in both the S1 and V1 of rats. These changes may indicate their involvement in key functional pathways and may account for the onset or progression of age-related pathologies. PMID:25788877

Proteomic changes associated with deletion of the Magnaporthe oryzae conidial morphology-regulating gene COM1

PubMed Central

2010-01-01

Background The rice blast disease caused by Magnaporthe oryzae is a major constraint on world rice production. The conidia produced by this fungal pathogen are the main source of disease dissemination. The morphology of conidia may be a critical factor in the spore dispersal and virulence of M. oryzae in the field. Deletion of a conidial morphology regulating gene encoding putative transcriptional regulator COM1 in M. oryzae resulted in aberrant conidial shape, reduced conidiation and attenuated virulence. Results In this study, a two-dimensional gel electrophoresis/matrix assisted laser desorption ionization- time of flight mass spectrometry (2-DE/MALDI-TOF MS) based proteomics approach was employed to identify the cellular and molecular components regulated by the COM1 protein (COM1p) that might contribute to the aberrant phenotypes in M. oryzae. By comparing the conidial proteomes of COM1 deletion mutant and its isogenic wild-type strain P131, we identified a potpourri of 31 proteins that exhibited statistically significant alterations in their abundance levels. Of these differentially regulated proteins, the abundance levels of nine proteins were elevated and twelve were reduced in the Δcom1 mutant. Three proteins were detected only in the Δcom1 conidial proteome, whereas seven proteins were apparently undetectable. The data obtained in the study suggest that the COM1p plays a key role in transcriptional reprogramming of genes implicated in melanin biosynthesis, carbon and energy metabolism, structural organization of cell, lipid metabolism, amino acid metabolism, etc. Semi-quantitative RT-PCR analysis revealed the down-regulation of genes encoding enzymes involved in melanin biosynthesis in the COM1 mutant. Conclusions Our results suggest that the COM1p may regulate the transcription of genes involved in various cellular processes indispensable for conidial development and appressorial penetration. These functions are likely to contribute to the effects of COM1p upon the aberrant phenotypes of M. oryzae. Reviewers This article is reviewed by George V. Shpakovski, Karthikeyan Sivaraman (nominated by M. Madan Babu) and Lakshminarayan M. Iyer. PMID:21040590

Kojic acid biosynthesis in Aspergillus oryzae is regulated by a Zn(II)(2)Cys(6) transcriptional activator and induced by kojic acid at the transcriptional level.

PubMed

Marui, Junichiro; Yamane, Noriko; Ohashi-Kunihiro, Sumiko; Ando, Tomohiro; Terabayashi, Yasunobu; Sano, Motoaki; Ohashi, Shinichi; Ohshima, Eiji; Tachibana, Kuniharu; Higa, Yoshitaka; Nishimura, Marie; Koike, Hideaki; Machida, Masayuki

2011-07-01

A gene encoding the Zn(II)(2)Cys(6) transcriptional factor is clustered with two genes involved in biosynthesis of a secondary metabolite, kojic acid (KA), in Aspergillus oryzae. We determined that the gene was essential for KA production and the transcriptional activation of KA biosynthetic genes, which were triggered by the addition of KA. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target

PubMed Central

Watanabe, Hideo; Francis, Joshua M.; Woo, Michele S.; Etemad, Banafsheh; Lin, Wenchu; Fries, Daniel F.; Peng, Shouyong; Snyder, Eric L.; Tata, Purushothama Rao; Izzo, Francesca; Schinzel, Anna C.; Cho, Jeonghee; Hammerman, Peter S.; Verhaak, Roel G.; Hahn, William C.; Rajagopal, Jayaraj; Jacks, Tyler; Meyerson, Matthew

2013-01-01

The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To study the transcriptional impact of NKX2-1 amplification, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma and analyzed DNA-binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation. Integration of these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1. Further cistromic and overexpression analyses indicated that NKX2-1 can cooperate with the forkhead box transcription factor FOXA1 to regulate LMO3 gene expression. RNAi analysis of NKX2-1-amplified cells compared with nonamplified cells demonstrated that LMO3 mediates cell survival downstream from NKX2-1. Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transcriptional signal transducer in NKX2-1-amplified lung adenocarcinomas. PMID:23322301

Evidence that activation of ASIC1a by acidosis increases osteoclast migration and adhesion by modulating integrin/Pyk2/Src signaling pathway.

PubMed

Li, X; Ye, J-X; Xu, M-H; Zhao, M-D; Yuan, F-L

2017-07-01

Activated acid-sensing ion channel 1a (ASIC1a) is involved in acid-induced osteoclastogenesis by regulating activation of the transcription factor NFATc1. These results indicated that ASIC1a activation by extracellular acid may cause osteoclast migration and adhesion through Ca 2+ -dependent integrin/Pyk2/Src signaling pathway. Osteoclast adhesion and migration are responsible for osteoporotic bone loss. Acidic conditions promote osteoclastogenesis. ASIC1a in osteoclasts is associated with acid-induced osteoclastogenesis through modulating transcription factor NFATc1 activation. However, the influence and the detailed mechanism of ASIC1a in regulating osteoclast adhesion and migration, in response to extracellular acid, are not well characterized. In this study, knockdown of ASIC1a was achieved in bone marrow macrophage cells using small interfering RNA (siRNA). The adhesion and migration abilities of osteoclast precursors and osteoclasts were determined by adhesion and migration assays, in vitro. Bone resorption was performed to measure osteoclast function. Cytoskeletal changes were assessed by F-actin ring formation. αvβ3 integrin expression in osteoclasts was measured by flow cytometry. Western blotting and co-immunoprecipitation were performed to measure alterations in integrin/Pyk2/Src signaling pathway. Our results showed that blockade of ASIC1a using ASIC1a-siRNA inhibited acid-induced osteoclast precursor migration and adhesion, as well as osteoclast adhesion and bone resorption; we also demonstrated that inhibition of ASIC1a decreased the cell surface αvβ3 integrin and β3 protein expression. Moreover, blocking of ASIC1a inhibited acidosis-induced actin ring formation and reduced Pyk2 and Src phosphorylation in osteoclasts and also inhibited the acid-induced association of the αvβ3 integrin/Src/Pyk2. Together, these results highlight a key functional role of ASIC1a/αvβ3 integrin/Pyk2/Src signaling pathway in migration and adhesion of osteoclasts.

Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant

PubMed Central

Nelson, Sven K.; Ariizumi, Tohru; Steber, Camille M.

2017-01-01

Plant embryos can survive years in a desiccated, quiescent state within seeds. In many species, seeds are dormant and unable to germinate at maturity. They acquire the capacity to germinate through a period of dry storage called after-ripening (AR), a biological process that occurs at 5–15% moisture when most metabolic processes cease. Because stored transcripts are among the first proteins translated upon water uptake, they likely impact germination potential. Transcriptome changes associated with the increased seed dormancy of the GA-insensitive sly1-2 mutant, and with dormancy loss through long sly1-2 after-ripening (19 months) were characterized in dry seeds. The SLY1 gene was needed for proper down-regulation of translation-associated genes in mature dry seeds, and for AR up-regulation of these genes in germinating seeds. Thus, sly1-2 seed dormancy may result partly from failure to properly regulate protein translation, and partly from observed differences in transcription factor mRNA levels. Two positive regulators of seed dormancy, DELLA GAI (GA-INSENSITIVE) and the histone deacetylase HDA6/SIL1 (MODIFIERS OF SILENCING1) were strongly AR-down-regulated. These transcriptional changes appeared to be functionally relevant since loss of GAI function and application of a histone deacetylase inhibitor led to decreased sly1-2 seed dormancy. Thus, after-ripening may increase germination potential over time by reducing dormancy-promoting stored transcript levels. Differences in transcript accumulation with after-ripening correlated to differences in transcript stability, such that stable mRNAs appeared AR-up-regulated, and unstable transcripts AR-down-regulated. Thus, relative transcript levels may change with dry after-ripening partly as a consequence of differences in mRNA turnover. PMID:29312402

Cryptochrome and Period Proteins Are Regulated by the CLOCK/BMAL1 Gene: Crosstalk between the PPARs/RXRα-Regulated and CLOCK/BMAL1-Regulated Systems

PubMed Central

Nakamura, Koh-ichi; Inoue, Ikuo; Takahashi, Seiichiro; Komoda, Tsugikazu; Katayama, Shigehiro

2008-01-01

Feeding and the circadian system regulate lipid absorption and metabolism, and the expression of enzymes involved in lipid metabolism is believed to be directly controlled by the clock system. To investigate the interaction between the lipid metabolism system and the circadian system, we analyzed the effect of a CLOCK/BMAL1 heterodimer on the transcriptional regulation of PPAR-controlled genes through PPAR response elements (PPREs). Transcription of acyl-CoA oxidase, cellular retinol binding protein II (CRBPII), and 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase was altered by CLOCK/BMAL1, and transcriptional activity via PPRE by PPARs/RXRα was enhanced by CLOCK/BMAL1 and/or by PPARs ligand/activators. We also found that CLOCK/BMAL1-mediated transcription of period (PER) and cryptochrome (CRY) was modulated by PPARα/RXRα. These results suggest that there may be crosstalk between the PPARs/RXRα-regulated system and the CLOCK/BMAL1-regulated system. PMID:18317514

DOE Office of Scientific and Technical Information (OSTI.GOV)

Versteeg, Gijs A.; Bredenbeek, Peter J.; Worm, Sjoerd H.E. van den

Many viruses encode antagonists to prevent interferon (IFN) induction. Infection of fibroblasts with the murine hepatitis coronavirus (MHV) and SARS-coronavirus (SARS-CoV) did not result in nuclear translocation of interferon-regulatory factor 3 (IRF3), a key transcription factor involved in IFN induction, and induction of IFN mRNA transcription. Furthermore, MHV and SARS-CoV infection could not prevent IFN induction by poly (I:C) or Sendai virus, suggesting that these CoVs do not inactivate IRF3-mediated transcription regulation, but apparently prevent detection of replicative RNA by cellular sensory molecules. Our data indicate that shielding of viral RNA to host cell sensors might be the main generalmore » mechanism for coronaviruses to prevent IFN induction.« less

PTEN regulates p300-dependent hypoxia-inducible factor 1 transcriptional activity through Forkhead transcription factor 3a (FOXO3a)

PubMed Central

Emerling, Brooke M.; Weinberg, Frank; Liu, Juinn-Lin; Mak, Tak W.; Chandel, Navdeep S.

2008-01-01

The tumor suppressor PTEN is mutated or deleted in many tumors, causing the activation of the PI3K pathway. Here, we show that the loss of PTEN increases the transcriptional activity of hypoxia-inducible factor 1 (HIF-1) through the inactivation of Forkhead transcription factors (FOXO) in PTEN-null cells. Reintroduction of PTEN into the nucleus, overexpression of a nonphosphorylatable FOXO3a, which accumulates in the nucleus, or inhibition of nuclear export of FOXO3a by leptomycin B represses HIF-1 transcriptional activity in PTEN-null cells. HIF-1 transcriptional activity increases in PTEN-positive cells depleted of FOXO3a with siRNA. PTEN and FOXO3a regulate the transactivation domain of HIF-1α. Chromatin immunoprecipitation indicates that FOXO3a complexes with HIF-1α and p300 on the Glut-1 promoter, a HIF-1 target gene. Overexpression of p300 reverses FOXO3a-mediated repression of HIF-1 transcriptional activity. Coimmunoprecipitation and GAL4-HIF-1α transactivation assays reveal that FOXO3a interferes with p300-dependent HIF-1 transcriptional activity. Thus, FOXO3a negatively regulates HIF-1 transcriptional activity. PMID:18268343

A novel GhBEE1-Like gene of cotton causes anther indehiscence in transgenic Arabidopsis under uncontrolled transcription level.

PubMed

Chen, Eryong; Wang, Xiaoqian; Gong, Qian; Butt, Hamama Islam; Chen, Yanli; Zhang, Chaojun; Yang, Zuoren; Wu, Zhixia; Ge, Xiaoyang; Zhang, Xianlong; Li, Fuguang; Zhang, Xueyan

2017-09-05

Male-sterile lines are very important for selective breeding, and anther dehiscence defect is an effective way to generate male-sterile lines. Although several bHLH-family proteins in Arabidopsis have been characterized, little is known about the role of bHLH-family proteins in cotton. Here, we isolated a novel bHLH protein from cotton (Gossypium hirsutum), named GhBEE1-Like. Protein domain analysis showed that GhBEE1-Like contained a basic domain and an HLH domain. Subcellular localization analysis revealed that GhBEE1-Like was a nuclear-localized protein. Expression pattern analysis showed GhBEE1-Like was highly expressed in floral organs, and its expression was induced by the active brassinosteroid (BR) substance 24-epi-BL. GhBEE1-Like overexpression in Arabidopsis resulted in two types of transgenic lines, one with normal anther dehiscence and the other with defective anther dehiscence. Semi-qRT-PCR and qRT-PCR analyses revealed that GhBEE1-Like transcript levels acted as a check-point determining how anther dehiscence proceeds in these transgenic lines; regulated transcript levels result in normal anther dehiscence, whereas uncontrolled transcript levels lead to anther indehiscence. These results suggest that GhBEE1-Like plays an important role via its accumulation in regulating anther dehiscence. Therefore, controlling the level of GhBEE1-Like expression in cotton could be a convenient tool for generating male-sterile lines to use in selective breeding. Copyright © 2017. Published by Elsevier B.V.

Estimating the size of the MSM populations for 38 European countries by calculating the survey-surveillance discrepancies (SSD) between self-reported new HIV diagnoses from the European MSM internet survey (EMIS) and surveillance-reported HIV diagnoses among MSM in 2009

PubMed Central

2013-01-01

Background Comparison of rates of newly diagnosed HIV infections among MSM across countries is challenging for a variety of reasons, including the unknown size of MSM populations. In this paper we propose a method of triangulating surveillance data with data collected in a pan-European MSM Internet Survey (EMIS) to estimate the sizes of the national MSM populations and the rates at which HIV is being diagnosed amongst them by calculating survey-surveillance discrepancies (SSD) as a measure of selection biases of survey participants. Methods In 2010, the first EMIS collected self-reported data on HIV diagnoses among more than 180,000 MSM in 38 countries of Europe. These data were compared with data from national HIV surveillance systems to explore possible sampling and reporting biases in the two approaches. The Survey-Surveillance Discrepancy (SSD) represents the ratio of survey members diagnosed in 2009 (HIVsvy) to total survey members (Nsvy), divided by the ratio of surveillance reports of diagnoses in 2009 (HIVpop) to the estimated total MSM population (Npop). As differences in household internet access may be a key component of survey selection biases, we analysed the relationship between household internet access and SSD in countries conducting consecutive MSM internet surveys at different time points with increasing levels of internet access. The empirically defined SSD was used to calculate the respective MSM population sizes (Npop), using the formula Npop = HIVpop*Nsvy*SSD/HIVsvy. Results Survey-surveillance discrepancies for consecutive MSM internet surveys between 2003 and 2010 with different levels of household internet access were best described by a potential equation, with high SSD at low internet access, declining to a level around 2 with broad access. The lowest SSD was calculated for the Netherlands with 1.8, the highest for Moldova with 9.0. Taking the best available estimate for surveillance reports of HIV diagnoses among MSM in 2009 (HIVpop), the relative MSM population sizes were between 0.03% and 5.6% of the adult male population aged 15–64. The correlation between recently diagnosed (2009) HIV in EMIS participants and HIV diagnosed among MSM in 2009 as reported in the national surveillance systems was very high (R2 = 0.88) when using the calculated MSM population size. Conclusions Npop and HIVpop were unreliably low for several countries. We discuss and identify possible measurement errors for countries with calculated MSM population sizes above 3% and below 1% of the adult male population. In most cases the number of new HIV diagnoses in MSM in the surveillance system appears too low. In some cases, measurement errors may be due to small EMIS sample sizes. It must be assumed that the SSD is modified by country-specific factors. Comparison of community-based survey data with surveillance data suggests only minor sampling biases in the former that – except for a few countries - do not seriously distort inter-country comparability, despite large variations in participation rates across countries. Internet surveys are useful complements to national surveillance systems, highlighting deficiencies and allowing estimates of the range of newly diagnosed infections among MSM in countries where surveillance systems fail to accurately provide such data. PMID:24088198

Magnetic domain interactions of Fe3O4 nanoparticles embedded in a SiO2 matrix.

PubMed

Fuentes-García, J A; Diaz-Cano, A I; Guillen-Cervantes, A; Santoyo-Salazar, J

2018-03-23

Currently, superparamagnetic functionalized systems of magnetite (Fe 3 O 4 ) nanoparticles (NPs) are promising options for applications in hyperthermia therapy, drug delivery and diagnosis. Fe 3 O 4 NPs below 20 nm have stable single domains (SSD), which can be oriented by magnetic field application. Dispersion of Fe 3 O 4 NPs in silicon dioxide (SiO 2 ) matrix allows local SSD response with uniaxial anisotropy and orientation to easy axis, 90° <001> or 180° <111>. A successful, easy methodology to produce Fe 3 O 4 NPs (6-17 nm) has been used with the Stöber modification. NPs were embedded in amorphous and biocompatible SiO 2 matrix by mechanical stirring in citrate and tetraethyl orthosilicate (TEOS). Fe 3 O 4 NPs dispersion was sampled in the range of 2-12 h to observe the SiO 2 matrix formation as time function. TEM characterization identified optimal conditions at 4 h stirring for separation of SSD Fe 3 O 4 in SiO 2 matrix. Low magnetization (M s ) of 0.001 emu and a coercivity (H c ) of 24.75 Oe indicate that the embedded SSD Fe 3 O 4 in amorphous SiO 2 reduces the M s by a diamagnetic barrier. Magnetic force microscopy (MFM) showed SSD Fe 3 O 4 of 1.2 nm on average embedded in SiO 2 matrix with uniaxial anisotropy response according to Fe 3+ and Fe 2+ electron spin coupling and rotation by intrinsic Neél contribution.

Refining the Magnitude of the Shallow Slip Deficit

NASA Astrophysics Data System (ADS)

Xu, X.; Tong, X.; Sandwell, D. T.; Milliner, C. W. D.

2014-12-01

Geodetic inversions for slip versus depth for several major (Mw > 7) strike-slip earthquakes (e.g. 1992 Landers, 1999 Hector Mine, 2010 El_Mayor-Cucapah) show a 10% to 40% reduction in slip near surface (depth < 2 km) compared to the slip at deeper depths (5 to 8 km). This has been called the shallow slip deficit (SSD). The large magnitude of this deficit has been an enigma since it cannot be explained by shallow creep during the interseismic period or by triggered slip from nearby earthquakes. One potential explanation for the SSD is that the previous geodetic inversions used incomplete data that do not go close to fault so the shallow portions of the slip models were poorly resolved and generally underestimated. In this study we improve the geodetic inversion, especially at shallow depth by: 1) refining the InSAR processing with non-boxcar phase filtering, model-dependent range corrections, more complete phase unwrapping by SNAPHU using a correlation mask and allowing a phase discontinuity along the rupture; 2) including near-fault offset data from optical imagery and SAR azimuth offsets; 3) using more detailed fault geometry; 4) and using additional campaign GPS data. With these improved observations, the slip inversion has significantly increased resolution at shallow depth. For the Landers rupture the SSD is reduced from 45% to 16%. Similarly for the Hector Mine rupture the SSD is reduced from 15% to 5%. We are assembling all the relevant co-seismic data for the El Major-Cucapah earthquake and will report the inversion result with its SSD at the meeting.

Co-design of application software and NAND flash memory in solid-state drive for relational database storage system

NASA Astrophysics Data System (ADS)

Miyaji, Kousuke; Sun, Chao; Soga, Ayumi; Takeuchi, Ken

2014-01-01

A relational database management system (RDBMS) is designed based on NAND flash solid-state drive (SSD) for storage. By vertically integrating the storage engine (SE) and the flash translation layer (FTL), system performance is maximized and the internal SSD overhead is minimized. The proposed RDBMS SE utilizes physical information about the NAND flash memory which is supplied from the FTL. The query operation is also optimized for SSD. By these treatments, page-copy-less garbage collection is achieved and data fragmentation in the NAND flash memory is suppressed. As a result, RDBMS performance increases by 3.8 times, power consumption of SSD decreases by 46% and SSD life time is increased by 61%. The effectiveness of the proposed scheme increases with larger erase block sizes, which matches the future scaling trend of three-dimensional (3D-) NAND flash memories. The preferable row data size of the proposed scheme is below 500 byte for 16 kbyte page size.

Structure of Vibrio cholerae ToxT reveals a mechanism for fatty acid regulation of virulence genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowden, Michael J.; Skorupski, Karen; Pellegrini, Maria

2010-03-04

Cholera is an acute intestinal infection caused by the bacterium Vibrio cholerae. In order for V. cholerae to cause disease, it must produce two virulence factors, the toxin-coregulated pilus (TCP) and cholera toxin (CT), whose expression is controlled by a transcriptional cascade culminating with the expression of the AraC-family regulator, ToxT. We have solved the 1.9 {angstrom} resolution crystal structure of ToxT, which reveals folds in the N- and C-terminal domains that share a number of features in common with AraC, MarA, and Rob as well as the unexpected presence of a buried 16-carbon fatty acid, cis-palmitoleate. The finding thatmore » cis-palmitoleic acid reduces TCP and CT expression in V. cholerae and prevents ToxT from binding to DNA in vitro provides a direct link between the host environment of V. cholerae and regulation of virulence gene expression.« less

v-Src oncogene product increases sphingosine kinase 1 expression through mRNA stabilization: alteration of AU-rich element-binding proteins.

PubMed

Sobue, S; Murakami, M; Banno, Y; Ito, H; Kimura, A; Gao, S; Furuhata, A; Takagi, A; Kojima, T; Suzuki, M; Nozawa, Y; Murate, T

2008-10-09

Sphingosine kinase 1 (SPHK1) is overexpressed in solid tumors and leukemia. However, the mechanism of SPHK1 overexpression by oncogenes has not been defined. We found that v-Src-transformed NIH3T3 cells showed a high SPHK1 mRNA, SPHK1 protein and SPHK enzyme activity. siRNA of SPHK1 inhibited the growth of v-Src-NIH3T3, suggesting the involvement of SPHK1 in v-Src-induced oncogenesis. v-Src-NIH3T3 showed activations of protein kinase C-alpha, signal transducers and activators of transcription 3 and c-Jun NH(2)-terminal kinase. Their inhibition suppressed SPHK1 expression in v-Src-NIH3T3, whereas their overexpression increased SPHK1 mRNA in NIH3T3. Unexpectedly, the nuclear run-on assay and the promoter analysis using 5'-promoter region of mouse SPHK1 did not show any significant difference between mock- and v-Src-NIH3T3. Furthermore, the half-life of SPHK1 mRNA in mock-NIH3T3 was nearly 15 min, whereas that of v-Src-NIH3T3 was much longer. Examination of two AU-rich region-binding proteins, AUF1 and HuR, that regulate mRNA decay reciprocally, showed decreased total AUF1 protein associated with increased tyrosine-phosphorylated form and increased serine-phosphorylated HuR protein in v-Src-NIH3T3. Modulation of AUF1 and HuR by their overexpression or siRNA revealed that SPHK1 mRNA in v-Src- and mock-NIH3T3 was regulated reciprocally by these factors. Our results showed, for the first time, a novel mechanism of v-Src-induced SPHK1 overexpression.

Aniline exposure associated with up-regulated transcriptional responses of three glutathione S-transferase Delta genes in Drosophila melanogaster.

PubMed

Chan, Wen-Chiao; Chien, Yi-Chih; Chien, Cheng-I

2015-03-01

Complex transcriptional profile of glutathione S-transferase Delta cluster genes occurred in the developmental process of the fruit fly Drosophila melanogaster. The purpose of this project was to quantify the expression levels of Gst Delta class genes altered by aniline exposure and to understand the relationship between aniline dosages and the variation of Gst Delta genes expressed in D. melanogaster. Using RT-PCR expression assays, the expression patterns of the transcript mRNAs of the glutathione S-transferase Delta genes were revealed and their expression levels were measured at eggs, larvae, pupae and adults. The adult stage was selected for further dose-response assays. After analysis, the results indicated that three Gst Delta genes (Gst D2, Gst D5 and Gst D6) were found to show a peak of up-regulated transcriptional response at 6-8h of exposure of aniline. Furthermore, the dose-response relationship of their induction levels within the dose regiments (from 1.2 to 2.0 μl/tube) had been measured. The expression patterns and annotations of these genes were discussed in the context. Copyright © 2015 Elsevier B.V. All rights reserved.

Fetal exposure to maternal stress and risk for schizophrenia spectrum disorders among offspring: Differential influences of fetal sex.

PubMed

Fineberg, Anna M; Ellman, Lauren M; Schaefer, Catherine A; Maxwell, Seth D; Shen, Ling; H Chaudhury, Nashid; Cook, Aundrea L; Bresnahan, Michaeline A; Susser, Ezra S; Brown, Alan S

2016-02-28

Exposure to adverse life events during pregnancy has been linked to increased risk of schizophrenia spectrum disorders (SSD) in offspring. Nevertheless, much of the previous work inferred maternal stress from severe life events rather than directly assessing maternal reports of stress. The present study aimed to examine maternal reports of stress during pregnancy and risk for offspring SSD. Participants were 95 SSD cases and 206 controls who were offspring from a large birth cohort study that followed pregnant women from 1959 to 1966. During pregnancy interviews, women were asked if anything worrisome had occurred recently. Interviews were qualitatively coded for stress-related themes, including reports of daily life stress, by two independent raters. None of the maternal psychosocial stress themes were significantly associated with increased odds of offspring SSD in analyses of the full sample. However, results indicated a significant daily life stress by infant sex interaction. Maternal daily life stress during pregnancy was associated with significantly increased odds of SSD among male offspring. Findings suggest sex-specific fetal sensitivity to maternal reported daily life stress during pregnancy on risk for SSD, with males appearing to be more vulnerable to the influences of maternal stress during pregnancy. Published by Elsevier Ireland Ltd.

Regulation of immunophenotype modulation of monocytes-macrophages from M1 into M2 by prostate cancer cell-culture supernatant via transcription factor STAT3.

PubMed

Solís-Martínez, R; Cancino-Marentes, M; Hernández-Flores, G; Ortiz-Lazareno, P; Mandujano-Álvarez, G; Cruz-Gálvez, C; Sierra-Díaz, E; Rodríguez-Padilla, C; Jave-Suárez, L F; Aguilar-Lemarroy, A; Bravo-Cuellar, A

2018-04-01

Transcription factor STAT3 has a prominent innate immunity effect on cancer progression. We determined the regulation of STAT3 in the immunophenotype modulation of macrophages from M1 into M2 induced by the cell-culture supernatant of the Prostate-Cancer line PC3. Monocytes-macrophages from healthy donors were cultured in the supernatant of PC3 cells, membrane proteins, and intracytoplasmic and phosphorylated STAT3 were measured using flow cytometry, while cytokines and growth factors were studied using luminescence. Cytotoxicity and nitric oxide were evaluated via colorimetric assays. The supernatant of PC3 prostate-tumor cells effectively induced macrophages toward an M2 profile, and the expression of phosphorylated STAT3 in the monocytes-macrophages notably increased, and mainly related to IL-10. In the group of monocytes-macrophages treated with a STAT3 inhibitor, the macrophages were induced toward an M1 phenotype. In this study, we showed that the secretion profile of PC3 prostate-cancer cells induces a change in macrophage phenotype from M1 into M2, and that the phenomenon is related to phosphorylation of transcription factor STAT3 and IL-10. Copyright © 2018. Published by Elsevier B.V.

Global transcriptional repression in C. elegans germline precursors by regulated sequestration of TAF-4.

PubMed

Guven-Ozkan, Tugba; Nishi, Yuichi; Robertson, Scott M; Lin, Rueyling

2008-10-03

In C. elegans, four asymmetric divisions, beginning with the zygote (P0), generate transcriptionally repressed germline blastomeres (P1-P4) and somatic sisters that become transcriptionally active. The protein PIE-1 represses transcription in the later germline blastomeres but not in the earlier germline blastomeres P0 and P1. We show here that OMA-1 and OMA-2, previously shown to regulate oocyte maturation, repress transcription in P0 and P1 by binding to and sequestering in the cytoplasm TAF-4, a component critical for assembly of TFIID and the pol II preinitiation complex. OMA-1/2 binding to TAF-4 is developmentally regulated, requiring phosphorylation by the DYRK kinase MBK-2, which is activated at meiosis II after fertilization. OMA-1/2 are normally degraded after the first mitosis, but ectopic expression of wild-type OMA-1 is sufficient to repress transcription in both somatic and later germline blastomeres. We propose that phosphorylation by MBK-2 serves as a developmental switch, converting OMA-1/2 from oocyte to embryo regulators.

Global transcriptional repression in C. elegans germline precursors by regulated sequestration of TFIID component TAF-4

PubMed Central

Guven-Ozkan, Tugba; Nishi, Yuichi; Robertson, Scott M.; Lin, Rueyling

2008-01-01

In C. elegans, four asymmetric divisions, beginning with the zygote (P0), generate transcriptionally repressed germline blastomeres (P1–P4) and somatic sisters that become transcriptionally active. The protein PIE-1 represses transcription in the later germline blastomeres, but not in the earlier germline blastomeres P0 and P1. We show here that OMA-1 and OMA-2, previously shown to regulate oocyte maturation, repress transcription in P0 and P1 by binding to and sequestering in the cytoplasm TAF-4, a component critical for assembly of TFIID and the pol II preinitiation complex. OMA-1/2 binding to TAF-4 is developmentally regulated, requiring phosphorylation by the DYRK kinase MBK-2, which is activated at meiosis II following fertilization. OMA-1/2 are normally degraded after the first mitosis, but ectopic expression of wildtype OMA-1 is sufficient to repress transcription in both somatic and later germline blastomeres. We propose that phosphorylation by MBK-2 serves as a developmental switch, converting OMA-1/2 from oocyte to embryo regulators. PMID:18854162

Modulation of HPA axis response to social stress in schizophrenia by childhood trauma.

PubMed

Lange, Claudia; Huber, Christian G; Fröhlich, Daniela; Borgwardt, Stefan; Lang, Undine E; Walter, Marc

2017-08-01

HPA axis functioning plays an important role in the etiology of schizophrenia spectrum disorders (SSD). However, only few studies have examined HPA axis responsivity to psychosocial stress in SSD, and results are heterogeneous. Furthermore, childhood trauma is known to influence psychopathology and treatment outcome in SSD, but studies on the influence of childhood trauma on stress related HPA axis activity are missing. The purpose of this study was to investigate cortisol response to a psychosocial stress challenge in SSD patients, and to examine its association with severity of childhood trauma. The present study included 25 subacutely ill patients with a current episode of a chronic SSD and 25 healthy controls. Participants underwent the modified Trier Social Stress Test, and salivary cortisol levels were assessed. The childhood trauma questionnaire was used to assess severity of adverse life events. Overall, cortisol response was blunted in the patient group compared to the control group (p<0.01). Furthermore, we identified two patient subgroups (cortisol responders (n=12) vs. non-responders (n=13) to the modified TSST) that differed in their severity of childhood trauma experience: responders had experienced more emotional abuse in their past (p<0.042). Therefore, childhood trauma might influence stress-related HPA axis activity in SSD. Our data contribute to the hypothesis that severity of childhood trauma may be of pathophysiological relevance in schizophrenia. In addition, it may be an overlooked factor contributing to inconsistent findings regarding HPA axis response to psychosocial stress in SSD. Copyright © 2017. Published by Elsevier Ltd.

Cognitive, Linguistic, and Motor Abilities in a Multigenerational Family with Childhood Apraxia of Speech.

PubMed

Carrigg, Bronwyn; Parry, Louise; Baker, Elise; Shriberg, Lawrence D; Ballard, Kirrie J

2016-10-05

This study describes the phenotype in a large family with a strong, multigenerational history of severe speech sound disorder (SSD) persisting into adolescence and adulthood in approximately half the cases. Aims were to determine whether a core phenotype, broader than speech, separated persistent from resolved SSD cases; and to ascertain the uniqueness of the phenotype relative to published cases. Eleven members of the PM family (9-55 years) were assessed across cognitive, language, literacy, speech, phonological processing, numeracy, and motor domains. Between group comparisons were made using the Mann-Whitney U-test (p < 0.01). Participant performances were compared to normative data using standardized tests and to the limited published data on persistent SSD phenotypes. Significant group differences were evident on multiple speech, language, literacy, phonological processing, and verbal intellect measures without any overlapping scores. Persistent cases performed within the impaired range on multiple measures. Phonological memory impairment and subtle literacy weakness were present in resolved SSD cases. A core phenotype distinguished persistent from resolved SSD cases that was characterized by a multiple verbal trait disorder, including Childhood Apraxia of Speech. Several phenotypic differences differentiated the persistent SSD phenotype in the PM family from the few previously reported studies of large families with SSD, including the absence of comorbid dysarthria and marked orofacial apraxia. This study highlights how comprehensive phenotyping can advance the behavioral study of disorders, in addition to forming a solid basis for future genetic and neural studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Relevance of risk predictions derived from a chronic species sensitivity distribution with cadmium to aquatic populations and ecosystems

USGS Publications Warehouse

Mebane, C.A.

2010-01-01

Criteria to protect aquatic life are intended to protect diverse ecosystems, but in practice are usually developed from compilations of single-species toxicity tests using standard test organisms that were tested in laboratory environments. Species sensitivity distributions (SSDs) developed from these compilations are extrapolated to set aquatic ecosystem criteria. The protectiveness of the approach was critically reviewed with a chronic SSD for cadmium comprising 27 species within 21 genera. Within the data set, one genus had lower cadmium effects concentrations than the SSD fifth percentile-based criterion, so in theory this genus, the amphipod Hyalella, could be lost or at least allowed some level of harm by this criteria approach. However, population matrix modeling projected only slightly increased extinction risks for a temperate Hyalella population under scenarios similar to the SSD fifth percentile criterion. The criterion value was further compared to cadmium effects concentrations in ecosystem experiments and field studies. Generally, few adverse effects were inferred from ecosystem experiments at concentrations less than the SSD fifth percentile criterion. Exceptions were behavioral impairments in simplified food web studies. No adverse effects were apparent in field studies under conditions that seldom exceeded the criterion. At concentrations greater than the SSD fifth percentile, the magnitudes of adverse effects in the field studies were roughly proportional to the laboratory-based fraction of species with adverse effects in the SSD. Overall, the modeling and field validation comparisons of the chronic criterion values generally supported the relevance and protectiveness of the SSD fifth percentile approach with cadmium. ?? 2009 Society for Risk Analysis.

[A clinical study on the relationship of autonomic nervous function and arteriosclerosis in patients with essential hypertension].

PubMed

Zhao, G; Li, S H; Tan, X

2016-03-01

To investigate the relationship between autonomic nervous function and arteriosclerosis in patients with essential hypertension. From January 2011 to December 2013, a total of 269 patients with essential hypertension hospitalized in Chang'an Branch of First People's Hospital of Liangshan were divided into normal PWV group (PWV<9 m/s, n=178) and high PWV group (PWV≥9 m/s, n=91) via the results of carotid-femoral pulse wave velocity (PWV). Synchronic 24 hours ambulatory blood pressure monitoring and dynamic electrocardiogram were performed for all participants to simultaneously monitor the heart rate variability (HRV) and blood pressure variability (BPV) in these patients. Pearson single factor analysis and multivariate logistic regression analysis were performed to define the relationship between PWV and HRV, BPV respectively. The level of nHR/dHR (index of heart rate variability), 24 hour'sSSD, dSSD, nSSD (indexes of blood pressure variability) increased significantly (all P<0.05), while the level of SDANN (index of heart rate variability) decreased significantly (P<0.05) in high PWV group compared with normal PWV group. Multiple linear regression analysis showed that PWV was positively correlated with 24 hour'sSSD, 24 hour'sPP, LF, LF/HF and night/day heart rate ratio (all P<0.05). HRV (LF, LF/HF, nHR/dHR) and BPV (24 hours'SSD, dSSD, nSSD) are positively correlated to arteriosclerosis in patients with essential hypertension. Our results show that sympathetic activation and vascular injury are closely related in patients with essential hypertension.

Synergistic cooperation of MDM2 and E2F1 contributes to TAp73 transcriptional activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kasim, Vivi, E-mail: vivikasim78@gmail.com; Huang, Can; Zhang, Jing

2014-07-04

Highlights: • MDM2 is a novel positive regulator of TAp73 transcriptional activity. • MDM2 colocalizes together and physically interacts with E2F1. • Synergistic cooperation of MDM2 and E2F1 is crucial for TAp73 transcription. • MDM2 regulates TAp73 transcriptional activity in a p53-independent manner. - Abstract: TAp73, a structural homologue of p53, plays an important role in tumorigenesis. E2F1 had been reported as a transcriptional regulator of TAp73, however, the detailed mechanism remains to be elucidated. Here we reported that MDM2-silencing reduced the activities of the TAp73 promoters and the endogenous TAp73 expression level significantly; while MDM2 overexpression upregulated them. Wemore » further revealed that the regulation of TAp73 transcriptional activity occurs as a synergistic effect of MDM2 and E2F1, most probably through their physical interaction in the nuclei. Furthermore, we also suggested that MDM2 might be involved in DNA damage-induced TAp73 transcriptional activity. Finally, we elucidated that MDM2-silencing reduced the proliferation rate of colon carcinoma cells regardless of the p53 status. Our data show a synergistic effect of MDM2 and E2F1 on TAp73 transcriptional activity, suggesting a novel regulation pathway of TAp73.« less

The Proximate Causes of Sexual Size Dimorphism in Phrynocephalus przewalskii

PubMed Central

Zhao, Wei; Liu, Nai-fa

2014-01-01

Sexual size dimorphism (SSD) is a common phenomenon and is a central topic in evolutionary biology. Recently, the importance of pursuing an ontogenetic perspective of SSD has been emphasized, to elucidate the proximate physiological mechanisms leading to its evolution. However, such research has seldom focused on the critical periods when males and females diverge. Using mark-recapture data, we investigated the development of SSD, sex-specific survivorship, and growth rates in Phrynocephalus przewalskii (Agamidae). We demonstrated that both male and female lizards are reproductively mature at age 10–11 months (including 5 months hibernation). Male-biased SSD in snout-vent length (SVL) was only found in adults and was fully expressed at age 11 months (June of the first full season of activity), just after sexual maturation. However, male-biased SSD in tail length (TL), hind-limb length (LL), and head width (HW) were fully expressed at age 9–10 months, just before sexual maturation. Analysis of age-specific linear growth rates identified sexually dimorphic growth during the fifth growth month (age 10–11 months) as the proximate cause of SSD in SVL. The males experienced higher mortality than females in the first 2 years and only survived better than females after SSD was well developed. This suggests that the critical period of divergence in the sizes of male and female P. przewalskii occurs between 10 and 11 months of age (May to June during the first full season of activity), and that the sexual difference in growth during this period is the proximate cause. However, the sexual difference in survivorship cannot explain the male-biased SSD in SVL. Our results indicate that performance-related characteristics, such as TL, HW, and LL diverged earlier than SVL. The physiological mechanisms underlying the different growth patterns of males and females may reflect different energy allocations associated with their different reproductive statuses. PMID:24465815

Comparative study of Silver Sulfadiazine with other materials for healing and infection prevention in burns: A systematic review and meta-analysis.

PubMed

Nímia, Heloisa Helena; Carvalho, Viviane Fernandes; Isaac, Cesar; Souza, Francisley Ávila; Gemperli, Rolf; Paggiaro, André Oliveira

2018-06-11

The aim of this systematic review with meta-analysis was to compare the effect of Silver Sulfadiazine (SSD) with other new dressings, with or without silver, on healing and infection prevention in burns. The electronic search was carried out in the electronic databases of Pubmed, ScienceDirect, Lilacs and BVS. The articles included were randomized clinical trials about burn treatment with SSD, which evaluated the healing and infection of burn wounds in humans. The exclusion criteria included articles, editorials and letters published in the form of abstracts, unpublished reports and case series, cross-sectional, observational experimental studies, and the use of sulfadiazine for other types of wounds. The search identified 873 references, and 24 studies were included in accordance with the eligibility criteria. The results showed a statistically favorable difference related to the time of healing for silver dressings (p<0.0001; MD 3.83; 95% CI 2.03-5.62) and dressings without silver (p<0.007; MD 2.9; 95% CI 0.81-5.00) in comparison with SSD. The rate of infection showed no difference in the group treated with SSD compared with the group treated with dressings containing silver (p>0.05). The rate of infection was significantly higher in the SSD group compared with the group treated with dressings without silver (p<0.005; MD 25.29% and MD 12.97%). Considering the clinical trials conducted up to the present time, the authors concluded that new dressings with and without silver show better results than SSD for wound healing, and burns treated with dressings without silver are less likely to become infected than burns with SSD. No differences between SSD and new silver materials were observed in relation to infection prevention. Copyright © 2018 Elsevier Ltd and ISBI. All rights reserved.

Is scoring system of computed tomography based metric parameters can accurately predicts shock wave lithotripsy stone-free rates and aid in the development of treatment strategies?

PubMed Central

Badran, Yasser Ali; Abdelaziz, Alsayed Saad; Shehab, Mohamed Ahmed; Mohamed, Hazem Abdelsabour Dief; Emara, Absel-Aziz Ali; Elnabtity, Ali Mohamed Ali; Ghanem, Maged Mohammed; ELHelaly, Hesham Abdel Azim

2016-01-01

Objective: The objective was to determine the predicting success of shock wave lithotripsy (SWL) using a combination of computed tomography based metric parameters to improve the treatment plan. Patients and Methods: Consecutive 180 patients with symptomatic upper urinary tract calculi 20 mm or less were enrolled in our study underwent extracorporeal SWL were divided into two main groups, according to the stone size, Group A (92 patients with stone ≤10 mm) and Group B (88 patients with stone >10 mm). Both groups were evaluated, according to the skin to stone distance (SSD) and Hounsfield units (≤500, 500–1000 and >1000 HU). Results: Both groups were comparable in baseline data and stone characteristics. About 92.3% of Group A rendered stone-free, whereas 77.2% were stone-free in Group B (P = 0.001). Furthermore, in both group SWL success rates was a significantly higher for stones with lower attenuation <830 HU than with stones >830 HU (P < 0.034). SSD were statistically differences in SWL outcome (P < 0.02). Simultaneous consideration of three parameters stone size, stone attenuation value, and SSD; we found that stone-free rate (SFR) was 100% for stone attenuation value <830 HU for stone <10 mm or >10 mm but total number SWL sessions and shock waves required for the larger stone group were higher than in the smaller group (P < 0.01). Furthermore, SFR was 83.3% and 37.5% for stone <10 mm, mean HU >830, SSD 90 mm and SSD >120 mm, respectively. On the other hand, SFR was 52.6% and 28.57% for stone >10 mm, mean HU >830, SSD <90 mm and SSD >120 mm, respectively. Conclusion: Stone size, stone density (HU), and SSD is simple to calculate and can be reported by radiologists to applying combined score help to augment predictive power of SWL, reduce cost, and improving of treatment strategies. PMID:27141192

Structural Analysis of the Phenol-Responsive Sensory Domain of the Transcription Activator PoxR.

PubMed

Patil, Vinod Vikas; Park, Kwang-Hyun; Lee, Seung-Goo; Woo, Euijeon

2016-04-05

Positive phenol-degradative gene regulator (PoxR) is a σ(54)-dependent AAA+ ATPase transcription activator that regulates the catabolism of phenols. The PoxR sensory domain detects phenols and relays signals for the activation of transcription. Here we report the first structure of the phenol sensory domain bound to phenol and five derivatives. It exists as a tightly intertwined homodimer with a phenol-binding pocket buried inside, placing two C termini on the same side of the dimer. His102 and Trp130 interact with the hydroxyl group of the phenol in a cavity surrounded by rigid hydrophobic residues on one side and a flexible region on the other. Each monomer has a V4R fold with a unique zinc-binding site. A shift at the C-terminal helix suggests that there is a possible conformational change upon ligand binding. The results provide a structural basis of chemical effector binding for transcriptional regulation with broad implications for protein engineering. Copyright © 2016 Elsevier Ltd. All rights reserved.

Silencing of IFN-stimulated gene transcription is regulated by histone H1 and its chaperone TAF-I

PubMed Central

Kadota, Shinichi; Nagata, Kyosuke

2014-01-01

Chromatin structure and its alteration play critical roles in the regulation of transcription. However, the transcriptional silencing mechanism with regard to the chromatin structure at an unstimulated state of the interferon (IFN)-stimulated gene (ISG) remains unclear. Here we investigated the role of template activating factor-I (TAF-I, also known as SET) in ISG transcription. Knockdown (KD) of TAF-I increased ISG transcript and simultaneously reduced the histone H1 level on the ISG promoters during the early stages of transcription after IFN stimulation from the unstimulated state. The transcription factor levels on the ISG promoters were increased in TAF-I KD cells only during the early stages of transcription. Furthermore, histone H1 KD also increased ISG transcript. TAF-I and histone H1 double KD did not show the additive effect in ISG transcription, suggesting that TAF-I and histone H1 may act on the same regulatory pathway to control ISG transcription. In addition, TAF-I KD and histone H1 KD affected the chromatin structure near the ISG promoters. On the basis of these findings, we propose that TAF-I and its target histone H1 are key regulators of the chromatin structure at the ISG promoter to maintain the silent state of ISG transcription. PMID:24878923

Inhibition of poly(ADP-ribose) polymerase-1 alters expression of mitochondria-related genes in PC12 cells: relevance to mitochondrial homeostasis in neurodegenerative disorders.

PubMed

Czapski, Grzegorz A; Cieślik, Magdalena; Wencel, Przemysław L; Wójtowicz, Sylwia; Strosznajder, Robert P; Strosznajder, Joanna B

2018-02-01

Alzheimer's disease (AD) is characterized by the release of amyloid beta peptides (Aβ) in the form of monomers/oligomers which may lead to oxidative stress, mitochondria dysfunction, synaptic loss, neuroinflammation and, in consequence, to overactivation of poly(ADP-ribose) polymerase-1 (PARP-1). However, Aβ peptides are also released in the brain ischemia, traumatic injury and in inflammatory response. PARP-1 is suggested to be a promising target in therapy of neurodegenerative disorders. We investigated the impact of PARP-1 inhibition on transcription of mitochondria-related genes in PC12 cells. Moreover, the effect of PARP-1 inhibitor (PJ34) on cells subjected to Aβ oligomers (AβO) - evoked stress was analyzed. Our data demonstrated that inhibition of PARP-1 in PC12 cells enhanced the transcription of genes for antioxidative enzymes (Sod1, Gpx1, Gpx4), activated genes regulating mitochondrial fission/fusion (Mfn1, Mfn2, Dnm1l, Opa1, Fis1), subunits of ETC complexes (mt-Nd1, Sdha, mt-Cytb) and modulated expression of several TFs, enhanced Foxo1 and decreased Nrf1, Stat6, Nfkb1. AβO elevated free radicals concentration, decreased mitochondria membrane potential (MMP) and cell viability after 24h. Gene transcription was not affected by AβO after 24h, but was significantly downregulated after 96h. In AβO stress, PJ34 exerted stimulatory effect on expression of several genes (Gpx1, Gpx4, Opa1, Mfn2, Fis1 and Sdha), decreased transcription of numerous TFs (Nrf1, Tfam, Stat3, Stat6, Trp53, Nfkb1) and prevented oxidative stress. Our results indicated that PARP-1 inhibition significantly enhanced transcription of genes involved in antioxidative defense and in regulation of mitochondria function, but was not able to ameliorate cells viability affected by Aβ. Copyright © 2017 Elsevier B.V. All rights reserved.

Expression of forkhead box transcription factor genes Foxp1 and Foxp2 during jaw development.

PubMed

Cesario, Jeffry M; Almaidhan, Asma A; Jeong, Juhee

2016-03-01

Development of the face is regulated by a large number of genes that are expressed in temporally and spatially specific patterns. While significant progress has been made on characterizing the genes that operate in the oral region of the face, those regulating development of the aboral (lateral) region remain largely unknown. Recently, we discovered that transcription factors LIM homeobox (LHX) 6 and LHX8, which are key regulators of oral development, repressed the expression of the genes encoding forkhead box transcription factors, Foxp1 and Foxp2, in the oral region. To gain insights into the potential role of the Foxp genes in region-specific development of the face, we examined their expression patterns in the first pharyngeal arch (primordium for the jaw) of mouse embryos at a high spatial and temporal resolution. Foxp1 and Foxp2 were preferentially expressed in the aboral and posterior parts of the first pharyngeal arch, including the developing temporomandibular joint. Through double immunofluorescence and double fluorescent RNA in situ hybridization, we found that Foxp1 was expressed in the progenitor cells for the muscle, bone, and connective tissue. Foxp2 was expressed in subsets of bone and connective tissue progenitors but not in the myoblasts. Neither gene was expressed in the dental mesenchyme nor in the oral half of the palatal shelf undergoing extensive growth and morphogenesis. Together, we demonstrated for the first time that Foxp1 and Foxp2 are expressed during craniofacial development. Our data suggest that the Foxp genes may regulate development of the aboral and posterior regions of the jaw. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamic regulation of six histone H3 lysine (K) methyltransferases in response to prolonged anoxia exposure in a freshwater turtle.

PubMed

Wijenayake, Sanoji; Hawkins, Liam J; Storey, Kenneth B

2018-04-05

The importance of histone lysine methylation is well established in health, disease, early development, aging, and cancer. However, the potential role of histone H3 methylation in regulating gene expression in response to extended periods of oxygen deprivation (anoxia) in a natural, anoxia-tolerant model system is underexplored. Red-eared sliders (Trachemys scripta elegans) can tolerate and survive three months of absolute anoxia and recover without incurring detrimental cellular damage, mainly by reducing the overall metabolic rate by 90% when compared to normoxia. Stringent regulation of gene expression is a vital aspect of metabolic rate depression in red-eared sliders, and as such we examined the anoxia-responsive regulation of histone lysine methylation in the liver during 5 h and 20 h anoxia exposure. Interestingly, this is the first study to illustrate the existence of histone lysine methyltransferases (HKMTs) and corresponding histone H3 lysine methylation levels in the liver of anoxia-tolerant red-eared sliders. In brief, H3K4me1, a histone mark associated with active transcription, and two corresponding histone lysine methyltransferases that modify H3K4me1 site, significantly increased in response to anoxia. On the contrary, H3K27me1, another transcriptionally active histone mark, significantly decreased during 20 h anoxia, and a transcriptionally repressive histone mark, H3K9me3, and the corresponding KMTs, similarly increased during 20 h anoxia. Overall, the results suggest a dynamic regulation of histone H3 lysine methylation in the liver of red-eared sliders that could theoretically aid in the selective upregulation of genes that are necessary for anoxia survival, while globally suppressing others to conserve energy. Copyright © 2018 Elsevier B.V. All rights reserved.

Effect of Malva sylvestris cream on burn injury and wounds in rats

PubMed Central

Nasiri, Ebrahim; Hosseinimehr, Seyed Jalal; Azadbakht, Mohammad; Akbari, Jafar; Enayati-fard, Reza; Azizi, Sohail

2015-01-01

Objectives: Burn injury is one of the most health-threatening problems in the world. Malva sylvestris (M. sylvestris) flowers have a high mucilage content and are used as a remedy for cut wound and dermal infected wounds in Iranian folklore Medicine. The purpose of this study was to investigate the effect of M. sylvestris cream on the second degree burn injury in rats. Materials and Methods: Five groups of 10 rats per group were burned with hot metal plate. Animals were administrated divided as control, normal saline, standard silver sulfadiazine 1% (SSD), 5% M. sylvestris, and 10% M. sylvestris into separate groups. Wound area, percentage of wound contraction, and histological and bacteriological assessments were evaluated. Results: Wound sizes were not significantly different among groups on 1st and 3rd days after burn injury, while they were significantly different among groups after 7th day post-burn injury. The average areas of wounds on the 15th day were 7.5±2.9, 6.7±2, 10.5±1.6, 4.7±2, and 4.5±2 cm2 for base cream, normal saline, SSD, 5% M. sylvestris, and 10% M. sylvestris, respectively. The results of histology exhibited well-formed horizontally-oriented collagen fibers in MS topical treatment groups. Microorganisms existed in the SSD group were most probably Staphilococcus epidermitis and for NS group were staphylococcus saprophiteccus. Conclusion: M. sylvestris cream improved histological changes of tissue components in the process of healing when compared with SSD cream. Therefore, it can be used as a topical treatment agent for burn wound. PMID:26909337

Identification of SNPs involved in regulating a novel alternative transcript of P450 CYP6ER1 in the brown planthopper.

PubMed

Liang, Zhi-Kun; Pang, Rui; Dong, Yi; Sun, Zhong-Xiang; Ling, Yan; Zhang, Wen-Qing

2017-04-29

Cytochrome P450-mediated metabolic resistance is one of the major mechanisms involved in insecticide resistance. Although the up-regulation of cytochrome P450 plays a vital role in insecticide metabolism, the molecular basis for the transcriptional regulation of cytochrome P450 remains largely unknown. The P450 gene CYP6ER1, has been reported to confer imidacloprid resistance to the brown planthopper, Nilaparvata lugens. Here, we identified a novel alternative transcript of CYP6ER1 (transcript A2) that had different expression patterns between resistant and susceptible populations, and was more stable after insecticide induction. The promoter of this transcript was sequenced and multiple single nucleotide polymorphisms (SNPs) were detected in individuals from susceptible and resistant field-collected populations. Resistant alleles of four SNPs were found to significantly enhance the promoter activity of the CYP6ER1 transcript A2. Electrophoretic mobility shift assays (EMSAs) revealed that these SNPs might regulate the binding of transcription factors to the promoter. Our findings provide novel evidence regarding the transcriptional regulation of a metabolic resistance-related gene and may be useful to understand the resistance mechanism of N. lugens in the field. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Rice LGD1 containing RNA binding activity affects growth and development through alternative promoters.

PubMed

Thangasamy, Saminathan; Chen, Pei-Wei; Lai, Ming-Hsing; Chen, Jychian; Jauh, Guang-Yuh

2012-07-01

Tiller initiation and panicle development are important agronomical traits for grain production in Oryza sativa L. (rice), but their regulatory mechanisms are not yet fully understood. In this study, T-DNA mutant and RNAi transgenic approaches were used to functionally characterize a unique rice gene, LAGGING GROWTH AND DEVELOPMENT 1 (LGD1). The lgd1 mutant showed slow growth, reduced tiller number and plant height, altered panicle architecture and reduced grain yield. The fewer unelongated internodes and cells in lgd1 led to respective reductions in tiller number and to semi-dwarfism. Several independent LGD1-RNAi lines exhibited defective phenotypes similar to those observed in lgd1. Interestingly, LGD1 encodes multiple transcripts with different transcription start sites (TSSs), which were validated by RNA ligase-mediated rapid amplification of 5' and 3' cDNA ends (RLM-RACE). Additionally, GUS assays and a luciferase promoter assay confirmed the promoter activities of LGD1.1 and LGD1.5. LGD1 encoding a von Willebrand factor type A (vWA) domain containing protein is a single gene in rice that is seemingly specific to grasses. GFP-tagged LGD1 isoforms were predominantly detected in the nucleus, and weakly in the cytoplasm. In vitro northwestern analysis showed the RNA-binding activity of the recombinant C-terminal LGD1 protein. Our results demonstrated that LGD1 pleiotropically regulated rice vegetative growth and development through both the distinct spatiotemporal expression patterns of its multiple transcripts and RNA binding activity. Hence, the study of LGD1 will strengthen our understanding of the molecular basis of the multiple transcripts, and their corresponding polypeptides with RNA binding activity, that regulate pleiotropic effects in rice. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

Transcription factor REST negatively influences the protein kinase C-dependent up-regulation of human mu-opioid receptor gene transcription.

PubMed

Bedini, Andrea; Baiula, Monica; Carbonari, Gioia; Spampinato, Santi

2010-01-01

Mu-opioid receptor expression increases during neurogenesis, regulates the survival of maturing neurons and is implicated in ischemia-induced neuronal death. The repressor element 1 silencing transcription factor (REST), a regulator of a subset of genes in differentiating and post-mitotic neurons, is involved in its transcriptional repression. Extracellular signaling molecules and mechanisms that control the human mu-opioid receptor (hMOR) gene transcription are not clearly understood. We examined the role of protein kinase C (PKC) on hMOR transcription in a model of neuronal cells and in the context of the potential influence of REST. In native SH-SY5Y neuroblastoma cells, PKC activation with phorbol 12-myristate 13-acetate (PMA, 16 nM, 24h) down-regulated hMOR transcription and concomitantly elevated the REST binding activity to repressor element 1 of the hMOR promoter. In contrast, PMA activated hMOR gene transcription when REST expression was knocked down by an antisense strategy or by retinoic acid-induced cell differentiation. PMA acts through a PKC-dependent pathway requiring downstream MAP kinases and the transcription factor AP-1. In a series of hMOR-luciferase promoter/reporter constructs transfected into SH-SY5Y cells and PC12 cells, PMA up-regulated hMOR transcription in PC12 cells lacking REST, and in SH-SY5Y cells either transfected with constructs deficient in the REST DNA binding element or when REST was down-regulated in retinoic acid-differentiated cells. These findings help explain how hMOR transcription is regulated and may clarify its contribution to epigenetic modifications and reprogramming of differentiated neuronal cells exposed to PKC-activating agents. Copyright 2009 Elsevier Ltd. All rights reserved.

SSD with generalized phase modulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rothenberg, J.

1996-01-09

Smoothing by spectral dispersion (SSD) with standard frequency modulation (FM), although simple to implement, has the disadvantage that low spatial frequencies present in the spectrum of the target illumination are not smoothed as effectively as with a more general smoothing method (eg, induced spatial incoherence method). The reduced smoothing performance of standard FM-SSD can result in spectral power of the speckle noise at these low spatial frequencies as much as one order of magnitude larger than that achieved with a more general method. In fact, at small integration times FM-SSD has no smoothing effect at all for a broad bandmore » of low spatial frequencies. This effect may have important implications for both direct and indirect drive ICF.« less

A spectral-spatial-dynamic hierarchical Bayesian (SSD-HB) model for estimating soybean yield

NASA Astrophysics Data System (ADS)

Kazama, Yoriko; Kujirai, Toshihiro

2014-10-01

A method called a "spectral-spatial-dynamic hierarchical-Bayesian (SSD-HB) model," which can deal with many parameters (such as spectral and weather information all together) by reducing the occurrence of multicollinearity, is proposed. Experiments conducted on soybean yields in Brazil fields with a RapidEye satellite image indicate that the proposed SSD-HB model can predict soybean yield with a higher degree of accuracy than other estimation methods commonly used in remote-sensing applications. In the case of the SSD-HB model, the mean absolute error between estimated yield of the target area and actual yield is 0.28 t/ha, compared to 0.34 t/ha when conventional PLS regression was applied, showing the potential effectiveness of the proposed model.

Aurora A regulates expression of AR-V7 in models of castrate resistant prostate cancer.

PubMed

Jones, Dominic; Noble, Martin; Wedge, Steve R; Robson, Craig N; Gaughan, Luke

2017-02-16

Androgen receptor variants (AR-Vs) provide a mechanism of therapy evasion in castrate-resistant prostate cancer (CRPC), yet mechanisms of regulation remain largely unknown. Here we investigate the role of Aurora A kinase on AR-Vs in models of CRPC and show depletion of Aurora A reduces AR-V target gene expression. Importantly, knockdown of Aurora A reconfigures splicing of AR pre-mRNA to discriminately down-regulate synthesis of AR-V transcripts, including AR-V7, without effecting full-length AR mRNA; and as a consequence, AR-V-driven proliferation and survival of CRPC cells is markedly reduced. Critically, these effects are reproduced by Aurora A inhibition. We show that Aurora A levels increase in advanced disease and AURKA is an AR-V target gene demonstrating a positive feedback mechanism of androgenic signalling in CRPC. In all, our data suggests that Aurora A plays a pivotal role in regulation of AR-V7 expression and represents a new therapeutic target in CRPC.

Aurora A regulates expression of AR-V7 in models of castrate resistant prostate cancer

PubMed Central

Jones, Dominic; Noble, Martin; Wedge, Steve R.; Robson, Craig N.; Gaughan, Luke

2017-01-01

Androgen receptor variants (AR-Vs) provide a mechanism of therapy evasion in castrate-resistant prostate cancer (CRPC), yet mechanisms of regulation remain largely unknown. Here we investigate the role of Aurora A kinase on AR-Vs in models of CRPC and show depletion of Aurora A reduces AR-V target gene expression. Importantly, knockdown of Aurora A reconfigures splicing of AR pre-mRNA to discriminately down-regulate synthesis of AR-V transcripts, including AR-V7, without effecting full-length AR mRNA; and as a consequence, AR-V-driven proliferation and survival of CRPC cells is markedly reduced. Critically, these effects are reproduced by Aurora A inhibition. We show that Aurora A levels increase in advanced disease and AURKA is an AR-V target gene demonstrating a positive feedback mechanism of androgenic signalling in CRPC. In all, our data suggests that Aurora A plays a pivotal role in regulation of AR-V7 expression and represents a new therapeutic target in CRPC. PMID:28205582

T cell fates ‘zipped up’: how the Bach2 basic leucine zipper transcriptional repressor directs T cell differentiation and function1

PubMed Central

Richer, Martin J.; Lang, Mark L.; Butler, Noah S.

2016-01-01

Recent data illustrate a key role for the transcriptional regulator Bach2 in orchestrating T cell differentiation and function. Although Bach2 has a well-described role in B cell differentiation, emerging data show that Bach2 is a prototypical member of a novel class of transcription factors that regulates transcriptional activity in T cells at super enhancers, or regions of high transcriptional activity. Accumulating data demonstrate specific roles for Bach2 in favoring regulatory T cell generation, restraining effector T cell differentiation and potentiating memory T cell development. Evidence suggests that Bach2 regulates various facets of T cell function by repressing other key transcriptional regulator such as Blimp-1. This review examines our current understanding of the role of Bach2 in T cell function and highlights the growing evidence that this transcriptional repressor functions as a key regulator involved in maintenance of T cell quiescence, T cell subset differentiation and memory T cell generation. PMID:27496973

CFLAP1 and CFLAP2 Are Two bHLH Transcription Factors Participating in Synergistic Regulation of AtCFL1-Mediated Cuticle Development in Arabidopsis

PubMed Central

Li, Shibai; Wang, Xiaochen; He, Shan; Li, Jieru; Huang, Qingpei; Imaizumi, Takato; Qu, Leqing; Qin, Genji; Qu, Li-Jia; Gu, Hongya

2016-01-01

The cuticle is a hydrophobic lipid layer covering the epidermal cells of terrestrial plants. Although many genes involved in Arabidopsis cuticle development have been identified, the transcriptional regulation of these genes is largely unknown. Previously, we demonstrated that AtCFL1 negatively regulates cuticle development by interacting with the HD-ZIP IV transcription factor HDG1. Here, we report that two bHLH transcription factors, AtCFL1 associated protein 1 (CFLAP1) and CFLAP2, are also involved in AtCFL1-mediated regulation of cuticle development. CFLAP1 and CFLAP2 interact with AtCFL1 both in vitro and in vivo. Overexpression of either CFLAP1 or CFLAP2 led to expressional changes of genes involved in fatty acids, cutin and wax biosynthesis pathways and caused multiple cuticle defective phenotypes such as organ fusion, breakage of the cuticle layer and decreased epicuticular wax crystal loading. Functional inactivation of CFLAP1 and CFLAP2 by chimeric repression technology caused opposite phenotypes to the CFLAP1 overexpressor plants. Interestingly, we find that, similar to the transcription factor HDG1, the function of CFLAP1 in cuticle development is dependent on the presence of AtCFL1. Furthermore, both HDG1 and CFLAP1/2 interact with the same C-terminal C4 zinc finger domain of AtCFL1, a domain that is essential for AtCFL1 function. These results suggest that AtCFL1 may serve as a master regulator in the transcriptional regulation of cuticle development, and that CFLAP1 and CFLAP2 are involved in the AtCFL1-mediated regulation pathway, probably through competing with HDG1 to bind to AtCFL1. PMID:26745719

The forkhead-like transcription factor (Fhl1p) maintains yeast replicative lifespan by regulating ribonucleotide reductase 1 (RNR1) gene transcription

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Akiko; Kamei, Yuka; Mukai, Yukio

In eukaryotes, numerous genetic factors contribute to the lifespan including metabolic enzymes, signal transducers, and transcription factors. As previously reported, the forkhead-like transcription factor (FHL1) gene was required for yeast replicative lifespan and cell proliferation. To determine how Fhl1p regulates the lifespan, we performed a DNA microarray analysis of a heterozygous diploid strain deleted for FHL1. We discovered numerous Fhl1p-target genes, which were then screened for lifespan-regulating activity. We identified the ribonucleotide reductase (RNR) 1 gene (RNR1) as a regulator of replicative lifespan. RNR1 encodes a large subunit of the RNR complex, which consists of two large (Rnr1p/Rnr3p) and twomore » small (Rnr2p/Rnr4p) subunits. Heterozygous deletion of FHL1 reduced transcription of RNR1 and RNR3, but not RNR2 and RNR4. Chromatin immunoprecipitation showed that Fhl1p binds to the promoter regions of RNR1 and RNR3. Cells harboring an RNR1 deletion or an rnr1-C428A mutation, which abolishes RNR catalytic activity, exhibited a short lifespan. In contrast, cells with a deletion of the other RNR genes had a normal lifespan. Overexpression of RNR1, but not RNR3, restored the lifespan of the heterozygous FHL1 mutant to the wild-type (WT) level. The Δfhl1/FHL1 mutant conferred a decrease in dNTP levels and an increase in hydroxyurea (HU) sensitivity. These findings reveal that Fhl1p regulates RNR1 gene transcription to maintain dNTP levels, thus modulating longevity by protection against replication stress. - Highlights: • Fhl1p regulates replicative lifespan and transcription of RNR large subunit genes. • Rnr1p uniquely acts as a lifespan regulator independent of the RNR complex. • dNTP levels modulate longevity by protection against replication stress.« less

Associations of DNA polymorphisms in growth hormone and its transcriptional regulators with growth and carcass traits in two populations of Brangus bulls.

PubMed

Thomas, M G; Enns, R M; Shirley, K L; Garcia, M D; Garrett, A J; Silver, G A

2007-03-30

Sequence polymorphisms in the growth hormone (GH) gene and its transcriptional regulators, Pit-1 and Prop-1, were evaluated for associations with growth and carcass traits in two populations of Brangus bulls Chihuahuan Desert Rangeland Research Center (CDRRC, N = 248 from 14 sires) and a cooperating breeding program (COOP, N = 186 from 34 sires). Polymorphisms were SNP mutations in intron 4 (C/T) and exon V (C/G) in GH, A/G in exon VI in Pit-1, and A/G in exon III in Prop-1. In the COOP population, bulls of Pit-1 GG genotype had a significantly greater percentage of intramuscular fat than bulls of the AA or AG genotype, and bulls of the Prop-1 AA genotype had significantly greater scrotal circumference than bulls of AG or GG genotypes at ~365 days of age. Also, heterozygous genotypes for the two GH polymorphisms appeared advantageous for traits of muscularity and adiposity in the COOP population. The heterozygous genotype of GH intron 4 SNP was associated with advantages in weight gain, scrotal circumference, and fat thickness in the CDRRC population. The two GH polymorphisms accounted for >/=27.7% of the variation in these traits in the CDRRC population; however, R(2) was <5% in the COOP population. Based on haplotype analyses the two GH SNPs appeared to be in phase; the haplotype analyses also paralleled with the genotype analyses. Polymorphisms in GH and its transcriptional regulators appear to be predictors of growth and carcass traits in Brangus bulls, particularly those with heterozygous GH genotypes.

The death-inducer obliterator 1 (Dido1) gene regulates embryonic stem cell self-renewal.

PubMed

Liu, Yinyin; Kim, Hyeung; Liang, Jiancong; Lu, Weisi; Ouyang, Bin; Liu, Dan; Songyang, Zhou

2014-02-21

The regulatory network of factors that center on master transcription factors such as Oct4, Nanog, and Sox2 help maintain embryonic stem (ES) cells and ensure their pluripotency. The target genes of these master transcription factors define the ES cell transcriptional landscape. In this study, we report our findings that Dido1, a target of canonical transcription factors such as Oct4, Sox2, and Nanog, plays an important role in regulating ES cell maintenance. We found that depletion of Dido1 in mouse ES cells led to differentiation, and ectopic expression of Dido1 inhibited differentiation induced by leukemia inhibitory factor withdrawal. We further demonstrated that whereas Nanog and Oct4 could occupy the Dido1 locus and promote its transcription, Dido1 could also target to the loci of pluripotency factors such as Nanog and Oct4 and positively regulate their expression. Through this feedback and feedforward loop, Dido1 is able to regulate self-renewal of mouse ES cells.

Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: prediction and validation.

PubMed

Datta, Moumita; Choudhury, Ananyo; Lahiri, Ansuman; Bhattacharyya, Nitai P

2011-09-26

HIP1 Protein Interactor (HIPPI) is a pro-apoptotic protein that induces Caspase8 mediated apoptosis in cell. We have shown earlier that HIPPI could interact with a specific 9 bp sequence motif, defined as the HIPPI binding site (HBS), present in the upstream promoter of Caspase1 gene and regulate its expression. We also have shown that HIPPI, without any known nuclear localization signal, could be transported to the nucleus by HIP1, a NLS containing nucleo-cytoplasmic shuttling protein. Thus our present work aims at the investigation of the role of HIPPI as a global transcription regulator. We carried out genome wide search for the presence of HBS in the upstream sequences of genes. Our result suggests that HBS was predominantly located within 2 Kb upstream from transcription start site. Transcription factors like CREBP1, TBP, OCT1, EVI1 and P53 half site were significantly enriched in the 100 bp vicinity of HBS indicating that they might co-operate with HIPPI for transcription regulation. To illustrate the role of HIPPI on transcriptome, we performed gene expression profiling by microarray. Exogenous expression of HIPPI in HeLa cells resulted in up-regulation of 580 genes (p < 0.05) while 457 genes were down-regulated. Several transcription factors including CBP, REST, C/EBP beta were altered by HIPPI in this study. HIPPI also interacted with P53 in the protein level. This interaction occurred exclusively in the nuclear compartment and was absent in cells where HIP1 was knocked down. HIPPI-P53 interaction was necessary for HIPPI mediated up-regulation of Caspase1 gene. Finally, we analyzed published microarray data obtained with post mortem brains of Huntington's disease (HD) patients to investigate the possible involvement of HIPPI in HD pathogenesis. We observed that along with the transcription factors like CREB, P300, SREBP1, Sp1 etc. which are already known to be involved in HD, HIPPI binding site was also significantly over-represented in the upstream sequences of genes altered in HD. Taken together, the results suggest that HIPPI could act as an important transcription regulator in cell regulating a vast array of genes, particularly transcription factors and at least, in part, play a role in transcription deregulation observed in HD.

Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: Prediction and validation

PubMed Central

2011-01-01

Background HIP1 Protein Interactor (HIPPI) is a pro-apoptotic protein that induces Caspase8 mediated apoptosis in cell. We have shown earlier that HIPPI could interact with a specific 9 bp sequence motif, defined as the HIPPI binding site (HBS), present in the upstream promoter of Caspase1 gene and regulate its expression. We also have shown that HIPPI, without any known nuclear localization signal, could be transported to the nucleus by HIP1, a NLS containing nucleo-cytoplasmic shuttling protein. Thus our present work aims at the investigation of the role of HIPPI as a global transcription regulator. Results We carried out genome wide search for the presence of HBS in the upstream sequences of genes. Our result suggests that HBS was predominantly located within 2 Kb upstream from transcription start site. Transcription factors like CREBP1, TBP, OCT1, EVI1 and P53 half site were significantly enriched in the 100 bp vicinity of HBS indicating that they might co-operate with HIPPI for transcription regulation. To illustrate the role of HIPPI on transcriptome, we performed gene expression profiling by microarray. Exogenous expression of HIPPI in HeLa cells resulted in up-regulation of 580 genes (p < 0.05) while 457 genes were down-regulated. Several transcription factors including CBP, REST, C/EBP beta were altered by HIPPI in this study. HIPPI also interacted with P53 in the protein level. This interaction occurred exclusively in the nuclear compartment and was absent in cells where HIP1 was knocked down. HIPPI-P53 interaction was necessary for HIPPI mediated up-regulation of Caspase1 gene. Finally, we analyzed published microarray data obtained with post mortem brains of Huntington's disease (HD) patients to investigate the possible involvement of HIPPI in HD pathogenesis. We observed that along with the transcription factors like CREB, P300, SREBP1, Sp1 etc. which are already known to be involved in HD, HIPPI binding site was also significantly over-represented in the upstream sequences of genes altered in HD. Conclusions Taken together, the results suggest that HIPPI could act as an important transcription regulator in cell regulating a vast array of genes, particularly transcription factors and at least, in part, play a role in transcription deregulation observed in HD. PMID:21943362

Deployment of the human immunodeficiency virus type 1 protein arsenal: combating the host to enhance viral transcription and providing targets for therapeutic development

PubMed Central

Dahiya, Satinder; Nonnemacher, Michael R.

2012-01-01

Despite the success of highly active antiretroviral therapy in combating human immunodeficiency virus type 1 (HIV-1) infection, the virus still persists in viral reservoirs, often in a state of transcriptional silence. This review focuses on the HIV-1 protein and regulatory machinery and how expanding knowledge of the function of individual HIV-1-coded proteins has provided valuable insights into understanding HIV transcriptional regulation in selected susceptible cell types. Historically, Tat has been the most studied primary transactivator protein, but emerging knowledge of HIV-1 transcriptional regulation in cells of the monocyte–macrophage lineage has more recently established that a number of the HIV-1 accessory proteins like Vpr may directly or indirectly regulate the transcriptional process. The viral proteins Nef and matrix play important roles in modulating the cellular activation pathways to facilitate viral replication. These observations highlight the cross talk between the HIV-1 transcriptional machinery and cellular activation pathways. The review also discusses the proposed transcriptional regulation mechanisms that intersect with the pathways regulated by microRNAs and how development of the knowledge of chromatin biology has enhanced our understanding of key protein–protein and protein–DNA interactions that form the HIV-1 transcriptome. Finally, we discuss the potential pharmacological approaches to target viral persistence and enhance effective transcription to purge the virus in cellular reservoirs, especially within the central nervous system, and the novel therapeutics that are currently in various stages of development to achieve a much superior prognosis for the HIV-1-infected population. PMID:22422068

Lewis type 1 antigen synthase (beta3Gal-T5) is transcriptionally regulated by homeoproteins.

PubMed

Isshiki, Soichiro; Kudo, Takashi; Nishihara, Shoko; Ikehara, Yuzuru; Togayachi, Akira; Furuya, Akiko; Shitara, Kenya; Kubota, Tetsuro; Watanabe, Masahiko; Kitajima, Masaki; Narimatsu, Hisashi

2003-09-19

The type 1 carbohydrate chain, Galbeta1-3GlcNAc, is synthesized by UDP-galactose:beta-N-acetylglucosamine beta1,3-galactosyltransferase (beta3Gal-T). Among six beta3Gal-Ts cloned to date, beta3Gal-T5 is an essential enzyme for the synthesis of type 1 chain in epithelium of digestive tracts or pancreatic tissue. It forms the type 1 structure on glycoproteins produced from such tissues. In the present study, we found that the transcriptional regulation of the beta3Gal-T5 gene is controlled by homeoproteins, i.e. members of caudal-related homeobox protein (Cdx) and hepatocyte nuclear factor (HNF) families. We found an important region (-151 to -121 from the transcription initiation site), named the beta3Gal-T5 control element (GCE), for the promoter activity. GCE contained the consensus sequences for members of the Cdx and HNF families. Mutations introduced into this sequence abolished the transcriptional activity. Four factors, Cdx1, Cdx2, HNF1alpha, and HNF1beta, could bind to GCE and transcriptionally activate the beta3Gal-T5 gene. Transcriptional regulation of the beta3Gal-T5 gene was consistent with that of members of the Cdx and HNF1 families in two in vivo systems. 1) During in vitro differentiation of Caco-2 cells, transcriptional up-regulation of beta3Gal-T5 was observed in correlation with the increase in transcripts for Cdx2 and HNF1alpha. 2) Both transcript and protein levels of beta3Gal-T5 were determined to be significantly reduced in colon cancer. This down-regulation was correlated with the decrease of Cdx1 and HNF1beta expression in cancer tissue. This is the first finding that a glycosyltransferase gene is transcriptionally regulated under the control of homeoproteins in a tissue-specific manner. beta3Gal-T5, controlled by the intestinal homeoproteins, may play an important role in the specific function of intestinal cells by modifying the carbohydrate structure of glycoproteins.

Baculovirus p35 gene is oppositely regulated by P53 and AP-1 like factors in Spodoptera frugiperda

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohareer, Krishnaveni; Institute of Life Sciences, University of Hyderabad Campus, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046; Sahdev, Sudhir

2011-11-04

Highlights: Black-Right-Pointing-Pointer Baculovirus p35 is regulated by both viral and host factors. Black-Right-Pointing-Pointer Baculovirus p35 is negatively regulated by SfP53-like factor. Black-Right-Pointing-Pointer Baculovirus p35 is positively regulated by SfAP-1-like factor. -- Abstract: Baculovirus p35 belongs to the early class of genes of AcMNPV and requires viral factors like Immediate Early protein-1 for its transcription. To investigate the role of host factors in regulating p35 gene expression, the putative transcription factor binding sites were examined in silico and the role of these factors in influencing the transcription of p35 gene was assessed. We focused our studies on AP-1 and P53-like factors,more » which are activated under oxidative stress conditions. The AP-1 motif is located at -1401 while P53 motif is at -1912 relative to p35 translation start site. The predicted AP-1 and P53 elements formed specific complexes with Spodoptera frugiperda nuclear extracts. Both AP-1 and P53 motif binding proteins were down regulated as a function of AcMNPV infection in Spodoptera cells. To address the question whether during an oxidative outburst, the p35 transcription is enhanced; we investigated the role of these oxidative stress induced host transcription factors in influencing p35 gene transcription. Reporter assays revealed that AP-1 element enhances the transcription of p35 by a factor of two. Interestingly, P53 element appears to repress the transcription of p35 gene.« less

Activation-induced cytidine deaminase (AID)-dependent somatic hypermutation requires a splice isoform of the serine/arginine-rich (SR) protein SRSF1

PubMed Central

Kanehiro, Yuichi; Todo, Kagefumi; Negishi, Misaki; Fukuoka, Junji; Gan, Wenjian; Hikasa, Takuya; Kaga, Yoshiaki; Takemoto, Masayuki; Magari, Masaki; Li, Xialu; Manley, James L.; Ohmori, Hitoshi; Kanayama, Naoki

2012-01-01

Somatic hypermutation (SHM) of Ig variable region (IgV) genes requires both IgV transcription and the enzyme activation-induced cytidine deaminase (AID). Identification of a cofactor responsible for the fact that IgV genes are much more sensitive to AID-induced mutagenesis than other genes is a key question in immunology. Here, we describe an essential role for a splice isoform of the prototypical serine/arginine-rich (SR) protein SRSF1, termed SRSF1-3, in AID-induced SHM in a DT40 chicken B-cell line. Unexpectedly, we found that SHM does not occur in a DT40 line lacking SRSF1-3 (DT40-ASF), although it is readily detectable in parental DT40 cells. Strikingly, overexpression of AID in DT40-ASF cells led to a large increase in nonspecific (off-target) mutations. In contrast, introduction of SRSF1-3, but not SRSF1, into these cells specifically restored SHM without increasing off-target mutations. Furthermore, we found that SRSF1-3 binds preferentially to the IgV gene and inhibits processing of the Ig transcript, providing a mechanism by which SRSF1-3 makes the IgV gene available for AID-dependent SHM. SRSF1 not only acts as an essential splicing factor but also regulates diverse aspects of mRNA metabolism and maintains genome stability. Our findings, thus, define an unexpected and important role for SRSF1, particularly for its splice variant, in enabling AID to function specifically on its natural substrate during SHM. PMID:22232677

Activation-induced cytidine deaminase (AID)-dependent somatic hypermutation requires a splice isoform of the serine/arginine-rich (SR) protein SRSF1.

PubMed

Kanehiro, Yuichi; Todo, Kagefumi; Negishi, Misaki; Fukuoka, Junji; Gan, Wenjian; Hikasa, Takuya; Kaga, Yoshiaki; Takemoto, Masayuki; Magari, Masaki; Li, Xialu; Manley, James L; Ohmori, Hitoshi; Kanayama, Naoki

2012-01-24

Somatic hypermutation (SHM) of Ig variable region (IgV) genes requires both IgV transcription and the enzyme activation-induced cytidine deaminase (AID). Identification of a cofactor responsible for the fact that IgV genes are much more sensitive to AID-induced mutagenesis than other genes is a key question in immunology. Here, we describe an essential role for a splice isoform of the prototypical serine/arginine-rich (SR) protein SRSF1, termed SRSF1-3, in AID-induced SHM in a DT40 chicken B-cell line. Unexpectedly, we found that SHM does not occur in a DT40 line lacking SRSF1-3 (DT40-ASF), although it is readily detectable in parental DT40 cells. Strikingly, overexpression of AID in DT40-ASF cells led to a large increase in nonspecific (off-target) mutations. In contrast, introduction of SRSF1-3, but not SRSF1, into these cells specifically restored SHM without increasing off-target mutations. Furthermore, we found that SRSF1-3 binds preferentially to the IgV gene and inhibits processing of the Ig transcript, providing a mechanism by which SRSF1-3 makes the IgV gene available for AID-dependent SHM. SRSF1 not only acts as an essential splicing factor but also regulates diverse aspects of mRNA metabolism and maintains genome stability. Our findings, thus, define an unexpected and important role for SRSF1, particularly for its splice variant, in enabling AID to function specifically on its natural substrate during SHM.

Aberrant methylation patterns affect the molecular pathogenesis of rheumatoid arthritis.

PubMed

Lin, Yang; Luo, Zhengqiang

2017-05-01

This study aims to investigate DNA methylation signatures in fibroblast-like synoviocytes (FLS) from patients with rheumatoid arthritis (RA), and to explore the relationship with transcription factors (TFs) that help to distinguish RA from osteoarthritis (OA). Microarray dataset of GSE46346, including six FLS samples from patients with RA and five FLS samples from patients with OA, was downloaded from the Gene Expression Omnibus database. RA and OA samples were screened for differentially methylated loci (DMLs). The corresponding differentially methylated genes (DMGs) were identified, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment analysis. A transcriptional regulatory network was built with TFs and their corresponding DMGs. Overall, 280 hypomethylated loci and 561 hypermethylated loci were screened. Genes containing hypermethylated loci were enriched in pathways in cancer, ECM-receptor interaction, focal adhesion and neurotrophin signaling pathways. Genes containing hypomethylated loci were enriched in the neurotrophin signaling pathway. Moreover, we found that CCCTC-binding factor (CTCF), Yin Yang 1 (YY1), v-myc avian myelocytomatosis viral oncogene homolog (c-MYC), and early growth response 1 (EGR1) were important TFs in the transcriptional regulatory network. Therefore, DMGs might participate in the neurotrophin signaling pathway, pathways in cancer, ECM-receptor interaction and focal adhesion pathways in RA. Furthermore, CTCF, c-MYC, YY1, and EGR1 may play important roles in RA through regulating DMGs. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification and determination of the saikosaponins in Radix bupleuri by accelerated solvent extraction combined with rapid-resolution LC-MS.

PubMed

Yang, Yun-Yun; Tang, You-Zhi; Fan, Chun-Lin; Luo, Hui-Tai; Guo, Peng-Ran; Chen, Jian-Xin

2010-07-01

A method based on accelerated solvent extraction combined with rapid-resolution LC-MS for efficient extraction, rapid separation, online identification and accurate determination of the saikosaponins (SSs) in Radix bupleuri (RB) was developed. The RB samples were extracted by accelerated solvent extraction using 70% aqueous ethanol v/v as solvent, at a temperature of 120 degrees C and pressure of 100 bar, with 10 min of static extraction time and three extraction cycles. Rapid-resolution LC separation was performed by using a C(18) column at gradient elution of water (containing 0.5% formic acid) and acetonitrile, and the major constituents were well separated within 20 min. A TOF-MS and an IT-MS were used for online identification of the major constituents, and 27 SSs were identified or tentatively identified. Five major bioactive SSs (SSa, SSc, SSd, 6''-O-acetyl-SSa and 6''-O-acetyl-SSd) with obvious peak areas and good resolution were chosen as benchmark substances, and a triple quadrupole MS operating in multiple-reaction monitoring mode was used for their quantitative analysis. A total of 16 RB samples from different regions of China were analyzed. The results indicated that the method was rapid, efficient, accurate and suitable for use in the quality control of RB.

The transcription factor Rap1p is required for tolerance to cell-wall perturbing agents and for cell-wall maintenance in Saccharomyces cerevisiae.

PubMed

Azad, Gajendra Kumar; Singh, Vikash; Baranwal, Shivani; Thakare, Mayur Jankiram; Tomar, Raghuvir S

2015-01-02

Yeast repressor activator protein (Rap1p) is involved in genomic stability and transcriptional regulation. We explored the function of Rap1p in yeast physiology using Rap1p truncation mutants. Our results revealed that the N-terminal truncation of Rap1p (Rap1ΔN) leads to hypersensitivity towards elevated temperature and cell-wall perturbing agents. Cell wall analysis showed an increase in the chitin and glucan content in Rap1ΔN cells as compared with wild type cells. Accordingly, mutant cells had a twofold thicker cell wall, as observed by electron microscopy. Furthermore, Rap1ΔN cells had increased levels of phosphorylated Slt2p, a MAP kinase of the cell wall integrity pathway. Mutant cells also had elevated levels of cell wall integrity response transcripts. Taken together, our findings suggest a connection between Rap1p and cell wall homeostasis. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Symptomatic subsyndromal depression in hospitalized hypertensive patients.

PubMed

Chiaie, Roberto Delle; Iannucci, Gino; Paroli, Marino; Salviati, Massimo; Caredda, Maria; Pasquini, Massimo; Biondi, Massimo

2011-12-01

Clinicians generally agree on the association between depression and hypertension. Less clear is if the nature of the link is direct or indirect and if this should be considered confined only to syndromal forms or if it concerns also subsyndromal affective presentations. This study investigated the nature of the association between hypertension and subsyndromal depression in hospitalized hypertensive patients. 196 hypertensive and 96 non hypertensive inpatients underwent a SCID interview, to exclude patients positive for any Axis I or Axis II diagnosis. Symptomatic Subsyndromal Depression (SSD) was identified according to criteria proposed by Judd. Psychopathological assessment was performed with Anxiety Sensitivity Index (ASI) and Hopkins Symptom Checklist-90 (SCL-90). Clinical assessments included blood pressure measurement, evaluation of general health conditions and screening cardiovascular risk factors (smoke, alcohol, body weight, sedentary life style). Hypertensives met more frequently criteria for SSD. They also scored higher on ASI and SCL-90. However, those with more severe physical conditions, if compared with more healthy patients, did not show increased psychopathological severity. Similarly, psychopathological symptom severity did not differ among hypertensives positive for other cardiovascular risk factors, commonly more frequent among depressed subjects. Further analyses are needed to explore the potential advantage obtained on blood pressure control by treating SSD. Hospitalized hypertensives, more frequently satisfied criteria for Symptomatic Subsyndromal Depression. These milder affective forms are probably directly linked to the presence of hypertension, rather than being indirectly associated to physical impairment or to higher prevalence of other cardiovascular risk factors. Copyright © 2011. Published by Elsevier B.V.

Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1

PubMed Central

Nishimura, Taisuke; Molinard, Guillaume; Petty, Tom J.; Broger, Larissa; Gabus, Caroline; Halazonetis, Thanos D.; Thore, Stéphane; Paszkowski, Jerzy

2012-01-01

Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks. However, exceptions to this rule suggest the existence of additional, as yet uncharacterized, layers of epigenetic regulation. MOM1, a protein of 2,001 amino acids that acts as a transcriptional silencer, represents such an exception. Here we define the 82 amino acid domain called CMM2 (Conserved MOM1 Motif 2) as a minimal MOM1 fragment capable of transcriptional regulation. As determined by X-ray crystallography, this motif folds into an unusual hendecad-based coiled-coil. Structure-based mutagenesis followed by transgenic complementation tests in plants demonstrate that CMM2 and its dimerization are effective for transcriptional suppression at chromosomal loci co-regulated by MOM1 and the siRNA pathway but not at loci controlled by MOM1 in an siRNA–independent fashion. These results reveal a surprising separation of epigenetic activities that enable the single, large MOM1 protein to coordinate cooperating mechanisms of epigenetic regulation. PMID:22346760

Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1.

PubMed

Nishimura, Taisuke; Molinard, Guillaume; Petty, Tom J; Broger, Larissa; Gabus, Caroline; Halazonetis, Thanos D; Thore, Stéphane; Paszkowski, Jerzy

2012-02-01

Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks. However, exceptions to this rule suggest the existence of additional, as yet uncharacterized, layers of epigenetic regulation. MOM1, a protein of 2,001 amino acids that acts as a transcriptional silencer, represents such an exception. Here we define the 82 amino acid domain called CMM2 (Conserved MOM1 Motif 2) as a minimal MOM1 fragment capable of transcriptional regulation. As determined by X-ray crystallography, this motif folds into an unusual hendecad-based coiled-coil. Structure-based mutagenesis followed by transgenic complementation tests in plants demonstrate that CMM2 and its dimerization are effective for transcriptional suppression at chromosomal loci co-regulated by MOM1 and the siRNA pathway but not at loci controlled by MOM1 in an siRNA-independent fashion. These results reveal a surprising separation of epigenetic activities that enable the single, large MOM1 protein to coordinate cooperating mechanisms of epigenetic regulation.

A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle.

PubMed

Linke, Christian; Chasapi, Anastasia; González-Novo, Alberto; Al Sawad, Istabrak; Tognetti, Silvia; Klipp, Edda; Loog, Mart; Krobitsch, Sylvia; Posas, Francesc; Xenarios, Ioannis; Barberis, Matteo

2017-01-01

Precise timing of cell division is achieved by coupling waves of cyclin-dependent kinase (Cdk) activity with a transcriptional oscillator throughout cell cycle progression. Although details of transcription of cyclin genes are known, it is unclear which is the transcriptional cascade that modulates their expression in a timely fashion. Here, we demonstrate that a Clb/Cdk1-mediated regulation of the Fkh2 transcription factor synchronizes the temporal mitotic CLB expression in budding yeast. A simplified kinetic model of the cyclin/Cdk network predicts a linear cascade where a Clb/Cdk1-mediated regulation of an activator molecule drives CLB3 and CLB2 expression. Experimental validation highlights Fkh2 as modulator of CLB3 transcript levels, besides its role in regulating CLB2 expression. A Boolean model based on the minimal number of interactions needed to capture the information flow of the Clb/Cdk1 network supports the role of an activator molecule in the sequential activation, and oscillatory behavior, of mitotic Clb cyclins. This work illustrates how transcription and phosphorylation networks can be coupled by a Clb/Cdk1-mediated regulation that synchronizes them.

Effect of L-arginine supplementation on immune responsiveness in patients with sickle cell disease.

PubMed

Scavella, Arnette; Leiva, Lily; Monjure, Hanh; Zea, Arnold H; Gardner, Renee V

2010-08-01

L-arginine (L-Arg) is deficient in sickle cell disease (SSD) during vasoocclusion. We investigated possible causal relationship between L-Arg deficiency and immune dysfunction in SSD in steady-state. Fifteen patients with SSD in steady-state and 13 controls were studied. Plasma L-Arg levels were measured using liquid chromatography. T cell subsets and CD3zeta (CD3zeta) chain expression were analyzed using flow cytometry. Lymphocyte proliferative response to phytohemagglutinin (PHA) and production of IL-6 and interferon-gamma (IFN-gamma) were evaluated with and without L-Arg. SSD patients had significantly lower L-Arg levels than controls. CD3 and CD19 cell populations were comparable for both groups, but SSD patients had above normal numbers of natural killer cells (P = 0.06). Patients and controls exhibited significantly increased lymphocyte blastogenesis to PHA after introduction of L-Arg to cultures; response of patients was significantly greater than values for control individuals. Proliferative response to candida in SSD patients was significantly lower than in controls; L-Arg supplementation did not increase this response. L-Arg had no effect on blastogenic response to PPD and candida albicans. No effect was likewise seen in production of IL-6 and IFN-gamma after addition of L-Arg. CD3zeta chain expression increased after addition of L-Arg in both groups; differences were insignificant. L-Arg levels in steady-state SSD are significantly lower than in controls. L-Arg supplementation enhanced lymphocyte blastogenesis to PHA for both controls and patients, but not in response to antigen. There were no significant differences in CD3zeta chain expression although upregulation of expression occurred after L-Arg supplementation for both groups. (c) 2010 Wiley-Liss, Inc.

A small-scale dynamo in feedback-dominated galaxies - III. Cosmological simulations

NASA Astrophysics Data System (ADS)

Rieder, Michael; Teyssier, Romain

2017-12-01

Magnetic fields are widely observed in the Universe in virtually all astrophysical objects, from individual stars to entire galaxies, even in the intergalactic medium, but their specific genesis has long been debated. Due to the development of more realistic models of galaxy formation, viable scenarios are emerging to explain cosmic magnetism, thanks to both deeper observations and more efficient and accurate computer simulations. We present here a new cosmological high-resolution zoom-in magnetohydrodynamic (MHD) simulation, using the adaptive mesh refinement technique, of a dwarf galaxy with an initially weak and uniform magnetic seed field that is amplified by a small-scale dynamo (SSD) driven by supernova-induced turbulence. As first structures form from the gravitational collapse of small density fluctuations, the frozen-in magnetic field separates from the cosmic expansion and grows through compression. In a second step, star formation sets in and establishes a strong galactic fountain, self-regulated by supernova explosions. Inside the galaxy, the interstellar medium becomes highly turbulent, dominated by strong supersonic shocks, as demonstrated by the spectral analysis of the gas kinetic energy. In this turbulent environment, the magnetic field is quickly amplified via a SSD process and is finally carried out into the circumgalactic medium by a galactic wind. This realistic cosmological simulation explains how initially weak magnetic seed fields can be amplified quickly in early, feedback-dominated galaxies, and predicts, as a consequence of the SSD process, that high-redshift magnetic fields are likely to be dominated by their small-scale components.

Hyaluronan-CD44v3 interaction with Oct4-Sox2-Nanog promotes miR-302 expression leading to self-renewal, clonal formation, and cisplatin resistance in cancer stem cells from head and neck squamous cell carcinoma.

PubMed

Bourguignon, Lilly Y W; Wong, Gabriel; Earle, Christine; Chen, Liqun

2012-09-21

Human head and neck squamous cell carcinoma (HNSCC) is a highly malignant cancer associated with major morbidity and mortality. In this study, we determined that human HNSCC-derived HSC-3 cells contain a subpopulation of cancer stem cells (CSCs) characterized by high levels of CD44v3 and aldehyde dehydrogenase-1 (ALDH1) expression. These tumor cells also express several stem cell markers (the transcription factors Oct4, Sox2, and Nanog) and display the hallmark CSC properties of self-renewal/clonal formation and the ability to generate heterogeneous cell populations. Importantly, hyaluronan (HA) stimulates the CD44v3 (an HA receptor) interaction with Oct4-Sox2-Nanog leading to both a complex formation and the nuclear translocation of three CSC transcription factors. Further analysis reveals that microRNA-302 (miR-302) is controlled by an upstream promoter containing Oct4-Sox2-Nanog-binding sites, whereas chromatin immunoprecipitation (ChIP) assays demonstrate that stimulation of miR-302 expression by HA-CD44 is Oct4-Sox2-Nanog-dependent in HNSCC-specific CSCs. This process results in suppression of several epigenetic regulators (AOF1/AOF2 and DNMT1) and the up-regulation of several survival proteins (cIAP-1, cIAP-2, and XIAP) leading to self-renewal, clonal formation, and cisplatin resistance. These CSCs were transfected with a specific anti-miR-302 inhibitor to silence miR-302 expression and block its target functions. Our results demonstrate that the anti-miR-302 inhibitor not only enhances the expression of AOF1/AOF2 and DNMT1 but also abrogates the production of cIAP-1, cIAP-2, and XIAP and HA-CD44v3-mediated cancer stem cell functions. Taken together, these findings strongly support the contention that the HA-induced CD44v3 interaction with Oct4-Sox2-Nanog signaling plays a pivotal role in miR-302 production leading to AOF1/AOF2/DNMT1 down-regulation and survival of protein activation. All of these events are critically important for the acquisition of cancer stem cell properties, including self-renewal, clonal formation, and chemotherapy resistance in HA-CD44v3-activated head and neck cancer.

Hyaluronan-CD44v3 Interaction with Oct4-Sox2-Nanog Promotes miR-302 Expression Leading to Self-renewal, Clonal Formation, and Cisplatin Resistance in Cancer Stem Cells from Head and Neck Squamous Cell Carcinoma*

PubMed Central

Bourguignon, Lilly Y. W.; Wong, Gabriel; Earle, Christine; Chen, Liqun

2012-01-01

Human head and neck squamous cell carcinoma (HNSCC) is a highly malignant cancer associated with major morbidity and mortality. In this study, we determined that human HNSCC-derived HSC-3 cells contain a subpopulation of cancer stem cells (CSCs) characterized by high levels of CD44v3 and aldehyde dehydrogenase-1 (ALDH1) expression. These tumor cells also express several stem cell markers (the transcription factors Oct4, Sox2, and Nanog) and display the hallmark CSC properties of self-renewal/clonal formation and the ability to generate heterogeneous cell populations. Importantly, hyaluronan (HA) stimulates the CD44v3 (an HA receptor) interaction with Oct4-Sox2-Nanog leading to both a complex formation and the nuclear translocation of three CSC transcription factors. Further analysis reveals that microRNA-302 (miR-302) is controlled by an upstream promoter containing Oct4-Sox2-Nanog-binding sites, whereas chromatin immunoprecipitation (ChIP) assays demonstrate that stimulation of miR-302 expression by HA-CD44 is Oct4-Sox2-Nanog-dependent in HNSCC-specific CSCs. This process results in suppression of several epigenetic regulators (AOF1/AOF2 and DNMT1) and the up-regulation of several survival proteins (cIAP-1, cIAP-2, and XIAP) leading to self-renewal, clonal formation, and cisplatin resistance. These CSCs were transfected with a specific anti-miR-302 inhibitor to silence miR-302 expression and block its target functions. Our results demonstrate that the anti-miR-302 inhibitor not only enhances the expression of AOF1/AOF2 and DNMT1 but also abrogates the production of cIAP-1, cIAP-2, and XIAP and HA-CD44v3-mediated cancer stem cell functions. Taken together, these findings strongly support the contention that the HA-induced CD44v3 interaction with Oct4-Sox2-Nanog signaling plays a pivotal role in miR-302 production leading to AOF1/AOF2/DNMT1 down-regulation and survival of protein activation. All of these events are critically important for the acquisition of cancer stem cell properties, including self-renewal, clonal formation, and chemotherapy resistance in HA-CD44v3-activated head and neck cancer. PMID:22847005

Preliminary evidence for school-based physical activity policy needs in Washington, DC.

PubMed

Goodman, Emily; Evans, W Douglas; DiPietro, Loretta

2012-01-01

The school setting could be a primary venue for promoting physical activity among inner-city children due to the structured natured of the school day. We examined differences in step counts between structured school days (SSD) and weekend days (WED) among a sample of public school children in Washington, DC. Subjects (N = 29) were third- to sixth-grade students enrolled in government-funded, extended-day enrichment programs. Step counts were measured using a pedometer (Bodytronics) over 2 SSD and 2 WED. Differences in mean step counts between SSD and WED were determined using multivariable linear regression, with adjustments for age, sex, and reported distance between house and school (miles). Recorded step counts were low on both SSD and WED (7735 ± 3540 and 8339 ± 5314 steps/day). Boys tended to record more steps on SSD compared with girls (8080 ± 3141 vs. 7491 ± 3872 steps/day, respectively), whereas girls recorded more steps on the WED compared with boys (9292 ± 6381 vs. 7194 ± 3669 steps/day). Parameter estimates from the regression modeling suggest distance from school (P < .01) to be the strongest predictor of daily step counts, independent of day (SSD/WED), sex, and age. Among inner-city school children, a safe walking route to and from school may provide an important opportunity for daily physical activity.

Sexual size dimorphism in three North Sea gadoids.

PubMed

Keyl, F; Kempf, A J; Sell, A F

2015-01-01

Existing biological data on whiting Merlangius merlangus, cod Gadus morhua and haddock Melanogrammus aeglefinus from a long-term international survey were analysed to address sexual size dimorphism (SSD) and its effect on their ecology and management. Results show that SSD, with larger females of the same age as males, is a result of higher growth rates in females. A direct consequence of SSD is the pronounced length-dependent female ratio that was found in all three gadoids in the North Sea. Female ratios of the three species changed from equality to female dominance at specific dominance transition lengths of c. 30, 35 and 60 cm for M. merlangus, G. morhua and M. aeglefinus, respectively. An analysis by area for M. merlangus also revealed length dependence of female ratios. SSD and length-dependent female ratios under most circumstances are inseparable. Higher overall energy demand as well as a higher energy uptake rate must result from the observed SSD and dimorphism in growth rates. Potential processes related to feeding, locomotion and physiology are proposed that could balance the increased energy investment of females. Potential consequences of SSD and length dependency of female ratios are the reduction of the reproductive potential of a stock due to size-selective fishing and biased assessment of the true size of the female spawning stock that could distort decisions in fisheries management. © 2014 The Fisheries Society of the British Isles.

Do reward-processing deficits in schizophrenia-spectrum disorders promote cannabis use? An investigation of physiological response to natural rewards and drug cues

PubMed Central

Cassidy, Clifford M.; Brodeur, Mathieu B.; Lepage, Martin; Malla, Ashok

2014-01-01

Background Dysfunctional reward processing is present in individuals with schizophrenia-spectrum disorders (SSD) and may confer vulnerability to addiction. Our objective was to identify a deficit in patients with SSD on response to rewarding stimuli and determine whether this deficit predicts cannabis use. Methods We divided a group of patients with SSD and nonpsychotic controls into cannabis users and nonusers. Response to emotional and cannabis-associated visual stimuli was assessed using self-report, event-related potentials (using the late positive potential [LPP]), facial electromyography and skin-conductance response. Results Our sample comprised 35 patients with SSD and 35 nonpsychotic controls. Compared with controls, the patients with SSD showed blunted LPP response to pleasant stimuli (p = 0.003). Across measures, cannabis-using controls showed greater response to pleasant stimuli than to cannabis stimuli whereas cannabis-using patients showed little bias toward pleasant stimuli. Reduced LPP response to pleasant stimuli was predictive of more frequent subsequent cannabis use (β = −0.24, p = 0.034). Limitations It is not clear if the deficit associated with cannabis use is specific to rewarding stimuli or nonspecific to any kind of emotionally salient stimuli. Conclusion The LPP captures a reward-processing deficit in patients with SSD and shows potential as a biomarker for identifying patients at risk of heavy cannabis use. PMID:24913137

Do reward-processing deficits in schizophrenia-spectrum disorders promote cannabis use? An investigation of physiological response to natural rewards and drug cues.

PubMed

Cassidy, Clifford M; Brodeur, Mathieu B; Lepage, Martin; Malla, Ashok

2014-09-01

Dysfunctional reward processing is present in individuals with schizophrenia-spectrum disorders (SSD) and may confer vulnerability to addiction. Our objective was to identify a deficit in patients with SSD on response to rewarding stimuli and determine whether this deficit predicts cannabis use. We divided a group of patients with SSD and nonpsychotic controls into cannabis users and nonusers. Response to emotional and cannabis-associated visual stimuli was assessed using self-report, event-related potentials (using the late positive potential [LPP]), facial electromyography and skin-conductance response. Our sample comprised 35 patients with SSD and 35 nonpsychotic controls. Compared with controls, the patients with SSD showed blunted LPP response to pleasant stimuli (p = 0.003). Across measures, cannabis-using controls showed greater response to pleasant stimuli than to cannabis stimuli whereas cannabis-using patients showed little bias toward pleasant stimuli. Reduced LPP response to pleasant stimuli was predictive of more frequent subsequent cannabis use (β = -0.24, p = 0.034). It is not clear if the deficit associated with cannabis use is specific to rewarding stimuli or nonspecific to any kind of emotionally salient stimuli. The LPP captures a reward-processing deficit in patients with SSD and shows potential as a biomarker for identifying patients at risk of heavy cannabis use.

Sexual selection accounts for the geographic reversal of sexual size dimorphism in the dung fly, sepsis punctum (Diptera: Sepsidae).

PubMed

Puniamoorthy, Nalini; Schäfer, Martin A; Blanckenhorn, Wolf U

2012-07-01

Sexual size dimorphism (SSD) varies widely across and within species. The differential equilibrium model of SSD explains dimorphism as the evolutionary outcome of consistent differences in natural and sexual selection between the sexes. Here, we comprehensively examine a unique cross-continental reversal in SSD in the dung fly, Sepsis punctum. Using common garden laboratory experiments, we establish that SSD is male-biased in Europe and female-biased in North America. When estimating sexual (pairing success) and fecundity selection (clutch size of female partner) on males under three operational sex ratios (OSRs), we find that the intensity of sexual selection is significantly stronger in European versus North American populations, increasing with male body size and OSR in the former only. Fecundity selection on female body size also increases strongly with egg number and weakly with egg volume, however, equally on both continents. Finally, viability selection on body size in terms of intrinsic (physiological) adult life span in the laboratory is overall nil and does not vary significantly across all seven populations. Although it is impossible to prove causality, our results confirm the differential equilibrium model of SSD in that differences in sexual selection intensity account for the reversal in SSD in European versus North American populations, presumably mediating the ongoing speciation process in S. punctum. © 2012 The Author(s).

Regulation of RE1 Protein Silencing Transcription Factor (REST) Expression by HIP1 Protein Interactor (HIPPI)*

PubMed Central

Datta, Moumita; Bhattacharyya, Nitai P.

2011-01-01

Earlier we have shown that the proapoptotic protein HIPPI (huntingtin interacting protein 1 (HIP1) protein interactor) along with its molecular partner HIP1 could regulate transcription of the caspase-1 gene. Here we report that RE1-silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) is a new transcriptional target of HIPPI. HIPPI could bind to the promoter of REST and increased its expression in neuronal as well as non-neuronal cells. Such activation of REST down-regulated expression of REST target genes, such as brain-derived neurotrophic factor (BDNF) or proenkephalin (PENK). The ability of HIPPI to activate REST gene transcription was dependent on HIP1, the nuclear transporter of HIPPI. Using a Huntington disease cell model, we have demonstrated that feeble interaction of HIP1 with mutant huntingtin protein resulted in increased nuclear accumulation of HIPPI and HIP1, leading to higher occupancy of HIPPI at the REST promoter, triggering its transcriptional activation and consequent repression of REST target genes. This novel transcription regulatory mechanism of REST by HIPPI may contribute to the deregulation of transcription observed in the cell model of Huntington disease. PMID:21832040

Regulation of RE1 protein silencing transcription factor (REST) expression by HIP1 protein interactor (HIPPI).

PubMed

Datta, Moumita; Bhattacharyya, Nitai P

2011-09-30

Earlier we have shown that the proapoptotic protein HIPPI (huntingtin interacting protein 1 (HIP1) protein interactor) along with its molecular partner HIP1 could regulate transcription of the caspase-1 gene. Here we report that RE1-silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) is a new transcriptional target of HIPPI. HIPPI could bind to the promoter of REST and increased its expression in neuronal as well as non-neuronal cells. Such activation of REST down-regulated expression of REST target genes, such as brain-derived neurotrophic factor (BDNF) or proenkephalin (PENK). The ability of HIPPI to activate REST gene transcription was dependent on HIP1, the nuclear transporter of HIPPI. Using a Huntington disease cell model, we have demonstrated that feeble interaction of HIP1 with mutant huntingtin protein resulted in increased nuclear accumulation of HIPPI and HIP1, leading to higher occupancy of HIPPI at the REST promoter, triggering its transcriptional activation and consequent repression of REST target genes. This novel transcription regulatory mechanism of REST by HIPPI may contribute to the deregulation of transcription observed in the cell model of Huntington disease.

Inducible, tunable and multiplex human gene regulation using CRISPR-Cpf1-based transcription factors | Office of Cancer Genomics

Cancer.gov

Targeted and inducible regulation of mammalian gene expression is a broadly important research capability that may also enable development of novel therapeutics for treating human diseases. Here we demonstrate that a catalytically inactive RNA-guided CRISPR-Cpf1 nuclease fused to transcriptional activation domains can up-regulate endogenous human gene expression. We engineered drug-inducible Cpf1-based activators and show how this system can be used to tune the regulation of endogenous gene transcription in human cells.

Acute tier-1 and tier-2 effect assessment approaches in the EFSA Aquatic Guidance Document: are they sufficiently protective for insecticides?

PubMed

van Wijngaarden, René P A; Maltby, Lorraine; Brock, Theo C M

2015-08-01

The objective of this paper is to evaluate whether the acute tier-1 and tier-2 methods as proposed by the Aquatic Guidance Document recently published by the European Food Safety Authority (EFSA) are appropriate for deriving regulatory acceptable concentrations (RACs) for insecticides. The tier-1 and tier-2 RACs were compared with RACs based on threshold concentrations from micro/mesocosm studies (ETO-RAC). A lower-tier RAC was considered as sufficiently protective, if less than the corresponding ETO-RAC. ETO-RACs were calculated for repeated (n = 13) and/or single pulsed applications (n = 17) of 26 insecticides to micro/mesocosms, giving a maximum of 30 insecticide × application combinations (i.e. cases) for comparison. Acute tier-1 RACs (for 24 insecticides) were lower than the corresponding ETO-RACs in 27 out of 29 cases, while tier-2 Geom-RACs (for 23 insecticides) were lower in 24 out of 26 cases. The tier-2 SSD-RAC (for 21 insecticides) using HC5 /3 was lower than the ETO-RAC in 23 out of 27 cases, whereas the tier-2 SSD-RAC using HC5 /6 was protective in 25 out of 27 cases. The tier-1 and tier-2 approaches proposed by EFSA for acute effect assessment are sufficiently protective for the majority of insecticides evaluated. Further evaluation may be needed for insecticides with more novel chemistries (neonicotinoids, biopesticides) and compounds that show delayed effects (insect growth regulators). © 2014 Society of Chemical Industry.

Nucleo-cytoplasmic shuttling dynamics of the transcriptional regulators XYR1 and CRE1 under conditions of cellulase and xylanase gene expression in Trichoderma reesei

PubMed Central

Lichius, Alexander; Seidl-Seiboth, Verena; Seiboth, Bernhard; Kubicek, Christian P

2014-01-01

Trichoderma reesei is a model for investigating the regulation of (hemi-)cellulase gene expression. Cellulases are formed adaptively, and the transcriptional activator XYR1 and the carbon catabolite repressor CRE1 are main regulators of their expression. We quantified the nucleo-cytoplasmic shuttling dynamics of GFP-fusion proteins of both transcription factors under cellulase and xylanase inducing conditions, and correlated their nuclear presence/absence with transcriptional changes. We also compared their subcellular localization in conidial germlings and mature hyphae. We show that cellulase gene expression requires de novo biosynthesis of XYR1 and its simultaneous nuclear import, whereas carbon catabolite repression is regulated through preformed CRE1 imported from the cytoplasmic pool. Termination of induction immediately stopped cellulase gene transcription and was accompanied by rapid nuclear degradation of XYR1. In contrast, nuclear CRE1 rapidly decreased upon glucose depletion, and became recycled into the cytoplasm. In mature hyphae, nuclei containing activated XYR1 were concentrated in the colony center, indicating that this is the main region of XYR1 synthesis and cellulase transcription. CRE1 was found to be evenly distributed throughout the entire mycelium. Taken together, our data revealed novel aspects of the dynamic shuttling and spatial bias of the major regulator of (hemi-)cellulase gene expression, XYR1, in T. reesei. PMID:25302561

Arsenic trioxide-mediated growth inhibition in gallbladder carcinoma cells via down-regulation of Cyclin D1 transcription mediated by Sp1 transcription factor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ai, Zhilong; Lu, Weiqi; Ton, Saixiong

2007-08-31

Gallbladder carcinoma (GBC), an aggressive and mostly lethal malignancy, is known to be resistant to a number of drug stimuli. Here, we demonstrated that arsenic trioxide inhibited the proliferation of gallbladder carcinoma in vivo and in vitro as well as the transcription of cell cycle-related protein Cyclin D1. And, Cyclin D1 overexpression inhibited the negative role of arsenic trioxide in cell cycle progression. We further explored the mechanisms by which arsenic trioxide affected Cyclin D1 transcription and found that the Sp1 transcription factor was down-regulated by arsenic trioxide, with a corresponding decrease in Cyclin D1 promoter activity. Taken together, thesemore » results suggested that arsenic trioxide inhibited gallbladder carcinoma cell proliferation via down-regulation of Cyclin D1 transcription in a Sp1-dependent manner, which provided a new mechanism of arsenic trioxide-involved cell proliferation and may have important therapeutic implications in gallbladder carcinoma patients.« less

Interaction between Saikosaponin D, Paeoniflorin, and Human Serum Albumin.

PubMed

Liang, Guo-Wu; Chen, Yi-Cun; Wang, Yi; Wang, Hong-Mei; Pan, Xiang-Yu; Chen, Pei-Hong; Niu, Qing-Xia

2018-01-27

Saikosaponin D (SSD) and paeoniflorin (PF) are the major active constituents of Bupleuri Radix and Paeonia lactiflora Pall , respectively, and have been widely used in China to treat liver and other diseases for many centuries. We explored the binding of SSD/PF to human serum albumin (HSA) by using fluorospectrophotometry, circular dichroism (CD) and molecular docking. Both SSD and PF produced a conformational change in HSA. Fluorescence quenching was accompanied by a blue shift in the fluorescence spectra. Co-binding of PF and SSD also induced quenching and a conformational change in HSA. The Stern-Volmer equation showed that quenching was dominated by static quenching. The binding constant for ternary interaction was below that for binary interaction. Site-competitive experiments demonstrated that SSD/PF bound to site I (subdomain IIA) and site II (subdomain IIIA) in HSA. Analysis of thermodynamic parameters indicated that hydrogen bonding and van der Waals forces were mostly responsible for the binary association. Also, there was energy transfer upon binary interaction. Molecular docking supported the experimental findings in conformation, binding sites and binding forces.

Concurrent maternal and pup postnatal tobacco smoke exposure in Wistar rats changes food preference and dopaminergic reward system parameters in the adult male offspring.

PubMed

Pinheiro, C R; Moura, E G; Manhães, A C; Fraga, M C; Claudio-Neto, S; Abreu-Villaça, Y; Oliveira, E; Lisboa, P C

2015-08-20

Children from pregnant smokers are more susceptible to become obese adults and to become drug or food addicts. Drugs and food activate the mesolimbic reward pathway, causing a sense of pleasure that induces further consumption. Here, we studied the relationship between tobacco smoke exposure during lactation with feeding, behavior and brain dopaminergic reward system parameters at adulthood. Nursing Wistar rats and their pups were divided into two groups: tobacco smoke-exposed (S: 4times/day, from the 3rd to the 21th day of lactation), and ambient air-exposed (C). On PN175, both offspring groups were subdivided for a food challenge: S and C that received standard chow (SC) or that chose between high-fat (HFD) and high-sucrose diets (HSDs). Food intake was recorded after 30min and 12h. Offspring were tested in the elevated plus maze and open field on PN178-179; they were euthanized for dopaminergic analysis on PN180. SSD (self-selected diet) animals presented a higher food intake compared to SC ones. S-SSD animals ate more than C-SSD ones at 30min and 12h. Both groups preferred the HFD. However, S-SSD animals consumed relatively more HFD than C-SSD at 30min. No behavioral differences were observed between groups. S animals presented lower tyrosine hydroxylase (TH) content in the ventral tegmental area, lower TH, dopaminergic receptor 2, higher dopaminergic receptor 1 contents in the nucleus accumbens and lower OBRb in hypothalamic arcuate nucleus. Tobacco-smoke exposure during lactation increases preference for fat in the adult progeny possibly due to alterations in the dopaminergic system. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

[Clinical, endoscopic and morphological manifestations of oesophageal lesion in systemic scleroderma].

PubMed

Karateev, A E; Movsiian, A E; Anan'eva, M M; Radenska-Lopovok, S G

2014-01-01

Oesophageal lesion is the commonest visceral manifestation of systemic scleroderma (SSD) affecting the quality of life and fraught with serious complications. The aim of this study was to evaluate clinical, endoscopic andmorphological manifestations of oesophageal lesion in systemic scleroderma and its relationships with other clinical symptoms and pharmacotherapy of the disease. 479 patients with SSD (93.7% women, 6.3% men, mean age 48.7 +/- 19.2 yr). All of them underwent EGDS in 2005-2010. 123 patients were examined for the detection of Barrett's oesophagus (BO), total screening regardless of complaints was conducted in 2010. Control group included 1018 age and sex-matched patients with RA who underwent EGDS in 2008-2009. Oesophageal lesions occurred much more frequently in SSD than in RA. Oesophageal symptoms were documented in 70.0 and 29.9% cases, non-erosive oesopahgitis in 28.8 and 1.5%, erosive esophagitis in 22.5 and 2.2% ulcers in 0.8 and 0% (p < 0.001). BO manifested as intestinal metaplasia (histological study of mucosal biopsy) was found in 30 SSD patients (4.2%). Screening revealed BO in 8.9% of the patients. The development of erosive oesophagitis was unrelated to the age of the patients, duration of the disease and its form (localized or diffusive), lung pathology or Sjogren's syndrome. Cytotoxic medicines significantly increased the frequency of erosive oesophagitis, it tended to increase under effect of NSAID and low doses of aspirin. Long-term intake of PPI did not reduce the risk of oesophagitis and BO. Half of the patients with SSD have oesophagitis. Over 20% of them suffer its complications (erosion and ulcers) and 9% have BO. All such patients need endoscopic study ofoesophagus regardless of clinical symptoms.

The pleiotropic transcriptional regulator COUP-TFI plays multiple roles in neural development and disease.

PubMed

Bertacchi, Michele; Parisot, Josephine; Studer, Michèle

2018-04-27

Transcription factors are expressed in a dynamic fashion both in time and space during brain development, and exert their roles by activating a cascade of multiple target genes. This implies that understanding the precise function of a transcription factor becomes a challenging task. In this review, we will focus on COUP-TFI (or NR2F1), a nuclear receptor belonging to the superfamily of the steroid/thyroid hormone receptors, and considered to be one of the major transcriptional regulators orchestrating cortical arealization, cell-type specification and maturation. Recent data have unraveled the multi-faceted functions of COUP-TFI in the development of several mouse brain structures, including the neocortex, hippocampus and ganglionic eminences. Despite NR2F1 mutations and deletions in humans have been linked to a complex neurodevelopmental disease mainly associated to optic atrophy and intellectual disability, its role during the formation of the retina and optic nerve remains unclear. In light of its major influence in cortical development, we predict that its haploinsufficiency might be the cause of other cognitive diseases, not identified so far. Mouse models offer a unique opportunity of dissecting COUP-TFI function in different regions during brain assembly; hence, the importance of comparing and discussing common points linking mouse models to human patients' symptoms. Copyright © 2018 Elsevier B.V. All rights reserved.

Silencing of IFN-stimulated gene transcription is regulated by histone H1 and its chaperone TAF-I.

PubMed

Kadota, Shinichi; Nagata, Kyosuke

2014-07-01

Chromatin structure and its alteration play critical roles in the regulation of transcription. However, the transcriptional silencing mechanism with regard to the chromatin structure at an unstimulated state of the interferon (IFN)-stimulated gene (ISG) remains unclear. Here we investigated the role of template activating factor-I (TAF-I, also known as SET) in ISG transcription. Knockdown (KD) of TAF-I increased ISG transcript and simultaneously reduced the histone H1 level on the ISG promoters during the early stages of transcription after IFN stimulation from the unstimulated state. The transcription factor levels on the ISG promoters were increased in TAF-I KD cells only during the early stages of transcription. Furthermore, histone H1 KD also increased ISG transcript. TAF-I and histone H1 double KD did not show the additive effect in ISG transcription, suggesting that TAF-I and histone H1 may act on the same regulatory pathway to control ISG transcription. In addition, TAF-I KD and histone H1 KD affected the chromatin structure near the ISG promoters. On the basis of these findings, we propose that TAF-I and its target histone H1 are key regulators of the chromatin structure at the ISG promoter to maintain the silent state of ISG transcription. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

H3K27 methylation and H3S28 phosphorylation-dependent transcriptional regulation by INHAT subunit SET/TAF-Iβ.

PubMed

Kim, Ji-Young; Kim, Kee-Beom; Son, Hye-Ju; Chae, Yun-Cheol; Oh, Si-Taek; Kim, Dong-Wook; Pak, Jhang Ho; Seo, Sang-Beom

2012-09-21

Significant progress has been made in understanding the relationship between histone modifications and 'reader' molecules and their effects on transcriptional regulation. A previously identified INHAT complex subunit, SET/TAF-Iβ, binds to histones and inhibits histone acetylation. To investigate the binding specificities of SET/TAF-Iβ to various histone modifications, we employed modified histone tail peptide array analyses. SET/TAF-Iβ strongly recognized PRC2-mediated H3K27me1/2/3; however, the bindings were completely disrupted by H3S28 phosphorylation. We have demonstrated that SET/TAF-Iβ is sequentially recruited to the target gene promoter ATF3 after the PRC2 complex via H3K27me recognition and may offer additive effects in the repression of the target gene. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Cloning of ubiquitin-activating enzyme and ubiquitin-conjugating enzyme genes from Gracilaria lemaneiformis and their activity under heat shock.

PubMed

Li, Guang-Qi; Zang, Xiao-Nan; Zhang, Xue-Cheng; Lu, Ning; Ding, Yan; Gong, Le; Chen, Wen-Chao

2014-03-15

To study the response of Gracilaria lemaneiformis to heat stress, two key enzymes - ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzyme (E2) - of the Ubiquitin/26S proteasome pathway (UPP) were studied in three strains of G. lemaneiformis-wild type, heat-tolerant cultivar 981 and heat-tolerant cultivar 07-2. The full length DNA sequence of E1 contained only one exon. The open reading frame (ORF) sequence was 981 nucleotides encoding 326 amino acids, which contained conserved ATP binding sites (LYDRQIRLWGLE, ELAKNVLLAGV, LKEMN, VVCAI) and the ubiquitin-activating domains (VVCAI…LMTEAC, VFLDLGDEYSYQ, AIVGGMWGRE). The gene sequence of E2 contained four exons and three introns. The sum of the four exons gave an open reading frame sequence of 444 nucleotides encoding 147 amino acids, which contained a conserved ubiquitin-activating domain (GSICLDIL), ubiquitin-conjugating domains (RIYHPNIN, KVLLSICSLL, DDPLV) and ubiquitin-ligase (E3) recognition sites (KRI, YPF, WSP). Real-time-PCR analysis of transcription levels of E1 and E2 under heat shock conditions (28°C and 32°C) showed that in wild type, transcriptions of E1 and E2 were up-regulated at 28°C, while at 32°C, transcriptions of the two enzymes were below the normal level. In cultivar 981 and cultivar 07-2 of G. lemaneiformis, the transcription levels of the two enzymes were up-regulated at 32°C, and transcription level of cultivar 07-2 was even higher than that of cultivar 981. These results suggest that the UPP plays an important role in high temperature resistance of G. lemaneiformis and the bioactivity of UPP is directly related to the heat-resistant ability of G. lemaneiformis. Copyright © 2013 Elsevier B.V. All rights reserved.

Advances in esophageal cancer: A new perspective on pathogenesis associated with long non-coding RNAs.

PubMed

Huang, Xiaomei; Zhou, Xi; Hu, Qing; Sun, Binyu; Deng, Mingming; Qi, Xiaolong; Lü, Muhan

2018-01-28

Esophageal cancer is a malignant digestive tract cancer with high mortality. Although studies have found that esophageal cancer is involved in a complex and important gene regulation network, the pathogenesis remains unclear. The recently described long non-coding RNAs (lncRNAs) are one effective part of the gene regulation network. However, in past decades, lncRNAs were thought to be "transcript noise" or "pseudogenes" and were thus ignored. Early studies indicated that lncRNAs play pivotal roles during evolution. However, in recent years, increasing research has revealed that many lncRNAs are associated with tumorigenesis. In particular, lncRNAs may act as important elements for epigenetic regulation, transcription, post-transcriptional regulation and post-translational modification of proteins. Additionally, they may be novel biomarkers for tumors and therapeutic targets in cancer. Here, we summarize the functions of lncRNAs in esophageal cancer, with an emphasis on lncRNA-mediated regulatory mechanisms that affect the biological characteristics of esophageal cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

The chrysanthemum leaf and root transcript profiling in response to salinity stress.

PubMed

Cheng, Peilei; Gao, Jiaojiao; Feng, Yitong; Zhang, Zixin; Liu, Yanan; Fang, Weimin; Chen, Sumei; Chen, Fadi; Jiang, Jiafu

2018-06-23

RNA-Seq was applied to capture the transcriptome of the leaf and root of non-treated and salinity-treated chrysanthemum cv. 'Jinba' plants. A total of 206,868 unigenes of mean length 849 nt and of N50 length 1363 nt was identified; of these about 64% (>132,000) could be functionally assigned. Depending on the severity of the salinity stress, differential transcription was observed for genes encoding proteins involved in osmotic adjustment, in ion transport, in reactive oxygen species scavenging and in the regulation of abscisic acid (ABA) signaling. The root stress response was dominated by the up-regulation of genes involved in ion transport and homeostasis, while that of the leaf reflected the plant's effort to make osmotic adjustments and to regulate ABA signaling. An array of known transcription factors (WRKY, AP2/ERF, MYB, bHLH and NAC) were differentially transcribed. Copyright © 2018. Published by Elsevier B.V.

Basic leucine zipper protein Cnc-C is a substrate and transcriptional regulator of the Drosophila 26S proteasome.

PubMed

Grimberg, Kristian Björk; Beskow, Anne; Lundin, Daniel; Davis, Monica M; Young, Patrick

2011-02-01

While the 26S proteasome is a key proteolytic complex, little is known about how proteasome levels are maintained in higher eukaryotic cells. Here we describe an RNA interference (RNAi) screen of Drosophila melanogaster that was used to identify transcription factors that may play a role in maintaining levels of the 26S proteasome. We used an RNAi library against 993 Drosophila transcription factor genes to identify genes whose suppression in Schneider 2 cells stabilized a ubiquitin-green fluorescent protein reporter protein. This screen identified Cnc (cap 'n' collar [CNC]; basic region leucine zipper) as a candidate transcriptional regulator of proteasome component expression. In fact, 20S proteasome activity was reduced in cells depleted of cnc. Immunoblot assays against proteasome components revealed a general decline in both 19S regulatory complex and 20S proteasome subunits after RNAi depletion of this transcription factor. Transcript-specific silencing revealed that the longest of the seven transcripts for the cnc gene, cnc-C, was needed for proteasome and p97 ATPase production. Quantitative reverse transcription-PCR confirmed the role of Cnc-C in activation of transcription of genes encoding proteasome components. Expression of a V5-His-tagged form of Cnc-C revealed that the transcription factor is itself a proteasome substrate that is stabilized when the proteasome is inhibited. We propose that this single cnc gene in Drosophila resembles the ancestral gene family of mammalian nuclear factor erythroid-derived 2-related transcription factors, which are essential in regulating oxidative stress and proteolysis.

MEDIATOR25 Acts as an Integrative Hub for the Regulation of Jasmonate-Responsive Gene Expression in Arabidopsis1[C][W

PubMed Central

Çevik, Volkan; Kidd, Brendan N.; Zhang, Peijun; Hill, Claire; Kiddle, Steve; Denby, Katherine J.; Holub, Eric B.; Cahill, David M.; Manners, John M.; Schenk, Peer M.; Beynon, Jim; Kazan, Kemal

2012-01-01

The PHYTOCHROME AND FLOWERING TIME1 gene encoding the MEDIATOR25 (MED25) subunit of the eukaryotic Mediator complex is a positive regulator of jasmonate (JA)-responsive gene expression in Arabidopsis (Arabidopsis thaliana). Based on the function of the Mediator complex as a bridge between DNA-bound transcriptional activators and the RNA polymerase II complex, MED25 has been hypothesized to function in association with transcriptional regulators of the JA pathway. However, it is currently not known mechanistically how MED25 functions to regulate JA-responsive gene expression. In this study, we show that MED25 physically interacts with several key transcriptional regulators of the JA signaling pathway, including the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factors OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59 and ERF1 as well as the master regulator MYC2. Physical interaction detected between MED25 and four group IX AP2/ERF transcription factors was shown to require the activator interaction domain of MED25 as well as the recently discovered Conserved Motif IX-1/EDLL transcription activation motif of MED25-interacting AP2/ERFs. Using transcriptional activation experiments, we also show that OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59- and ERF1-dependent activation of PLANT DEFENSIN1.2 as well as MYC2-dependent activation of VEGETATIVE STORAGE PROTEIN1 requires a functional MED25. In addition, MED25 is required for MYC2-dependent repression of pathogen defense genes. These results suggest an important role for MED25 as an integrative hub within the Mediator complex during the regulation of JA-associated gene expression. PMID:22822211

Intervention efficacy and intensity for children with speech sound disorder.

PubMed

Allen, Melissa M

2013-06-01

Clinicians do not have an evidence base they can use to recommend optimum intervention intensity for preschool children who present with speech sound disorder (SSD). This study examined the effect of dose frequency on phonological performance and the efficacy of the multiple oppositions approach. Fifty-four preschool children with SSD were randomly assigned to one of three intervention conditions. Two intervention conditions received the multiple oppositions approach either 3 times per week for 8 weeks (P3) or once weekly for 24 weeks (P1). A control (C) condition received a storybook intervention. Percentage of consonants correct (PCC) was evaluated at 8 weeks and after 24 sessions. PCC gain was examined after a 6-week maintenance period. The P3 condition had a significantly better phonological outcome than the P1 and C conditions at 8 weeks and than the P1 condition after 24 weeks. There were no significant differences between the P1 and C conditions. There was no significant difference between the P1 and P3 conditions in PCC gain during the maintenance period. Preschool children with SSD who received the multiple oppositions approach made significantly greater gains when they were provided with a more intensive dose frequency and when cumulative intervention intensity was held constant.

The Hog1p kinase regulates Aft1p transcription factor to control iron accumulation.

PubMed

Martins, Telma S; Pereira, Clara; Canadell, David; Vilaça, Rita; Teixeira, Vítor; Moradas-Ferreira, Pedro; de Nadal, Eulàlia; Posas, Francesc; Costa, Vítor

2018-01-01

Iron acquisition systems have to be tightly regulated to assure a continuous supply of iron, since it is essential for survival, but simultaneously to prevent iron overload that is toxic to the cells. In budding yeast, the low‑iron sensing transcription factor Aft1p is a master regulator of the iron regulon. Our previous work revealed that bioactive sphingolipids modulate iron homeostasis as yeast cells lacking the sphingomyelinase Isc1p exhibit an upregulation of the iron regulon. In this study, we show that Isc1p impacts on iron accumulation and localization. Notably, Aft1p is activated in isc1Δ cells due to a decrease in its phosphorylation and an increase in its nuclear levels. Consistently, the expression of a phosphomimetic version of Aft1p-S210/S224 that favours its nuclear export abolished iron accumulation in isc1Δ cells. Notably, the Hog1p kinase, homologue of mammalian p38, interacts with and directly phosphorylates Aft1p at residues S210 and S224. However, Hog1p-Aft1p interaction decreases in isc1Δ cells, which likely contributes to Aft1p dephosphorylation and consequently to Aft1p activation and iron overload in isc1Δ cells. These results suggest that alterations in sphingolipid composition in isc1Δ cells may impact on iron homeostasis by disturbing the regulation of Aft1p by Hog1p. To our knowledge, Hog1p is the first kinase reported to directly regulate Aft1p, impacting on iron homeostasis. Copyright © 2017 Elsevier B.V. All rights reserved.

The metabolic activator FOXO1 binds hepatitis B virus DNA and activates its transcription

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shlomai, Amir, E-mail: amirsh@tasmc.health.gov.il; Institute for Gastroenterology and Liver disease, Tel-Aviv Sourasky Medical Center, 6 Weizmann street, Tel-Aviv; Shaul, Yosef

2009-04-17

Hepatitis B virus (HBV) is a small DNA virus that targets the liver and infects humans worldwide. Recently we have shown that the metabolic regulator PGC-1{alpha} coactivates HBV transcription thereby rendering the virus susceptible to fluctuations in the nutritional status of the liver. PGC-1{alpha} coactivation of HBV is mediated through the liver-enriched nuclear receptor HNF4{alpha} and through another yet unknown transcription factor(s). Here we show that the forkhead transcription factor FOXO1, a known target for PGC-1{alpha} coactivation and a central mediator of glucose metabolism in the liver, binds HBV core promoter and activates its transcription. This activation is further enhancedmore » in the presence of PGC-1{alpha}, implying that FOXO1 is a target for PGC-1{alpha} coactivation of HBV transcription. Thus, our results identify another key metabolic regulator as an activator of HBV transcription, thereby supporting the principle that HBV gene expression is regulated in a similar way to key hepatic metabolic genes.« less

Cloning and Characterization of an Outer Membrane Protein of Vibrio vulnificus Required for Heme Utilization: Regulation of Expression and Determination of the Gene Sequence

PubMed Central

Litwin, Christine M.; Byrne, Burke L.

1998-01-01

Vibrio vulnificus is a halophilic, marine pathogen that has been associated with septicemia and serious wound infections in patients with iron overload and preexisting liver disease. For V. vulnificus, the ability to acquire iron from the host has been shown to correlate with virulence. V. vulnificus is able to use host iron sources such as hemoglobin and heme. We previously constructed a fur mutant of V. vulnificus which constitutively expresses at least two iron-regulated outer membrane proteins, of 72 and 77 kDa. The N-terminal amino acid sequence of the 77-kDa protein purified from the V. vulnificus fur mutant had 67% homology with the first 15 amino acids of the mature protein of the Vibrio cholerae heme receptor, HutA. In this report, we describe the cloning, DNA sequence, mutagenesis, and analysis of transcriptional regulation of the structural gene for HupA, the heme receptor of V. vulnificus. DNA sequencing of hupA demonstrated a single open reading frame of 712 amino acids that was 50% identical and 66% similar to the sequence of V. cholerae HutA and similar to those of other TonB-dependent outer membrane receptors. Primer extension analysis localized one promoter for the V. vulnificus hupA gene. Analysis of the promoter region of V. vulnificus hupA showed a sequence homologous to the consensus Fur box. Northern blot analysis showed that the transcript was strongly regulated by iron. An internal deletion in the V. vulnificus hupA gene, done by using marker exchange, resulted in the loss of expression of the 77-kDa protein and the loss of the ability to use hemin or hemoglobin as a source of iron. The hupA deletion mutant of V. vulnificus will be helpful in future studies of the role of heme iron in V. vulnificus pathogenesis. PMID:9632577

S-nitrosylation in the regulation of gene transcription☆

PubMed Central

Sha, Yonggang; Marshall, Harvey E.

2015-01-01

Background Post-translational modification of proteins by S-nitrosylation serves as a major mode of signaling in mammalian cells and a growing body of evidence has shown that transcription factors and their activating pathways are primary targets. S-nitrosylation directly modifies a number of transcription factors, including NF-κB, HIF-1, and AP-1. In addition, S-nitrosylation can indirectly regulate gene transcription by modulating other cell signaling pathways, in particular JNK kinase and ras. Scope of review The evolution of S-nitrosylation as a signaling mechanism in the regulation of gene transcription, physiological advantages of protein S-nitrosylation in the control of gene transcription, and discussion of the many transcriptional proteins modulated by S-nitrosylation is summarized. Major conclusions S-nitrosylation plays a crucial role in the control of mammalian gene transcription with numerous transcription factors regulated by this modification. Many of these proteins serve as immunomodulators, and inducible nitric oxide synthase (iNOS) is regarded as a principal mediatiator of NO-dependent S-nitrosylation. However, additional targets within the nucleus (e.g. histone deacetylases) and alternative mechanisms of S-nitrosylation (e.g. GAPDH-mediated trans-nitrosylation) are thought to play a role in NOS-dependent transcriptional regulation. General significance Derangement of SNO-regulated gene transcription is an important factor in a variety of pathological conditions including neoplasia and sepsis. A better understanding of protein S-nitrosylation as it relates to gene transcription and the physiological mechanisms behind this process is likely to lead to novel therapies for these disorders. This article is part of a Special Issue entitled Regulation of Cellular Processes by S-nitrosylation. PMID:21640163

SMAD3 augments FoxO3-induced MuRF-1 promoter activity in a DNA-binding-dependent manner

PubMed Central

Bollinger, Lance M.; Witczak, Carol A.; Houmard, Joseph A.

2014-01-01

Muscle-specific RING finger-1 (MuRF-1), a ubiquitin ligase and key regulator of proteasome-dependent protein degradation, is highly expressed during skeletal muscle atrophy. The transcription factor forkhead box O3 (FoxO3) induces MuRF-1 expression, but the direct role of other major atrophy-related transcription factors, such as SMAD3, is largely unknown. The goal of this study was to determine whether SMAD3 individually regulates, or with FoxO3 coordinately regulates, MuRF-1 expression. In cultured myotubes or human embryonic kidney cells, MuRF-1 mRNA content and promoter activity were increased by FoxO3 but not by SMAD3 overexpression. However, FoxO3 and SMAD3 coexpression synergistically increased MuRF-1 mRNA and promoter activity. Mutation of the SMAD-binding element (SBE) in the proximal MuRF-1 promoter or overexpression of a SMAD3 DNA-binding mutant attenuated FoxO3-dependent MuRF-1 promoter activation, showing that SMAD binding to DNA is required for optimal activation of FoxO3-induced transcription of MuRF-1. Using chromatin immunoprecipitation, SMAD3 DNA binding increased FoxO3 abundance and SBE mutation reduced FoxO3 abundance on the MuRF-1 promoter. Furthermore, SMAD3 overexpression dose-dependently increased FoxO3 protein content, and coexpression of FoxO3 and SMAD3 synergistically increased FoxO-dependent gene transcription [assessed with a FoxO response element (FRE)-driven reporter]. Collectively, these results show that SMAD3 regulates transcription of MuRF-1 by increasing FoxO3 binding at a conserved FRE-SBE motif within the proximal promoter region, and by increasing FoxO3 protein content and transcriptional activity. These data are the first to indicate that two major transcription factors regulating protein degradation, FoxO3 and SMAD3, converge to coordinately and directly regulate transcription of MuRF-1. PMID:24920680

Cherenkov imaging method for rapid optimization of clinical treatment geometry in total skin electron beam therapy

PubMed Central

Zhang, Rongxiao; Gladstone, David J.; Williams, Benjamin B.; Glaser, Adam K.; Pogue, Brian W.; Jarvis, Lesley A.

2016-01-01

Purpose: A method was developed utilizing Cherenkov imaging for rapid and thorough determination of the two gantry angles that produce the most uniform treatment plane during dual-field total skin electron beam therapy (TSET). Methods: Cherenkov imaging was implemented to gather 2D measurements of relative surface dose from 6 MeV electron beams on a white polyethylene sheet. An intensified charge-coupled device camera time-gated to the Linac was used for Cherenkov emission imaging at sixty-two different gantry angles (1° increments, from 239.5° to 300.5°). Following a modified Stanford TSET technique, which uses two fields per patient position for full body coverage, composite images were created as the sum of two beam images on the sheet; each angle pair was evaluated for minimum variation across the patient region of interest. Cherenkov versus dose correlation was verified with ionization chamber measurements. The process was repeated at source to surface distance (SSD) = 441, 370.5, and 300 cm to determine optimal angle spread for varying room geometries. In addition, three patients receiving TSET using a modified Stanford six-dual field technique with 6 MeV electron beams at SSD = 441 cm were imaged during treatment. Results: As in previous studies, Cherenkov intensity was shown to directly correlate with dose for homogenous flat phantoms (R2 = 0.93), making Cherenkov imaging an appropriate candidate to assess and optimize TSET setup geometry. This method provided dense 2D images allowing 1891 possible treatment geometries to be comprehensively analyzed from one data set of 62 single images. Gantry angles historically used for TSET at their institution were 255.5° and 284.5° at SSD = 441 cm; however, the angles optimized for maximum homogeneity were found to be 252.5° and 287.5° (+6° increase in angle spread). Ionization chamber measurements confirmed improvement in dose homogeneity across the treatment field from a range of 24.4% at the initial angles, to only 9.8% with the angles optimized. A linear relationship between angle spread and SSD was observed, ranging from 35° at 441 cm, to 39° at 300 cm, with no significant variation in percent-depth dose at midline (R2 = 0.998). For patient studies, factors influencing in vivo correlation between Cherenkov intensity and measured surface dose are still being investigated. Conclusions: Cherenkov intensity correlates to relative dose measured at depth of maximum dose in a uniform, flat phantom. Imaging of phantoms can thus be used to analyze and optimize TSET treatment geometry more extensively and rapidly than thermoluminescent dosimeters or ionization chambers. This work suggests that there could be an expanded role for Cherenkov imaging as a tool to efficiently improve treatment protocols and as a potential verification tool for routine monitoring of unique patient treatments. PMID:26843259

Cherenkov imaging method for rapid optimization of clinical treatment geometry in total skin electron beam therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andreozzi, Jacqueline M., E-mail: Jacqueline.M.Andreozzi.th@dartmouth.edu, E-mail: Lesley.A.Jarvis@hitchcock.org; Glaser, Adam K.; Zhang, Rongxiao

2016-02-15

Purpose: A method was developed utilizing Cherenkov imaging for rapid and thorough determination of the two gantry angles that produce the most uniform treatment plane during dual-field total skin electron beam therapy (TSET). Methods: Cherenkov imaging was implemented to gather 2D measurements of relative surface dose from 6 MeV electron beams on a white polyethylene sheet. An intensified charge-coupled device camera time-gated to the Linac was used for Cherenkov emission imaging at sixty-two different gantry angles (1° increments, from 239.5° to 300.5°). Following a modified Stanford TSET technique, which uses two fields per patient position for full body coverage, compositemore » images were created as the sum of two beam images on the sheet; each angle pair was evaluated for minimum variation across the patient region of interest. Cherenkov versus dose correlation was verified with ionization chamber measurements. The process was repeated at source to surface distance (SSD) = 441, 370.5, and 300 cm to determine optimal angle spread for varying room geometries. In addition, three patients receiving TSET using a modified Stanford six-dual field technique with 6 MeV electron beams at SSD = 441 cm were imaged during treatment. Results: As in previous studies, Cherenkov intensity was shown to directly correlate with dose for homogenous flat phantoms (R{sup 2} = 0.93), making Cherenkov imaging an appropriate candidate to assess and optimize TSET setup geometry. This method provided dense 2D images allowing 1891 possible treatment geometries to be comprehensively analyzed from one data set of 62 single images. Gantry angles historically used for TSET at their institution were 255.5° and 284.5° at SSD = 441 cm; however, the angles optimized for maximum homogeneity were found to be 252.5° and 287.5° (+6° increase in angle spread). Ionization chamber measurements confirmed improvement in dose homogeneity across the treatment field from a range of 24.4% at the initial angles, to only 9.8% with the angles optimized. A linear relationship between angle spread and SSD was observed, ranging from 35° at 441 cm, to 39° at 300 cm, with no significant variation in percent-depth dose at midline (R{sup 2} = 0.998). For patient studies, factors influencing in vivo correlation between Cherenkov intensity and measured surface dose are still being investigated. Conclusions: Cherenkov intensity correlates to relative dose measured at depth of maximum dose in a uniform, flat phantom. Imaging of phantoms can thus be used to analyze and optimize TSET treatment geometry more extensively and rapidly than thermoluminescent dosimeters or ionization chambers. This work suggests that there could be an expanded role for Cherenkov imaging as a tool to efficiently improve treatment protocols and as a potential verification tool for routine monitoring of unique patient treatments.« less

The gga-let-7 family post-transcriptionally regulates TGFBR1 and LIN28B during the differentiation process in early chick development.

PubMed

Lee, Sang In; Jeon, Mi-Hyang; Kim, Jeom Sun; Jeon, Ik-Soo; Byun, Sung June

2015-12-01

Early chick embryogenesis is governed by a complex mechanism involving transcriptional and post-transcriptional regulation, although how post-transcriptional processes influence the balance between pluripotency and differentiation during early chick development have not been previously investigated. Here, we characterized the microRNA (miRNA) signature associated with differentiation in the chick embryo, and found that as expression of the gga-let-7 family increases through early development, expression of their direct targets, TGFBR1 and LIN28B, decreases; indeed, gga-let-7a-5p and gga-let-7b miRNAs directly bind to TGFBR1 and LIN28B transcripts. Our data further indicate that TGFBR1 and LIN28B maintain pluripotency by regulating POUV, NANOG, and CRIPTO. Therefore, gga-let-7 miRNAs act as post-transcriptional regulators of differentiation in blastodermal cells by repressing the expression of the TGFBR1 and LIN28B, which intrinsically controls blastodermal cell differentiation in early chick development. © 2015 Wiley Periodicals, Inc.

Unexpected distribution of CA19.9 and other type 1 chain Lewis antigens in normal and cancer tissues of colon and pancreas: Importance of the detection method and role of glycosyltransferase regulation.

PubMed

Aronica, Adele; Avagliano, Laura; Caretti, Anna; Tosi, Delfina; Bulfamante, Gaetano Pietro; Trinchera, Marco

2017-01-01

CA19.9 antigen has been assumed as an abundant product of cancer cells, due to the reactivity found by immunohistochemical staining of cancer tissues with anti-CA19.9 antibody. Expression and biosynthesis of type 1 chain Lewis antigens in the colon and the pancreas were studied by immunodetection in tissue sections and lysates, quantification of glycosyltransferase transcripts, bisulfite sequencing, and chromatin immunoprecipitation assays. CA19.9 was poorly detectable in normal colon mucosa and almost undetectable in colon cancer, while it was easily detected in the pancreatic ducts, together with Lewis b antigen, under both normal and cancer conditions. B3GALT5 transcripts were down-regulated in colon cancer, while they remained expressed in pancreatic cancer. Even ST3GAL3 transcript appeared well expressed in the pancreas but poorly in the colon, irrespective of normal or cancer conditions. CpG islands flanking B3GALT5 native promoter presented an extremely low degree of methylation in pancreatic cancer with respect to colon cancer. In a DNA region about 1kb away from the B3GALT5 retroviral promoter, a stretch of CG dinucleotides presented a methylation pattern potentially associated with transcription. Such a DNA region and the transcription factor binding site provided overlapping results by chromatin immunoprecipitation assays, corroborating the hypothesis. CA19.9 appears as a physiological product whose synthesis strongly depends on the tissue specific and epigenetically-regulated expression of B3GALT5 and ST3GAL3. CA19.9 and other Lewis antigens acquire tumor marker properties in the pancreas due to mechanisms giving rise to reabsorption into vessels and elevation in circulating levels. Copyright © 2016 Elsevier B.V. All rights reserved.

Genome-wide analysis of AR binding and comparison with transcript expression in primary human fetal prostate fibroblasts and cancer associated fibroblasts.

PubMed

Nash, Claire; Boufaied, Nadia; Mills, Ian G; Franco, Omar E; Hayward, Simon W; Thomson, Axel A

2017-05-05

The androgen receptor (AR) is a transcription factor, and key regulator of prostate development and cancer, which has discrete functions in stromal versus epithelial cells. AR expressed in mesenchyme is necessary and sufficient for prostate development while loss of stromal AR is predictive of prostate cancer progression. Many studies have characterized genome-wide binding of AR in prostate tumour cells but none have used primary mesenchyme or stroma. We applied ChIPseq to identify genomic AR binding sites in primary human fetal prostate fibroblasts and patient derived cancer associated fibroblasts, as well as the WPMY1 cell line overexpressing AR. We identified AR binding sites that were specific to fetal prostate fibroblasts (7534), cancer fibroblasts (629), WPMY1-AR (2561) as well as those common among all (783). Primary fibroblasts had a distinct AR binding profile versus prostate cancer cell lines and tissue, and showed a localisation to gene promoter binding sites 1 kb upstream of the transcriptional start site, as well as non-classical AR binding sequence motifs. We used RNAseq to define transcribed genes associated with AR binding sites and derived cistromes for embryonic and cancer fibroblasts as well as a cistrome common to both. These were compared to several in vivo ChIPseq and transcript expression datasets; which identified subsets of AR targets that were expressed in vivo and regulated by androgens. This analysis enabled us to deconvolute stromal AR targets active in stroma within tumour samples. Taken together, our data suggest that the AR shows significantly different genomic binding site locations in primary prostate fibroblasts compared to that observed in tumour cells. Validation of our AR binding site data with transcript expression in vitro and in vivo suggests that the AR target genes we have identified in primary fibroblasts may contribute to clinically significant and biologically important AR-regulated changes in prostate tissue. Copyright © 2017. Published by Elsevier B.V.

Coordination of NF-kappaB and NFAT antagonism by the forkhead transcription factor Foxd1.

PubMed

Lin, Ling; Peng, Stanford L

2006-04-15

Forkhead transcription factors play critical roles in the maintenance of immune homeostasis. In this study, we demonstrate that this regulation most likely involves intricate interactions between the forkhead family members and inflammatory transcription factors: the forkhead member Foxd1 coordinates the regulation of the activity of two key inflammatory transcription factors, NF-AT and NF-kappaB, with Foxd1 deficiency resulting in multiorgan, systemic inflammation, exaggerated Th cell-derived cytokine production, and T cell proliferation in autologous MLRs. Foxd1-deficient T cells possess increased activity of both NF-AT and NF-kappaB: the former correlates with the ability of Foxd1 to regulate casein kinase 1, an NF-AT inhibitory kinase; the latter with the ability of Foxd1 to regulate Foxj1, which regulates the NF-kappaB inhibitory subunit IkappaB beta. Thus, Foxd1 modulates inflammatory reactions and prevents autoimmunity by directly regulating anti-inflammatory regulators of the NF-AT pathway, and by coordinating the suppression of the NF-kappaB pathway via Foxj1. These findings indicate the presence of a general network of forkhead proteins that enforce T cell quiescence.

Glycogen synthase kinase-3 inhibitors suppress the AR-V7-mediated transcription and selectively inhibit cell growth in AR-V7-positive prostate cancer cells.

PubMed

Nakata, Daisuke; Koyama, Ryokichi; Nakayama, Kazuhide; Kitazawa, Satoshi; Watanabe, Tatsuya; Hara, Takahito

2017-06-01

Recent evidence suggests that androgen receptor (AR) splice variants, including AR-V7, play a pivotal role in resistance to androgen blockade in prostate cancer treatment. The development of new therapeutic agents that can suppress the transcriptional activities of AR splice variants has been anticipated as the next generation treatment of castration-resistant prostate cancer. High-throughput screening of AR-V7 signaling inhibitors was performed using an AR-V7 reporter system. The effects of a glycogen synthase kinase-3 (GSK3) inhibitor, LY-2090314, on endogenous AR-V7 signaling were evaluated in an AR-V7-positive cell line, JDCaP-hr, by quantitative reverse transcription polymerase chain reaction. The relationship between AR-V7 signaling and β-catenin signaling was assessed using RNA interference. The effect of LY-2090314 on cell growth in various prostate cancer cell lines was also evaluated. We identified GSK3 inhibitors as transcriptional suppressors of AR-V7 using a high-throughput screen with an AR-V7 reporter system. LY-2090314 suppressed the reporter activity and endogenous AR-V7 activity in JDCaP-hr cells. Because silencing of β-catenin partly rescued the suppression, it was evident that the suppression was mediated, at least partially, via the activation of β-catenin signaling. AR-V7 signaling and β-catenin signaling reciprocally regulate each other in JDCaP-hr cells, and therefore, GSK3 inhibition can repress AR-V7 transcriptional activity by accumulating intracellular β-catenin. Notably, LY-2090314 selectively inhibited the growth of AR-V7-positive prostate cancer cells in vitro. Our findings demonstrate the potential of GSK3 inhibitors in treating advanced prostate cancer driven by AR splice variants. In vivo evaluation of AR splice variant-positive prostate cancer models will help illustrate the overall significance of GSK3 inhibitors in treating prostate cancer. © 2017 Wiley Periodicals, Inc.

Tissue-Specific 5′ Heterogeneity of PPARα Transcripts and Their Differential Regulation by Leptin

PubMed Central

Garratt, Emma S.; Vickers, Mark H.; Gluckman, Peter D.; Hanson, Mark A.

2013-01-01

The genes encoding nuclear receptors comprise multiple 5′untranslated exons, which give rise to several transcripts encoding the same protein, allowing tissue-specific regulation of expression. Both human and mouse peroxisome proliferator activated receptor (PPAR) α genes have multiple promoters, although their function is unknown. Here we have characterised the rat PPARα promoter region and have identified three alternative PPARα transcripts, which have different transcription start sites owing to the utilisation of distinct first exons. Moreover these alternative PPARα transcripts were differentially expressed between adipose tissue and liver. We show that while the major adipose (P1) and liver (P2) transcripts were both induced by dexamethasone, they were differentially regulated by the PPARα agonist, clofibric acid, and leptin. Leptin had no effect on the adipose-specific P1 transcript, but induced liver-specific P2 promoter activity via a STAT3/Sp1 mechanism. Moreover in Wistar rats, leptin treatment between postnatal day 3–13 led to an increase in P2 but not P1 transcription in adipose tissue which was sustained into adulthood. This suggests that the expression of the alternative PPARα transcripts are in part programmed by early life exposure to leptin leading to persistent change in adipose tissue fatty acid metabolism through specific activation of a quiescent PPARα promoter. Such complexity in the regulation of PPARα may allow the expression of PPARα to be finely regulated in response to environmental factors. PMID:23825665

Zinc finger transcription factor CASZ1 interacts with histones, DNA repair proteins and recruits NuRD complex to regulate gene transcription.

PubMed

Liu, Zhihui; Lam, Norris; Thiele, Carol J

2015-09-29

The zinc finger transcription factor CASZ1 has been found to control neural fate-determination in flies, regulate murine and frog cardiac development, control murine retinal cell progenitor expansion and function as a tumor suppressor gene in humans. However, the molecular mechanism by which CASZ1 regulates gene transcription to exert these diverse biological functions has not been described. Here we identify co-factors that are recruited by CASZ1b to regulate gene transcription using co-immunoprecipitation (co-IP) and mass spectrometry assays. We find that CASZ1b binds to the nucleosome remodeling and histone deacetylase (NuRD) complex, histones and DNA repair proteins. Mutagenesis of the CASZ1b protein assay demonstrates that the N-terminus of CASZ1b is required for NuRD binding, and a poly(ADP-ribose) binding motif in the CASZ1b protein is required for histone H3 and DNA repair proteins binding. The N-terminus of CASZ1b fused to an artificial DNA-binding domain (GAL4DBD) causes a significant repression of transcription (5xUAS-luciferase assay), which could be blocked by treatment with an HDAC inhibitor. Realtime PCR results show that the transcriptional activity of CASZ1b mutants that abrogate NuRD or histone H3/DNA binding is significantly decreased. This indicates a model in which CASZ1b binds to chromatin and recruits NuRD complexes to orchestrate epigenetic-mediated transcriptional programs.

c-Jun induces apoptosis of starved BM2 monoblasts by activating cyclin A-CDK2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vanhara, Petr; Bryja, Vitezslav; Horvath, Viktor

2007-02-02

c-Jun is one of the major components of the activating protein-1 (AP-1), the transcription factor that participates in regulation of proliferation, differentiation, and apoptosis. In this study, we explored functional interactions of the c-Jun protein with several regulators of the G1/S transition in serum-deprived v-myb-transformed chicken monoblasts BM2. We show that the c-Jun protein induces expression of cyclin A, thus up-regulating activity of cyclin A-associated cyclin-dependent kinase 2 (CDK2), and causing massive programmed cell death of starved BM2cJUN cells. Specific inhibition of CDK2 suppresses frequency of apoptosis of BM2cJUN cells. We conclude that up-regulation of cyclin A expression and CDK2more » activity can represent important link between the c-Jun protein, cell cycle machinery, and programmed cell death pathway in leukemic cells.« less

Mitochondrial AtTrxo1 is transcriptionally regulated by AtbZIP9 and AtAZF2 and affects seed germination under saline conditions

PubMed Central

Ortiz-Espín, Ana; Iglesias-Fernández, Raquel; Calderón, Aingeru; Carbonero, Pilar; Sevilla, Francisca

2017-01-01

Abstract Mitochondrial thioredoxin-o (AtTrxo1) was characterized and its expression examined in different organs of Arabidopsis thaliana. AtTrxo1 transcript levels were particularly high in dry seeds and cotyledons where they reached a maximum 36 h after imbibition with water, coinciding with 50% germination. Expression was lower in seeds germinating in 100 mM NaCl. To gain insight into the transcriptional regulation of the AtTrxo1 gene, a phylogenomic analysis was coupled with the screening of an arrayed library of Arabidopsis transcription factors in yeast. The basic leucine zipper AtbZIP9 and the zinc finger protein AZF2 were identified as putative transcriptional regulators. Transcript regulation of AtbZIP9 and AtAFZ2 during germination was compatible with the proposed role in transcriptional regulation of AtTrxo1. Transient over-expression of AtbZIP9 and AtAZF2 in Nicotiana benthamiana leaves demonstrated an activation effect of AtbZIP9 and a repressor effect of AtAZF2 on AtTrxo1 promoter-driven reporter expression. Although moderate concentrations of salt delayed germination in Arabidopsis wild-type seeds, those of two different AtTrxo1 knock-out mutants germinated faster and accumulated higher H2O2 levels than the wild-type. All these data indicate that AtTrxo1 has a role in redox homeostasis during seed germination under salt conditions. PMID:28184497

Differential regulation of HIF-1α and HIF-2α in neuroblastoma: Estrogen-related receptor alpha (ERRα) regulates HIF2A transcription and correlates to poor outcome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamidian, Arash; Stedingk, Kristoffer von; Munksgaard Thorén, Matilda

2015-06-05

Hypoxia-inducible factors (HIFs) are differentially regulated in tumor cells. While the current paradigm supports post-translational regulation of the HIF-α subunits, we recently showed that hypoxic HIF-2α is also transcriptionally regulated via insulin-like growth factor (IGF)-II in the childhood tumor neuroblastoma. Here, we demonstrate that transcriptional regulation of HIF-2α seems to be restricted to neural cell-derived tumors, while HIF-1α is canonically regulated at the post-translational level uniformly across different tumor forms. Enhanced expression of HIF2A mRNA at hypoxia is due to de novo transcription rather than increased mRNA stability, and chemical stabilization of the HIF-α proteins at oxygen-rich conditions unexpectedly leadsmore » to increased HIF2A transcription. The enhanced HIF2A levels do not seem to be dependent on active HIF-1. Using a transcriptome array approach, we identified members of the Peroxisome proliferator-activated receptor gamma coactivator (PGC)/Estrogen-related receptor (ERR) complex families as potential regulators of HIF2A. Knockdown or inhibition of one of the members, ERRα, leads to decreased expression of HIF2A, and high expression of the ERRα gene ESRRA correlates with poor overall and progression-free survival in a clinical neuroblastoma material consisting of 88 tumors. Thus, targeting of ERRα and pathways regulating transcriptional HIF-2α are promising therapeutic avenues in neuroblastoma. - Highlights: • Transcriptional control of HIF-2α is restricted to neural cell-derived tumors. • Enhanced transcription of HIF2A is not due to increased mRNA stability. • Chemical stabilization of the HIF-α subunits leads to increased HIF2A transcription. • ERRα regulates HIF2A mRNA expression in neuroblastoma. • High expression of ESRRA correlates to poor outcome in neuroblastoma.« less

Comparative Monomethylarginine Proteomics Suggests that Protein Arginine Methyltransferase 1 (PRMT1) is a Significant Contributor to Arginine Monomethylation in Toxoplasma gondii

PubMed Central

Yakubu, Rama R.; Silmon de Monerri, Natalie C.; Nieves, Edward; Kim, Kami; Weiss, Louis M.

2017-01-01

Arginine methylation is a common posttranslational modification found on nuclear and cytoplasmic proteins that has roles in transcriptional regulation, RNA metabolism and DNA repair. The protozoan parasite Toxoplasma gondii has a complex life cycle requiring transcriptional plasticity and has unique transcriptional regulatory pathways. Arginine methylation may play an important part in transcriptional regulation and splicing biology in this organism. The T. gondii genome contains five putative protein arginine methyltransferases (PRMTs), of which PRMT1 is important for cell division and growth. In order to better understand the function(s) of the posttranslational modification monomethyl arginine (MMA) in T. gondii, we performed a proteomic analysis of MMA proteins using affinity purification employing anti-MMA specific antibodies followed by mass spectrometry. The arginine monomethylome of T. gondii contains a large number of RNA binding proteins and multiple ApiAP2 transcription factors, suggesting a role for arginine methylation in RNA biology and transcriptional regulation. Surprisingly, 90% of proteins that are arginine monomethylated were detected as being phosphorylated in a previous phosphoproteomics study which raises the possibility of interplay between MMA and phosphorylation in this organism. Supporting this, a number of kinases are also arginine methylated. Because PRMT1 is thought to be a major PRMT in T. gondii, an organism which lacks a MMA-specific PRMT, we applied comparative proteomics to understand how PRMT1 might contribute to the MMA proteome in T. gondii. We identified numerous putative PRMT1 substrates, which include RNA binding proteins, transcriptional regulators (e.g. AP2 transcription factors), and kinases. Together, these data highlight the importance of MMA and PRMT1 in arginine methylation in T. gondii, as a potential regulator of a large number of processes including RNA biology and transcription. PMID:28143887

Transcriptional regulation by FOXP1, FOXP2, and FOXP4 dimerization.

PubMed

Sin, Cora; Li, Hongyan; Crawford, Dorota A

2015-02-01

FOXP1, FOXP2, and FOXP4 are three members of the FOXP gene subfamily of transcription factors involved in the development of the central nervous system. Previous studies have shown that the transcriptional activity of FOXP1/2/4 is regulated by homo- and heterodimerization. However, their transcriptional gene targets in the developing brain are still largely unknown. FOXP2 regulates the expression of many genes important in embryonic development, including WNT and Notch signaling pathways. In this study, we investigate whether dimerization of FOXP1/2/4 leads to differential expression of ten known FOXP2 target genes (CER1, SFRP4, WISP2, PRICKLE1, NCOR2, SNW1, NEUROD2, PAX3, EFNB3, and SLIT1). FOXP1/2/4 open-reading frames were stably transfected into HEK293 cells, and the expression level of these FOXP2 target genes was quantified using real-time polymerase chain reaction. Our results revealed that the specific combination of FOXP1/2/4 dimers regulates transcription of various FOXP2 target genes involved in early neuronal development.

Mga2 Transcription Factor Regulates an Oxygen-responsive Lipid Homeostasis Pathway in Fission Yeast*

PubMed Central

Burr, Risa; Stewart, Emerson V.; Shao, Wei; Zhao, Shan; Hannibal-Bach, Hans Kristian; Ejsing, Christer S.; Espenshade, Peter J.

2016-01-01

Eukaryotic lipid synthesis is oxygen-dependent with cholesterol synthesis requiring 11 oxygen molecules and fatty acid desaturation requiring 1 oxygen molecule per double bond. Accordingly, organisms evaluate oxygen availability to control lipid homeostasis. The sterol regulatory element-binding protein (SREBP) transcription factors regulate lipid homeostasis. In mammals, SREBP-2 controls cholesterol biosynthesis, whereas SREBP-1 controls triacylglycerol and glycerophospholipid biosynthesis. In the fission yeast Schizosaccharomyces pombe, the SREBP-2 homolog Sre1 regulates sterol homeostasis in response to changing sterol and oxygen levels. However, notably missing is an SREBP-1 analog that regulates triacylglycerol and glycerophospholipid homeostasis in response to low oxygen. Consistent with this, studies have shown that the Sre1 transcription factor regulates only a fraction of all genes up-regulated under low oxygen. To identify new regulators of low oxygen adaptation, we screened the S. pombe nonessential haploid deletion collection and identified 27 gene deletions sensitive to both low oxygen and cobalt chloride, a hypoxia mimetic. One of these genes, mga2, is a putative transcriptional activator. In the absence of mga2, fission yeast exhibited growth defects under both normoxia and low oxygen conditions. Mga2 transcriptional targets were enriched for lipid metabolism genes, and mga2Δ cells showed disrupted triacylglycerol and glycerophospholipid homeostasis, most notably with an increase in fatty acid saturation. Indeed, addition of exogenous oleic acid to mga2Δ cells rescued the observed growth defects. Together, these results establish Mga2 as a transcriptional regulator of triacylglycerol and glycerophospholipid homeostasis in S. pombe, analogous to mammalian SREBP-1. PMID:27053105

Overexpression of a DENND1A isoform produces a polycystic ovary syndrome theca phenotype

PubMed Central

McAllister, Jan M.; Modi, Bhavi; Miller, Bruce A.; Biegler, Jessica; Bruggeman, Richard; Legro, Richard S.; Strauss, Jerome F.

2014-01-01

Polycystic ovary syndrome (PCOS), characterized by increased ovarian androgen biosynthesis, anovulation, and infertility, affects 5–7% of reproductive-age women. Genome-wide association studies identified PCOS candidate loci that were replicated in subsequent reports, including DENND1A, which encodes a protein associated with clathrin-coated pits where cell-surface receptors reside. However, these studies provided no information about functional roles for DENND1A in the pathogenesis of PCOS. DENND1A protein was located in the cytoplasm as well as nuclei of theca cells, suggesting a possible role in gene regulation. DENND1A immunostaining was more intense in the theca of PCOS ovaries. Using theca cells isolated and propagated from normal cycling and PCOS women, we found that DENND1A variant 2 (DENND1A.V2) protein and mRNA levels are increased in PCOS theca cells. Exosomal DENND1A.V2 RNA was significantly elevated in urine from PCOS women compared with normal cycling women. Forced overexpression of DENND1A.V2 in normal theca cells resulted in a PCOS phenotype of augmented CYP17A1 and CYP11A1 gene transcription, mRNA abundance, and androgen biosynthesis. Knock-down of DENND1A.V2 in PCOS theca cells reduced androgen biosynthesis and CYP17A1 and CYP11A1 gene transcription. An IgG specific to DENND1A.V2 also reduced androgen biosynthesis and CYP17 and CYP11A1 mRNA when added to the medium of cultured PCOS theca cells. We conclude that the PCOS candidate gene, DENND1A, plays a key role in the hyperandrogenemia associated with PCOS. These observations have both diagnostic and therapeutic implications for this common disorder. PMID:24706793

Transcriptional analysis reveals the critical role of RNA polymerase-binding transcription factor, DksA, in regulating multi-drug resistance of Escherichia coli.

PubMed

Wang, Jiawei; Cao, Li; Yang, Xiaowen; Wu, Qingmin; Lu, Lin; Wang, Zhen

2018-05-07

The objective of this study was to comprehensively identify the target genes regulated by the RNA polymerase-binding transcription factor DksA in Escherichia coli, and to clarify the role of DksA in multi-drug resistance. A clinical E. coli strain, E8, was selected to construct the dksA gene deletion mutant by using the Red recombination system. The minimum inhibitory concentrations (MICs) of 12 antibiotics in the E8ΔdksA (mutant) were markedly lower than those in the wild-type strain, E8. Genes differentially expressed in the wild-type and dksA mutant were detected using RNA-Seq and were validated by performing quantitative real-time PCR (qRT-PCR). In total, 168 differentially expressed genes were identified in E8ΔdksA, including 81 up-regulated and 87 down-regulated genes. Many of the genes identified are involved in metabolism, two-component systems, transcriptional regulators, and transport/membrane proteins. Interestingly, genes encoding the transcriptional regulator, MarR, which is known to repress the multiple drug resistance operon, marRAB; MdfA, a transport protein that exhibits multidrug efflux activities; oligopeptide transport system proteins OppA and OppD were among those differentially expressed, and could potentially contribute to the increased drug susceptibility of E8ΔdksA. In conclusion, DksA plays an important role in the multi-drug resistance of this E. coli strain, and directly or indirectly regulates the expression of several genes related to antibiotic resistance. Copyright © 2018. Published by Elsevier B.V.

Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells

PubMed Central

Li, LiQi; Jothi, Raja; Cui, Kairong; Lee, Jan Y; Cohen, Tsadok; Gorivodsky, Marat; Tzchori, Itai; Zhao, Yangu; Hayes, Sandra M; Bresnick, Emery H; Zhao, Keji; Westphal, Heiner; Love, Paul E

2013-01-01

The nuclear adaptor Ldb1 functions as a core component of multiprotein transcription complexes that regulate differentiation in diverse cell types. In the hematopoietic lineage, Ldb1 forms a complex with the non–DNA-binding adaptor Lmo2 and the transcription factors E2A, Scl and GATA-1 (or GATA-2). Here we demonstrate a critical and continuous requirement for Ldb1 in the maintenance of both fetal and adult mouse hematopoietic stem cells (HSCs). Deletion of Ldb1 in hematopoietic progenitors resulted in the downregulation of many transcripts required for HSC maintenance. Genome-wide profiling by chromatin immunoprecipitation followed by sequencing (ChIP-Seq) identified Ldb1 complex–binding sites at highly conserved regions in the promoters of genes involved in HSC maintenance. Our results identify a central role for Ldb1 in regulating the transcriptional program responsible for the maintenance of HSCs. PMID:21186366

Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells.

PubMed

Li, LiQi; Jothi, Raja; Cui, Kairong; Lee, Jan Y; Cohen, Tsadok; Gorivodsky, Marat; Tzchori, Itai; Zhao, Yangu; Hayes, Sandra M; Bresnick, Emery H; Zhao, Keji; Westphal, Heiner; Love, Paul E

2011-02-01

The nuclear adaptor Ldb1 functions as a core component of multiprotein transcription complexes that regulate differentiation in diverse cell types. In the hematopoietic lineage, Ldb1 forms a complex with the non-DNA-binding adaptor Lmo2 and the transcription factors E2A, Scl and GATA-1 (or GATA-2). Here we demonstrate a critical and continuous requirement for Ldb1 in the maintenance of both fetal and adult mouse hematopoietic stem cells (HSCs). Deletion of Ldb1 in hematopoietic progenitors resulted in the downregulation of many transcripts required for HSC maintenance. Genome-wide profiling by chromatin immunoprecipitation followed by sequencing (ChIP-Seq) identified Ldb1 complex-binding sites at highly conserved regions in the promoters of genes involved in HSC maintenance. Our results identify a central role for Ldb1 in regulating the transcriptional program responsible for the maintenance of HSCs.

Soft sediment deformation structures in a lacustrine sedimentary succession induced by volcano-tectonic activities: An example from the Cretaceous Beolgeumri Formation, Wido Volcanics, Korea

NASA Astrophysics Data System (ADS)

Ko, Kyoungtae; Kim, Sung Won; Lee, Hong-Jin; Hwang, In Gul; Kim, Bok Chul; Kee, Won-Seo; Kim, Young-Seog; Gihm, Yong Sik

2017-08-01

The Cretaceous Beolgeumri Formation is composed of laminated mudstones intercalated with sandstones, chert, and a bed of lapilli tuff that were deposited in a lacustrine environment at the terminal part of a regional strike-slip fault systems on the southwestern Korean Peninsula. The Beolgeumri Formation contains various types of soft sediment deformation (SSD) structures that are characterized by a wide extent (< 4 km), lateral continuity (< 200 m), and vertical repetition. The SSD structures can be classified into six categories based on their morphological features and deformation styles: 1) fold structures, 2) load structures, 3) water-escape structures, 4) rip-down structures, 5) boudin structures, and 6) synsedimentary fault structures. Field examination of SSD structures together with an analysis of the sedimentological records of the Beolgeumri Formation indicate that the SSD structures formed largely by liquefaction and/or fluidization triggered by ground shaking during earthquakes. To constrain the timing of the development of SSD structures in the Beolgeumri Formation, we conducted sensitive high-resolution ion microprobe (SHRIMP) U-Pb zircon age dating of block sized lithic clasts bearing volcaniclastic deposits that conformably underlie (the Mangryeongbong Tuff) and overlie (the Ttandallae Tuff) the Beolgeumri Formation. The Mangryeongbong and Ttandallae Tuffs have ages of 86.63 ± 0.83 Ma and 87.24 ± 0.36 Ma, respectively, indicating that the Beolgeumri Formation was deposited during a short interval between major volcanic eruptions. The large lithic clasts of volcaniclastic deposits suggest that the Beolgeumri Formation was deposited adjacent to an active volcanic edifice(s). Syndepositional magmatic activities are suggested by the occurrence of a lapilli tuff bed in the Beolgeumri Formation and an igneous intrusion (intermediate sill) that is crosscut by a sand dike, as well as the similar age results of the underlying and overlying volcaniclastic deposits. Thus, we infer that the earthquakes that caused the development of SSD structures in the study area were closely related to syndepositional magmatic activities, as is the case for modern tectonic earthquakes around active volcanoes.

Regulation of MDM2 Activity by Nucleolin

DTIC Science & Technology

2006-06-01

UbcH5), p53 (1 ml produced in a wheat germ transcription-coupled in vitro translation system (Pro- mega)), GST-Mdm2 (400 ng) and 10 mg ubiquitin (Sigma... Acids Res. 28, 446 (2000). 22. V. Sirri, P. Roussel, M. C. Gendron, D. Hernandez-Verdun, Cytometry 28, 147 (1997). 23. J. Bartkova et al., Nature...DO-1). Immunoprecipitation and GST-pulldown Transfected cells were lysed in 20mM N-2-hydroxyethylpiper- azine-N0-2-ethanesulfonic acid , pH 7.4, 100mM

Investigation of facial emotion recognition, alexithymia, and levels of anxiety and depression in patients with somatic symptoms and related disorders

PubMed Central

Öztürk, Ahmet; Kiliç, Alperen; Deveci, Erdem; Kirpinar, İsmet

2016-01-01

Background The concept of facial emotion recognition is well established in various neuropsychiatric disorders. Although emotional disturbances are strongly associated with somatoform disorders, there are a restricted number of studies that have investigated facial emotion recognition in somatoform disorders. Furthermore, there have been no studies that have regarded this issue using the new diagnostic criteria for somatoform disorders as somatic symptoms and related disorders (SSD). In this study, we aimed to compare the factors of facial emotion recognition between patients with SSD and age- and sex-matched healthy controls (HC) and to retest and investigate the factors of facial emotion recognition using the new criteria for SSD. Patients and methods After applying the inclusion and exclusion criteria, 54 patients who were diagnosed with SSD according to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) criteria and 46 age- and sex-matched HC were selected to participate in the present study. Facial emotion recognition, alexithymia, and the status of anxiety and depression were compared between the groups. Results Patients with SSD had significantly decreased scores of facial emotion for fear faces, disgust faces, and neutral faces compared with age- and sex-matched HC (t=−2.88, P=0.005; t=−2.86, P=0.005; and t=−2.56, P=0.009, respectively). After eliminating the effects of alexithymia and depressive and anxious states, the groups were found to be similar in terms of their responses to facial emotion and mean reaction time to facial emotions. Discussion Although there have been limited numbers of studies that have examined the recognition of facial emotion in patients with somatoform disorders, our study is the first to investigate facial recognition in patients with SSD diagnosed according to the DSM-5 criteria. Recognition of facial emotion was found to be disturbed in patients with SSD. However, our findings suggest that disturbances in facial recognition were significantly associated with alexithymia and the status of depression and anxiety, which is consistent with the previous studies. Further studies are needed to highlight the associations between facial emotion recognition and SSD. PMID:27199559

SomethiNG 2 talk about-Transcriptional regulation in embryonic and adult oligodendrocyte precursors.

PubMed

Küspert, Melanie; Wegner, Michael

2016-05-01

Glial cells that express the chondroitin sulfate proteoglycan NG2 represent an inherently heterogeneous population. These so-called NG2-glia are present during development and in the adult CNS, where they are referred to as embryonic oligodendrocyte precursors and adult NG2-glia, respectively. They give rise to myelinating oligodendrocytes at all times of life. Over the years much has been learnt about the transcriptional network in embryonic oligodendrocyte precursors, and several transcription factors from the HLH, HMG-domain, zinc finger and homeodomain protein families have been identified as main constituents. Much less is known about the corresponding network in adult NG2-glia. Here we summarize and discuss current knowledge on functions of each of these transcription factor families in NG2-glia, and where possible compare transcriptional regulation in embryonic oligodendrocyte precursors and adult NG2-glia. This article is part of a Special Issue entitled SI:NG2-glia (Invited only). Copyright © 2015 Elsevier B.V. All rights reserved.

TCPs, WUSs, and WINDs: families of transcription factors that regulate shoot meristem formation, stem cell maintenance, and somatic cell differentiation.

PubMed

Ikeda, Miho; Ohme-Takagi, Masaru

2014-01-01

In contrast to somatic mammalian cells, which cannot alter their fate, plant cells can dedifferentiate to form totipotent callus cells and regenerate a whole plant, following treatment with specific phytohormones. However, the regulatory mechanisms and key factors that control differentiation-dedifferentiation and cell totipotency have not been completely clarified in plants. Recently, several plant transcription factors that regulate meristem formation and dedifferentiation have been identified and include members of the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP), WUSCHEL (WUS), and WOUND INDUCED DEDIFFERENTIATION (WIND1) families. WUS and WIND positively control plant cell totipotency, while TCP negatively controls it. Interestingly, TCP is a transcriptional activator that acts as a negative regulator of shoot meristem formation, and WUS is a transcriptional repressor that positively maintains totipotency of the stem cells of the shoot meristem. We describe here the functions of TCP, WUS, and WIND transcription factors in the regulation of differentiation-dedifferentiation by positive and negative transcriptional regulators.

Zinc Finger-Containing Cellular Transcription Corepressor ZBTB25 Promotes Influenza Virus RNA Transcription and Is a Target for Zinc Ejector Drugs.

PubMed

Chen, Shu-Chuan; Jeng, King-Song; Lai, Michael M C

2017-10-15

Influenza A virus (IAV) replication relies on an intricate interaction between virus and host cells. How the cellular proteins are usurped for IAV replication remains largely obscure. The aim of this study was to search for novel and potential cellular factors that participate in IAV replication. ZBTB25, a transcription repressor of a variety of cellular genes, was identified by an RNA interference (RNAi) genomic library screen. Depletion of ZBTB25 significantly reduced IAV production. Conversely, overexpression of ZBTB25 enhanced it. ZBTB25 interacted with the viral RNA-dependent RNA polymerase (RdRp) protein and modulated its transcription activity. In addition, ZBTB25 also functioned as a viral RNA (vRNA)-binding protein, binding preferentially to the U-rich sequence within the 5' untranslated region (UTR) of vRNA. Both protein-protein and protein-RNA interactions involving ZBTB25 facilitated viral RNA transcription and replication. In addition, ZBTB25 suppressed interferon production, further enhancing viral replication. ZBTB25-associated functions required an intact zinc finger domain and posttranslational SUMO-1 modification of ZBTB25. Furthermore, treatment with disulfiram (a zinc ejector) of ZBTB25-overexpressing cells showed significantly reduced IAV production as a result of reduced RNA synthesis. Our findings indicate that IAV usurps ZBTB25 for IAV RNA synthesis and serves as a novel and potential therapeutic antiviral target. IMPORTANCE IAV-induced seasonal influenza causes severe illness and death in high-risk populations. However, IAV has developed resistance to current antiviral drugs due to its high mutation rate. Therefore, development of drugs targeting cellular factors required for IAV replication is an attractive alternative for IAV therapy. Here, we discovered a cellular protein, ZBTB25, that enhances viral RdRp activity by binding to both viral RdRp and viral RNA to stimulate viral RNA synthesis. A unique feature of ZBTB25 in the regulation of viral replication is its dual transcription functions, namely, promoting viral RNA transcription through binding to the U-rich region of vRNA and suppressing cellular interferon production. ZBTB25 contains a zinc finger domain that is required for RNA-inhibitory activity by chelating zinc ions. Disulfiram treatment disrupts the zinc finger functions, effectively repressing IAV replication. Based on our findings, we demonstrate that ZBTB25 regulates IAV RNA transcription and replication and serves as a promising antiviral target for IAV treatment. Copyright © 2017 American Society for Microbiology.

Zinc Finger-Containing Cellular Transcription Corepressor ZBTB25 Promotes Influenza Virus RNA Transcription and Is a Target for Zinc Ejector Drugs

PubMed Central

Chen, Shu-Chuan; Jeng, King-Song

2017-01-01

ABSTRACT Influenza A virus (IAV) replication relies on an intricate interaction between virus and host cells. How the cellular proteins are usurped for IAV replication remains largely obscure. The aim of this study was to search for novel and potential cellular factors that participate in IAV replication. ZBTB25, a transcription repressor of a variety of cellular genes, was identified by an RNA interference (RNAi) genomic library screen. Depletion of ZBTB25 significantly reduced IAV production. Conversely, overexpression of ZBTB25 enhanced it. ZBTB25 interacted with the viral RNA-dependent RNA polymerase (RdRp) protein and modulated its transcription activity. In addition, ZBTB25 also functioned as a viral RNA (vRNA)-binding protein, binding preferentially to the U-rich sequence within the 5′ untranslated region (UTR) of vRNA. Both protein-protein and protein-RNA interactions involving ZBTB25 facilitated viral RNA transcription and replication. In addition, ZBTB25 suppressed interferon production, further enhancing viral replication. ZBTB25-associated functions required an intact zinc finger domain and posttranslational SUMO-1 modification of ZBTB25. Furthermore, treatment with disulfiram (a zinc ejector) of ZBTB25-overexpressing cells showed significantly reduced IAV production as a result of reduced RNA synthesis. Our findings indicate that IAV usurps ZBTB25 for IAV RNA synthesis and serves as a novel and potential therapeutic antiviral target. IMPORTANCE IAV-induced seasonal influenza causes severe illness and death in high-risk populations. However, IAV has developed resistance to current antiviral drugs due to its high mutation rate. Therefore, development of drugs targeting cellular factors required for IAV replication is an attractive alternative for IAV therapy. Here, we discovered a cellular protein, ZBTB25, that enhances viral RdRp activity by binding to both viral RdRp and viral RNA to stimulate viral RNA synthesis. A unique feature of ZBTB25 in the regulation of viral replication is its dual transcription functions, namely, promoting viral RNA transcription through binding to the U-rich region of vRNA and suppressing cellular interferon production. ZBTB25 contains a zinc finger domain that is required for RNA-inhibitory activity by chelating zinc ions. Disulfiram treatment disrupts the zinc finger functions, effectively repressing IAV replication. Based on our findings, we demonstrate that ZBTB25 regulates IAV RNA transcription and replication and serves as a promising antiviral target for IAV treatment. PMID:28768860

Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis.

PubMed

Norton, Gareth J; Lou-Hing, Daniel E; Meharg, Andrew A; Price, Adam H

2008-01-01

Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

Rice–arsenate interactions in hydroponics: whole genome transcriptional analysis

PubMed Central

Norton, Gareth J.; Lou-Hing, Daniel E.; Meharg, Andrew A.; Price, Adam H.

2008-01-01

Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 μM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the Bala×Azucena mapping population. PMID:18453530

DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts

PubMed Central

Paraskevopoulou, Maria D.; Vlachos, Ioannis S.; Karagkouni, Dimitra; Georgakilas, Georgios; Kanellos, Ilias; Vergoulis, Thanasis; Zagganas, Konstantinos; Tsanakas, Panayiotis; Floros, Evangelos; Dalamagas, Theodore; Hatzigeorgiou, Artemis G.

2016-01-01

microRNAs (miRNAs) are short non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of coding gene expression. Long non-coding RNAs (lncRNAs) have been recently reported to interact with miRNAs. The sponge-like function of lncRNAs introduces an extra layer of complexity in the miRNA interactome. DIANA-LncBase v1 provided a database of experimentally supported and in silico predicted miRNA Recognition Elements (MREs) on lncRNAs. The second version of LncBase (www.microrna.gr/LncBase) presents an extensive collection of miRNA:lncRNA interactions. The significantly enhanced database includes more than 70 000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. The new experimental module presents a 14-fold increase compared to the previous release. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm. The relevant module provides millions of predicted miRNA binding sites, accompanied with detailed metadata and MRE conservation metrics. LncBase v2 caters information regarding cell type specific miRNA:lncRNA regulation and enables users to easily identify interactions in 66 different cell types, spanning 36 tissues for human and mouse. Database entries are also supported by accurate lncRNA expression information, derived from the analysis of more than 6 billion RNA-Seq reads. PMID:26612864

Regulation of pokemon 1 activity by sumoylation.

PubMed

Roh, Hee-Eun; Lee, Min-Nyung; Jeon, Bu-Nam; Choi, Won-Il; Kim, Yoo-Jin; Yu, Mi-Young; Hur, Man-Wook

2007-01-01

Pokemon 1 is a proto-oncogenic transcriptional regulator that contains a POZ domain at the N-terminus and four Kruppel-like zinc fingers at the C-terminus. Pokemon 1 plays an important role in adipogenesis, osteogenesis, oncogenesis, and transcription of NF-kB responsive genes. Recent reports have shown that biological activities of transcription factors are regulated by sumolylation. We investigated whether Pokemon 1 is post-translationally modified by sumoylation and whether the modification affects Pokemon 1's transcriptional properties. We found that Pokemon 1 is sumoylated in vitro and in vivo. Upon careful analysis of the amino acid sequence of Pokemon 1, we found ten potential sumoylation sites located at lysines 61, 354, 371, 379, 383, 396, 486, 487, 536 and 539. We mutated each of these amino acids into arginine and tested whether the mutation could affect the transcriptional properties of Pokemon 1 on the Pokemon 1 responsive genes, such as ADH5/FDH and pG5-FRE-Luc. Wild-type Pokemon 1 potently represses transcription of ADH5/FDH. Most of the mutants, however, were weaker transcription repressors and repressed transcription 1.3-3.3 fold less effective. Although potential sumoylation sites were located close to the DNA binding domain or the nuclear localization sequence, the mutations did not alter nuclear localization or DNA binding activity. In addition, on the pG5-FRE-Luc test promoter construct, ectopic SUMO-1 repressed transcription in the presence of Pokemon 1. The sumoylation target lysine residue at amino acid 61, which is located in the middle of the POZ-domain, is important because K61R mutation resulted in a much weaker molecular interaction with corepressors. Our data suggest that Pokemon 1's activity as a transcription factor may involve sumoylation, and that sumoylation might be important in the regulation of transcription by Pokemon 1.

Bipartite functions of the CREB co-activators selectively direct alternative splicing or transcriptional activation

PubMed Central

Amelio, Antonio L; Caputi, Massimo; Conkright, Michael D

2009-01-01

The CREB regulated transcription co-activators (CRTCs) regulate many biological processes by integrating and converting environmental inputs into transcriptional responses. Although the mechanisms by which CRTCs sense cellular signals are characterized, little is known regarding how CRTCs contribute to the regulation of cAMP inducible genes. Here we show that these dynamic regulators, unlike other co-activators, independently direct either pre-mRNA splice-site selection or transcriptional activation depending on the cell type or promoter context. Moreover, in other scenarios, the CRTC co-activators coordinately regulate transcription and splicing. Mutational analyses showed that CRTCs possess distinct functional domains responsible for regulating either pre-mRNA splicing or transcriptional activation. Interestingly, the CRTC1–MAML2 oncoprotein lacks the splicing domain and is incapable of altering splice-site selection despite robustly activating transcription. The differential usage of these distinct domains allows CRTCs to selectively mediate multiple facets of gene regulation, indicating that co-activators are not solely restricted to coordinating alternative splicing with increase in transcriptional activity. PMID:19644446

Development and Performance of a Suprathermal Electron Spectrometer to Study Auroral Precipitations

NASA Technical Reports Server (NTRS)

Ogasawara, Keiichi; Grubbs, Guy, II; Michell, Robert G.; Samara, Maria; Stange, Jason L.; Trevino, John A.; Webster, James; Jahn, Jorg-Micha

2016-01-01

The design, development, and performance of Medium-energy Electron SPectrometer (MESP), dedicated to the in situ observation of suprathermal electrons in the auroral ionosphere, are summarized in this paper. MESP employs a permanent magnet filter with a light tight structure to select electrons with proper energies guided to the detectors. A combination of two avalanche photodiodes and a large area solid-state detector (SSD) provided 46 total energy bins (1 keV resolution for 3-20 keV range for APDs, and 7 keV resolution for greater than 20 keV range for SSDs). Multi-channel ultra-low power application-specific integrated circuits are also verified for the flight operation to read-out and analyze the detector signals. MESP was launched from Poker F1at Research Range on 3 March 2014 as a part of ground-to-rocket electrodynamics-electrons correlative experiment (GREECE) mission. MESP successfully measured the precipitating electrons from 3 to 120 keV in 120-ms time resolution and characterized the features of suprathermal distributions associated with auroral arcs throughout the flight. The measured electrons were showing the inverted-V type spectra, consistent with the past measurements. In addition, investigations of the suprathermal electron population indicated the existence of the energetic non-thermal distribution corresponding to the brightest aurora.

Bifidobacterium breve - HT-29 cell line interaction: modulation of TNF-α induced gene expression.

PubMed

Boesten, R J; Schuren, F H J; Willemsen, L E M; Vriesema, A; Knol, J; De Vos, W M

2011-06-01

To provide insight in the molecular basis for intestinal host-microbe interactions, we determined the genome-wide transcriptional response of human intestinal epithelial cells following exposure to cells of Bifidobacterium breve. To select an appropriate test system reflecting inflammatory conditions, the responsiveness to TNF-α was compared in T84, Caco-2 and HT-29 cells. The highest TNF-α response was observed in HT-29 cells and this cell line was selected for exposure to the B. breve strains M-16V, NR246 and UCC2003. After one hour of bacterial pre-incubation followed by two hours of additional TNF-α stimulation, B. breve M-16V (86%), but to a much lesser extent strains NR246 (50%) or UCC2003 (32%), showed a strain-specific reduction of the HT-29 transcriptional response to the inflammatory treatment. The most important functional groups of genes that were transcriptionally suppressed by the presence of B. breve M-16V, were found to be involved in immune regulation and apoptotic processes. About 54% of the TNF-α induced genes were solely suppressed by the presence of B. breve M-16V. These included apoptosis-related cysteine protease caspase 7 (CASP7), interferon regulatory factor 3 (IRF3), amyloid beta (A4) precursor proteinbinding family A member 1 (APBA1), NADPH oxidase (NOX5), and leukemia inhibitory factor receptor (LIFR). The extracellular IL-8 concentration was determined by an immunological assay but did not change significantly, indicating that B. breve M-16V only partially modulates the TNF-α pathway. In conclusion, this study shows that B. breve strains modulate gene expression in HT-29 cells under inflammatory conditions in a strain-specific way.

Translational Upregulation of an Individual p21Cip1 Transcript Variant by GCN2 Regulates Cell Proliferation and Survival under Nutrient Stress

PubMed Central

Lehman, Stacey L.; Cerniglia, George J.; Johannes, Gregg J.; Ye, Jiangbin; Ryeom, Sandra; Koumenis, Constantinos

2015-01-01

Multiple transcripts encode for the cell cycle inhibitor p21Cip1. These transcripts produce identical proteins but differ in their 5’ untranslated regions (UTRs). Although several stresses that induce p21 have been characterized, the mechanisms regulating the individual transcript variants and their functional significance are unknown. Here we demonstrate through 35S labeling, luciferase reporter assays, and polysome transcript profiling that activation of the Integrated Stress Response (ISR) kinase GCN2 selectively upregulates the translation of a p21 transcript variant containing 5’ upstream open reading frames (uORFs) through phosphorylation of the eukaryotic translation initiation factor eIF2α. Mutational analysis reveals that the uORFs suppress translation under basal conditions, but promote translation under stress. Functionally, ablation of p21 ameliorates G1/S arrest and reduces cell survival in response to GCN2 activation. These findings uncover a novel mechanism of p21 post-transcriptional regulation, offer functional significance for the existence of multiple p21 transcripts, and support a key role for GCN2 in regulating the cell cycle under stress. PMID:26102367

Deficit of heat shock transcription factor 1-heat shock 70 kDa protein 1A axis determines the cell death vulnerability in a model of spinocerebellar ataxia type 6.

PubMed

Li, Li; Saegusa, Hironao; Tanabe, Tsutomu

2009-11-01

Spinocerebellar ataxia type 6 (SCA6) is caused by a small expansion of polyglutamine (polyQ)-encoding CAG repeat in Ca(v)2.1 calcium channel gene. To gain insights into pathogenic mechanism of SCA6, we used HEK293 cells expressing fusion protein of enhanced green fluorescent protein and Ca(v)2.1 carboxyl terminal fragment (EGFP-Ca(v)2.1CT) [L24 and S13 cells containing 24 polyQ (disease range) and 13 polyQ (normal range), respectively] and examined their responses to some stressors. When exposed to CdCl(2), L24 cells showed lower viability than the control S13 cells and caspase-dependent apoptosis was enhanced more in L24 cells. Localization of EGFP-Ca(v)2.1CT was almost confined to the nucleus, where it existed as speckle-like structures. Interestingly, CdCl(2) treatment resulted in disruption of more promyelocytic leukemia nuclear bodies (PML-NBs) in L24 cells than in S13 cells and in cells where PML-NBs were disrupted, aggregates of EGFP-Ca(v)2.1CT became larger. Furthermore, a large number of aggregates were formed in L24 cells than in S13 cells. Results of RNAi experiments indicated that HSPA1A determined the difference against CdCl(2) toxicity. Furthermore, protein expression of heat shock transcription factor 1 (HSF1), which activates HSPA1A expression, was down-regulated in L24 cells. Therefore, HSF1-HSPA1A axis is critical for the vulnerability in L24 cells.

Heme oxygenase up-regulation under ultraviolet-B radiation is not epigenetically restricted and involves specific stress-related transcriptions factors.

PubMed

Santa-Cruz, Diego; Pacienza, Natalia; Zilli, Carla; Pagano, Eduardo; Balestrasse, Karina; Yannarelli, Gustavo

2017-08-01

Heme oxygenase-1 (HO-1) plays a protective role against oxidative stress in plants. The mechanisms regulating its expression, however, remain unclear. Here we studied the methylation state of a GC rich HO-1 promoter region and the expression of several stress-related transcription factors (TFs) in soybean plants subjected to ultraviolet-B (UV-B) radiation. Genomic DNA and total RNA were isolated from leaves of plants irradiated with 7.5 and 15kJm-2 UV-B. A 304bp HO-1 promoter region was amplified by PCR from sodium bisulfite-treated DNA, cloned into pGEMT plasmid vector and evaluated by DNA sequencing. Bisulfite sequencing analysis showed similar HO-1 promoter methylation levels in control and UV-B-treated plants (C: 3.4±1.3%; 7.5: 2.6±0.5%; 15: 3.1±1.1%). Interestingly, HO-1 promoter was strongly unmethylated in control plants. Quantitative RT-PCR analysis of TFs showed that GmMYB177, GmMYBJ6, GmWRKY21, GmNAC11, GmNAC20 and GmGT2A but not GmWRK13 and GmDREB were induced by UV-B radiation. The expression of several TFs was also enhanced by hemin, a potent and specific HO inducer, inferring that they may mediate HO-1 up-regulation. These results suggest that soybean HO-1 gene expression is not epigenetically regulated. Moreover, the low level of HO-1 promoter methylation suggests that this antioxidant enzyme can rapidly respond to environmental stress. Finally, this study has identified some stress-related TFs involved in HO-1 up-regulation under UV-B radiation. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

MicroRNA-20a/b regulates cholesterol efflux through post-transcriptional repression of ATP-binding cassette transporter A1.

PubMed

Liang, Bin; Wang, Xin; Song, Xiaosu; Bai, Rui; Yang, Huiyu; Yang, Zhiming; Xiao, Chuanshi; Bian, Yunfei

2017-09-01

ATP-binding cassette transporter A1 (ABCA1) plays a crucial role in reverse cholesterol transport and exhibits anti-atherosclerosis effects. Some microRNAs (miRs) regulate ABCA1 expression, and recent studies have shown that miR-20a/b might play a critical role in atherosclerotic diseases. Here, we attempted to clarify the potential contribution of miR-20a/b in post-transcriptional regulation of ABCA1, cholesterol efflux, and atherosclerosis. We performed bioinformatics analysis and found that miR-20a/b was highly conserved and directly bound to ABCA1 mRNA with low binding free energy. Luciferase-reporter assay also confirmed that miR-20a/b significantly reduced luciferase activity associated with the ABCA1 3' untranslated region reporter construct. Additionally, miR-20a/b decreased ABCA1 expression, which, in turn, decreased cholesterol efflux and increased cholesterol content in THP-1 and RAW 264.7 macrophage-derived foam cells. In contrast, miR-20a/b inhibitors increased ABCA1 expression and cholesterol efflux, decreased cholesterol content, and inhibited foam-cell formation. Consistent with our in vitro results, miR-20a/b-treated ApoE -/- mice showed decreased ABCA1expression in the liver and reductions of reverse cholesterol transport in vivo. Furthermore, miR-20a/b regulated the formation of nascent high-density lipoprotein and promoted atherosclerotic development, whereas miR-20a/b knockdown attenuated atherosclerotic formation. miR-20 is a new miRNA capable of targeting ABCA1 and regulating ABCA1 expression. Therefore, miR-20 inhibition constitutes a new strategy for ABCA1-based treatment of atherosclerosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Transcriptional regulation of the cytosolic chaperonin theta subunit gene, Cctq, by Ets domain transcription factors Elk-1, Sap-1a, and Net in the absence of serum response factor.

PubMed

Yamazaki, Yuji; Kubota, Hiroshi; Nozaki, Masami; Nagata, Kazuhiro

2003-08-15

The chaperonin-containing t-complex polypeptide 1 (CCT) is a molecular chaperone that facilitates protein folding in eukaryotic cytosol, and the expression of CCT is highly dependent on cell growth. We show here that transcription of the gene encoding the theta subunit of mouse CCT, Cctq, is regulated by the ternary complex factors (TCFs), Elk-1, Sap-1a, and Net (Sap-2). Reporter gene assay using HeLa cells indicated that the Cctq gene promoter contains a cis-acting element of the CCGGAAGT sequence (CQE1) at -36 bp. The major CQE1-binding proteins in HeLa cell nuclear extract was recognized by anti-Elk-1 or anti-Sap-1a antibodies in electrophoretic mobility shift assay, and recombinant Elk-1, Sap-1a, or Net specifically recognized CQE1. The CQE1-dependent transcriptional activity in HeLa cells was virtually abolished by overexpression of the DNA binding domains of TCFs. Overexpression of full-length TCFs with Ras indicated that exogenous TCFs can regulate the CQE1-dependent transcription in a Ras-dependent manner. PD98059, an inhibitor of MAPK, significantly repressed the CQE1-dependent transcription. However, no serum response factor was detected by electrophoretic mobility shift assay using the CQE1 element. These results indicate that transcription of the Cctq gene is regulated by TCFs under the control of the Ras/MAPK pathway, probably independently of serum response factor.

The histone modifications governing TFF1 transcription mediated by estrogen receptor.

PubMed

Li, Yanyan; Sun, Luyang; Zhang, Yu; Wang, Dandan; Wang, Feng; Liang, Jing; Gui, Bin; Shang, Yongfeng

2011-04-22

Transcription regulation by histone modifications is a major contributing factor to the structural and functional diversity in biology. These modifications are encrypted as histone codes or histone languages and function to establish and maintain heritable epigenetic codes that define the identity and the fate of the cell. Despite recent advances revealing numerous histone modifications associated with transcription regulation, how such modifications dictate the process of transcription is not fully understood. Here we describe spatial and temporal analyses of the histone modifications that are introduced during estrogen receptor α (ERα)-activated transcription. We demonstrated that aborting RNA polymerase II caused a disruption of the histone modifications that are associated with transcription elongation but had a minimal effect on modifications deposited during transcription initiation. We also found that the histone H3S10 phosphorylation mark is catalyzed by mitogen- and stress-activated protein kinase 1 (MSK1) and is recognized by a 14-3-3ζ/14-3-3ε heterodimer through its interaction with H3K4 trimethyltransferase SMYD3 and the p52 subunit of TFIIH. We showed that H3S10 phosphorylation is a prerequisite for H3K4 trimethylation. In addition, we demonstrated that SET8/PR-Set7/KMT5A is required for ERα-regulated transcription and its catalyzed H4K20 monomethylation is implicated in both transcription initiation and elongation. Our experiments provide a relatively comprehensive analysis of histone modifications associated with ERα-regulated transcription and define the biological meaning of several key components of the histone code that governs ERα-regulated transcription.

VasH Is a Transcriptional Regulator of the Type VI Secretion System Functional in Endemic and Pandemic Vibrio cholerae▿†

PubMed Central

Kitaoka, Maya; Miyata, Sarah T.; Brooks, Teresa M.; Unterweger, Daniel; Pukatzki, Stefan

2011-01-01

The Gram-negative bacterium Vibrio cholerae is the etiological agent of cholera, a disease characterized by the release of high volumes of watery diarrhea. Many medically important proteobacteria, including V. cholerae, carry one or multiple copies of the gene cluster that encodes the bacterial type VI secretion system (T6SS) to confer virulence or interspecies competitiveness. Structural similarity and sequence homology between components of the T6SS and the cell-puncturing device of T4 bacteriophage suggest that the T6SS functions as a molecular syringe to inject effector molecules into prokaryotic and eukaryotic target cells. Although our understanding of how the structural T6SS apparatus assembles is developing, little is known about how this system is regulated. Here, we report on the contribution of the activator of the alternative sigma factor 54, VasH, as a global regulator of the V. cholerae T6SS. Using bioinformatics and mutational analyses, we identified domains of the VasH polypeptide that are essential for its ability to initiate transcription of T6SS genes and established a universal role for VasH in endemic and pandemic V. cholerae strains. PMID:21949076

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

PubMed Central

Menet, Jerome S; Rodriguez, Joseph; Abruzzi, Katharine C; Rosbash, Michael

2012-01-01

A substantial fraction of the metazoan transcriptome undergoes circadian oscillations in many cells and tissues. Based on the transcription feedback loops important for circadian timekeeping, it is commonly assumed that this mRNA cycling reflects widespread transcriptional regulation. To address this issue, we directly measured the circadian dynamics of mouse liver transcription using Nascent-Seq (genome-wide sequencing of nascent RNA). Although many genes are rhythmically transcribed, many rhythmic mRNAs manifest poor transcriptional rhythms, indicating a prominent contribution of post-transcriptional regulation to circadian mRNA expression. This analysis of rhythmic transcription also showed that the rhythmic DNA binding profile of the transcription factors CLOCK and BMAL1 does not determine the transcriptional phase of most target genes. This likely reflects gene-specific collaborations of CLK:BMAL1 with other transcription factors. These insights from Nascent-Seq indicate that it should have broad applicability to many other gene expression regulatory issues. DOI: http://dx.doi.org/10.7554/eLife.00011.001 PMID:23150795

Purification and characterisation of a new hypothalamic satiety peptide, cocaine and amphetamine regulated transcript (CART), produced in yeast.

PubMed

Thim, L; Nielsen, P F; Judge, M E; Andersen, A S; Diers, I; Egel-Mitani, M; Hastrup, S

1998-05-29

Cocaine and amphetamine regulated transcript (CART) is a newly discovered hypothalamic peptide with a potent appetite suppressing activity following intracerebroventricular administration. When the mature rat CART sequence encoding CART(1-102) was inserted in the yeast expression plasmid three CART peptides could be purified from the fermentation broth reflecting processing at dibasic sequences. None of these corresponded to the naturally occurring CART(55-102). In order to obtain CART(55-102) the precursor Glu-Glu-Ile-Asp-CART(55-102) has been produced and CART(55-102) was generated by digestion of the precursor with dipeptidylaminopeptidase-1. All four generated CART peptides have been characterised by N-terminal amino acid sequencing and mass spectrometry. The CART peptides contain six cysteine residues and using the yeast expressed CART(62-102) the disulphide bond configuration was found to be I-III, II-V and IV-VI. When the four CART peptides were intracerebroventricularly injected in fasted mice (0.1 to 2.0 microg) they all produced a dose dependent inhibition of food intake.

Prevalence and Predictors of Persistent Speech Sound Disorder at Eight Years Old: Findings From a Population Cohort Study

PubMed Central

Miller, Laura L.; Peters, Tim J.; Emond, Alan; Roulstone, Sue

2016-01-01

Purpose The purpose of this study was to determine prevalence and predictors of persistent speech sound disorder (SSD) in children aged 8 years after disregarding children presenting solely with common clinical distortions (i.e., residual errors). Method Data from the Avon Longitudinal Study of Parents and Children (Boyd et al., 2012) were used. Children were classified as having persistent SSD on the basis of percentage of consonants correct measures from connected speech samples. Multivariable logistic regression analyses were performed to identify predictors. Results The estimated prevalence of persistent SSD was 3.6%. Children with persistent SSD were more likely to be boys and from families who were not homeowners. Early childhood predictors identified as important were weak sucking at 4 weeks, not often combining words at 24 months, limited use of word morphology at 38 months, and being unintelligible to strangers at age 38 months. School-age predictors identified as important were maternal report of difficulty pronouncing certain sounds and hearing impairment at age 7 years, tympanostomy tube insertion at any age up to 8 years, and a history of suspected coordination problems. The contribution of these findings to our understanding of risk factors for persistent SSD and the nature of the condition is considered. Conclusion Variables identified as predictive of persistent SSD suggest that factors across motor, cognitive, and linguistic processes may place a child at risk. PMID:27367606

Motor sequencing deficit as an endophenotype of speech sound disorder: a genome-wide linkage analysis in a multigenerational family.

PubMed

Peter, Beate; Matsushita, Mark; Raskind, Wendy H

2012-10-01

The aim of this pilot study was to investigate a measure of motor sequencing deficit as a potential endophenotype of speech sound disorder (SSD) in a multigenerational family with evidence of familial SSD. In a multigenerational family with evidence of a familial motor-based SSD, affectation status and a measure of motor sequencing during oral motor testing were obtained. To further investigate the role of motor sequencing as an endophenotype for genetic studies, parametric and nonparametric linkage analyses were carried out using a genome-wide panel of 404 microsatellites. In seven of the 10 family members with available data, SSD affectation status and motor sequencing status coincided. Linkage analysis revealed four regions of interest, 6p21, 7q32, 7q36, and 8q24, primarily identified with the measure of motor sequencing ability. The 6p21 region overlaps with a locus implicated in rapid alternating naming in a recent genome-wide dyslexia linkage study. The 7q32 locus contains a locus implicated in dyslexia. The 7q36 locus borders on a gene known to affect the component traits of language impairment. The results are consistent with a motor-based endophenotype of SSD that would be informative for genetic studies. The linkage results in this first genome-wide study in a multigenerational family with SSD warrant follow-up in additional families and with fine mapping or next-generation approaches to gene identification.

Efficacy of Bone-Anchored Hearing Aids in Single-Sided Deafness: A Systematic Review.

PubMed

Kim, Gaeun; Ju, Hyun Mi; Lee, Sun Hee; Kim, Hee-Soon; Kwon, Jeong A; Seo, Young Joon

2017-04-01

Bone-anchored hearing aids (BAHAs) have been known to partially restore some of the functions lost in subjects with single-sided deafness (SSD). Our aims in this systemic review were to analyze the present capabilities of BAHAs in the context of SSD, and to evaluate the efficacy of BAHAs in improving speech recognition in noisy conditions, sound localization, and subjective outcomes. A systematic search was undertaken until August 2015 by two independent reviewers, with disagreements resolved by consensus. Among 286 references, we analyzed 14 studies that used both subjective and objective indicators to assess the capabilities of a total of 296 patients in the unaided and aided situations. Although there was "no benefit" of BAHA implantation for sound localization, BAHAs certainly improved subjects' speech discrimination in noisy circumstances. In the six studies that dealt with sound localization, no significant difference was found after the implantation. Twelve studies showed the benefits of BAHAs for speech discrimination in noise. Regarding subjective outcomes of using the prosthesis in patients with SSD (abbreviated profile of hearing aid benefit [APHAB] and the Glasgow hearing aid benefit profile [GHABP], etc.), we noticed an improvement in the quality of life. This systematic review has indicated that BAHAs may successfully rehabilitate patients with SSD by alleviating the hearing handicap to a certain degree, which could improve patients' quality of life. This report has presented additional evidence of effective auditory rehabilitation for SSD and will be helpful to clinicians counseling patients regarding treatment options for SSD.